[{"file_date_updated":"2024-01-02T09:23:57Z","license":"https://creativecommons.org/licenses/by/4.0/","year":"2023","pmid":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"author":[{"full_name":"Del Bianco, Marta","first_name":"Marta","last_name":"Del Bianco"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Strader, Lucia","first_name":"Lucia","last_name":"Strader"},{"last_name":"Kepinski","first_name":"Stefan","full_name":"Kepinski, Stefan"}],"date_created":"2023-12-24T23:00:53Z","date_updated":"2024-01-02T09:29:24Z","volume":74,"month":"12","publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38038239"]},"quality_controlled":"1","doi":"10.1093/jxb/erad420","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Amid the delays due to the global pandemic, in early October 2022, the auxin community gathered in the idyllic peninsula of Cavtat, Croatia. More than 170 scientists from across the world converged to discuss the latest advancements in fundamental and applied research in the field. The topics, from signalling and transport to plant architecture and response to the environment, show how auxin research must bridge from the molecular realm to macroscopic developmental responses. This is mirrored in this collection of reviews, contributed by participants of the Auxin 2022 meeting.","lang":"eng"}],"issue":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14709","title":"Auxin research: Creating tools for a greener future","ddc":["580"],"status":"public","intvolume":" 74","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_JourExperimentalBotany_DelBianco.pdf","file_size":425194,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14724","checksum":"f66fb960fd791dea53fd0e087f2fbbe8","success":1,"date_updated":"2024-01-02T09:23:57Z","date_created":"2024-01-02T09:23:57Z"}],"scopus_import":"1","day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","publication":"Journal of Experimental Botany","citation":{"ieee":"M. Del Bianco, J. Friml, L. Strader, and S. Kepinski, “Auxin research: Creating tools for a greener future,” Journal of Experimental Botany, vol. 74, no. 22. Oxford University Press, pp. 6889–6892, 2023.","apa":"Del Bianco, M., Friml, J., Strader, L., & Kepinski, S. (2023). Auxin research: Creating tools for a greener future. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erad420","ista":"Del Bianco M, Friml J, Strader L, Kepinski S. 2023. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 74(22), 6889–6892.","ama":"Del Bianco M, Friml J, Strader L, Kepinski S. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 2023;74(22):6889-6892. doi:10.1093/jxb/erad420","chicago":"Del Bianco, Marta, Jiří Friml, Lucia Strader, and Stefan Kepinski. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany. Oxford University Press, 2023. https://doi.org/10.1093/jxb/erad420.","short":"M. Del Bianco, J. Friml, L. Strader, S. Kepinski, Journal of Experimental Botany 74 (2023) 6889–6892.","mla":"Del Bianco, Marta, et al. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany, vol. 74, no. 22, Oxford University Press, 2023, pp. 6889–92, doi:10.1093/jxb/erad420."},"article_type":"original","page":"6889-6892","date_published":"2023-12-01T00:00:00Z"},{"date_updated":"2024-01-10T13:41:10Z","date_created":"2024-01-10T09:24:35Z","volume":24,"author":[{"last_name":"Teplova","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia"},{"full_name":"Pigidanov, Artemii A.","first_name":"Artemii A.","last_name":"Pigidanov"},{"full_name":"Serebryakova, Marina V.","last_name":"Serebryakova","first_name":"Marina V."},{"last_name":"Golyshev","first_name":"Sergei A.","full_name":"Golyshev, Sergei A."},{"full_name":"Galiullina, Raisa A.","first_name":"Raisa A.","last_name":"Galiullina"},{"full_name":"Chichkova, Nina V.","first_name":"Nina V.","last_name":"Chichkova"},{"first_name":"Andrey B.","last_name":"Vartapetian","full_name":"Vartapetian, Andrey B."}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"MDPI","acknowledgement":"We thank C.U.T. Hellen for critically reading the manuscript. The MALDI MS facility and CLSM became available to us in the framework of Moscow State University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071.","year":"2023","pmid":1,"file_date_updated":"2024-01-10T13:39:42Z","article_number":"16527","language":[{"iso":"eng"}],"doi":"10.3390/ijms242216527","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38003717"],"isi":["001113792600001"]},"month":"11","publication_identifier":{"issn":["1422-0067"]},"file":[{"access_level":"open_access","file_name":"2023_IJMS_Teplova.pdf","content_type":"application/pdf","file_size":2637784,"creator":"dernst","relation":"main_file","file_id":"14791","checksum":"4df7d206ba022b7f54eff1f0aec1659a","success":1,"date_created":"2024-01-10T13:39:42Z","date_updated":"2024-01-10T13:39:42Z"}],"oa_version":"Published Version","title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","ddc":["580"],"status":"public","intvolume":" 24","_id":"14776","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident.","lang":"eng"}],"issue":"22","type":"journal_article","date_published":"2023-11-01T00:00:00Z","article_type":"original","publication":"International Journal of Molecular Sciences","citation":{"apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., & Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms242216527","ieee":"A. Teplova et al., “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” International Journal of Molecular Sciences, vol. 24, no. 22. MDPI, 2023.","ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527.","ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 2023;24(22). doi:10.3390/ijms242216527","chicago":"Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms242216527.","short":"A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina, N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences 24 (2023).","mla":"Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal of Molecular Sciences, vol. 24, no. 22, 16527, MDPI, 2023, doi:10.3390/ijms242216527."},"day":"01","article_processing_charge":"Yes","has_accepted_license":"1","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"]},{"month":"07","publication_identifier":{"eissn":["1674-2052"],"issn":["1752-9867"]},"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["37393433"],"isi":["001044410900001"]},"oa":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2023.06.007","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2024-01-29T10:37:05Z","ec_funded":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Elsevier ","year":"2023","acknowledgement":"We thank all the authors for sharing the published materials. This research was supported by the Lab Support Facility and the Imaging and Optics Facility of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This project was funded by the European Research Council Advanced Grant (ETAP-742985).","pmid":1,"date_created":"2023-07-12T07:32:46Z","date_updated":"2024-01-29T10:38:57Z","volume":16,"author":[{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","first_name":"Huihuang","last_name":"Chen","full_name":"Chen, Huihuang"},{"orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin","full_name":"Li, Lanxin"},{"last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","first_name":"Linlin"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_type":"letter_note","page":"1117-1119","publication":"Molecular Plant","citation":{"ama":"Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 2023;16(7):1117-1119. doi:10.1016/j.molp.2023.06.007","ista":"Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119.","apa":"Chen, H., Li, L., Zou, M., Qi, L., & Friml, J. (2023). Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. Elsevier . https://doi.org/10.1016/j.molp.2023.06.007","ieee":"H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and AFB1 receptors in auxin signalling.,” Molecular Plant, vol. 16, no. 7. Elsevier , pp. 1117–1119, 2023.","mla":"Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant, vol. 16, no. 7, Elsevier , 2023, pp. 1117–19, doi:10.1016/j.molp.2023.06.007.","short":"H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.","chicago":"Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant. Elsevier , 2023. https://doi.org/10.1016/j.molp.2023.06.007."},"date_published":"2023-07-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast.","lang":"eng"}],"issue":"7","status":"public","title":"Distinct functions of TIR1 and AFB1 receptors in auxin signalling.","ddc":["580"],"intvolume":" 16","_id":"13212","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"2023_MolecularPlant_Chen.pdf","access_level":"open_access","file_size":1000871,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14894","date_created":"2024-01-29T10:37:05Z","date_updated":"2024-01-29T10:37:05Z","checksum":"6012b7e4a2f680ee6c1f84001e2b945f","success":1}]},{"file_date_updated":"2024-01-29T11:21:43Z","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","acknowledgement":"We gratefully acknowledge our brave colleagues, whose excellent efforts kept the plant cAMP research going in the last two decades. The authors were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.","year":"2023","pmid":1,"date_created":"2023-07-23T22:01:13Z","date_updated":"2024-01-29T11:21:55Z","volume":240,"author":[{"orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","last_name":"Qi","first_name":"Linlin","full_name":"Qi, Linlin"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"month":"10","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"isi":1,"quality_controlled":"1","project":[{"_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123","name":"Peptide receptor complexes for auxin canalization and regeneration in Arabidopsis"},{"name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051"}],"external_id":{"isi":["001026321500001"],"pmid":["37434303"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/nph.19123","type":"journal_article","abstract":[{"lang":"eng","text":"The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general."}],"issue":"2","title":"Tale of cAMP as a second messenger in auxin signaling and beyond","ddc":["580"],"status":"public","intvolume":" 240","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13266","file":[{"checksum":"6d9bbd45b8e7bb3ceee2586d447bacb2","success":1,"date_created":"2024-01-29T11:21:43Z","date_updated":"2024-01-29T11:21:43Z","relation":"main_file","file_id":"14898","content_type":"application/pdf","file_size":974464,"creator":"dernst","access_level":"open_access","file_name":"2023_NewPhytologist_Qi.pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","page":"489-495","publication":"New Phytologist","citation":{"ista":"Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 240(2), 489–495.","ieee":"L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling and beyond,” New Phytologist, vol. 240, no. 2. Wiley, pp. 489–495, 2023.","apa":"Qi, L., & Friml, J. (2023). Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. Wiley. https://doi.org/10.1111/nph.19123","ama":"Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 2023;240(2):489-495. doi:10.1111/nph.19123","chicago":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” New Phytologist. Wiley, 2023. https://doi.org/10.1111/nph.19123.","mla":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” New Phytologist, vol. 240, no. 2, Wiley, 2023, pp. 489–95, doi:10.1111/nph.19123.","short":"L. Qi, J. Friml, New Phytologist 240 (2023) 489–495."},"date_published":"2023-10-01T00:00:00Z"},{"date_created":"2023-07-12T07:32:00Z","date_updated":"2024-01-30T10:55:34Z","volume":4,"author":[{"last_name":"Xia","first_name":"Jing","full_name":"Xia, Jing"},{"last_name":"Kong","first_name":"Mengjuan","full_name":"Kong, Mengjuan"},{"first_name":"Zhisen","last_name":"Yang","full_name":"Yang, Zhisen"},{"last_name":"Sun","first_name":"Lianghanxiao","full_name":"Sun, Lianghanxiao"},{"first_name":"Yakun","last_name":"Peng","full_name":"Peng, Yakun"},{"last_name":"Mao","first_name":"Yanbo","full_name":"Mao, Yanbo"},{"full_name":"Wei, Hong","last_name":"Wei","first_name":"Hong"},{"full_name":"Ying, Wei","first_name":"Wei","last_name":"Ying"},{"first_name":"Yongxiao","last_name":"Gao","full_name":"Gao, Yongxiao"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"first_name":"Jianping","last_name":"Weng","full_name":"Weng, Jianping"},{"full_name":"Liu, Xin","last_name":"Liu","first_name":"Xin"},{"first_name":"Linfeng","last_name":"Sun","full_name":"Sun, Linfeng"},{"first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Elsevier ","acknowledgement":"This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB37020103 to Linfeng Sun); research funds from the Center for Advanced Interdisciplinary Science\r\nand Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China (QYPY20220012 to S.T.); start-up funding from the University of Science and Technology of China and the\r\nChinese Academy of Sciences (GG9100007007, KY9100000026,KY9100000051, and KJ2070000079 to S.T.); the National Natural Science Foundation of China (31900885 to X.L. and 31870732 to Linfeng Sun); the Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun); the Fundamental Research Funds for the Central Universities (WK9100000021 to S.T. and WK9100000031 to Linfeng Sun); and the USTC Research Funds of the Double First-Class Initiative (YD9100002016 to S.T. and YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation.We thank Dr. Yang Zhao for sharing published materials (Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences) and the Cryo-EM Center of the University of Science and Technology of China for the EM facility support. We are grateful to Y. Gao and all other staff members for their technical support on cryo-EM data collection. ","year":"2023","pmid":1,"file_date_updated":"2024-01-30T10:54:40Z","article_number":"100632","language":[{"iso":"eng"}],"doi":"10.1016/j.xplc.2023.100632","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["37254481"],"isi":["001113003000001"]},"month":"11","publication_identifier":{"eissn":["2590-3462"]},"oa_version":"Published Version","file":[{"file_id":"14900","relation":"main_file","success":1,"checksum":"f8ef92af6096834f91ce38587fb1db9f","date_created":"2024-01-30T10:54:40Z","date_updated":"2024-01-30T10:54:40Z","access_level":"open_access","file_name":"2023_PlantCommunications_Xia.pdf","creator":"dernst","content_type":"application/pdf","file_size":1434862}],"ddc":["580"],"title":"Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen","status":"public","intvolume":" 4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13209","abstract":[{"text":"The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we reveal that naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated developmental processes. Additional cellular and biochemical evidence indicates that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analyses confirm that naproxen binds directly to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate. Thus, by combining cellular, biochemical, and structural approaches, this study clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of this compound may advance our understanding of the molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in auxin biology and agriculture.","lang":"eng"}],"issue":"6","type":"journal_article","date_published":"2023-11-13T00:00:00Z","article_type":"original","publication":"Plant Communications","citation":{"mla":"Xia, Jing, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” Plant Communications, vol. 4, no. 6, 100632, Elsevier , 2023, doi:10.1016/j.xplc.2023.100632.","short":"J. Xia, M. Kong, Z. Yang, L. Sun, Y. Peng, Y. Mao, H. Wei, W. Ying, Y. Gao, J. Friml, J. Weng, X. Liu, L. Sun, S. Tan, Plant Communications 4 (2023).","chicago":"Xia, Jing, Mengjuan Kong, Zhisen Yang, Lianghanxiao Sun, Yakun Peng, Yanbo Mao, Hong Wei, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” Plant Communications. Elsevier , 2023. https://doi.org/10.1016/j.xplc.2023.100632.","ama":"Xia J, Kong M, Yang Z, et al. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. 2023;4(6). doi:10.1016/j.xplc.2023.100632","ista":"Xia J, Kong M, Yang Z, Sun L, Peng Y, Mao Y, Wei H, Ying W, Gao Y, Friml J, Weng J, Liu X, Sun L, Tan S. 2023. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. 4(6), 100632.","apa":"Xia, J., Kong, M., Yang, Z., Sun, L., Peng, Y., Mao, Y., … Tan, S. (2023). Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. Elsevier . https://doi.org/10.1016/j.xplc.2023.100632","ieee":"J. Xia et al., “Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen,” Plant Communications, vol. 4, no. 6. Elsevier , 2023."},"day":"13","article_processing_charge":"Yes","has_accepted_license":"1"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"12","citation":{"chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2221313120.","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:10.1073/pnas.2221313120.","short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2221313120","ieee":"Y. Wang et al., “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25. National Academy of Sciences, 2023.","ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(25). doi:10.1073/pnas.2221313120"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_type":"original","date_published":"2023-06-12T00:00:00Z","type":"journal_article","issue":"25","abstract":[{"lang":"eng","text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability."}],"_id":"13201","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 120","ddc":["570"],"title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","status":"public","oa_version":"Published Version","file":[{"file_name":"2023_PNAS_Wang.pdf","access_level":"open_access","creator":"alisjak","file_size":5244581,"content_type":"application/pdf","embargo":"2023-12-12","file_id":"13204","relation":"main_file","date_created":"2023-07-10T08:48:40Z","date_updated":"2023-12-13T23:30:03Z","checksum":"d800e06252eaefba28531fa9440f23f0"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"06","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["37307446"],"isi":["001030689600003"]},"quality_controlled":"1","isi":1,"doi":"10.1073/pnas.2221313120","language":[{"iso":"eng"}],"article_number":"e2221313120","file_date_updated":"2023-12-13T23:30:03Z","pmid":1,"year":"2023","acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), Hainan Provincial Natural Science Foundation of China (323CXTD379), Chinese Universities Scientific Fund (2023TC019), Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, and China Postdoctoral Science Foundation (BH2020259460).","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"first_name":"Yalu","last_name":"Wang","full_name":"Wang, Yalu"},{"full_name":"Yuan, Zhi","last_name":"Yuan","first_name":"Zhi"},{"full_name":"Wang, Jinyi","last_name":"Wang","first_name":"Jinyi"},{"first_name":"Huixin","last_name":"Xiao","full_name":"Xiao, Huixin"},{"full_name":"Wan, Lu","last_name":"Wan","first_name":"Lu"},{"last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"full_name":"Guo, Yan","last_name":"Guo","first_name":"Yan"},{"full_name":"Gong, Zhizhong","first_name":"Zhizhong","last_name":"Gong"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Zhang, Jing","last_name":"Zhang","first_name":"Jing"}],"volume":120,"date_created":"2023-07-09T22:01:12Z","date_updated":"2023-12-13T23:30:04Z"},{"_id":"14510","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","ddc":["570"],"oa_version":"Published Version","file":[{"checksum":"3d5e680bfc61f98e308c434f45cc9bd6","date_updated":"2023-11-20T09:18:51Z","date_created":"2023-11-20T09:18:51Z","file_id":"14567","relation":"source_file","creator":"ngnyliuk","file_size":20824903,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"Thesis_Gnyliukh_final_08_11_23.docx"},{"file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","embargo_to":"open_access","access_level":"closed","creator":"ngnyliuk","content_type":"application/pdf","file_size":24871844,"embargo":"2024-11-23","file_id":"14568","relation":"main_file","date_updated":"2023-11-23T13:10:55Z","date_created":"2023-11-20T09:23:11Z","checksum":"bfc96d47fc4e7e857dd71656097214a4"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"citation":{"short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria."},"page":"180","date_published":"2023-11-10T00:00:00Z","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"article_processing_charge":"No","has_accepted_license":"1","day":"10","year":"2023","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14591"},{"relation":"part_of_dissertation","status":"public","id":"9887"},{"id":"8139","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","first_name":"Nataliia"}],"date_created":"2023-11-10T09:10:06Z","date_updated":"2024-03-28T23:30:46Z","ec_funded":1,"file_date_updated":"2023-11-23T13:10:55Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"doi":"10.15479/at:ista:14510","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"month":"11"},{"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10016","title":"Fourteen stations of auxin","status":"public","intvolume":" 14","abstract":[{"text":"Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research. ","lang":"eng"}],"issue":"5","type":"journal_article","date_published":"2022-05-27T00:00:00Z","publication":"Cold Spring Harbor Perspectives in Biology","citation":{"ama":"Friml J. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 2022;14(5). doi:10.1101/cshperspect.a039859 ","ieee":"J. Friml, “Fourteen stations of auxin,” Cold Spring Harbor Perspectives in Biology, vol. 14, no. 5. Cold Spring Harbor Laboratory, 2022.","apa":"Friml, J. (2022). Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a039859 ","ista":"Friml J. 2022. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 14(5), a039859.","short":"J. Friml, Cold Spring Harbor Perspectives in Biology 14 (2022).","mla":"Friml, Jiří. “Fourteen Stations of Auxin.” Cold Spring Harbor Perspectives in Biology, vol. 14, no. 5, a039859, Cold Spring Harbor Laboratory, 2022, doi:10.1101/cshperspect.a039859 .","chicago":"Friml, Jiří. “Fourteen Stations of Auxin.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/cshperspect.a039859 ."},"article_type":"review","day":"27","article_processing_charge":"No","scopus_import":"1","author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"date_updated":"2023-08-02T06:54:42Z","date_created":"2021-09-14T11:36:53Z","volume":14,"year":"2022","acknowledgement":"The author thanks the whole community of researchers consciously or unconsciously working on questions related to auxin, whose hard work and enthusiasm contributed to development of this exciting story. Particular thanks go to many\r\nbrilliant present and past members of the Friml group and our numerous excellent collaborators, without whom my own personal journey would not be possible. The way of the cross with its 14 stations is a popular devotion among Roman Catholics and inspires them to make a spiritual pilgrimage through contemplation of Christ on his last day. Its aspects of gradual progress, struggle, passion, and revelation served as an inspiration for the formal depiction of our journey to understanding auxin as described in this review. It is in no way intended to reflect the personal beliefs of the author and readers. I am grateful to Nick Barton, Eva Benková, Lenka Caisová, Matyáš Fendrych, Lukáš Fiedler, Monika Frátriková, Jarmila Frimlová, Michelle Gallei, Jakub Hajný, Lukas Hoermayer, Alexandra Mally, Ondrˇej Novák, Jan Petrášek, Aleš Pěnčík, Steffen Vanneste, Tongda Xu, and Zhenbiao Yang for their valuable comments. Special thanks go to Michelle Gallei for her invaluable assistance with the figures.","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Cold Spring Harbor Laboratory","article_number":"a039859","doi":"10.1101/cshperspect.a039859 ","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a039859 ","open_access":"1"}],"external_id":{"isi":["000806563000003"],"pmid":["34400554"]},"quality_controlled":"1","isi":1,"month":"05","publication_identifier":{"issn":["1943-0264"]}},{"publication_identifier":{"issn":["0032-0781"],"eissn":["1471-9053"]},"month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/pcp/pcab149"}],"external_id":{"isi":["000877899400009"],"pmid":["34791413"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1093/pcp/pcab149","language":[{"iso":"eng"}],"pmid":1,"year":"2022","acknowledgement":"The authors thank Ralf Stracke (Bielefeld University, Bielefeld, Germany) for providing the myb mutants and their colleagues Bert De Rybel for the tmo5t;mo5l1 double mutant, Boris Parizot for tips on the RNA-seq analysis, Veronique Storme for statistical help on both the RNA-seq and lateral root density, and Martine De Cock for help in preparing the manuscript.","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","publication_status":"published","author":[{"first_name":"Sylwia","last_name":"Struk","full_name":"Struk, Sylwia"},{"full_name":"Braem, Lukas","last_name":"Braem","first_name":"Lukas"},{"full_name":"Matthys, Cedrick","last_name":"Matthys","first_name":"Cedrick"},{"last_name":"Walton","first_name":"Alan","full_name":"Walton, Alan"},{"first_name":"Nick","last_name":"Vangheluwe","full_name":"Vangheluwe, Nick"},{"full_name":"Van Praet, Stan","last_name":"Van Praet","first_name":"Stan"},{"full_name":"Jiang, Lingxiang","last_name":"Jiang","first_name":"Lingxiang"},{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Baster","full_name":"Baster, Pawel"},{"full_name":"De Cuyper, Carolien","last_name":"De Cuyper","first_name":"Carolien"},{"full_name":"Boyer, Francois-Didier","first_name":"Francois-Didier","last_name":"Boyer"},{"full_name":"Stes, Elisabeth","last_name":"Stes","first_name":"Elisabeth"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Gevaert, Kris","last_name":"Gevaert","first_name":"Kris"},{"first_name":"Sofie","last_name":"Goormachtig","full_name":"Goormachtig, Sofie"}],"volume":63,"date_created":"2021-12-28T11:44:18Z","date_updated":"2023-08-02T13:40:43Z","scopus_import":"1","keyword":["flavonols","MAX2","rac-Gr24","RNA-seq","root development","transcriptional regulation"],"article_processing_charge":"No","day":"21","citation":{"apa":"Struk, S., Braem, L., Matthys, C., Walton, A., Vangheluwe, N., Van Praet, S., … Goormachtig, S. (2022). Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. Plant & Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcab149","ieee":"S. Struk et al., “Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density,” Plant & Cell Physiology, vol. 63, no. 1. Oxford University Press, pp. 104–119, 2022.","ista":"Struk S, Braem L, Matthys C, Walton A, Vangheluwe N, Van Praet S, Jiang L, Baster P, De Cuyper C, Boyer F-D, Stes E, Beeckman T, Friml J, Gevaert K, Goormachtig S. 2022. Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. Plant & Cell Physiology. 63(1), 104–119.","ama":"Struk S, Braem L, Matthys C, et al. Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. Plant & Cell Physiology. 2022;63(1):104-119. doi:10.1093/pcp/pcab149","chicago":"Struk, Sylwia, Lukas Braem, Cedrick Matthys, Alan Walton, Nick Vangheluwe, Stan Van Praet, Lingxiang Jiang, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density.” Plant & Cell Physiology. Oxford University Press, 2022. https://doi.org/10.1093/pcp/pcab149.","short":"S. Struk, L. Braem, C. Matthys, A. Walton, N. Vangheluwe, S. Van Praet, L. Jiang, P. Baster, C. De Cuyper, F.-D. Boyer, E. Stes, T. Beeckman, J. Friml, K. Gevaert, S. Goormachtig, Plant & Cell Physiology 63 (2022) 104–119.","mla":"Struk, Sylwia, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density.” Plant & Cell Physiology, vol. 63, no. 1, Oxford University Press, 2022, pp. 104–19, doi:10.1093/pcp/pcab149."},"publication":"Plant & Cell Physiology","page":"104-119","article_type":"original","date_published":"2022-01-21T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"The synthetic strigolactone (SL) analog, rac-GR24, has been instrumental in studying the role of SLs as well as karrikins because it activates the receptors DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2) of their signaling pathways, respectively. Treatment with rac-GR24 modifies the root architecture at different levels, such as decreasing the lateral root density (LRD), while promoting root hair elongation or flavonol accumulation. Previously, we have shown that the flavonol biosynthesis is transcriptionally activated in the root by rac-GR24 treatment, but, thus far, the molecular players involved in that response have remained unknown. To get an in-depth insight into the changes that occur after the compound is perceived by the roots, we compared the root transcriptomes of the wild type and the more axillary growth2 (max2) mutant, affected in both SL and karrikin signaling pathways, with and without rac-GR24 treatment. Quantitative reverse transcription (qRT)-PCR, reporter line analysis and mutant phenotyping indicated that the flavonol response and the root hair elongation are controlled by the ELONGATED HYPOCOTYL 5 (HY5) and MYB12 transcription factors, but HY5, in contrast to MYB12, affects the LRD as well. Furthermore, we identified the transcription factors TARGET OF MONOPTEROS 5 (TMO5) and TMO5 LIKE1 as negative and the Mediator complex as positive regulators of the rac-GR24 effect on LRD. Altogether, hereby, we get closer toward understanding the molecular mechanisms that underlay the rac-GR24 responses in the root.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10583","intvolume":" 63","title":"Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density","status":"public","oa_version":"Published Version"},{"author":[{"last_name":"Wang","first_name":"R","full_name":"Wang, R"},{"last_name":"Himschoot","first_name":"E","full_name":"Himschoot, E"},{"first_name":"M","last_name":"Grenzi","full_name":"Grenzi, M"},{"full_name":"Chen, J","last_name":"Chen","first_name":"J"},{"full_name":"Safi, A","first_name":"A","last_name":"Safi"},{"full_name":"Krebs, M","first_name":"M","last_name":"Krebs"},{"first_name":"K","last_name":"Schumacher","full_name":"Schumacher, K"},{"last_name":"Nowack","first_name":"MK","full_name":"Nowack, MK"},{"last_name":"Moeder","first_name":"W","full_name":"Moeder, W"},{"last_name":"Yoshioka","first_name":"K","full_name":"Yoshioka, K"},{"full_name":"Van Damme, D","first_name":"D","last_name":"Van Damme"},{"full_name":"De Smet, I","first_name":"I","last_name":"De Smet"},{"full_name":"Geelen, D","last_name":"Geelen","first_name":"D"},{"full_name":"Beeckman, T","first_name":"T","last_name":"Beeckman"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Costa, A","first_name":"A","last_name":"Costa"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"}],"date_updated":"2023-08-02T14:07:58Z","date_created":"2022-02-03T09:19:01Z","volume":73,"acknowledgement":"We thank Joerg Kudla (WWU Munster, Germany), Petra Dietrich (F.A. University of Erlangen-Nurnberg, Germany) for sharing published materials, and NASC for providing seeds. We thank Veronique Storme for help with the statistical analyses. Part of the imaging analysis was carried out at NOLIMITS, an advanced imaging facility established by the University of Milan.\r\nThis work was supported by grants of the China Scholarship Council (CSC) to RW and JC; Fonds Wetenschappelijk Onderzoek (FWO) to TB and (G002220N) SV; the special research fund of Ghent University to EH; the Deutsche Forschungsgemeinschaft (DFG) through Grants within FOR964 (MK and KS); Piano di Sviluppo di Ateneo 2019 (University of Milan) to AC; the European Research Council (ERC) T-Rex project 682436 to DVD; the ERC ETAP project 742985 to JF, and by a PhD fellowship from the University of Milan to MG.","year":"2022","pmid":1,"publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"JiFr"}],"ec_funded":1,"article_number":"erac019","doi":"10.1093/jxb/erac019","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["35085386"],"isi":["000764220900001"]},"main_file_link":[{"url":"https://biblio.ugent.be/publication/8738721","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"month":"04","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10717","status":"public","title":"Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots","intvolume":" 73","abstract":[{"lang":"eng","text":"Much of what we know about the role of auxin in plant development derives from exogenous manipulations of auxin distribution and signaling, using inhibitors, auxins and auxin analogs. In this context, synthetic auxin analogs, such as 1-Naphtalene Acetic Acid (1-NAA), are often favored over the endogenous auxin indole-3-acetic acid (IAA), in part due to their higher stability. While such auxin analogs have proven to be instrumental to reveal the various faces of auxin, they display in some cases distinct bioactivities compared to IAA. Here, we focused on the effect of auxin analogs on the accumulation of PIN proteins in Brefeldin A-sensitive endosomal aggregations (BFA bodies), and the correlation with the ability to elicit Ca 2+ responses. For a set of commonly used auxin analogs, we evaluated if auxin-analog induced Ca 2+ signaling inhibits PIN accumulation. Not all auxin analogs elicited a Ca 2+ response, and their differential ability to elicit Ca 2+ responses correlated partially with their ability to inhibit BFA-body formation. However, in tir1/afb and cngc14, 1-NAA-induced Ca 2+ signaling was strongly impaired, yet 1-NAA still could inhibit PIN accumulation in BFA bodies. This demonstrates that TIR1/AFB-CNGC14-dependent Ca 2+ signaling does not inhibit BFA body formation in Arabidopsis roots."}],"issue":"8","type":"journal_article","date_published":"2022-04-18T00:00:00Z","publication":"Journal of Experimental Botany","citation":{"ama":"Wang R, Himschoot E, Grenzi M, et al. Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. Journal of Experimental Botany. 2022;73(8). doi:10.1093/jxb/erac019","apa":"Wang, R., Himschoot, E., Grenzi, M., Chen, J., Safi, A., Krebs, M., … Vanneste, S. (2022). Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. Journal of Experimental Botany. Oxford Academic. https://doi.org/10.1093/jxb/erac019","ieee":"R. Wang et al., “Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots,” Journal of Experimental Botany, vol. 73, no. 8. Oxford Academic, 2022.","ista":"Wang R, Himschoot E, Grenzi M, Chen J, Safi A, Krebs M, Schumacher K, Nowack M, Moeder W, Yoshioka K, Van Damme D, De Smet I, Geelen D, Beeckman T, Friml J, Costa A, Vanneste S. 2022. Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. Journal of Experimental Botany. 73(8), erac019.","short":"R. Wang, E. Himschoot, M. Grenzi, J. Chen, A. Safi, M. Krebs, K. Schumacher, M. Nowack, W. Moeder, K. Yoshioka, D. Van Damme, I. De Smet, D. Geelen, T. Beeckman, J. Friml, A. Costa, S. Vanneste, Journal of Experimental Botany 73 (2022).","mla":"Wang, R., et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” Journal of Experimental Botany, vol. 73, no. 8, erac019, Oxford Academic, 2022, doi:10.1093/jxb/erac019.","chicago":"Wang, R, E Himschoot, M Grenzi, J Chen, A Safi, M Krebs, K Schumacher, et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” Journal of Experimental Botany. Oxford Academic, 2022. https://doi.org/10.1093/jxb/erac019."},"article_type":"original","day":"18","article_processing_charge":"No","scopus_import":"1"},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2022-02-01T00:00:00Z","citation":{"ista":"Yu Z, Zhang F, Friml J, Ding Z. 2022. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 64(2), 371–392.","apa":"Yu, Z., Zhang, F., Friml, J., & Ding, Z. (2022). Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13225","ieee":"Z. Yu, F. Zhang, J. Friml, and Z. Ding, “Auxin signaling: Research advances over the past 30 years,” Journal of Integrative Plant Biology, vol. 64, no. 2. Wiley, pp. 371–392, 2022.","ama":"Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 2022;64(2):371-392. doi:10.1111/jipb.13225","chicago":"Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances over the Past 30 Years.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13225.","mla":"Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.” Journal of Integrative Plant Biology, vol. 64, no. 2, Wiley, 2022, pp. 371–92, doi:10.1111/jipb.13225.","short":"Z. Yu, F. Zhang, J. Friml, Z. Ding, Journal of Integrative Plant Biology 64 (2022) 371–392."},"publication":"Journal of Integrative Plant Biology","page":"371-392","article_type":"review","issue":"2","abstract":[{"text":"Auxin, one of the first identified and most widely studied phytohormones, has been and will remain a hot topic in plant biology. After more than a century of passionate exploration, the mysteries of its synthesis, transport, signaling, and metabolism have largely been unlocked. Due to the rapid development of new technologies, new methods, and new genetic materials, the study of auxin has entered the fast lane over the past 30 years. Here, we highlight advances in understanding auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional and non-transcriptional branches, and the epigenetic regulation of auxin signaling. We also focus on feedback inhibition mechanisms that prevent the over-amplification of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional regulation to coordinate plant growth and development. The identification of additional auxin signaling components and their regulation will continue to open new avenues of research in this field, leading to an increasingly deeper, more comprehensive understanding of how auxin signals are interpreted at the cellular level to regulate plant growth and development.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","_id":"10719","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 64","title":"Auxin signaling: Research advances over the past 30 years","status":"public","publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"month":"02","doi":"10.1111/jipb.13225","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jipb.13225"}],"external_id":{"pmid":["35018726"],"isi":["000761281200011"]},"oa":1,"isi":1,"quality_controlled":"1","author":[{"first_name":"Z","last_name":"Yu","full_name":"Yu, Z"},{"full_name":"Zhang, F","last_name":"Zhang","first_name":"F"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Ding, Z","last_name":"Ding","first_name":"Z"}],"volume":64,"date_updated":"2023-08-02T14:08:30Z","date_created":"2022-02-03T09:52:59Z","pmid":1,"acknowledgement":"This research was financially supported by the National Natural Science Foundation of China and the Israel Science Foundation (NSFC-ISF; 32061143005), National Natural Science Foundation of China (32000225), Natural Science Foundation of Shandong Province (ZR2020QC036), and China Postdoctoral Science Foundation (2020M682165).\r\n","year":"2022","publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published"},{"article_number":"102174","file_date_updated":"2022-03-10T13:34:09Z","year":"2022","acknowledgement":"The authors apologize to those researchers whose work was not cited. In addition, exciting topics such as PIN polarization in context of phyllotaxis, shoot branching and termination of gravitropic bending, or role of additional auxin transporters could not have been included owing to lack of space. This work was supported by the Czech Science Foundation GAČR (GA18-26981S). The authors also acknowledge the EMBO for supporting J.H. with a long-term fellowship (ALTF217-2021).","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Elsevier","author":[{"full_name":"Hajny, Jakub","last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"date_updated":"2023-08-02T14:29:12Z","date_created":"2022-02-20T23:01:32Z","volume":65,"month":"02","publication_identifier":{"issn":["1369-5266"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000758724700004"],"pmid":["35123880"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.pbi.2022.102174","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Among the most fascinated properties of the plant hormone auxin is its ability to promote formation of its own directional transport routes. These gradually narrowing auxin channels form from the auxin source toward the sink and involve coordinated, collective polarization of individual cells. Once established, the channels provide positional information, along which new vascular strands form, for example, during organogenesis, regeneration, or leave venation. The main prerequisite of this still mysterious auxin canalization mechanism is a feedback between auxin signaling and its directional transport. This is manifested by auxin-induced re-arrangements of polar, subcellular localization of PIN-FORMED (PIN) auxin exporters. Immanent open questions relate to how position of auxin source and sink as well as tissue context are sensed and translated into tissue polarization and how cells communicate to polarize coordinately. Recently, identification of the first molecular players opens new avenues into molecular studies of this intriguing example of self-organizing plant development."}],"issue":"2","_id":"10768","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Auxin canalization: From speculative models toward molecular players","ddc":["580"],"intvolume":" 65","file":[{"creator":"dernst","content_type":"application/pdf","file_size":820322,"access_level":"open_access","file_name":"2022_CurrentOpPlantBiology_Hajny.pdf","success":1,"checksum":"f1ee02b6fb4200934eeb31fa69120885","date_created":"2022-03-10T13:34:09Z","date_updated":"2022-03-10T13:34:09Z","file_id":"10844","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Current Opinion in Plant Biology","citation":{"mla":"Hajny, Jakub, et al. “Auxin Canalization: From Speculative Models toward Molecular Players.” Current Opinion in Plant Biology, vol. 65, no. 2, 102174, Elsevier, 2022, doi:10.1016/j.pbi.2022.102174.","short":"J. Hajny, S. Tan, J. Friml, Current Opinion in Plant Biology 65 (2022).","chicago":"Hajny, Jakub, Shutang Tan, and Jiří Friml. “Auxin Canalization: From Speculative Models toward Molecular Players.” Current Opinion in Plant Biology. Elsevier, 2022. https://doi.org/10.1016/j.pbi.2022.102174.","ama":"Hajny J, Tan S, Friml J. Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. 2022;65(2). doi:10.1016/j.pbi.2022.102174","ista":"Hajny J, Tan S, Friml J. 2022. Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. 65(2), 102174.","apa":"Hajny, J., Tan, S., & Friml, J. (2022). Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2022.102174","ieee":"J. Hajny, S. Tan, and J. Friml, “Auxin canalization: From speculative models toward molecular players,” Current Opinion in Plant Biology, vol. 65, no. 2. Elsevier, 2022."},"article_type":"original","date_published":"2022-02-01T00:00:00Z"},{"doi":"10.1093/plcell/koac071","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"external_id":{"pmid":["35218346"],"isi":["000767438800001"]},"oa":1,"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"month":"06","author":[{"full_name":"Dahhan, DA","first_name":"DA","last_name":"Dahhan"},{"first_name":"GD","last_name":"Reynolds","full_name":"Reynolds, GD"},{"full_name":"Cárdenas, JJ","first_name":"JJ","last_name":"Cárdenas"},{"first_name":"D","last_name":"Eeckhout","full_name":"Eeckhout, D"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson"},{"full_name":"Yperman, K","first_name":"K","last_name":"Yperman"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vang","first_name":"N","full_name":"Vang, N"},{"last_name":"Yan","first_name":"X","full_name":"Yan, X"},{"first_name":"I","last_name":"Hwang","full_name":"Hwang, I"},{"full_name":"Heese, A","last_name":"Heese","first_name":"A"},{"last_name":"De Jaeger","first_name":"G","full_name":"De Jaeger, G"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"first_name":"J","last_name":"Pan","full_name":"Pan, J"},{"full_name":"Bednarek, SY","last_name":"Bednarek","first_name":"SY"}],"volume":34,"date_updated":"2023-08-02T14:46:48Z","date_created":"2022-03-08T13:47:51Z","pmid":1,"acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","year":"2022","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publisher":"Oxford Academic","publication_status":"published","date_published":"2022-06-01T00:00:00Z","citation":{"ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 2022;34(6):2150-2173. doi:10.1093/plcell/koac071","ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","ieee":"D. Dahhan et al., “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” Plant Cell, vol. 34, no. 6. Oxford Academic, pp. 2150–2173, 2022.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. Oxford Academic. https://doi.org/10.1093/plcell/koac071","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell, vol. 34, no. 6, Oxford Academic, 2022, pp. 2150–73, doi:10.1093/plcell/koac071.","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell. Oxford Academic, 2022. https://doi.org/10.1093/plcell/koac071."},"publication":"Plant Cell","page":"2150-2173","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","_id":"10841","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 34","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","status":"public","issue":"6","abstract":[{"text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.","lang":"eng"}],"type":"journal_article"},{"article_type":"original","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ieee":"Q. Lu et al., “Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 11. Proceedings of the National Academy of Sciences, 2022.","apa":"Lu, Q., Zhang, Y., Hellner, J., Giannini, C., Xu, X., Pauwels, J., … Russinova, E. (2022). Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2118220119","ista":"Lu Q, Zhang Y, Hellner J, Giannini C, Xu X, Pauwels J, Ma Q, Dejonghe W, Han H, Van De Cotte B, Impens F, Gevaert K, De Smet I, Friml J, Molina DM, Russinova E. 2022. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 119(11), e2118220119.","ama":"Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(11). doi:10.1073/pnas.2118220119","chicago":"Lu, Qing, Yonghong Zhang, Joakim Hellner, Caterina Giannini, Xiangyu Xu, Jarne Pauwels, Qian Ma, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2118220119.","short":"Q. Lu, Y. Zhang, J. Hellner, C. Giannini, X. Xu, J. Pauwels, Q. Ma, W. Dejonghe, H. Han, B. Van De Cotte, F. Impens, K. Gevaert, I. De Smet, J. Friml, D.M. Molina, E. Russinova, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 11, e2118220119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2118220119."},"date_published":"2022-03-07T00:00:00Z","scopus_import":"1","day":"07","has_accepted_license":"1","article_processing_charge":"No","ddc":["580"],"title":"Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling","status":"public","intvolume":" 119","_id":"10888","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2022_PNAS_Lu.pdf","creator":"dernst","content_type":"application/pdf","file_size":2169534,"file_id":"10910","relation":"main_file","success":1,"checksum":"83e0fea7919570d0b519b41193342571","date_created":"2022-03-21T09:19:47Z","date_updated":"2022-03-21T09:19:47Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Despite the growing interest in using chemical genetics in plant research, small molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or posttranslational modifications, allows the discovery of drug targets or the study of protein–metabolite and protein–protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf, thus revealing cross-talk between brassinosteroid and auxin signaling."}],"issue":"11","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["35254915"],"isi":["000771756300008"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2118220119","month":"03","publication_identifier":{"eissn":["1091-6490"]},"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"JiFr"}],"acknowledgement":"We thank Yanhai Yin for providing the anti-BES1 antibody, Johan Winne and Brenda Callebaut for synthesizing bikinin, Yuki Kondo and Hiroo Fukuda for published materials, Tomasz Nodzy\u0003nski for useful advice, and Martine De Cock for help in preparing the manuscript. This\r\nwork was supported by the China Scholarship Council for predoctoral (Q.L. and X.X.) and postdoctoral (Y.Z.) fellowships; the Agency for Innovation by Science and Technology for a predoctoral fellowship (W.D.); the Research Foundation-Flanders, Projects G009018N and G002121N (E.R.); and the VIB TechWatch Fund (E.R.).","year":"2022","pmid":1,"date_updated":"2023-08-03T06:06:27Z","date_created":"2022-03-20T23:01:39Z","volume":119,"author":[{"full_name":"Lu, Qing","first_name":"Qing","last_name":"Lu"},{"first_name":"Yonghong","last_name":"Zhang","full_name":"Zhang, Yonghong"},{"last_name":"Hellner","first_name":"Joakim","full_name":"Hellner, Joakim"},{"last_name":"Giannini","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina"},{"full_name":"Xu, Xiangyu","first_name":"Xiangyu","last_name":"Xu"},{"first_name":"Jarne","last_name":"Pauwels","full_name":"Pauwels, Jarne"},{"full_name":"Ma, Qian","last_name":"Ma","first_name":"Qian"},{"full_name":"Dejonghe, Wim","first_name":"Wim","last_name":"Dejonghe"},{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van De Cotte, Brigitte","first_name":"Brigitte","last_name":"Van De Cotte"},{"first_name":"Francis","last_name":"Impens","full_name":"Impens, Francis"},{"full_name":"Gevaert, Kris","last_name":"Gevaert","first_name":"Kris"},{"last_name":"De Smet","first_name":"Ive","full_name":"De Smet, Ive"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"last_name":"Molina","first_name":"Daniel Martinez","full_name":"Molina, Daniel Martinez"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"}],"article_number":"e2118220119","file_date_updated":"2022-03-21T09:19:47Z"},{"author":[{"last_name":"Wang","first_name":"Ren","full_name":"Wang, Ren"},{"first_name":"Ellie","last_name":"Himschoot","full_name":"Himschoot, Ellie"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"first_name":"Marie","last_name":"Boudsocq","full_name":"Boudsocq, Marie"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"}],"related_material":{"link":[{"url":"https://doi.org/10.3389/fpls.2022.1100792","relation":"erratum"}]},"date_updated":"2023-08-03T12:01:47Z","date_created":"2022-07-17T22:01:54Z","volume":13,"acknowledgement":"RW and JC predoctoral fellows that were supported by the Chinese Science Counsil. The IPS2 benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).\r\nWe thank Jen Sheen for establishing and generously sharing the CKP family clone sets, and for providing useful feedback on the manuscript.","year":"2022","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Frontiers","file_date_updated":"2022-07-18T08:05:15Z","article_number":"862398","doi":"10.3389/fpls.2022.862398","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["35783951"],"isi":["000819250500001"]},"quality_controlled":"1","isi":1,"month":"06","publication_identifier":{"eissn":["1664-462X"]},"oa_version":"Published Version","file":[{"file_name":"2022_FrontiersPlantScience_Wang.pdf","access_level":"open_access","creator":"dernst","file_size":5040638,"content_type":"application/pdf","file_id":"11596","relation":"main_file","date_created":"2022-07-18T08:05:15Z","date_updated":"2022-07-18T08:05:15Z","success":1,"checksum":"95313515637c0f84de591d204375d764"}],"_id":"11589","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","ddc":["580"],"status":"public","intvolume":" 13","abstract":[{"text":"Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana.","lang":"eng"}],"type":"journal_article","date_published":"2022-06-16T00:00:00Z","publication":"Frontiers in Plant Science","citation":{"ista":"Wang R, Himschoot E, Chen J, Boudsocq M, Geelen D, Friml J, Beeckman T, Vanneste S. 2022. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 13, 862398.","ieee":"R. Wang et al., “Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana,” Frontiers in Plant Science, vol. 13. Frontiers, 2022.","apa":"Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste, S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2022.862398","ama":"Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 2022;13. doi:10.3389/fpls.2022.862398","chicago":"Wang, Ren, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří Friml, Tom Beeckman, and Steffen Vanneste. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” Frontiers in Plant Science. Frontiers, 2022. https://doi.org/10.3389/fpls.2022.862398.","mla":"Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” Frontiers in Plant Science, vol. 13, 862398, Frontiers, 2022, doi:10.3389/fpls.2022.862398.","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022)."},"article_type":"original","day":"16","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"scopus_import":"1","keyword":["Multidisciplinary"],"day":"25","article_processing_charge":"No","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences","citation":{"chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2121058119.","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences 119 (2022).","mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences, vol. 119, no. 31, e2121058119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2121058119.","ieee":"L. Li et al., “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” Proceedings of the National Academy of Sciences, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., & Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2121058119","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. 119(31), e2121058119.","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences. 2022;119(31). doi:10.1073/pnas.2121058119"},"article_type":"original","date_published":"2022-07-25T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term."}],"issue":"31","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11723","ddc":["580"],"status":"public","title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","intvolume":" 119","file":[{"creator":"dernst","file_size":2506262,"content_type":"application/pdf","file_name":"2022_PNAS_Li.pdf","access_level":"open_access","date_updated":"2022-08-08T07:42:09Z","date_created":"2022-08-08T07:42:09Z","success":1,"checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","file_id":"11747","relation":"main_file"}],"oa_version":"Published Version","month":"07","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351"}],"doi":"10.1073/pnas.2121058119","language":[{"iso":"eng"}],"article_number":"e2121058119","file_date_updated":"2022-08-08T07:42:09Z","acknowledgement":"We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”","year":"2022","pmid":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publisher":"Proceedings of the National Academy of Sciences","author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li","full_name":"Li, Lanxin"},{"last_name":"Chen","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang"},{"first_name":"Saqer S.","last_name":"Alotaibi","full_name":"Alotaibi, Saqer S."},{"full_name":"Pěnčík, Aleš","first_name":"Aleš","last_name":"Pěnčík"},{"full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2022-08-04T20:06:49Z","date_updated":"2023-08-03T12:43:53Z","volume":119},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"4816-4839","publication":"The Plant Cell","citation":{"ama":"Tian Z, Zhang Y, Zhu L, et al. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. 2022;34(12):4816-4839. doi:10.1093/plcell/koac270","ista":"Tian Z, Zhang Y, Zhu L, Jiang B, Wang H, Gao R, Friml J, Xiao G. 2022. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. 34(12), 4816–4839.","ieee":"Z. Tian et al., “Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum),” The Plant Cell, vol. 34, no. 12. Oxford University Press, pp. 4816–4839, 2022.","apa":"Tian, Z., Zhang, Y., Zhu, L., Jiang, B., Wang, H., Gao, R., … Xiao, G. (2022). Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac270","mla":"Tian, Z., et al. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” The Plant Cell, vol. 34, no. 12, Oxford University Press, 2022, pp. 4816–39, doi:10.1093/plcell/koac270.","short":"Z. Tian, Y. Zhang, L. Zhu, B. Jiang, H. Wang, R. Gao, J. Friml, G. Xiao, The Plant Cell 34 (2022) 4816–4839.","chicago":"Tian, Z, Yuzhou Zhang, L Zhu, B Jiang, H Wang, R Gao, Jiří Friml, and G Xiao. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” The Plant Cell. Oxford University Press, 2022. https://doi.org/10.1093/plcell/koac270."},"date_published":"2022-12-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Strigolactones (SLs) are a class of phytohormones that regulate plant shoot branching and adventitious root development. However, little is known regarding the role of SLs in controlling the behavior of the smallest unit of the organism, the single cell. Here, taking advantage of a classic single-cell model offered by the cotton (Gossypium hirsutum) fiber cell, we show that SLs, whose biosynthesis is fine-tuned by gibberellins (GAs), positively regulate cell elongation and cell wall thickness by promoting the biosynthesis of very-long-chain fatty acids (VLCFAs) and cellulose, respectively. Furthermore, we identified two layers of transcription factors (TFs) involved in the hierarchical regulation of this GA-SL crosstalk. The top-layer TF GROWTH-REGULATING FACTOR 4 (GhGRF4) directly activates expression of the SL biosynthetic gene DWARF27 (D27) to increase SL accumulation in fiber cells and GAs induce GhGRF4 expression. SLs induce the expression of four second-layer TF genes (GhNAC100-2, GhBLH51, GhGT2, and GhB9SHZ1), which transmit SL signals downstream to two ketoacyl-CoA synthase genes (KCS) and three cellulose synthase (CesA) genes by directly activating their transcription. Finally, the KCS and CesA enzymes catalyze the biosynthesis of very long chain fatty acids and cellulose, respectively, to regulate development of high-grade cotton fibers. In addition to providing a theoretical basis for cotton fiber improvement, our results shed light on SL signaling in plant development at the single-cell level.","lang":"eng"}],"issue":"12","status":"public","ddc":["580"],"title":"Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum)","intvolume":" 34","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12053","file":[{"date_updated":"2023-01-20T08:29:12Z","date_created":"2023-01-20T08:29:12Z","success":1,"checksum":"1c606d9545f29dfca15235f69ad27b58","file_id":"12318","relation":"main_file","creator":"dernst","file_size":3282540,"content_type":"application/pdf","file_name":"2022_PlantCell_Tian.pdf","access_level":"open_access"}],"oa_version":"Published Version","month":"12","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF"}],"external_id":{"isi":["000852753000001"],"pmid":["36040191"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/plcell/koac270","file_date_updated":"2023-01-20T08:29:12Z","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"acknowledgement":"This work was supported by the National Natural Science Foundation of China (32070549), Shaanxi Youth Entrusted Talent Program (20190205), Fundamental Research Funds for the Central Universities (GK202002005 and GK202201017), Young Elite Scientists Sponsorship Program by China Association for Science and Technology (CAST) (2019-2021QNRC001), State Key Laboratory of Cotton Biology Open Fund (CB2020A12 and CB2021A21) and FWF Stand-alone Project (P29988).","year":"2022","pmid":1,"date_created":"2022-09-07T14:19:39Z","date_updated":"2023-08-03T13:41:06Z","volume":34,"author":[{"full_name":"Tian, Z","first_name":"Z","last_name":"Tian"},{"first_name":"Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou"},{"full_name":"Zhu, L","last_name":"Zhu","first_name":"L"},{"first_name":"B","last_name":"Jiang","full_name":"Jiang, B"},{"last_name":"Wang","first_name":"H","full_name":"Wang, H"},{"full_name":"Gao, R","first_name":"R","last_name":"Gao"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Xiao, G","first_name":"G","last_name":"Xiao"}],"related_material":{"link":[{"url":"https://doi.org/10.1093/plcell/koac342","relation":"erratum"}]}},{"month":"09","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-022-32888-8","language":[{"iso":"eng"}],"external_id":{"isi":["000848744900004"],"pmid":["36050482"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"file_date_updated":"2022-09-08T07:46:16Z","article_number":"5147","author":[{"full_name":"Konstantinova, N","last_name":"Konstantinova","first_name":"N"},{"full_name":"Hörmayer, Lukas","last_name":"Hörmayer","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"full_name":"Keshkeih, R","last_name":"Keshkeih","first_name":"R"},{"full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Di Donato, M","last_name":"Di Donato","first_name":"M"},{"full_name":"Retzer, K","first_name":"K","last_name":"Retzer"},{"full_name":"Moulinier-Anzola, J","first_name":"J","last_name":"Moulinier-Anzola"},{"full_name":"Schwihla, M","first_name":"M","last_name":"Schwihla"},{"first_name":"B","last_name":"Korbei","full_name":"Korbei, B"},{"last_name":"Geisler","first_name":"M","full_name":"Geisler, M"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Luschnig, C","last_name":"Luschnig","first_name":"C"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-33198-9","relation":"erratum"}]},"date_updated":"2023-08-03T13:40:32Z","date_created":"2022-09-07T14:19:26Z","volume":13,"acknowledgement":"We would like to thank Tatsuo Sakai, Marcus Heisler, Toru Fujiwara, Lucia Strader, Christian Hardtke, Malcolm Bennett, Claus Schwechheimer, Gerd Jürgens and Remko Offringa for sharing published materials and Alba Grau Gimeno for support. We are greatly indebted to Bert de Rybel for supporting N.K. and M.G. to work on the final stages of manuscript preparation as postdocs in his laboratory. A full-length SOR1 cDNA clone (J090099M14) was obtained from the National Agriculture and Food Research Organization (NARO, Japan). Support by the Multiscale Imaging Core Facility at the BOKU is greatly acknowledged. This work has been supported by grants from the Austrian Science Fund (FWF P25931-B16; P31493-B25 to Christian Luschnig; I3630-B25 to Jiří Friml; P30850-B32 to Barbara Korbei) and from the Swiss National Funds (31003A-165877/1 to Markus Geisler) and the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant agreement No 885979 to Matouš Glanc).","year":"2022","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","day":"01","has_accepted_license":"1","article_processing_charge":"No","date_published":"2022-09-01T00:00:00Z","publication":"Nature Communications","citation":{"ama":"Konstantinova N, Hörmayer L, Glanc M, et al. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. 2022;13. doi:10.1038/s41467-022-32888-8","ieee":"N. Konstantinova et al., “WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions,” Nature Communications, vol. 13. Springer Nature, 2022.","apa":"Konstantinova, N., Hörmayer, L., Glanc, M., Keshkeih, R., Tan, S., Di Donato, M., … Luschnig, C. (2022). WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-32888-8","ista":"Konstantinova N, Hörmayer L, Glanc M, Keshkeih R, Tan S, Di Donato M, Retzer K, Moulinier-Anzola J, Schwihla M, Korbei B, Geisler M, Friml J, Luschnig C. 2022. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. 13, 5147.","short":"N. Konstantinova, L. Hörmayer, M. Glanc, R. Keshkeih, S. Tan, M. Di Donato, K. Retzer, J. Moulinier-Anzola, M. Schwihla, B. Korbei, M. Geisler, J. Friml, C. Luschnig, Nature Communications 13 (2022).","mla":"Konstantinova, N., et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” Nature Communications, vol. 13, 5147, Springer Nature, 2022, doi:10.1038/s41467-022-32888-8.","chicago":"Konstantinova, N, Lukas Hörmayer, Matous Glanc, R Keshkeih, Shutang Tan, M Di Donato, K Retzer, et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-32888-8."},"article_type":"original","abstract":[{"text":"Directionality in the intercellular transport of the plant hormone auxin is determined by polar plasma membrane localization of PIN-FORMED (PIN) auxin transport proteins. However, apart from PIN phosphorylation at conserved motifs, no further determinants explicitly controlling polar PIN sorting decisions have been identified. Here we present Arabidopsis WAVY GROWTH 3 (WAV3) and closely related RING-finger E3 ubiquitin ligases, whose loss-of-function mutants show a striking apical-to-basal polarity switch in PIN2 localization in root meristem cells. WAV3 E3 ligases function as essential determinants for PIN polarity, acting independently from PINOID/WAG-dependent PIN phosphorylation. They antagonize ectopic deposition of de novo synthesized PIN proteins already immediately following completion of cell division, presumably via preventing PIN sorting into basal, ARF GEF-mediated trafficking. Our findings reveal an involvement of E3 ligases in the selective targeting of apically localized PINs in higher plants.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2022-09-08T07:46:16Z","date_created":"2022-09-08T07:46:16Z","success":1,"checksum":"43336758c89cd6c045839089af070afe","file_id":"12063","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":6678579,"file_name":"2022_NatureCommunications_Konstantinova.pdf","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12052","status":"public","ddc":["580"],"title":"WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions","intvolume":" 13"},{"issue":"7927","abstract":[{"lang":"eng","text":"Polar auxin transport is unique to plants and coordinates their growth and development1,2. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and drive polar auxin transport3,4; however, their structures and transport mechanisms remain largely unknown. Here, we report three inward-facing conformation structures of Arabidopsis thaliana PIN1: the apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The transmembrane domain of PIN1 shares a conserved NhaA fold5. In the substrate-bound structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding. NPA competes with IAA for the same site at the intracellular pocket, but with a much higher affinity. These findings inform our understanding of the substrate recognition and transport mechanisms of PINs and set up a framework for future research on directional auxin transport, one of the most crucial processes underlying plant development."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":32344580,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_Nature_Yang.pdf","success":1,"checksum":"3136a585f8e1c7e73b5e1418b3d01898","date_created":"2022-09-08T08:02:54Z","date_updated":"2022-09-08T08:02:54Z","file_id":"12064","relation":"main_file"}],"intvolume":" 609","title":"Structural insights into auxin recognition and efflux by Arabidopsis PIN1","status":"public","ddc":["580"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12054","has_accepted_license":"1","article_processing_charge":"No","day":"02","scopus_import":"1","date_published":"2022-08-02T00:00:00Z","page":"611-615","article_type":"original","citation":{"chicago":"Yang, Z, J Xia, J Hong, C Zhang, H Wei, W Ying, C Sun, et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05143-9.","mla":"Yang, Z., et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” Nature, vol. 609, no. 7927, Springer Nature, 2022, pp. 611–15, doi:10.1038/s41586-022-05143-9.","short":"Z. Yang, J. Xia, J. Hong, C. Zhang, H. Wei, W. Ying, C. Sun, L. Sun, Y. Mao, Y. Gao, S. Tan, J. Friml, D. Li, X. Liu, L. Sun, Nature 609 (2022) 611–615.","ista":"Yang Z, Xia J, Hong J, Zhang C, Wei H, Ying W, Sun C, Sun L, Mao Y, Gao Y, Tan S, Friml J, Li D, Liu X, Sun L. 2022. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. 609(7927), 611–615.","ieee":"Z. Yang et al., “Structural insights into auxin recognition and efflux by Arabidopsis PIN1,” Nature, vol. 609, no. 7927. Springer Nature, pp. 611–615, 2022.","apa":"Yang, Z., Xia, J., Hong, J., Zhang, C., Wei, H., Ying, W., … Sun, L. (2022). Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05143-9","ama":"Yang Z, Xia J, Hong J, et al. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. 2022;609(7927):611-615. doi:10.1038/s41586-022-05143-9"},"publication":"Nature","file_date_updated":"2022-09-08T08:02:54Z","volume":609,"date_created":"2022-09-07T14:19:52Z","date_updated":"2023-08-03T13:41:44Z","author":[{"first_name":"Z","last_name":"Yang","full_name":"Yang, Z"},{"full_name":"Xia, J","first_name":"J","last_name":"Xia"},{"last_name":"Hong","first_name":"J","full_name":"Hong, J"},{"first_name":"C","last_name":"Zhang","full_name":"Zhang, C"},{"full_name":"Wei, H","last_name":"Wei","first_name":"H"},{"full_name":"Ying, W","first_name":"W","last_name":"Ying"},{"full_name":"Sun, C","first_name":"C","last_name":"Sun"},{"last_name":"Sun","first_name":"L","full_name":"Sun, L"},{"full_name":"Mao, Y","first_name":"Y","last_name":"Mao"},{"full_name":"Gao, Y","last_name":"Gao","first_name":"Y"},{"full_name":"Tan, S","first_name":"S","last_name":"Tan"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Li, D","first_name":"D","last_name":"Li"},{"full_name":"Liu, X","first_name":"X","last_name":"Liu"},{"full_name":"Sun, L","last_name":"Sun","first_name":"L"}],"department":[{"_id":"JiFr"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2022","acknowledgement":"We thank the Cryo-EM Center of the University of Science and Technology of China (USTC) and the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science, for the EM facility support; we thank B. Zhu, X. Huang and all the other staff members for their technical support on cryo-EM data collection. We thank J. Ren for his technical support with the transport assays and M. Seeger for providing the sybody libraries. This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB 37020204 to D.L. and XDB37020103 to Linfeng Sun), National Natural Science Foundation of China (82151215 and 31870726 to D.L., 31900885 to X.L., and 31870732 to Linfeng Sun), Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun), the Fundamental Research Funds for the Central Universities (WK9100000031 to Linfeng Sun), and the USTC Research Funds of the Double First-Class Initiative (YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation, and a Young Scholar Award from the Cyrus Tang Foundation.","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1038/s41586-022-05143-9","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000848082900002"],"pmid":["35917925"]}},{"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"month":"12","doi":"10.1083/jcb.202203139","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["36260289"],"isi":["000932958800001"]},"quality_controlled":"1","isi":1,"file_date_updated":"2023-01-23T10:30:11Z","article_number":"e202203139","author":[{"full_name":"Zhao, Jierui","first_name":"Jierui","last_name":"Zhao"},{"last_name":"Bui","first_name":"Mai Thu","full_name":"Bui, Mai Thu"},{"last_name":"Ma","first_name":"Juncai","full_name":"Ma, Juncai"},{"full_name":"Künzl, Fabian","first_name":"Fabian","last_name":"Künzl"},{"full_name":"Picchianti, Lorenzo","first_name":"Lorenzo","last_name":"Picchianti"},{"last_name":"De La Concepcion","first_name":"Juan Carlos","full_name":"De La Concepcion, Juan Carlos"},{"full_name":"Chen, Yixuan","first_name":"Yixuan","last_name":"Chen"},{"full_name":"Petsangouraki, Sofia","first_name":"Sofia","last_name":"Petsangouraki"},{"full_name":"Mohseni, Azadeh","first_name":"Azadeh","last_name":"Mohseni"},{"full_name":"García-Leon, Marta","last_name":"García-Leon","first_name":"Marta"},{"full_name":"Gomez, Marta Salas","last_name":"Gomez","first_name":"Marta Salas"},{"full_name":"Giannini, Caterina","first_name":"Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"first_name":"Dubois","last_name":"Gwennogan","full_name":"Gwennogan, Dubois"},{"first_name":"Roksolana","last_name":"Kobylinska","full_name":"Kobylinska, Roksolana"},{"full_name":"Clavel, Marion","first_name":"Marion","last_name":"Clavel"},{"full_name":"Schellmann, Swen","last_name":"Schellmann","first_name":"Swen"},{"last_name":"Jaillais","first_name":"Yvon","full_name":"Jaillais, Yvon"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Kang, Byung-Ho","last_name":"Kang","first_name":"Byung-Ho"},{"first_name":"Yasin","last_name":"Dagdas","full_name":"Dagdas, Yasin"}],"volume":221,"date_created":"2023-01-12T11:57:10Z","date_updated":"2023-08-03T14:20:15Z","pmid":1,"acknowledgement":"We thank Suayip Ustün, Karin Schumacher, Erika Isono, Gerd Juergens, Takashi Ueda, Daniel Hofius, and Liwen Jiang for sharing published materials.\r\nWe acknowledge funding from Austrian Academy of Sciences, Austrian Science Fund (FWF, P 32355, P 34944), Austrian Science Fund (FWF-SFB F79), Vienna Science and Technology\r\nFund (WWTF, LS17-047) to Y. Dagdas; Austrian Academy of Sciences DOC Fellowship to J. Zhao, Marie Curie VIP2 Fellowship to J.C. De La Concepcion and M. Clavel; Hong Kong Research Grant Council (GRF14121019, 14113921, AoE/M-05/12, C4002-17G) to B.-H. Kang. We thank Vienna Biocenter Core Facilities (VBCF) Protein Chemistry, Biooptics, Plant Sciences, Molecular Biology, and Protein Technologies. We thank J. Matthew Watson\r\nand members of the Dagdas lab for the critical reading and editing of the manuscript.","year":"2022","department":[{"_id":"JiFr"}],"publisher":"Rockefeller University Press","publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","keyword":["Cell Biology"],"date_published":"2022-12-01T00:00:00Z","citation":{"mla":"Zhao, Jierui, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” Journal of Cell Biology, vol. 221, no. 12, e202203139, Rockefeller University Press, 2022, doi:10.1083/jcb.202203139.","short":"J. Zhao, M.T. Bui, J. Ma, F. Künzl, L. Picchianti, J.C. De La Concepcion, Y. Chen, S. Petsangouraki, A. Mohseni, M. García-Leon, M.S. Gomez, C. Giannini, D. Gwennogan, R. Kobylinska, M. Clavel, S. Schellmann, Y. Jaillais, J. Friml, B.-H. Kang, Y. Dagdas, Journal of Cell Biology 221 (2022).","chicago":"Zhao, Jierui, Mai Thu Bui, Juncai Ma, Fabian Künzl, Lorenzo Picchianti, Juan Carlos De La Concepcion, Yixuan Chen, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” Journal of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202203139.","ama":"Zhao J, Bui MT, Ma J, et al. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 2022;221(12). doi:10.1083/jcb.202203139","ista":"Zhao J, Bui MT, Ma J, Künzl F, Picchianti L, De La Concepcion JC, Chen Y, Petsangouraki S, Mohseni A, García-Leon M, Gomez MS, Giannini C, Gwennogan D, Kobylinska R, Clavel M, Schellmann S, Jaillais Y, Friml J, Kang B-H, Dagdas Y. 2022. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 221(12), e202203139.","apa":"Zhao, J., Bui, M. T., Ma, J., Künzl, F., Picchianti, L., De La Concepcion, J. C., … Dagdas, Y. (2022). Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202203139","ieee":"J. Zhao et al., “Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole,” Journal of Cell Biology, vol. 221, no. 12. Rockefeller University Press, 2022."},"publication":"Journal of Cell Biology","article_type":"original","issue":"12","abstract":[{"lang":"eng","text":"Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"12342","checksum":"050b5cc4b25e6b94fe3e3cbfe0f5c06b","success":1,"date_created":"2023-01-23T10:30:11Z","date_updated":"2023-01-23T10:30:11Z","access_level":"open_access","file_name":"2022_JCB_Zhao.pdf","content_type":"application/pdf","file_size":10365777,"creator":"dernst"}],"oa_version":"Published Version","_id":"12121","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 221","status":"public","title":"Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole","ddc":["580"]},{"has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"date_published":"2022-11-15T00:00:00Z","citation":{"ieee":"J. Huang et al., “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” Nature Communications, vol. 13. Springer Nature, 2022.","apa":"Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-34723-6","ista":"Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J, Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 13, 6960.","ama":"Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 2022;13. doi:10.1038/s41467-022-34723-6","chicago":"Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-34723-6.","short":"J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen, J. Friml, D. Zhao, Nature Communications 13 (2022).","mla":"Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” Nature Communications, vol. 13, 6960, Springer Nature, 2022, doi:10.1038/s41467-022-34723-6."},"publication":"Nature Communications","article_type":"original","abstract":[{"text":"Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"12346","relation":"main_file","date_updated":"2023-01-23T11:17:33Z","date_created":"2023-01-23T11:17:33Z","success":1,"checksum":"233922a7b9507d9d48591e6799e4526e","file_name":"2022_NatureCommunications_Huang.pdf","access_level":"open_access","creator":"dernst","file_size":3375249,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12130","intvolume":" 13","ddc":["580"],"status":"public","title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","publication_identifier":{"issn":["2041-1723"]},"month":"11","doi":"10.1038/s41467-022-34723-6","language":[{"iso":"eng"}],"external_id":{"isi":["000884426700001"],"pmid":["36379956"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2023-01-23T11:17:33Z","article_number":"6960","author":[{"first_name":"Jian","last_name":"Huang","full_name":"Huang, Jian"},{"last_name":"Zhao","first_name":"Lei","full_name":"Zhao, Lei"},{"full_name":"Malik, Shikha","last_name":"Malik","first_name":"Shikha"},{"full_name":"Gentile, Benjamin R.","first_name":"Benjamin R.","last_name":"Gentile"},{"full_name":"Xiong, Va","first_name":"Va","last_name":"Xiong"},{"full_name":"Arazi, Tzahi","last_name":"Arazi","first_name":"Tzahi"},{"first_name":"Heather A.","last_name":"Owen","full_name":"Owen, Heather A."},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Zhao","first_name":"Dazhong","full_name":"Zhao, Dazhong"}],"volume":13,"date_created":"2023-01-12T12:02:41Z","date_updated":"2023-08-04T08:52:01Z","pmid":1,"acknowledgement":"We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari for critically reading the manuscript; E. Xiong and G. Zhang for preparing some experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1 cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP, pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP spl and pin1-5 seeds. This work was supported by the US National Science Foundation (NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796) and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist Award from the Greater Milwaukee Foundation, USDA National Institute of Food and Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System Applied Research Funding Programs.","year":"2022","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","publication_status":"published"},{"article_type":"original","page":"1533-1542","publication":"Molecular Plant","citation":{"chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant. Elsevier, 2022. https://doi.org/10.1016/j.molp.2022.09.003.","mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:10.1016/j.molp.2022.09.003.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., & Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2022.09.003","ieee":"A. J. Johnson et al., “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” Molecular Plant, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 2022;15(10):1533-1542. doi:10.1016/j.molp.2022.09.003"},"date_published":"2022-10-03T00:00:00Z","keyword":["Plant Science","Molecular Biology"],"scopus_import":"1","day":"03","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","ddc":["580"],"status":"public","intvolume":" 15","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12239","file":[{"relation":"main_file","file_id":"12435","checksum":"04d5c12490052d03e4dc4412338a43dd","success":1,"date_updated":"2023-01-30T07:46:51Z","date_created":"2023-01-30T07:46:51Z","access_level":"open_access","file_name":"2022_MolecularPlant_Johnson.pdf","content_type":"application/pdf","file_size":2307251,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"issue":"10","isi":1,"quality_controlled":"1","project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000882769800009"],"pmid":["36081349"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2022.09.003","month":"10","publication_identifier":{"issn":["1674-2052"]},"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","year":"2022","pmid":1,"date_created":"2023-01-16T09:51:49Z","date_updated":"2023-08-04T09:39:24Z","volume":15,"author":[{"full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843"},{"last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer"},{"first_name":"Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso"},{"first_name":"Dana A.","last_name":"Dahhan","full_name":"Dahhan, Dana A."},{"full_name":"Bednarek, Sebastian Y.","last_name":"Bednarek","first_name":"Sebastian Y."},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"file_date_updated":"2023-01-30T07:46:51Z"},{"language":[{"iso":"eng"}],"doi":"10.3390/ijms23116352","isi":1,"quality_controlled":"1","project":[{"name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["35683031"],"isi":["000808733300001"]},"month":"06","publication_identifier":{"issn":["1422-0067"]},"date_updated":"2023-08-09T10:13:57Z","date_created":"2022-07-05T15:14:34Z","volume":23,"author":[{"full_name":"Bilanovičová, V","last_name":"Bilanovičová","first_name":"V"},{"full_name":"Rýdza, N","first_name":"N","last_name":"Rýdza"},{"full_name":"Koczka, L","first_name":"L","last_name":"Koczka"},{"first_name":"M","last_name":"Hess","full_name":"Hess, M"},{"last_name":"Feraru","first_name":"E","full_name":"Feraru, E"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Nodzyński, T","last_name":"Nodzyński","first_name":"T"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"MDPI","year":"2022","acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","pmid":1,"file_date_updated":"2022-07-06T07:36:59Z","date_published":"2022-06-06T00:00:00Z","article_type":"original","page":"6352","publication":"International Journal of Molecular Sciences","citation":{"short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” International Journal of Molecular Sciences, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:10.3390/ijms23116352.","chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” International Journal of Molecular Sciences. MDPI, 2022. https://doi.org/10.3390/ijms23116352.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 2022;23(11):6352. doi:10.3390/ijms23116352","ieee":"V. Bilanovičová et al., “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” International Journal of Molecular Sciences, vol. 23, no. 11. MDPI, p. 6352, 2022.","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., & Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms23116352","ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352."},"day":"06","article_processing_charge":"Yes","has_accepted_license":"1","oa_version":"Published Version","file":[{"file_name":"2022_IntJMolSci_Bilanovicova.pdf","access_level":"open_access","file_size":2324542,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"11492","date_created":"2022-07-06T07:36:59Z","date_updated":"2022-07-06T07:36:59Z","checksum":"e997a57a928ec9d51fad8ce824a05935","success":1}],"ddc":["570"],"status":"public","title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","intvolume":" 23","_id":"11489","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors."}],"issue":"11","type":"journal_article"},{"_id":"12144","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Adenylate cyclase activity of TIR1/AFB auxin receptors in plants","intvolume":" 611","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants."}],"issue":"7934","publication":"Nature","citation":{"ista":"Qi L, Kwiatkowski M, Chen H, Hörmayer L, Sinclair SA, Zou M, del Genio CI, Kubeš MF, Napier R, Jaworski K, Friml J. 2022. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 611(7934), 133–138.","ieee":"L. Qi et al., “Adenylate cyclase activity of TIR1/AFB auxin receptors in plants,” Nature, vol. 611, no. 7934. Springer Nature, pp. 133–138, 2022.","apa":"Qi, L., Kwiatkowski, M., Chen, H., Hörmayer, L., Sinclair, S. A., Zou, M., … Friml, J. (2022). Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05369-7","ama":"Qi L, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 2022;611(7934):133-138. doi:10.1038/s41586-022-05369-7","chicago":"Qi, Linlin, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hörmayer, Scott A Sinclair, Minxia Zou, Charo I. del Genio, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05369-7.","mla":"Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” Nature, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38, doi:10.1038/s41586-022-05369-7.","short":"L. Qi, M. Kwiatkowski, H. Chen, L. Hörmayer, S.A. Sinclair, M. Zou, C.I. del Genio, M.F. Kubeš, R. Napier, K. Jaworski, J. Friml, Nature 611 (2022) 133–138."},"article_type":"original","page":"133-138","date_published":"2022-11-03T00:00:00Z","scopus_import":"1","day":"03","article_processing_charge":"No","year":"2022","acknowledgement":"This research was supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria. We thank C. Gehring for suggestions and advice; and K. U. Torii and G. Stacey for seeds and plasmids. This project was funded by a European Research Council Advanced Grant (ETAP-742985). M.F.K. and R.N. acknowledge the support of the EU MSCA-IF project CrysPINs (792329). M.K. was supported by the project POWR.03.05.00-00-Z302/17 Universitas Copernicana Thoruniensis in Futuro–IDS “Academia Copernicana”. CIDG acknowledges support from UKRI under Future Leaders Fellowship grant number MR/T020652/1.","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"author":[{"last_name":"Qi","first_name":"Linlin","orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin"},{"last_name":"Kwiatkowski","first_name":"Mateusz","full_name":"Kwiatkowski, Mateusz"},{"full_name":"Chen, Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","last_name":"Chen","first_name":"Huihuang"},{"full_name":"Hörmayer, Lukas","last_name":"Hörmayer","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sinclair, Scott A","last_name":"Sinclair","first_name":"Scott A","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zou, Minxia","last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"full_name":"del Genio, Charo I.","first_name":"Charo I.","last_name":"del Genio"},{"full_name":"Kubeš, Martin F.","first_name":"Martin F.","last_name":"Kubeš"},{"first_name":"Richard","last_name":"Napier","full_name":"Napier, Richard"},{"full_name":"Jaworski, Krzysztof","last_name":"Jaworski","first_name":"Krzysztof"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"}],"date_created":"2023-01-12T12:06:05Z","date_updated":"2023-10-03T11:04:53Z","volume":611,"ec_funded":1,"main_file_link":[{"url":"http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf","open_access":"1"}],"oa":1,"external_id":{"pmid":["36289340"],"isi":["000875061600013"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41586-022-05369-7","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"11","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]}},{"issue":"23","abstract":[{"lang":"eng","text":"Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth."}],"type":"journal_article","oa_version":"None","intvolume":" 57","title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12120","article_processing_charge":"No","day":"05","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"scopus_import":"1","date_published":"2022-12-05T00:00:00Z","page":"2638-2651.e6","article_type":"original","citation":{"ieee":"H. Xiao et al., “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” Developmental Cell, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022.","apa":"Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022). Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2022.11.006","ista":"Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6.","ama":"Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 2022;57(23):2638-2651.e6. doi:10.1016/j.devcel.2022.11.006","chicago":"Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.11.006.","short":"H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6.","mla":"Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental Cell, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:10.1016/j.devcel.2022.11.006."},"publication":"Developmental Cell","volume":57,"date_created":"2023-01-12T11:57:00Z","date_updated":"2023-10-04T08:23:20Z","author":[{"full_name":"Xiao, Huixin","last_name":"Xiao","first_name":"Huixin"},{"full_name":"Hu, Yumei","first_name":"Yumei","last_name":"Hu"},{"full_name":"Wang, Yaping","last_name":"Wang","first_name":"Yaping"},{"full_name":"Cheng, Jinkui","first_name":"Jinkui","last_name":"Cheng"},{"first_name":"Jinyi","last_name":"Wang","full_name":"Wang, Jinyi"},{"first_name":"Guojingwei","last_name":"Chen","full_name":"Chen, Guojingwei"},{"last_name":"Li","first_name":"Qian","full_name":"Li, Qian"},{"first_name":"Shuwei","last_name":"Wang","full_name":"Wang, Shuwei"},{"full_name":"Wang, Yalu","last_name":"Wang","first_name":"Yalu"},{"full_name":"Wang, Shao-Shuai","last_name":"Wang","first_name":"Shao-Shuai"},{"last_name":"Wang","first_name":"Yi","full_name":"Wang, Yi"},{"full_name":"Xuan, Wei","last_name":"Xuan","first_name":"Wei"},{"last_name":"Li","first_name":"Zhen","full_name":"Li, Zhen"},{"full_name":"Guo, Yan","first_name":"Yan","last_name":"Guo"},{"first_name":"Zhizhong","last_name":"Gong","full_name":"Gong, Zhizhong"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"last_name":"Zhang","first_name":"Jing","full_name":"Zhang, Jing"}],"publisher":"Elsevier","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2022","acknowledgement":"The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu Jiang for helpful discussions. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153).","publication_identifier":{"issn":["1534-5807"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2022.11.006","isi":1,"quality_controlled":"1","external_id":{"isi":["000919603800005"],"pmid":["36473460"]}},{"article_processing_charge":"No","has_accepted_license":"1","day":"15","scopus_import":"1","date_published":"2022-09-15T00:00:00Z","page":"575-581","article_type":"original","citation":{"apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05187-x","ieee":"J. Friml et al., “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” Nature, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 2022;609(7927):575-581. doi:10.1038/s41586-022-05187-x","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05187-x.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” Nature, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:10.1038/s41586-022-05187-x."},"publication":"Nature","issue":"7927","abstract":[{"lang":"eng","text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization."}],"type":"journal_article","file":[{"creator":"amally","content_type":"application/pdf","file_size":79774945,"access_level":"open_access","file_name":"Friml Nature 2022_merged.pdf","success":1,"checksum":"a6055c606aefb900bf62ae3e7d15f921","date_created":"2023-11-02T17:12:37Z","date_updated":"2023-11-02T17:12:37Z","file_id":"14483","relation":"main_file"}],"oa_version":"Submitted Version","intvolume":" 609","ddc":["580"],"status":"public","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","_id":"12291","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"month":"09","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"doi":"10.1038/s41586-022-05187-x","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000851357500002"],"pmid":["36071161"]},"ec_funded":1,"file_date_updated":"2023-11-02T17:12:37Z","volume":609,"date_updated":"2023-11-07T08:16:09Z","date_created":"2023-01-16T10:04:48Z","author":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C"},{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","first_name":"Zuzana","last_name":"Gelová","full_name":"Gelová, Zuzana"},{"last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","first_name":"Aline"},{"first_name":"Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge"},{"last_name":"Živanović","first_name":"Branka D.","full_name":"Živanović, Branka D."},{"full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","last_name":"Zou"},{"full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986","last_name":"Fiedler","first_name":"Lukas"},{"full_name":"Giannini, Caterina","last_name":"Giannini","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","last_name":"Hrtyan","first_name":"Mónika"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"first_name":"Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","last_name":"Randuch","full_name":"Randuch, Marek"},{"first_name":"Nikola","last_name":"Rýdza","full_name":"Rýdza, Nikola"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan"},{"id":"e3736151-106c-11ec-b916-c2558e2762c6","first_name":"Anastasiia","last_name":"Teplova","full_name":"Teplova, Anastasiia"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"}],"publisher":"Springer Nature","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"publication_status":"published","pmid":1,"year":"2022","acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910)."},{"has_accepted_license":"1","article_processing_charge":"No","day":"20","page":"248","citation":{"ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","apa":"Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","mla":"Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626."},"date_published":"2022-07-20T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth."}],"status":"public","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","ddc":["575"],"_id":"11626","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"file_id":"11645","relation":"main_file","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","date_created":"2022-07-25T09:08:47Z","date_updated":"2022-07-25T09:08:47Z","access_level":"open_access","file_name":"Thesis_Gallei.pdf","creator":"mgallei","content_type":"application/pdf","file_size":9730864},{"checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","date_created":"2022-07-25T09:09:09Z","date_updated":"2022-07-25T09:39:58Z","relation":"source_file","file_id":"11646","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":19560720,"creator":"mgallei","access_level":"closed","file_name":"Thesis_Gallei_source.docx"},{"creator":"mgallei","content_type":"application/pdf","file_size":24542837,"access_level":"closed","description":"This is the print version of the thesis including the full appendix","file_name":"Thesis_Gallei_to_print.pdf","checksum":"3994f7f20058941b5bb8a16886b21e71","date_updated":"2022-07-25T09:39:58Z","date_created":"2022-07-25T09:09:32Z","file_id":"11647","relation":"source_file"},{"file_id":"11650","relation":"main_file","date_updated":"2022-07-25T11:48:45Z","date_created":"2022-07-25T11:48:45Z","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","file_name":"Thesis_Gallei_Appendix.pdf","access_level":"open_access","creator":"mgallei","content_type":"application/pdf","file_size":15435966}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-019-0"]},"month":"07","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shani, Eilon","first_name":"Eilon","last_name":"Shani"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:11626","ec_funded":1,"file_date_updated":"2022-07-25T11:48:45Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"publication_status":"published","year":"2022","date_updated":"2023-11-07T08:20:13Z","date_created":"2022-07-20T11:21:53Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8931"},{"id":"9287","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7142"},{"id":"7465","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8138"},{"relation":"part_of_dissertation","status":"public","id":"6260"},{"relation":"part_of_dissertation","status":"public","id":"10411"}]},"author":[{"full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei"}]},{"oa":1,"external_id":{"isi":["000793707900005"],"pmid":["34848141"]},"project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.tplants.2021.11.006","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1360-1385"]},"month":"05","pmid":1,"acknowledgement":"The authors thank Alexandra Mally for editing the text. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 to Jiří Friml and the DOC Fellowship of the Austrian Academy of Sciences to Lanxin Li. All figures were created with BioRender.com.","year":"2022","department":[{"_id":"JiFr"}],"publisher":"Cell Press","publication_status":"published","related_material":{"record":[{"id":"11626","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin"},{"full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"volume":27,"date_created":"2021-12-05T23:01:43Z","date_updated":"2023-11-07T08:20:14Z","file_date_updated":"2023-11-02T17:00:03Z","citation":{"mla":"Li, Lanxin, et al. “Bending to Auxin: Fast Acid Growth for Tropisms.” Trends in Plant Science, vol. 27, no. 5, Cell Press, 2022, pp. 440–49, doi:10.1016/j.tplants.2021.11.006.","short":"L. Li, M.C. Gallei, J. Friml, Trends in Plant Science 27 (2022) 440–449.","chicago":"Li, Lanxin, Michelle C Gallei, and Jiří Friml. “Bending to Auxin: Fast Acid Growth for Tropisms.” Trends in Plant Science. Cell Press, 2022. https://doi.org/10.1016/j.tplants.2021.11.006.","ama":"Li L, Gallei MC, Friml J. Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. 2022;27(5):440-449. doi:10.1016/j.tplants.2021.11.006","ista":"Li L, Gallei MC, Friml J. 2022. Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. 27(5), 440–449.","apa":"Li, L., Gallei, M. C., & Friml, J. (2022). Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2021.11.006","ieee":"L. Li, M. C. Gallei, and J. Friml, “Bending to auxin: Fast acid growth for tropisms,” Trends in Plant Science, vol. 27, no. 5. Cell Press, pp. 440–449, 2022."},"publication":"Trends in Plant Science","page":"440-449","article_type":"original","date_published":"2022-05-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","_id":"10411","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 27","status":"public","title":"Bending to auxin: Fast acid growth for tropisms","ddc":["580"],"oa_version":"Submitted Version","file":[{"file_size":805779,"content_type":"application/pdf","creator":"amally","file_name":"Li Plants 2021_accepted.pdf","access_level":"open_access","date_created":"2023-11-02T17:00:03Z","date_updated":"2023-11-02T17:00:03Z","checksum":"3d94980ee1ff6bec100dd813f6a921a6","success":1,"relation":"main_file","file_id":"14480"}],"type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"The phytohormone auxin is the major growth regulator governing tropic responses including gravitropism. Auxin build-up at the lower side of stimulated shoots promotes cell expansion, whereas in roots it inhibits growth, leading to upward shoot bending and downward root bending, respectively. Yet it remains an enigma how the same signal can trigger such opposite cellular responses. In this review, we discuss several recent unexpected insights into the mechanisms underlying auxin regulation of growth, challenging several existing models. We focus on the divergent mechanisms of apoplastic pH regulation in shoots and roots revisiting the classical Acid Growth Theory and discuss coordinated involvement of multiple auxin signaling pathways. From this emerges a more comprehensive, updated picture how auxin regulates growth."}]},{"year":"2022","acknowledgement":"The research leading to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme ERC-2013-STG (grant agreement: 335691), the Austrian Science Fund (I 3033-B22), the Austrian Academy of Sciences, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy EXC-2070-390732324 (PhenoRob) and DFG grant (DJ 64/5-1).\r\nWe would like to thank the GMI/IMBA/IMP core facilities for their excellent technical support. We would like to acknowledge Dr. Sinéad A. O’Sullivan from DZNE, University of Bonn for providing anti-GFP antibodies. The authors are thankful to the Excellence University of Bonn for providing infrastructure and instrumentation facilities at the INRES-Plant Pathology department.","department":[{"_id":"JiFr"}],"publisher":"Frontiers Media","publication_status":"published","author":[{"first_name":"Kishor D.","last_name":"Ingole","full_name":"Ingole, Kishor D."},{"last_name":"Nagarajan","first_name":"Nithya","full_name":"Nagarajan, Nithya"},{"full_name":"Uhse, Simon","first_name":"Simon","last_name":"Uhse"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina"},{"first_name":"Armin","last_name":"Djamei","full_name":"Djamei, Armin"}],"volume":3,"date_created":"2023-07-16T22:01:12Z","date_updated":"2024-03-06T14:01:57Z","article_number":"1029114","file_date_updated":"2023-07-17T11:46:34Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.3389/ffunb.2022.1029114","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2673-6128"]},"month":"10","_id":"13240","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 3","ddc":["579"],"title":"Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis","status":"public","file":[{"file_size":27966699,"content_type":"application/pdf","creator":"dernst","file_name":"2023_FrontiersFungalBio_Ingole.pdf","access_level":"open_access","date_created":"2023-07-17T11:46:34Z","date_updated":"2023-07-17T11:46:34Z","checksum":"2254e0119c0749d6f7237084fefcece6","success":1,"relation":"main_file","file_id":"13242"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Ustilago maydis is a biotrophic phytopathogenic fungus that causes corn smut disease. As a well-established model system, U. maydis is genetically fully accessible with large omics datasets available and subject to various biological questions ranging from DNA-repair, RNA-transport, and protein secretion to disease biology. For many genetic approaches, tight control of transgene regulation is important. Here we established an optimised version of the Tetracycline-ON (TetON) system for U. maydis. We demonstrate the Tetracycline concentration-dependent expression of fluorescent protein transgenes and the system’s suitability for the induced expression of the toxic protein BCL2 Associated X-1 (Bax1). The Golden Gate compatible vector system contains a native minimal promoter from the mating factor a-1 encoding gene, mfa with ten copies of the tet-regulated operator (tetO) and a codon optimised Tet-repressor (tetR*) which is translationally fused to the native transcriptional corepressor Mql1 (UMAG_05501). The metabolism-independent transcriptional regulator system is functional both, in liquid culture as well as on solid media in the presence of the inducer and can become a useful tool for toxin-antitoxin studies, identification of antifungal proteins, and to study functions of toxic gene products in Ustilago maydis."}],"citation":{"mla":"Ingole, Kishor D., et al. “Tetracycline-Controlled (TetON) Gene Expression System for the Smut Fungus Ustilago Maydis.” Frontiers in Fungal Biology, vol. 3, 1029114, Frontiers Media, 2022, doi:10.3389/ffunb.2022.1029114.","short":"K.D. Ingole, N. Nagarajan, S. Uhse, C. Giannini, A. Djamei, Frontiers in Fungal Biology 3 (2022).","chicago":"Ingole, Kishor D., Nithya Nagarajan, Simon Uhse, Caterina Giannini, and Armin Djamei. “Tetracycline-Controlled (TetON) Gene Expression System for the Smut Fungus Ustilago Maydis.” Frontiers in Fungal Biology. Frontiers Media, 2022. https://doi.org/10.3389/ffunb.2022.1029114.","ama":"Ingole KD, Nagarajan N, Uhse S, Giannini C, Djamei A. Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. 2022;3. doi:10.3389/ffunb.2022.1029114","ista":"Ingole KD, Nagarajan N, Uhse S, Giannini C, Djamei A. 2022. Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. 3, 1029114.","apa":"Ingole, K. D., Nagarajan, N., Uhse, S., Giannini, C., & Djamei, A. (2022). Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. Frontiers Media. https://doi.org/10.3389/ffunb.2022.1029114","ieee":"K. D. Ingole, N. Nagarajan, S. Uhse, C. Giannini, and A. Djamei, “Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis,” Frontiers in Fungal Biology, vol. 3. Frontiers Media, 2022."},"publication":"Frontiers in Fungal Biology","article_type":"original","date_published":"2022-10-19T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"19"},{"type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"abstract":[{"lang":"eng","text":"Tropisms are among the most important growth responses for plant adaptation to the surrounding environment. One of the most common tropisms is root gravitropism. Root gravitropism enables the plant to anchor securely to the soil enabling the absorption of water and nutrients. Most of the knowledge related to the plant gravitropism has been acquired from the flowering plants, due to limited research in non-seed plants. Limited research on non-seed plants is due in large part to the lack of standard research methods. Here, we describe the experimental methods to evaluate gravitropism in representative non-seed plant species, including the non-vascular plant moss Physcomitrium patens, the early diverging extant vascular plant lycophyte Selaginella moellendorffii and fern Ceratopteris richardii. In addition, we introduce the methods used for statistical analysis of the root gravitropism in non-seed plant species."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10267","status":"public","title":"Evaluation of gravitropism in non-seed plants","intvolume":" 2368","oa_version":"None","scopus_import":"1","series_title":"MIMB","day":"14","article_processing_charge":"No","publication":"Plant Gravitropism","citation":{"chicago":"Zhang, Yuzhou, Lanxin Li, and Jiří Friml. “Evaluation of Gravitropism in Non-Seed Plants.” In Plant Gravitropism, edited by Elison B Blancaflor, 2368:43–51. MIMB. Springer Nature, 2021. https://doi.org/10.1007/978-1-0716-1677-2_2.","short":"Y. Zhang, L. Li, J. Friml, in:, E.B. Blancaflor (Ed.), Plant Gravitropism, Springer Nature, 2021, pp. 43–51.","mla":"Zhang, Yuzhou, et al. “Evaluation of Gravitropism in Non-Seed Plants.” Plant Gravitropism, edited by Elison B Blancaflor, vol. 2368, Springer Nature, 2021, pp. 43–51, doi:10.1007/978-1-0716-1677-2_2.","apa":"Zhang, Y., Li, L., & Friml, J. (2021). Evaluation of gravitropism in non-seed plants. In E. B. Blancaflor (Ed.), Plant Gravitropism (Vol. 2368, pp. 43–51). Springer Nature. https://doi.org/10.1007/978-1-0716-1677-2_2","ieee":"Y. Zhang, L. Li, and J. Friml, “Evaluation of gravitropism in non-seed plants,” in Plant Gravitropism, vol. 2368, E. B. Blancaflor, Ed. Springer Nature, 2021, pp. 43–51.","ista":"Zhang Y, Li L, Friml J. 2021.Evaluation of gravitropism in non-seed plants. In: Plant Gravitropism. Methods in Molecular Biology, vol. 2368, 43–51.","ama":"Zhang Y, Li L, Friml J. Evaluation of gravitropism in non-seed plants. In: Blancaflor EB, ed. Plant Gravitropism. Vol 2368. MIMB. Springer Nature; 2021:43-51. doi:10.1007/978-1-0716-1677-2_2"},"page":"43-51","date_published":"2021-10-14T00:00:00Z","ec_funded":1,"acknowledgement":"The Ceratopteris richardii spores were obtained from the lab of Jo Ann Banks at Purdue University. This work was supported by funding from the European Union’s Horizon 2020 research and innovation program (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), IST Fellow program and DOC Fellowship of the Austrian Academy of Sciences.","year":"2021","pmid":1,"publication_status":"published","editor":[{"first_name":"Elison B","last_name":"Blancaflor","full_name":"Blancaflor, Elison B"}],"publisher":"Springer Nature","department":[{"_id":"JiFr"}],"author":[{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","last_name":"Zhang","full_name":"Zhang, Yuzhou"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li","full_name":"Li, Lanxin"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"date_created":"2021-11-11T09:26:10Z","date_updated":"2022-08-26T09:13:00Z","volume":2368,"month":"10","publication_identifier":{"eisbn":["978-1-0716-1677-2"],"isbn":["978-1-0716-1676-5"]},"external_id":{"pmid":["34647246"]},"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"doi":"10.1007/978-1-0716-1677-2_2","language":[{"iso":"eng"}]},{"author":[{"full_name":"Hörmayer, Lukas","last_name":"Hörmayer","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous"}],"date_created":"2021-11-11T10:03:30Z","date_updated":"2022-06-03T06:47:06Z","volume":2382,"acknowledgement":"We thank B. De Rybel for allowing M.G. to work on this manuscript during a postdoc in his laboratory, and EMBO for supporting M.G. with a Long-Term fellowship (ALTF 1005-2019) during this time. We acknowledge the service and support by the Bioimaging Facility at IST Austria, and finally, we thank A. Mally for proofreading and correcting the manuscript.","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Humana Press","month":"10","publication_identifier":{"issn":["1064-3745"],"eisbn":["978-1-0716-1744-1"],"isbn":["978-1-0716-1743-4"],"eissn":["1940-6029"]},"doi":"10.1007/978-1-0716-1744-1_6","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["34705235"]},"quality_controlled":"1","abstract":[{"text":"The analysis of dynamic cellular processes such as plant cytokinesis stands and falls with live-cell time-lapse confocal imaging. Conventional approaches to time-lapse imaging of cell division in Arabidopsis root tips are tedious and have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous imaging of multiple root tips on a vertical-stage confocal microscope with automated root tracking. We also provide modifications of the basic protocol to implement this imaging method in the analysis of genetic, pharmacological or laser ablation wounding-mediated experimental manipulations. Our method dramatically improves the efficiency of cell division time-lapse imaging by increasing the throughput, while reducing the person-hour requirements of such experiments.","lang":"eng"}],"type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10268","status":"public","title":"Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy","intvolume":" 2382","day":"28","article_processing_charge":"No","scopus_import":"1","series_title":"MIMB","date_published":"2021-10-28T00:00:00Z","publication":"Plant Cell Division","citation":{"ieee":"L. Hörmayer, J. Friml, and M. Glanc, “Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy,” in Plant Cell Division, vol. 2382, Humana Press, 2021, pp. 105–114.","apa":"Hörmayer, L., Friml, J., & Glanc, M. (2021). Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In Plant Cell Division (Vol. 2382, pp. 105–114). Humana Press. https://doi.org/10.1007/978-1-0716-1744-1_6","ista":"Hörmayer L, Friml J, Glanc M. 2021.Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: Plant Cell Division. Methods in Molecular Biology, vol. 2382, 105–114.","ama":"Hörmayer L, Friml J, Glanc M. Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: Plant Cell Division. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:10.1007/978-1-0716-1744-1_6","chicago":"Hörmayer, Lukas, Jiří Friml, and Matous Glanc. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” In Plant Cell Division, 2382:105–14. MIMB. Humana Press, 2021. https://doi.org/10.1007/978-1-0716-1744-1_6.","short":"L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114.","mla":"Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” Plant Cell Division, vol. 2382, Humana Press, 2021, pp. 105–14, doi:10.1007/978-1-0716-1744-1_6."},"page":"105-114"},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear.\r\nHere, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains.\r\nPharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane.\r\nThis study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems."}],"intvolume":" 229","ddc":["580"],"title":"Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8582","file":[{"file_name":"2021_NewPhytologist_Li.pdf","access_level":"open_access","creator":"dernst","file_size":4061962,"content_type":"application/pdf","file_id":"9084","relation":"main_file","date_created":"2021-02-04T09:44:17Z","date_updated":"2021-02-04T09:44:17Z","success":1,"checksum":"b45621607b4cab97eeb1605ab58e896e"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","page":"351-369","article_type":"original","citation":{"apa":"Li, H., von Wangenheim, D., Zhang, X., Tan, S., Darwish-Miranda, N., Naramoto, S., … Friml, J. (2021). Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.16887","ieee":"H. Li et al., “Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana,” New Phytologist, vol. 229, no. 1. Wiley, pp. 351–369, 2021.","ista":"Li H, von Wangenheim D, Zhang X, Tan S, Darwish-Miranda N, Naramoto S, Wabnik KT, de Rycke R, Kaufmann W, Gütl DJ, Tejos R, Grones P, Ke M, Chen X, Dettmer J, Friml J. 2021. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 229(1), 351–369.","ama":"Li H, von Wangenheim D, Zhang X, et al. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 2021;229(1):351-369. doi:10.1111/nph.16887","chicago":"Li, Hongjiang, Daniel von Wangenheim, Xixi Zhang, Shutang Tan, Nasser Darwish-Miranda, Satoshi Naramoto, Krzysztof T Wabnik, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.16887.","short":"H. Li, D. von Wangenheim, X. Zhang, S. Tan, N. Darwish-Miranda, S. Naramoto, K.T. Wabnik, R. de Rycke, W. Kaufmann, D.J. Gütl, R. Tejos, P. Grones, M. Ke, X. Chen, J. Dettmer, J. Friml, New Phytologist 229 (2021) 351–369.","mla":"Li, Hongjiang, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” New Phytologist, vol. 229, no. 1, Wiley, 2021, pp. 351–69, doi:10.1111/nph.16887."},"publication":"New Phytologist","date_published":"2021-01-01T00:00:00Z","ec_funded":1,"file_date_updated":"2021-02-04T09:44:17Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"EvBe"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"We thank Dr Ingo Heilmann (Martin‐Luther‐University Halle‐Wittenberg) for the XVE>>PIP5K1‐YFP line, Dr Brad Day (Michigan State University) for the ndr1‐1 mutant and the complementation lines, and Dr Patricia C. Zambryski (University of California, Berkeley) for the 35S::P30‐GFP line, the Bioimaging team (IST Austria) for assistance with imaging, group members for discussions, Martine De Cock for help in preparing the manuscript and Nataliia Gnyliukh for critical reading and revision of the manuscript. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 742985) and Comisión Nacional de Investigación Científica y Tecnológica (Project CONICYT‐PAI 82130047). DvW received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007‐2013) under REA grant agreement no. 291734.","year":"2021","volume":229,"date_created":"2020-09-28T08:59:28Z","date_updated":"2023-08-04T11:01:21Z","author":[{"full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Hongjiang"},{"full_name":"von Wangenheim, Daniel","first_name":"Daniel","last_name":"von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang"},{"full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"id":"39CD9926-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8821-8236","first_name":"Nasser","last_name":"Darwish-Miranda","full_name":"Darwish-Miranda, Nasser"},{"full_name":"Naramoto, Satoshi","first_name":"Satoshi","last_name":"Naramoto"},{"first_name":"Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T"},{"full_name":"de Rycke, Riet","last_name":"de Rycke","first_name":"Riet"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter"},{"full_name":"Gütl, Daniel J","id":"381929CE-F248-11E8-B48F-1D18A9856A87","last_name":"Gütl","first_name":"Daniel J"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Grones"},{"full_name":"Ke, Meiyu","first_name":"Meiyu","last_name":"Ke"},{"full_name":"Chen, Xu","last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Dettmer","full_name":"Dettmer, Jan"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"publication_identifier":{"issn":["0028646X"],"eissn":["14698137"]},"month":"01","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000570187900001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1111/nph.16887"},{"publication_identifier":{"issn":["1467-7644","1467-7652"]},"month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["32981232"],"isi":["000577682300001"]},"isi":1,"quality_controlled":"1","doi":"10.1111/pbi.13484","language":[{"iso":"eng"}],"file_date_updated":"2021-04-12T12:29:07Z","pmid":1,"acknowledgement":"We are thankful to Professor Yuxian Zhu from Wuhan University for his extremely valuable remarks and helpful comments on the manuscript. This work was supported by the Shaanxi Natural Science Foundation (2019JQ‐062 and 2020JQ‐410), Shaanxi Youth Entrusted Talents Program (20190205), China Postdoctoral Science Foundation (2018M640947, 2020T130394), Shaanxi Postdoctoral Project (2018BSHYDZZ76), Natural Science Basic Research Plan in Shaanxi Province of China (2018JZ3006), Fundamental Research Funds for the Central Universities (GK201903064, GK201901004, GK202002005 and GK202001004), and State Key Laboratory of Cotton Biology Open Fund (CB2020A12).","year":"2021","department":[{"_id":"JiFr"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"He, P","last_name":"He","first_name":"P"},{"full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Li, H","last_name":"Li","first_name":"H"},{"first_name":"X","last_name":"Fu","full_name":"Fu, X"},{"full_name":"Shang, H","last_name":"Shang","first_name":"H"},{"first_name":"C","last_name":"Zou","full_name":"Zou, C"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"full_name":"Xiao, G","first_name":"G","last_name":"Xiao"}],"volume":19,"date_updated":"2023-08-04T11:03:10Z","date_created":"2020-10-05T12:44:33Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"ista":"He P, Zhang Y, Li H, Fu X, Shang H, Zou C, Friml J, Xiao G. 2021. GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. Plant Biotechnology Journal. 19(3), 548–562.","ieee":"P. He et al., “GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton,” Plant Biotechnology Journal, vol. 19, no. 3. Wiley, pp. 548–562, 2021.","apa":"He, P., Zhang, Y., Li, H., Fu, X., Shang, H., Zou, C., … Xiao, G. (2021). GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. Plant Biotechnology Journal. Wiley. https://doi.org/10.1111/pbi.13484","ama":"He P, Zhang Y, Li H, et al. GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. Plant Biotechnology Journal. 2021;19(3):548-562. doi:10.1111/pbi.13484","chicago":"He, P, Yuzhou Zhang, H Li, X Fu, H Shang, C Zou, Jiří Friml, and G Xiao. “GhARF16-1 Modulates Leaf Development by Transcriptionally Regulating the GhKNOX2-1 Gene in Cotton.” Plant Biotechnology Journal. Wiley, 2021. https://doi.org/10.1111/pbi.13484.","mla":"He, P., et al. “GhARF16-1 Modulates Leaf Development by Transcriptionally Regulating the GhKNOX2-1 Gene in Cotton.” Plant Biotechnology Journal, vol. 19, no. 3, Wiley, 2021, pp. 548–62, doi:10.1111/pbi.13484.","short":"P. He, Y. Zhang, H. Li, X. Fu, H. Shang, C. Zou, J. Friml, G. Xiao, Plant Biotechnology Journal 19 (2021) 548–562."},"publication":"Plant Biotechnology Journal","page":"548-562","article_type":"original","date_published":"2021-03-01T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"text":"The leaf is a crucial organ evolved with remarkable morphological diversity to maximize plant photosynthesis. The leaf shape is a key trait that affects photosynthesis, flowering rates, disease resistance, and yield. Although many genes regulating leaf development have been identified in the past years, the precise regulatory architecture underlying the generation of diverse leaf shapes remains to be elucidated. We used cotton as a reference model to probe the genetic framework underlying divergent leaf forms. Comparative transcriptome analysis revealed that the GhARF16‐1 and GhKNOX2‐1 genes might be potential regulators of leaf shape. We functionally characterized the auxin‐responsive factor ARF16‐1 acting upstream of GhKNOX2‐1 to determine leaf morphology in cotton. The transcription of GhARF16‐1 was significantly higher in lobed‐leaved cotton than in smooth‐leaved cotton. Furthermore, the overexpression of GhARF16‐1 led to the upregulation of GhKNOX2‐1 and resulted in more and deeper serrations in cotton leaves, similar to the leaf shape of cotton plants overexpressing GhKNOX2‐1. We found that GhARF16‐1 specifically bound to the promoter of GhKNOX2‐1 to induce its expression. The heterologous expression of GhARF16‐1 and GhKNOX2‐1 in Arabidopsis led to lobed and curly leaves, and a genetic analysis revealed that GhKNOX2‐1 is epistatic to GhARF16‐1 in Arabidopsis, suggesting that the GhARF16‐1 and GhKNOX2‐1 interaction paradigm also functions to regulate leaf shape in Arabidopsis. To our knowledge, our results uncover a novel mechanism by which auxin, through the key component ARF16‐1 and its downstream‐activated gene KNOX2‐1, determines leaf morphology in eudicots.","lang":"eng"}],"_id":"8606","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 19","title":"GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton","status":"public","ddc":["580"],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9321","date_created":"2021-04-12T12:29:07Z","date_updated":"2021-04-12T12:29:07Z","checksum":"63845be37fb962586e0c7773f2355970","success":1,"file_name":"2021_PlantBiotechJournal_He.pdf","access_level":"open_access","file_size":15691871,"content_type":"application/pdf","creator":"dernst"}]},{"ec_funded":1,"file_date_updated":"2021-01-07T14:03:53Z","volume":14,"date_updated":"2023-08-04T11:21:13Z","date_created":"2021-01-03T23:01:23Z","author":[{"orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"department":[{"_id":"JiFr"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"This work was supported by the European Union’s Horizon 2020 Program (ERC grant agreement no. 742985 to J.F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). C.L. is supported by the Austrian Science Fund (FWF; P 31493).","publication_identifier":{"eissn":["17529867"],"issn":["16742052"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2020.11.004","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Long Term Fellowship","_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000605359400014"],"pmid":["33186755"]},"oa":1,"issue":"1","abstract":[{"text":"The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"917e60e57092f22e16beac70b1775ea6","success":1,"date_updated":"2021-01-07T14:03:53Z","date_created":"2021-01-07T14:03:53Z","relation":"main_file","file_id":"8995","file_size":871088,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_MolecularPlant_Tan.pdf"}],"intvolume":" 14","ddc":["580"],"title":"Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling","status":"public","_id":"8992","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","day":"04","scopus_import":"1","date_published":"2021-01-04T00:00:00Z","page":"151-165","article_type":"original","citation":{"ista":"Tan S, Luschnig C, Friml J. 2021. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular Plant. 14(1), 151–165.","apa":"Tan, S., Luschnig, C., & Friml, J. (2021). Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.11.004","ieee":"S. Tan, C. Luschnig, and J. Friml, “Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling,” Molecular Plant, vol. 14, no. 1. Elsevier, pp. 151–165, 2021.","ama":"Tan S, Luschnig C, Friml J. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular Plant. 2021;14(1):151-165. doi:10.1016/j.molp.2020.11.004","chicago":"Tan, Shutang, Christian Luschnig, and Jiří Friml. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” Molecular Plant. Elsevier, 2021. https://doi.org/10.1016/j.molp.2020.11.004.","mla":"Tan, Shutang, et al. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” Molecular Plant, vol. 14, no. 1, Elsevier, 2021, pp. 151–65, doi:10.1016/j.molp.2020.11.004.","short":"S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165."},"publication":"Molecular Plant"},{"article_number":"e2020857118","ec_funded":1,"publisher":"National Academy of Sciences","department":[{"_id":"JiFr"},{"_id":"LeSa"}],"publication_status":"published","pmid":1,"acknowledgement":"This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript.","year":"2021","volume":118,"date_created":"2021-01-03T23:01:23Z","date_updated":"2023-08-07T13:29:23Z","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2102232118","relation":"erratum"}]},"author":[{"last_name":"Abas","first_name":"Lindy","full_name":"Abas, Lindy"},{"last_name":"Kolb","first_name":"Martina","full_name":"Kolb, Martina"},{"full_name":"Stadlmann, Johannes","first_name":"Johannes","last_name":"Stadlmann"},{"full_name":"Janacek, Dorina P.","last_name":"Janacek","first_name":"Dorina P."},{"first_name":"Kristina","last_name":"Lukic","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1581-881X","full_name":"Lukic, Kristina"},{"first_name":"Claus","last_name":"Schwechheimer","full_name":"Schwechheimer, Claus"},{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mach, Lukas","last_name":"Mach","first_name":"Lukas"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"first_name":"Ulrich Z.","last_name":"Hammes","full_name":"Hammes, Ulrich Z."}],"publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"month":"01","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.2020857118","open_access":"1"}],"external_id":{"isi":["000607270100073"],"pmid":["33443187"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2020857118","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism."}],"intvolume":" 118","status":"public","title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","_id":"8993","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"05","article_type":"original","citation":{"ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 2021;118(1). doi:10.1073/pnas.2020857118","apa":"Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2020857118","ieee":"L. Abas et al., “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” PNAS, vol. 118, no. 1. National Academy of Sciences, 2021.","ista":"Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. PNAS. 118(1), e2020857118.","short":"L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, PNAS 118 (2021).","mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” PNAS, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:10.1073/pnas.2020857118.","chicago":"Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2020857118."},"publication":"PNAS","date_published":"2021-01-05T00:00:00Z"},{"file_date_updated":"2021-03-22T11:18:58Z","article_number":"1657","author":[{"last_name":"Hu","first_name":"Yangjie","full_name":"Hu, Yangjie"},{"full_name":"Omary, Moutasem","first_name":"Moutasem","last_name":"Omary"},{"first_name":"Yun","last_name":"Hu","full_name":"Hu, Yun"},{"full_name":"Doron, Ohad","last_name":"Doron","first_name":"Ohad"},{"last_name":"Hörmayer","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas"},{"last_name":"Chen","first_name":"Qingguo","full_name":"Chen, Qingguo"},{"first_name":"Or","last_name":"Megides","full_name":"Megides, Or"},{"last_name":"Chekli","first_name":"Ori","full_name":"Chekli, Ori"},{"last_name":"Ding","first_name":"Zhaojun","full_name":"Ding, Zhaojun"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Zhao, Yunde","last_name":"Zhao","first_name":"Yunde"},{"last_name":"Tsarfaty","first_name":"Ilan","full_name":"Tsarfaty, Ilan"},{"full_name":"Shani, Eilon","last_name":"Shani","first_name":"Eilon"}],"date_created":"2021-03-21T23:01:19Z","date_updated":"2023-08-07T14:17:55Z","volume":12,"year":"2021","acknowledgement":"This work was supported by grants from the Israel Science Foundation (2378/19 to E.S.), the Joint NSFC-ISF Research Grant (3419/20 to E.S. and Z.D.), the Human Frontier Science Program (HFSP—LIY000540/2020 to E.S.), the European Research Council Starting Grant (757683- RobustHormoneTrans to E.S.), PBC postdoctoral fellowships (to Y.H. and M.O.), NIH (GM114660 to Y.Z.), Breast Cancer Research Foundation (BCRF to I.T.).","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"month":"03","publication_identifier":{"eissn":["20411723"]},"doi":"10.1038/s41467-021-21802-3","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000630419400048"],"pmid":["33712581"]},"quality_controlled":"1","isi":1,"abstract":[{"text":"Auxin is a key regulator of plant growth and development. Local auxin biosynthesis and intercellular transport generates regional gradients in the root that are instructive for processes such as specification of developmental zones that maintain root growth and tropic responses. Here we present a toolbox to study auxin-mediated root development that features: (i) the ability to control auxin synthesis with high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic analysis infrastructure. Integration of these two features enables cutting-edge analysis of root development at single-cell resolution based on morphokinetic parameters under normal growth conditions and during cell-type-specific induction of auxin biosynthesis. We show directional auxin flow in the root and refine the contributions of key players in this process. In addition, we determine the quantitative kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic insights into root development, the tools developed here will enable biologists to study kinetics and morphology of various critical processes at the single cell-level in whole organisms.","lang":"eng"}],"type":"journal_article","file":[{"date_created":"2021-03-22T11:18:58Z","date_updated":"2021-03-22T11:18:58Z","checksum":"e1022f3aee349853ded2b2b3e092362d","success":1,"relation":"main_file","file_id":"9275","file_size":8602096,"content_type":"application/pdf","creator":"dernst","file_name":"2021_NatureComm_Hu.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9254","status":"public","ddc":["580"],"title":"Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing","intvolume":" 12","day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2021-03-12T00:00:00Z","publication":"Nature Communications","citation":{"chicago":"Hu, Yangjie, Moutasem Omary, Yun Hu, Ohad Doron, Lukas Hörmayer, Qingguo Chen, Or Megides, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-21802-3.","short":"Y. Hu, M. Omary, Y. Hu, O. Doron, L. Hörmayer, Q. Chen, O. Megides, O. Chekli, Z. Ding, J. Friml, Y. Zhao, I. Tsarfaty, E. Shani, Nature Communications 12 (2021).","mla":"Hu, Yangjie, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” Nature Communications, vol. 12, 1657, Springer Nature, 2021, doi:10.1038/s41467-021-21802-3.","apa":"Hu, Y., Omary, M., Hu, Y., Doron, O., Hörmayer, L., Chen, Q., … Shani, E. (2021). Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-21802-3","ieee":"Y. Hu et al., “Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing,” Nature Communications, vol. 12. Springer Nature, 2021.","ista":"Hu Y, Omary M, Hu Y, Doron O, Hörmayer L, Chen Q, Megides O, Chekli O, Ding Z, Friml J, Zhao Y, Tsarfaty I, Shani E. 2021. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 12, 1657.","ama":"Hu Y, Omary M, Hu Y, et al. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 2021;12. doi:10.1038/s41467-021-21802-3"},"article_type":"original"},{"language":[{"iso":"eng"}],"doi":"10.1093/plcell/koab122","isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"external_id":{"pmid":["33944955"],"isi":["000703938100026"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"07","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"date_created":"2021-06-02T13:13:58Z","date_updated":"2023-08-08T13:54:32Z","volume":33,"author":[{"full_name":"Ruiz-Lopez, N","last_name":"Ruiz-Lopez","first_name":"N"},{"last_name":"Pérez-Sancho","first_name":"J","full_name":"Pérez-Sancho, J"},{"full_name":"Esteban Del Valle, A","last_name":"Esteban Del Valle","first_name":"A"},{"full_name":"Haslam, RP","last_name":"Haslam","first_name":"RP"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"last_name":"Catalá","first_name":"R","full_name":"Catalá, R"},{"full_name":"Perea-Resa, C","first_name":"C","last_name":"Perea-Resa"},{"full_name":"Van Damme, D","first_name":"D","last_name":"Van Damme"},{"first_name":"S","last_name":"García-Hernández","full_name":"García-Hernández, S"},{"first_name":"A","last_name":"Albert","full_name":"Albert, A"},{"full_name":"Vallarino, J","last_name":"Vallarino","first_name":"J"},{"full_name":"Lin, J","last_name":"Lin","first_name":"J"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"last_name":"Macho","first_name":"AP","full_name":"Macho, AP"},{"last_name":"Salinas","first_name":"J","full_name":"Salinas, J"},{"last_name":"Rosado","first_name":"A","full_name":"Rosado, A"},{"full_name":"Napier, JA","first_name":"JA","last_name":"Napier"},{"first_name":"V","last_name":"Amorim-Silva","full_name":"Amorim-Silva, V"},{"last_name":"Botella","first_name":"MA","full_name":"Botella, MA"}],"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"acknowledgement":"We would also like to thank Lothar Willmitzer for the lipidomic analysis at the Max Planck Institute of Molecular Plant Physiology (Potsdam, Germany). We thank Manuela Vega from SCI for her technical assistance in image analysis. We thank John R. Pearson and the Bionand Nanoimaging Unit, F. David Navas Fernández and the SCAI Imaging Facility and The Plant Cell Biology facility at the Shanghai Center for Plant Stress Biology for assistance with confocal microscopy. The FaFAH1 clone was a gift from Iraida Amaya Saavedra (IFAPA-Centro de Churriana, Málaga, Spain). The AHA3 antibody against the H+-ATPase was a gift from Ramón Serrano Salom (Instituto de Biología Molecular y Celular de Plantas, Valencia, Spain). The MAP-mTU2-SAC1 construct was provided by Yvon Jaillais (Laboratoire Reproduction et Développement des Plantes, Univ Lyon, France). The pGWB5 from the pGWB vector series, was provided by Tsuyoshi Nakagawa (Department of Molecular and Functional Genomics, Shimane University). We thank Plan Propio from the University of Málaga for financial support.\r\nFunding","year":"2021","pmid":1,"file_date_updated":"2021-10-14T13:36:38Z","ec_funded":1,"date_published":"2021-07-01T00:00:00Z","article_type":"original","page":"2431-2453","publication":"Plant Cell","citation":{"chicago":"Ruiz-Lopez, N, J Pérez-Sancho, A Esteban Del Valle, RP Haslam, S Vanneste, R Catalá, C Perea-Resa, et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab122.","mla":"Ruiz-Lopez, N., et al. “Synaptotagmins at the Endoplasmic Reticulum-Plasma Membrane Contact Sites Maintain Diacylglycerol Homeostasis during Abiotic Stress.” Plant Cell, vol. 33, no. 7, American Society of Plant Biologists, 2021, pp. 2431–53, doi:10.1093/plcell/koab122.","short":"N. Ruiz-Lopez, J. Pérez-Sancho, A. Esteban Del Valle, R. Haslam, S. Vanneste, R. Catalá, C. Perea-Resa, D. Van Damme, S. García-Hernández, A. Albert, J. Vallarino, J. Lin, J. Friml, A. Macho, J. Salinas, A. Rosado, J. Napier, V. Amorim-Silva, M. Botella, Plant Cell 33 (2021) 2431–2453.","ista":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, Haslam R, Vanneste S, Catalá R, Perea-Resa C, Van Damme D, García-Hernández S, Albert A, Vallarino J, Lin J, Friml J, Macho A, Salinas J, Rosado A, Napier J, Amorim-Silva V, Botella M. 2021. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 33(7), 2431–2453.","ieee":"N. Ruiz-Lopez et al., “Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress,” Plant Cell, vol. 33, no. 7. American Society of Plant Biologists, pp. 2431–2453, 2021.","apa":"Ruiz-Lopez, N., Pérez-Sancho, J., Esteban Del Valle, A., Haslam, R., Vanneste, S., Catalá, R., … Botella, M. (2021). Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab122","ama":"Ruiz-Lopez N, Pérez-Sancho J, Esteban Del Valle A, et al. Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress. Plant Cell. 2021;33(7):2431-2453. doi:10.1093/plcell/koab122"},"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_PlantCell_RuizLopez.pdf","file_size":2952028,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"10141","checksum":"22d596678d00310d793611864a6d0fcd","success":1,"date_updated":"2021-10-14T13:36:38Z","date_created":"2021-10-14T13:36:38Z"}],"status":"public","title":"Synaptotagmins at the endoplasmic reticulum-plasma membrane contact sites maintain diacylglycerol homeostasis during abiotic stress","ddc":["580"],"intvolume":" 33","_id":"9443","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Endoplasmic reticulum–plasma membrane contact sites (ER–PM CS) play fundamental roles in all eukaryotic cells. Arabidopsis thaliana mutants lacking the ER–PM protein tether synaptotagmin1 (SYT1) exhibit decreased PM integrity under multiple abiotic stresses, such as freezing, high salt, osmotic stress, and mechanical damage. Here, we show that, together with SYT1, the stress-induced SYT3 is an ER–PM tether that also functions in maintaining PM integrity. The ER–PM CS localization of SYT1 and SYT3 is dependent on PM phosphatidylinositol-4-phosphate and is regulated by abiotic stress. Lipidomic analysis revealed that cold stress increased the accumulation of diacylglycerol at the PM in a syt1/3 double mutant relative to wild-type while the levels of most glycerolipid species remain unchanged. In addition, the SYT1-green fluorescent protein fusion preferentially binds diacylglycerol in vivo with little affinity for polar glycerolipids. Our work uncovers a SYT-dependent mechanism of stress adaptation counteracting the detrimental accumulation of diacylglycerol at the PM produced during episodes of abiotic stress.","lang":"eng"}],"issue":"7","type":"journal_article"},{"date_published":"2021-07-07T00:00:00Z","article_type":"original","page":"2981–3003","publication":"Plant Cell","citation":{"mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:10.1093/plcell/koab183.","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” Plant Cell. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plcell/koab183.","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 2021;33(9):2981–3003. doi:10.1093/plcell/koab183","ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","ieee":"Z. Gao et al., “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” Plant Cell, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1093/plcell/koab183"},"day":"07","has_accepted_license":"1","article_processing_charge":"No","file":[{"access_level":"open_access","file_name":"2021_PlantCell_Gao.pdf","file_size":10566921,"content_type":"application/pdf","creator":"cziletti","relation":"main_file","file_id":"9691","checksum":"6715712ec306c321f0204c817b7f8ae7","success":1,"date_created":"2021-07-19T12:13:34Z","date_updated":"2021-07-19T12:13:34Z"}],"oa_version":"Published Version","title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","status":"public","ddc":["580"],"intvolume":" 33","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9657","abstract":[{"text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia.","lang":"eng"}],"issue":"9","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1093/plcell/koab183","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000702165300012"],"pmid":["34240197"]},"oa":1,"month":"07","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"date_created":"2021-07-14T15:32:43Z","date_updated":"2023-08-10T14:01:41Z","volume":33,"author":[{"first_name":"Z","last_name":"Gao","full_name":"Gao, Z"},{"full_name":"Chen, Z","first_name":"Z","last_name":"Chen"},{"last_name":"Cui","first_name":"Y","full_name":"Cui, Y"},{"last_name":"Ke","first_name":"M","full_name":"Ke, M"},{"first_name":"H","last_name":"Xu","full_name":"Xu, H"},{"first_name":"Q","last_name":"Xu","full_name":"Xu, Q"},{"last_name":"Chen","first_name":"J","full_name":"Chen, J"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"last_name":"Huang","first_name":"L","full_name":"Huang, L"},{"full_name":"Zhao, H","first_name":"H","last_name":"Zhao"},{"last_name":"Huang","first_name":"D","full_name":"Huang, D"},{"last_name":"Mai","first_name":"S","full_name":"Mai, S"},{"full_name":"Xu, T","last_name":"Xu","first_name":"T"},{"full_name":"Liu, X","first_name":"X","last_name":"Liu"},{"first_name":"S","last_name":"Li","full_name":"Li, S"},{"full_name":"Guan, Y","last_name":"Guan","first_name":"Y"},{"full_name":"Yang, W","first_name":"W","last_name":"Yang"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Petrášek","first_name":"J","full_name":"Petrášek, J"},{"full_name":"Zhang, J","last_name":"Zhang","first_name":"J"},{"full_name":"Chen, X","first_name":"X","last_name":"Chen"}],"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"year":"2021","pmid":1,"file_date_updated":"2021-07-19T12:13:34Z"},{"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2021-10-01T00:00:00Z","publication":"New Phytologist","citation":{"chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17617.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” New Phytologist, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:10.1111/nph.17617.","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” New Phytologist, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., & Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. Wiley. https://doi.org/10.1111/nph.17617","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 2021;232(2):510-522. doi:10.1111/nph.17617"},"article_type":"original","page":"510-522","abstract":[{"text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2021-10-07T13:42:47Z","date_created":"2021-10-07T13:42:47Z","success":1,"checksum":"6422a6eb329b52d96279daaee0fcf189","file_id":"10105","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":1939800,"file_name":"2021_NewPhytologist_Han.pdf","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9656","status":"public","title":"PIN-mediated polar auxin transport regulations in plant tropic responses","ddc":["580"],"intvolume":" 232","month":"10","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"doi":"10.1111/nph.17617","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000680587100001"],"pmid":["34254313"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"file_date_updated":"2021-10-07T13:42:47Z","ec_funded":1,"author":[{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski"},{"first_name":"Linlin","last_name":"Qi","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin"},{"first_name":"SS","last_name":"Alotaibi","full_name":"Alotaibi, SS"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"date_updated":"2023-08-10T14:02:41Z","date_created":"2021-07-14T15:29:14Z","volume":232,"acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","year":"2021","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"JiFr"}]},{"intvolume":" 12","title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","status":"public","ddc":["580","570"],"_id":"9909","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_Genes_Zeng.pdf","content_type":"application/pdf","file_size":1340305,"creator":"asandaue","relation":"main_file","file_id":"9919","checksum":"3d99535618cf9a5b14d264408fa52e97","success":1,"date_updated":"2021-08-16T09:02:40Z","date_created":"2021-08-16T09:02:40Z"}],"type":"journal_article","issue":"8","abstract":[{"text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.","lang":"eng"}],"article_type":"original","citation":{"ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 2021;12(8). doi:10.3390/genes12081141","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","ieee":"Y. Zeng et al., “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” Genes, vol. 12, no. 8. MDPI, 2021.","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. MDPI. https://doi.org/10.3390/genes12081141","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” Genes, vol. 12, no. 8, 1141, MDPI, 2021, doi:10.3390/genes12081141.","short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12081141."},"publication":"Genes","date_published":"2021-07-27T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"27","publisher":"MDPI","department":[{"_id":"JiFr"}],"publication_status":"published","acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","year":"2021","volume":12,"date_created":"2021-08-15T22:01:28Z","date_updated":"2023-08-11T10:32:21Z","author":[{"full_name":"Zeng, Yinwei","last_name":"Zeng","first_name":"Yinwei"},{"full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten"},{"full_name":"Trinh, Hoang Khai","first_name":"Hoang Khai","last_name":"Trinh"},{"full_name":"Heugebaert, Thomas","last_name":"Heugebaert","first_name":"Thomas"},{"last_name":"Stevens","first_name":"Christian V.","full_name":"Stevens, Christian V."},{"full_name":"Garcia-Maquilon, Irene","first_name":"Irene","last_name":"Garcia-Maquilon"},{"first_name":"Pedro L.","last_name":"Rodriguez","full_name":"Rodriguez, Pedro L."},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Danny","last_name":"Geelen","full_name":"Geelen, Danny"}],"article_number":"1141","file_date_updated":"2021-08-16T09:02:40Z","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000690558000001"]},"language":[{"iso":"eng"}],"doi":"10.3390/genes12081141","publication_identifier":{"eissn":["20734425"]},"month":"07"},{"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"month":"11","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2","open_access":"1"}],"external_id":{"pmid":["34637542"],"isi":["000714678100001"]},"language":[{"iso":"eng"}],"doi":"10.1111/nph.17792","publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"acknowledgement":"We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests.","year":"2021","volume":233,"date_updated":"2023-08-14T11:46:43Z","date_created":"2021-11-14T23:01:24Z","author":[{"full_name":"Kashkan, Ivan","last_name":"Kashkan","first_name":"Ivan"},{"last_name":"Hrtyan","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika"},{"last_name":"Retzer","first_name":"Katarzyna","full_name":"Retzer, Katarzyna"},{"full_name":"Humpolíčková, Jana","last_name":"Humpolíčková","first_name":"Jana"},{"full_name":"Jayasree, Aswathy","first_name":"Aswathy","last_name":"Jayasree"},{"full_name":"Filepová, Roberta","last_name":"Filepová","first_name":"Roberta"},{"last_name":"Vondráková","first_name":"Zuzana","full_name":"Vondráková, Zuzana"},{"full_name":"Simon, Sibu","first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741"},{"full_name":"Rombaut, Debbie","last_name":"Rombaut","first_name":"Debbie"},{"last_name":"Jacobs","first_name":"Thomas B.","full_name":"Jacobs, Thomas B."},{"last_name":"Frilander","first_name":"Mikko J.","full_name":"Frilander, Mikko J."},{"first_name":"Jan","last_name":"Hejátko","full_name":"Hejátko, Jan"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"last_name":"Růžička","first_name":"Kamil","full_name":"Růžička, Kamil"}],"scopus_import":"1","article_processing_charge":"No","day":"05","page":"329-343","article_type":"original","citation":{"chicago":"Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17792.","short":"I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2021) 329–343.","mla":"Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist, vol. 233, Wiley, 2021, pp. 329–43, doi:10.1111/nph.17792.","ieee":"I. Kashkan et al., “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” New Phytologist, vol. 233. Wiley, pp. 329–343, 2021.","apa":"Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2021). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.17792","ista":"Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2021. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233, 329–343.","ama":"Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 2021;233:329-343. doi:10.1111/nph.17792"},"publication":"New Phytologist","date_published":"2021-11-05T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development."}],"intvolume":" 233","status":"public","title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10282","oa_version":"Preprint"},{"doi":"10.1038/s41477-021-01011-y","language":[{"iso":"eng"}],"external_id":{"isi":["000717408000002"],"pmid":["34764442"]},"isi":1,"quality_controlled":"1","month":"11","publication_identifier":{"eissn":["2055-0278"]},"author":[{"full_name":"Xu, Enjun","first_name":"Enjun","last_name":"Xu"},{"last_name":"Chai","first_name":"Liang","full_name":"Chai, Liang"},{"last_name":"Zhang","first_name":"Shiqi","full_name":"Zhang, Shiqi"},{"full_name":"Yu, Ruixue","last_name":"Yu","first_name":"Ruixue"},{"last_name":"Zhang","first_name":"Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","full_name":"Zhang, Xixi"},{"first_name":"Chongyi","last_name":"Xu","full_name":"Xu, Chongyi"},{"last_name":"Hu","first_name":"Yuxin","full_name":"Hu, Yuxin"}],"date_updated":"2023-08-14T11:54:02Z","date_created":"2021-11-21T23:01:30Z","volume":7,"acknowledgement":"We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055).","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","date_published":"2021-11-11T00:00:00Z","publication":"Nature Plants","citation":{"chicago":"Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants. Springer Nature, 2021. https://doi.org/10.1038/s41477-021-01011-y.","mla":"Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:10.1038/s41477-021-01011-y.","short":"E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504.","ista":"Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504.","ieee":"E. Xu et al., “Catabolism of strigolactones by a carboxylesterase,” Nature Plants, vol. 7. Springer Nature, pp. 1495–1504, 2021.","apa":"Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., & Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-021-01011-y","ama":"Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 2021;7:1495–1504. doi:10.1038/s41477-021-01011-y"},"article_type":"original","page":"1495–1504 ","day":"11","article_processing_charge":"No","scopus_import":"1","oa_version":"None","_id":"10326","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Catabolism of strigolactones by a carboxylesterase","status":"public","intvolume":" 7","abstract":[{"text":"Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants.","lang":"eng"}],"type":"journal_article"},{"oa_version":"Published Version","_id":"9368","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth","intvolume":" 186","abstract":[{"lang":"eng","text":"The quality control system for messenger RNA (mRNA) is fundamental for cellular activities in eukaryotes. To elucidate the molecular mechanism of 3'-Phosphoinositide-Dependent Protein Kinase1 (PDK1), a master regulator that is essential throughout eukaryotic growth and development, we employed a forward genetic approach to screen for suppressors of the loss-of-function T-DNA insertion double mutant pdk1.1 pdk1.2 in Arabidopsis thaliana. Notably, the severe growth attenuation of pdk1.1 pdk1.2 was rescued by sop21 (suppressor of pdk1.1 pdk1.2), which harbours a loss-of-function mutation in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast (Saccharomyces cerevisiae) DOM34p, which each form a heterodimeric complex with the GTPase HBS1 (HSP70 SUBFAMILY B SUPPRESSOR1, also called SUPERKILLER PROTEIN7, SKI7), a protein that is responsible for ribosomal rescue and thereby assures the quality and fidelity of mRNA molecules during translation. Genetic analysis further revealed that a dysfunctional PEL1-HBS1 complex failed to degrade the T-DNA-disrupted PDK1 transcripts, which were truncated but functional, and thus rescued the growth and developmental defects of pdk1.1 pdk1.2. Our studies demonstrated the functionality of a homologous PELOTA-HBS1 complex and identified its essential regulatory role in plants, providing insights into the mechanism of mRNA quality control."}],"issue":"4","type":"journal_article","date_published":"2021-04-30T00:00:00Z","publication":"Plant Physiology","citation":{"ama":"Kong W, Tan S, Zhao Q, et al. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 2021;186(4):2003-2020. doi:10.1093/plphys/kiab199","ista":"Kong W, Tan S, Zhao Q, Lin D, Xu Z, Friml J, Xue H. 2021. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 186(4), 2003–2020.","ieee":"W. Kong et al., “mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth,” Plant Physiology, vol. 186, no. 4. American Society of Plant Biologists, pp. 2003–2020, 2021.","apa":"Kong, W., Tan, S., Zhao, Q., Lin, D., Xu, Z., Friml, J., & Xue, H. (2021). mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1093/plphys/kiab199","mla":"Kong, W., et al. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” Plant Physiology, vol. 186, no. 4, American Society of Plant Biologists, 2021, pp. 2003–20, doi:10.1093/plphys/kiab199.","short":"W. Kong, S. Tan, Q. Zhao, D. Lin, Z. Xu, J. Friml, H. Xue, Plant Physiology 186 (2021) 2003–2020.","chicago":"Kong, W, Shutang Tan, Q Zhao, DL Lin, ZH Xu, Jiří Friml, and HW Xue. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” Plant Physiology. American Society of Plant Biologists, 2021. https://doi.org/10.1093/plphys/kiab199."},"article_type":"original","page":"2003-2020","day":"30","article_processing_charge":"No","author":[{"last_name":"Kong","first_name":"W","full_name":"Kong, W"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang"},{"first_name":"Q","last_name":"Zhao","full_name":"Zhao, Q"},{"full_name":"Lin, DL","last_name":"Lin","first_name":"DL"},{"full_name":"Xu, ZH","last_name":"Xu","first_name":"ZH"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Xue, HW","first_name":"HW","last_name":"Xue"}],"date_updated":"2023-09-05T12:20:27Z","date_created":"2021-05-03T13:28:20Z","volume":186,"acknowledgement":"We gratefully acknowledge the Arabidopsis Biological Resource Centre (ABRC) for providing T-DNA insertional mutants, and Prof. Remko Offringa for sharing published seeds. We thank Yuchuan Liu (Shanghai OE Biotech Co., Ltd) for help with proteomics data analysis, Xixi Zhang (IST Austria) for providing the pDONR-P4P1r-mCherry plasmid, and Yao Xiao (Technical University of Munich), Alexander Johnson (IST Austria) and Hana Semeradova (IST Austria) for helpful discussions. The study was supported by National Natural Science Foundation of China (NSFC, 31721001, 91954206, to H.-W. X.), “Ten-Thousand Talent Program” (to H.-W. X.) and Collaborative Innovation Center of Crop Stress Biology, Henan Province, and Austrian Science Fund (FWF): I 3630-B25 (to J. F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015).","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","doi":"10.1093/plphys/kiab199","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000703922000025"],"pmid":["33930167"]},"main_file_link":[{"url":"https://doi.org/10.1093/plphys/kiab199","open_access":"1"}],"quality_controlled":"1","isi":1,"project":[{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","grant_number":"723-2015","name":"Long Term Fellowship"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]}},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000653077800004"],"pmid":["33705718"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"doi":"10.1016/j.cub.2021.02.028","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"acknowledgement":"We acknowledge Ben Scheres, Christian Luschnig, and Claus Schwechheimer for sharing published material. We thank Monika Hrtyan and Dorota Jaworska at IST Austria and Gerda Lamers and Ward de Winter at IBL Netherlands for technical assistance; Corinna Hartinger, Jakub Hajný, Lesia Rodriguez, Mingyue Li, and Lindy Abas for experimental support; and the Bioimaging Facility at IST Austria and the Bioimaging Core at VIB for imaging support. We are grateful to Christian Luschnig, Lindy Abas, and Roman Pleskot for valuable discussions. We also acknowledge the EMBO for supporting M.G. with a long-term fellowship ( ALTF 1005-2019 ) during the finalization and revision of this manuscript in the laboratory of B.D.R., and we thank R. Pierik for allowing K.V.G. to work on this manuscript during a postdoc in his laboratory at Utrecht University. This work was supported by grants from the European Research Council under the European Union’s Seventh Framework Programme (ERC grant agreements 742985 to J.F., 714055 to B.D.R., and 803048 to M.F.), the Austrian Science Fund (FWF; I 3630-B25 to J.F.), Chemical Sciences (partly) financed by the Dutch Research Council (NWO-CW TOP 700.58.301 to R.O.), the Dutch Research Council (NWO-VICI 865.17.002 to R. Pierik), Grants-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology, Japan (KAKENHI grant 17K17595 to S.N.), the Ministry of Education, Youth and Sports of the Czech Republic (MŠMT project NPUI-LO1417 ), and a China Scholarship Council (to X.W.).","year":"2021","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JiFr"}],"author":[{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc"},{"first_name":"K","last_name":"Van Gelderen","full_name":"Van Gelderen, K"},{"full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","first_name":"Lukas"},{"last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"full_name":"Naramoto, S","first_name":"S","last_name":"Naramoto"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","first_name":"Xixi"},{"last_name":"Domjan","first_name":"David","orcid":"0000-0003-2267-106X","id":"C684CD7A-257E-11EA-9B6F-D8588B4F947F","full_name":"Domjan, David"},{"full_name":"Vcelarova, L","first_name":"L","last_name":"Vcelarova"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson"},{"last_name":"de Koning","first_name":"E","full_name":"de Koning, E"},{"last_name":"van Dop","first_name":"M","full_name":"van Dop, M"},{"full_name":"Rademacher, E","last_name":"Rademacher","first_name":"E"},{"first_name":"S","last_name":"Janson","full_name":"Janson, S"},{"last_name":"Wei","first_name":"X","full_name":"Wei, X"},{"full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar"},{"first_name":"Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas"},{"full_name":"De Rybel, B","first_name":"B","last_name":"De Rybel"},{"first_name":"R","last_name":"Offringa","full_name":"Offringa, R"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"date_created":"2021-03-26T12:09:33Z","date_updated":"2023-09-05T13:03:34Z","volume":31,"file_date_updated":"2021-04-01T10:53:42Z","ec_funded":1,"publication":"Current Biology","citation":{"short":"M. Glanc, K. Van Gelderen, L. Hörmayer, S. Tan, S. Naramoto, X. Zhang, D. Domjan, L. Vcelarova, R. Hauschild, A.J. Johnson, E. de Koning, M. van Dop, E. Rademacher, S. Janson, X. Wei, G. Molnar, M. Fendrych, B. De Rybel, R. Offringa, J. Friml, Current Biology 31 (2021) 1918–1930.","mla":"Glanc, Matous, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” Current Biology, vol. 31, no. 9, Elsevier, 2021, pp. 1918–30, doi:10.1016/j.cub.2021.02.028.","chicago":"Glanc, Matous, K Van Gelderen, Lukas Hörmayer, Shutang Tan, S Naramoto, Xixi Zhang, David Domjan, et al. “AGC Kinases and MAB4/MEL Proteins Maintain PIN Polarity by Limiting Lateral Diffusion in Plant Cells.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2021.02.028.","ama":"Glanc M, Van Gelderen K, Hörmayer L, et al. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. 2021;31(9):1918-1930. doi:10.1016/j.cub.2021.02.028","apa":"Glanc, M., Van Gelderen, K., Hörmayer, L., Tan, S., Naramoto, S., Zhang, X., … Friml, J. (2021). AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2021.02.028","ieee":"M. Glanc et al., “AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells,” Current Biology, vol. 31, no. 9. Elsevier, pp. 1918–1930, 2021.","ista":"Glanc M, Van Gelderen K, Hörmayer L, Tan S, Naramoto S, Zhang X, Domjan D, Vcelarova L, Hauschild R, Johnson AJ, de Koning E, van Dop M, Rademacher E, Janson S, Wei X, Molnar G, Fendrych M, De Rybel B, Offringa R, Friml J. 2021. AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells. Current Biology. 31(9), 1918–1930."},"article_type":"original","page":"1918-1930","date_published":"2021-03-10T00:00:00Z","day":"10","has_accepted_license":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9290","status":"public","title":"AGC kinases and MAB4/MEL proteins maintain PIN polarity by limiting lateral diffusion in plant cells","ddc":["580"],"intvolume":" 31","oa_version":"Published Version","file":[{"creator":"dernst","file_size":4324371,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_CurrentBiology_Glanc.pdf","success":1,"checksum":"b1723040ecfd8c81194185472eb62546","date_updated":"2021-04-01T10:53:42Z","date_created":"2021-04-01T10:53:42Z","file_id":"9303","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Polar subcellular localization of the PIN exporters of the phytohormone auxin is a key determinant of directional, intercellular auxin transport and thus a central topic of both plant cell and developmental biology. Arabidopsis mutants lacking PID, a kinase that phosphorylates PINs, or the MAB4/MEL proteins of unknown molecular function display PIN polarity defects and phenocopy pin mutants, but mechanistic insights into how these factors convey PIN polarity are missing. Here, by combining protein biochemistry with quantitative live-cell imaging, we demonstrate that PINs, MAB4/MELs, and AGC kinases interact in the same complex at the plasma membrane. MAB4/MELs are recruited to the plasma membrane by the PINs and in concert with the AGC kinases maintain PIN polarity through limiting lateral diffusion-based escape of PINs from the polar domain. The PIN-MAB4/MEL-PID protein complex has self-reinforcing properties thanks to positive feedback between AGC kinase-mediated PIN phosphorylation and MAB4/MEL recruitment. We thus uncover the molecular mechanism by which AGC kinases and MAB4/MEL proteins regulate PIN localization and plant development."}],"issue":"9"},{"month":"01","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"external_id":{"isi":["000614361000039"],"pmid":["33157019"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1016/j.cub.2020.10.011","language":[{"iso":"eng"}],"file_date_updated":"2021-02-04T11:37:50Z","year":"2021","acknowledgement":"We thank the SiCE group for discussions and comments; S. Yalovsky, B. Scheres, and the NASC/ABRC collection for providing transgenic Arabidopsis lines and plasmids; L. Kalmbach and M. Barberon for the gift of pLOK180_pFR7m34GW; A. Lacroix, J. Berger, and P. Bolland for plant care; and M. Fendrych for help with microfluidics in the J.F. lab. We acknowledge\r\nthe contribution of the SFR Biosciences (UMS3444/CNRS, US8/Inser m, ENS de Lyon, UCBL) facilities: C. Lionet, E. Chatre, and J. Brocard at LBIPLATIM-MICROSCOPY for assistance with imaging, and V. GuegenChaignon and A. Page at the Protein Science Facility (PSF) for assistance with protein purification and mass spectrometry. Y.J. was funded by ERC\r\ngrant 3363360-APPL under FP/2007–2013. Y.J. and Z.L.N. were funded by an ANR- and NSF-supported ERA-CAPS project (SICOPID: ANR-17-CAPS0003-01/NSF PGRP IOS-1841917). A.I.C.-D. is funded by an ERC consolidator grant (ERC-2015-CoG–683163) and BIO2016-78955 grant from the Spanish Ministry of Economy and Competitiveness. Exchanges between the Y.J. and T.B. laboratories were funded by Tournesol grant 35656NB. B.K.M. was\r\nfunded by the Omics@vib Marie Curie COFUND and Research Foundation Flanders for a postdoctoral fellowship.","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Elsevier","author":[{"last_name":"Marquès-Bueno","first_name":"MM","full_name":"Marquès-Bueno, MM"},{"first_name":"L","last_name":"Armengot","full_name":"Armengot, L"},{"full_name":"Noack, LC","last_name":"Noack","first_name":"LC"},{"first_name":"J","last_name":"Bareille","full_name":"Bareille, J"},{"full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","first_name":"Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"first_name":"MP","last_name":"Platre","full_name":"Platre, MP"},{"last_name":"Bayle","first_name":"V","full_name":"Bayle, V"},{"full_name":"Liu, M","first_name":"M","last_name":"Liu"},{"full_name":"Opdenacker, D","last_name":"Opdenacker","first_name":"D"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"full_name":"Möller, BK","last_name":"Möller","first_name":"BK"},{"full_name":"Nimchuk, ZL","first_name":"ZL","last_name":"Nimchuk"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"last_name":"Caño-Delgado","first_name":"AI","full_name":"Caño-Delgado, AI"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jaillais, Y","last_name":"Jaillais","first_name":"Y"}],"date_updated":"2023-09-05T13:03:15Z","date_created":"2020-12-01T13:39:46Z","volume":31,"day":"11","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Current Biology","citation":{"mla":"Marquès-Bueno, MM, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” Current Biology, vol. 31, no. 1, Elsevier, 2021, doi:10.1016/j.cub.2020.10.011.","short":"M. Marquès-Bueno, L. Armengot, L. Noack, J. Bareille, L. Rodriguez Solovey, M. Platre, V. Bayle, M. Liu, D. Opdenacker, S. Vanneste, B. Möller, Z. Nimchuk, T. Beeckman, A. Caño-Delgado, J. Friml, Y. Jaillais, Current Biology 31 (2021).","chicago":"Marquès-Bueno, MM, L Armengot, LC Noack, J Bareille, Lesia Rodriguez Solovey, MP Platre, V Bayle, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” Current Biology. Elsevier, 2021. https://doi.org/10.1016/j.cub.2020.10.011.","ama":"Marquès-Bueno M, Armengot L, Noack L, et al. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 2021;31(1). doi:10.1016/j.cub.2020.10.011","ista":"Marquès-Bueno M, Armengot L, Noack L, Bareille J, Rodriguez Solovey L, Platre M, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller B, Nimchuk Z, Beeckman T, Caño-Delgado A, Friml J, Jaillais Y. 2021. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 31(1).","ieee":"M. Marquès-Bueno et al., “Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism,” Current Biology, vol. 31, no. 1. Elsevier, 2021.","apa":"Marquès-Bueno, M., Armengot, L., Noack, L., Bareille, J., Rodriguez Solovey, L., Platre, M., … Jaillais, Y. (2021). Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2020.10.011"},"article_type":"original","date_published":"2021-01-11T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface."}],"issue":"1","_id":"8824","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"status":"public","title":"Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism","intvolume":" 31","oa_version":"Published Version","file":[{"checksum":"30b3393d841fb2b1e2b22fb42b5c8fff","success":1,"date_updated":"2021-02-04T11:37:50Z","date_created":"2021-02-04T11:37:50Z","relation":"main_file","file_id":"9090","file_size":3458646,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2021_CurrentBiology_MarquesBueno.pdf"}]},{"scopus_import":"1","article_processing_charge":"No","day":"17","page":"2275-2291","article_type":"original","citation":{"ieee":"I. El Houari et al., “Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport,” New Phytologist, vol. 230, no. 6. Wiley, pp. 2275–2291, 2021.","apa":"El Houari, I., Van Beirs, C., Arents, H., Han, H., Chanoca, A., Opdenacker, D., … Vanholme, B. (2021). Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. Wiley. https://doi.org/10.1111/nph.17349","ista":"El Houari I, Van Beirs C, Arents H, Han H, Chanoca A, Opdenacker D, Pollier J, Storme V, Steenackers W, Quareshy M, Napier R, Beeckman T, Friml J, De Rybel B, Boerjan W, Vanholme B. 2021. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. 230(6), 2275–2291.","ama":"El Houari I, Van Beirs C, Arents H, et al. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytologist. 2021;230(6):2275-2291. doi:10.1111/nph.17349","chicago":"El Houari, I, C Van Beirs, HE Arents, Huibin Han, A Chanoca, D Opdenacker, J Pollier, et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE Are Caused by Perturbations in Auxin Transport.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17349.","short":"I. El Houari, C. Van Beirs, H. Arents, H. Han, A. Chanoca, D. Opdenacker, J. Pollier, V. Storme, W. Steenackers, M. Quareshy, R. Napier, T. Beeckman, J. Friml, B. De Rybel, W. Boerjan, B. Vanholme, New Phytologist 230 (2021) 2275–2291.","mla":"El Houari, I., et al. “Seedling Developmental Defects upon Blocking CINNAMATE-4-HYDROXYLASE Are Caused by Perturbations in Auxin Transport.” New Phytologist, vol. 230, no. 6, Wiley, 2021, pp. 2275–91, doi:10.1111/nph.17349."},"publication":"New Phytologist","date_published":"2021-03-17T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"• The phenylpropanoid pathway serves a central role in plant metabolism, providing numerous compounds involved in diverse physiological processes. Most carbon entering the pathway is incorporated into lignin. Although several phenylpropanoid pathway mutants show seedling growth arrest, the role for lignin in seedling growth and development is unexplored.\r\n• We use complementary pharmacological and genetic approaches to block CINNAMATE‐4‐HYDROXYLASE (C4H) functionality in Arabidopsis seedlings and a set of molecular and biochemical techniques to investigate the underlying phenotypes.\r\n• Blocking C4H resulted in reduced lateral rooting and increased adventitious rooting apically in the hypocotyl. These phenotypes coincided with an inhibition in auxin transport. The upstream accumulation in cis‐cinnamic acid was found to likely cause polar auxin transport inhibition. Conversely, a downstream depletion in lignin perturbed phloem‐mediated auxin transport. Restoring lignin deposition effectively reestablished phloem transport and, accordingly, auxin homeostasis.\r\n• Our results show that the accumulation of bioactive intermediates and depletion in lignin jointly cause the aberrant phenotypes upon blocking C4H, and demonstrate that proper deposition of lignin is essential for the establishment of auxin distribution in seedlings. Our data position the phenylpropanoid pathway and lignin in a new physiological framework, consolidating their importance in plant growth and development.","lang":"eng"}],"intvolume":" 230","title":"Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9288","oa_version":"Published Version","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"month":"03","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000639552400001"],"pmid":["33728703"]},"main_file_link":[{"url":"https://biblio.ugent.be/publication/8703799/file/8703800.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1111/nph.17349","publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2021","volume":230,"date_created":"2021-03-26T12:09:01Z","date_updated":"2023-09-05T15:46:55Z","author":[{"full_name":"El Houari, I","first_name":"I","last_name":"El Houari"},{"full_name":"Van Beirs, C","last_name":"Van Beirs","first_name":"C"},{"last_name":"Arents","first_name":"HE","full_name":"Arents, HE"},{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"first_name":"A","last_name":"Chanoca","full_name":"Chanoca, A"},{"full_name":"Opdenacker, D","first_name":"D","last_name":"Opdenacker"},{"first_name":"J","last_name":"Pollier","full_name":"Pollier, J"},{"first_name":"V","last_name":"Storme","full_name":"Storme, V"},{"last_name":"Steenackers","first_name":"W","full_name":"Steenackers, W"},{"full_name":"Quareshy, M","first_name":"M","last_name":"Quareshy"},{"full_name":"Napier, R","first_name":"R","last_name":"Napier"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Rybel","first_name":"B","full_name":"De Rybel, B"},{"last_name":"Boerjan","first_name":"W","full_name":"Boerjan, W"},{"full_name":"Vanholme, B","last_name":"Vanholme","first_name":"B"}]},{"date_published":"2021-01-01T00:00:00Z","publication":"New Phytologist","citation":{"ista":"Ke M, Ma Z, Wang D, Sun Y, Wen C, Huang D, Chen Z, Yang L, Tan S, Li R, Friml J, Miao Y, Chen X. 2021. Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. 229(2), 963–978.","apa":"Ke, M., Ma, Z., Wang, D., Sun, Y., Wen, C., Huang, D., … Chen, X. (2021). Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.16915","ieee":"M. Ke et al., “Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana,” New Phytologist, vol. 229, no. 2. Wiley, pp. 963–978, 2021.","ama":"Ke M, Ma Z, Wang D, et al. Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. 2021;229(2):963-978. doi:10.1111/nph.16915","chicago":"Ke, M, Z Ma, D Wang, Y Sun, C Wen, D Huang, Z Chen, et al. “Salicylic Acid Regulates PIN2 Auxin Transporter Hyper-Clustering and Root Gravitropic Growth via Remorin-Dependent Lipid Nanodomain Organization in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.16915.","mla":"Ke, M., et al. “Salicylic Acid Regulates PIN2 Auxin Transporter Hyper-Clustering and Root Gravitropic Growth via Remorin-Dependent Lipid Nanodomain Organization in Arabidopsis Thaliana.” New Phytologist, vol. 229, no. 2, Wiley, 2021, pp. 963–78, doi:10.1111/nph.16915.","short":"M. Ke, Z. Ma, D. Wang, Y. Sun, C. Wen, D. Huang, Z. Chen, L. Yang, S. Tan, R. Li, J. Friml, Y. Miao, X. Chen, New Phytologist 229 (2021) 963–978."},"article_type":"original","page":"963-978","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_NewPhytologist_Ke.pdf","creator":"dernst","file_size":3674502,"content_type":"application/pdf","file_id":"9085","relation":"main_file","success":1,"checksum":"d36b6a8c6fafab66264e0d27114dae63","date_created":"2021-02-04T09:53:16Z","date_updated":"2021-02-04T09:53:16Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8608","ddc":["580"],"status":"public","title":"Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana","intvolume":" 229","abstract":[{"text":"To adapt to the diverse array of biotic and abiotic cues, plants have evolved sophisticated mechanisms to sense changes in environmental conditions and modulate their growth. Growth-promoting hormones and defence signalling fine tune plant development antagonistically. During host-pathogen interactions, this defence-growth trade-off is mediated by the counteractive effects of the defence hormone salicylic acid (SA) and the growth hormone auxin. Here we revealed an underlying mechanism of SA regulating auxin signalling by constraining the plasma membrane dynamics of PIN2 auxin efflux transporter in Arabidopsis thaliana roots. The lateral diffusion of PIN2 proteins is constrained by SA signalling, during which PIN2 proteins are condensed into hyperclusters depending on REM1.2-mediated nanodomain compartmentalisation. Furthermore, membrane nanodomain compartmentalisation by SA or Remorin (REM) assembly significantly suppressed clathrin-mediated endocytosis. Consequently, SA-induced heterogeneous surface condensation disrupted asymmetric auxin distribution and the resultant gravitropic response. Our results demonstrated a defence-growth trade-off mechanism by which SA signalling crosstalked with auxin transport by concentrating membrane-resident PIN2 into heterogeneous compartments.","lang":"eng"}],"issue":"2","type":"journal_article","doi":"10.1111/nph.16915","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000573568000001"],"pmid":["32901934"]},"isi":1,"quality_controlled":"1","month":"01","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"author":[{"first_name":"M","last_name":"Ke","full_name":"Ke, M"},{"full_name":"Ma, Z","last_name":"Ma","first_name":"Z"},{"full_name":"Wang, D","first_name":"D","last_name":"Wang"},{"full_name":"Sun, Y","first_name":"Y","last_name":"Sun"},{"full_name":"Wen, C","last_name":"Wen","first_name":"C"},{"full_name":"Huang, D","last_name":"Huang","first_name":"D"},{"full_name":"Chen, Z","last_name":"Chen","first_name":"Z"},{"last_name":"Yang","first_name":"L","full_name":"Yang, L"},{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang"},{"full_name":"Li, R","last_name":"Li","first_name":"R"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Miao, Y","last_name":"Miao","first_name":"Y"},{"first_name":"X","last_name":"Chen","full_name":"Chen, X"}],"date_created":"2020-10-05T12:45:36Z","date_updated":"2023-09-05T16:06:24Z","volume":229,"acknowledgement":"This work was supported by the National Key Research andDevelopment Programme of China (2017YFA0506100), theNational Natural Science Foundation of China (31870170 and31701168), and the Fok Ying Tung Education Foundation(161027) to XC; NTU startup grant (M4081533) and NIM/01/2016 (NTU, Singapore) to YM. We thank Lei Shi andZhongquan Lin for microscopy assistance.","year":"2021","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"JiFr"}],"file_date_updated":"2021-02-04T09:53:16Z"},{"publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"month":"02","oa":1,"external_id":{"pmid":["33634751"],"isi":["000636121800001"]},"main_file_link":[{"url":"https://doi.org/10.1080/15548627.2020.1797280","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1080/15548627.2020.1797280","language":[{"iso":"eng"}],"pmid":1,"acknowledgement":"This work was supported by the National Institute of General Medical Sciences [GM131919]. Due to space and other limitations, it is not possible to include all other sources of financial support.","year":"2021","department":[{"_id":"JiFr"},{"_id":"CaHe"}],"publisher":"Taylor & Francis","publication_status":"published","author":[{"full_name":"Klionsky, Daniel J.","first_name":"Daniel J.","last_name":"Klionsky"},{"last_name":"Abdel-Aziz","first_name":"Amal Kamal","full_name":"Abdel-Aziz, Amal Kamal"},{"full_name":"Abdelfatah, Sara","first_name":"Sara","last_name":"Abdelfatah"},{"last_name":"Abdellatif","first_name":"Mahmoud","full_name":"Abdellatif, Mahmoud"},{"last_name":"Abdoli","first_name":"Asghar","full_name":"Abdoli, Asghar"},{"full_name":"Abel, Steffen","last_name":"Abel","first_name":"Steffen"},{"last_name":"Abeliovich","first_name":"Hagai","full_name":"Abeliovich, Hagai"},{"full_name":"Abildgaard, Marie H.","last_name":"Abildgaard","first_name":"Marie H."},{"first_name":"Yakubu Princely","last_name":"Abudu","full_name":"Abudu, Yakubu Princely"},{"full_name":"Acevedo-Arozena, Abraham","last_name":"Acevedo-Arozena","first_name":"Abraham"},{"full_name":"Adamopoulos, Iannis E.","last_name":"Adamopoulos","first_name":"Iannis E."},{"last_name":"Adeli","first_name":"Khosrow","full_name":"Adeli, Khosrow"},{"last_name":"Adolph","first_name":"Timon E.","full_name":"Adolph, Timon E."},{"last_name":"Adornetto","first_name":"Annagrazia","full_name":"Adornetto, Annagrazia"},{"first_name":"Elma","last_name":"Aflaki","full_name":"Aflaki, Elma"},{"first_name":"Galila","last_name":"Agam","full_name":"Agam, Galila"},{"full_name":"Agarwal, Anupam","first_name":"Anupam","last_name":"Agarwal"},{"full_name":"Aggarwal, Bharat B.","last_name":"Aggarwal","first_name":"Bharat B."},{"last_name":"Agnello","first_name":"Maria","full_name":"Agnello, Maria"},{"full_name":"Agostinis, Patrizia","first_name":"Patrizia","last_name":"Agostinis"},{"last_name":"Agrewala","first_name":"Javed N.","full_name":"Agrewala, Javed N."},{"full_name":"Agrotis, Alexander","last_name":"Agrotis","first_name":"Alexander"},{"first_name":"Patricia V.","last_name":"Aguilar","full_name":"Aguilar, Patricia V."},{"first_name":"S. 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Weiergräber, C.C. Weihl, G. Weindl, R. Weiskirchen, A. Wells, R.H. Wen, X. Wen, A. Werner, B. Weykopf, S.P. Wheatley, J.L. Whitton, A.J. Whitworth, K. Wiktorska, M.E. Wildenberg, T. Wileman, S. Wilkinson, D. Willbold, B. Williams, R.S.B. Williams, R.L. Williams, P.R. Williamson, R.A. Wilson, B. Winner, N.J. Winsor, S.S. Witkin, H. Wodrich, U. Woehlbier, T. Wollert, E. Wong, J.H. Wong, R.W. Wong, V.K.W. Wong, W.W.L. Wong, A.G. Wu, C. Wu, J. Wu, J. Wu, K.K. Wu, M. Wu, S.Y. Wu, S. Wu, S.Y. Wu, S. Wu, W.K.K. Wu, X. Wu, X. Wu, Y.W. Wu, Y. Wu, R.J. Xavier, H. Xia, L. Xia, Z. Xia, G. Xiang, J. Xiang, M. Xiang, W. Xiang, B. Xiao, G. Xiao, H. Xiao, H.T. Xiao, J. Xiao, L. Xiao, S. Xiao, Y. Xiao, B. Xie, C.M. Xie, M. Xie, Y. Xie, Z. Xie, Z. Xie, M. Xilouri, C. Xu, E. Xu, H. Xu, J. Xu, J.R. Xu, L. Xu, W.W. Xu, X. Xu, Y. Xue, S.M.S. Yakhine-Diop, M. Yamaguchi, O. Yamaguchi, A. Yamamoto, S. Yamashina, S. Yan, S.J. Yan, Z. Yan, Y. Yanagi, C. Yang, D.S. Yang, H. Yang, H.T. Yang, H. Yang, J.M. Yang, J. Yang, J. Yang, L. Yang, L. Yang, M. Yang, P.M. Yang, Q. Yang, S. Yang, S. Yang, S.F. Yang, W. Yang, W.Y. Yang, X. Yang, X. Yang, Y. Yang, Y. Yang, H. Yao, S. Yao, X. Yao, Y.G. Yao, Y.M. Yao, T. Yasui, M. Yazdankhah, P.M. Yen, C. Yi, X.M. Yin, Y. Yin, Z. Yin, Z. Yin, M. Ying, Z. Ying, C.K. Yip, S.P.T. Yiu, Y.H. Yoo, K. Yoshida, S.R. Yoshii, T. Yoshimori, B. Yousefi, B. Yu, H. Yu, J. Yu, J. Yu, L. Yu, M.L. Yu, S.W. Yu, V.C. Yu, W.H. Yu, Z. Yu, Z. Yu, J. Yuan, L.Q. Yuan, S. Yuan, S.S.F. Yuan, Y. Yuan, Z. Yuan, J. Yue, Z. Yue, J. Yun, R.L. Yung, D.N. Zacks, G. Zaffagnini, V.O. Zambelli, I. Zanella, Q.S. Zang, S. Zanivan, S. Zappavigna, P. Zaragoza, K.S. Zarbalis, A. Zarebkohan, A. Zarrouk, S.O. Zeitlin, J. Zeng, J.D. Zeng, E. Žerovnik, L. Zhan, B. Zhang, D.D. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H.L. Zhang, J. Zhang, J. Zhang, J.P. Zhang, K.Y.B. Zhang, L.W. Zhang, L. Zhang, L. Zhang, L. Zhang, L. Zhang, M. Zhang, P. Zhang, S. Zhang, W. Zhang, X. Zhang, X.W. Zhang, X. Zhang, X. Zhang, X. Zhang, X. Zhang, X.D. Zhang, Y. Zhang, Y. Zhang, Y. Zhang, Y.D. Zhang, Y. Zhang, Y.Y. Zhang, Y. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, H. Zhao, L. Zhao, S. Zhao, T. Zhao, X.F. Zhao, Y. Zhao, Y. Zhao, Y. Zhao, Y. Zhao, G. Zheng, K. Zheng, L. Zheng, S. Zheng, X.L. Zheng, Y. Zheng, Z.G. Zheng, B. Zhivotovsky, Q. Zhong, A. Zhou, B. Zhou, C. Zhou, G. Zhou, H. Zhou, H. Zhou, H. Zhou, J. Zhou, J. Zhou, J. Zhou, J. Zhou, K. Zhou, R. Zhou, X.J. Zhou, Y. Zhou, Y. Zhou, Y. Zhou, Z.Y. Zhou, Z. Zhou, B. Zhu, C. Zhu, G.Q. Zhu, H. Zhu, H. Zhu, H. Zhu, W.G. Zhu, Y. Zhu, Y. Zhu, H. Zhuang, X. Zhuang, K. Zientara-Rytter, C.M. Zimmermann, E. Ziviani, T. Zoladek, W.X. Zong, D.B. Zorov, A. Zorzano, W. Zou, Z. Zou, Z. Zou, S. Zuryn, W. Zwerschke, B. Brand-Saberi, X.C. Dong, C.S. Kenchappa, Z. Li, Y. Lin, S. Oshima, Y. Rong, J.C. Sluimer, C.L. Stallings, C.K. Tong, Autophagy 17 (2021) 1–382.","mla":"Klionsky, Daniel J., et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” Autophagy, vol. 17, no. 1, Taylor & Francis, 2021, pp. 1–382, doi:10.1080/15548627.2020.1797280.","chicago":"Klionsky, Daniel J., Amal Kamal Abdel-Aziz, Sara Abdelfatah, Mahmoud Abdellatif, Asghar Abdoli, Steffen Abel, Hagai Abeliovich, et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” Autophagy. Taylor & Francis, 2021. https://doi.org/10.1080/15548627.2020.1797280."},"publication":"Autophagy","page":"1-382","article_type":"review","date_published":"2021-02-08T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. ","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9298","intvolume":" 17","title":"Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)","status":"public","oa_version":"Published Version"},{"_id":"10223","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 599","status":"public","title":"Cell surface and intracellular auxin signalling for H+ fluxes in root growth","oa_version":"Preprint","type":"journal_article","issue":"7884","abstract":[{"text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments.","lang":"eng"}],"citation":{"chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-04037-6.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:10.1038/s41586-021-04037-6.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 599(7884), 273–277.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277. doi:10.1038/s41586-021-04037-6"},"publication":"Nature","page":"273-277","article_type":"original","date_published":"2021-11-11T00:00:00Z","scopus_import":"1","keyword":["Multidisciplinary"],"article_processing_charge":"No","day":"11","pmid":1,"year":"2021","acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","publisher":"Springer Nature","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"publication_status":"published","related_material":{"link":[{"url":"https://ist.ac.at/en/news/stop-and-grow/","relation":"press_release","description":"News on IST Webpage"}],"record":[{"status":"public","relation":"earlier_version","id":"10095"}]},"author":[{"orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin","full_name":"Li, Lanxin"},{"full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark","last_name":"Roosjen","full_name":"Roosjen, Mark"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"first_name":"Lesia","last_name":"Rodriguez Solovey","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chen, Jian","last_name":"Chen","first_name":"Jian"},{"full_name":"Shabala, Lana","first_name":"Lana","last_name":"Shabala"},{"last_name":"Smet","first_name":"Wouter","full_name":"Smet, Wouter"},{"full_name":"Ren, Hong","first_name":"Hong","last_name":"Ren"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"last_name":"Kinoshita","first_name":"Toshinori","full_name":"Kinoshita, Toshinori"},{"last_name":"Gray","first_name":"William M.","full_name":"Gray, William M."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"volume":599,"date_created":"2021-11-07T23:01:25Z","date_updated":"2023-10-18T08:30:53Z","ec_funded":1,"main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"external_id":{"isi":["000713338100006"],"pmid":["34707283"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41586-021-04037-6","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"month":"11"},{"volume":44,"date_updated":"2023-11-07T08:18:36Z","date_created":"2021-02-24T10:07:21Z","author":[{"full_name":"Zhao, Y","last_name":"Zhao","first_name":"Y"},{"full_name":"Wu, L","first_name":"L","last_name":"Wu"},{"full_name":"Fu, Q","first_name":"Q","last_name":"Fu"},{"first_name":"D","last_name":"Wang","full_name":"Wang, D"},{"last_name":"Li","first_name":"J","full_name":"Li, J"},{"last_name":"Yao","first_name":"B","full_name":"Yao, B"},{"first_name":"S","last_name":"Yu","full_name":"Yu, S"},{"last_name":"Jiang","first_name":"L","full_name":"Jiang, L"},{"full_name":"Qian, J","first_name":"J","last_name":"Qian"},{"full_name":"Zhou, X","last_name":"Zhou","first_name":"X"},{"first_name":"L","last_name":"Han","full_name":"Han, L"},{"first_name":"S","last_name":"Zhao","full_name":"Zhao, S"},{"last_name":"Ma","first_name":"C","full_name":"Ma, C"},{"full_name":"Zhang, Y","first_name":"Y","last_name":"Zhang"},{"full_name":"Luo, C","last_name":"Luo","first_name":"C"},{"full_name":"Dong, Q","first_name":"Q","last_name":"Dong"},{"full_name":"Li, S","first_name":"S","last_name":"Li"},{"full_name":"Zhang, L","last_name":"Zhang","first_name":"L"},{"full_name":"Jiang, X","first_name":"X","last_name":"Jiang"},{"full_name":"Li, Y","first_name":"Y","last_name":"Li"},{"full_name":"Luo, H","last_name":"Luo","first_name":"H"},{"first_name":"K","last_name":"Li","full_name":"Li, K"},{"full_name":"Yang, J","first_name":"J","last_name":"Yang"},{"full_name":"Luo, Q","last_name":"Luo","first_name":"Q"},{"last_name":"Li","first_name":"L","full_name":"Li, L"},{"full_name":"Peng, S","last_name":"Peng","first_name":"S"},{"full_name":"Huang, H","last_name":"Huang","first_name":"H"},{"last_name":"Zuo","first_name":"Z","full_name":"Zuo, Z"},{"full_name":"Liu, C","last_name":"Liu","first_name":"C"},{"last_name":"Wang","first_name":"L","full_name":"Wang, L"},{"first_name":"C","last_name":"Li","full_name":"Li, C"},{"full_name":"He, X","last_name":"He","first_name":"X"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Du, Y","first_name":"Y","last_name":"Du"}],"publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2021","file_date_updated":"2023-11-02T17:02:11Z","language":[{"iso":"eng"}],"doi":"10.1111/pce.14029","quality_controlled":"1","isi":1,"external_id":{"pmid":["33576018"],"isi":["000625398600001"]},"oa":1,"publication_identifier":{"issn":["0140-7791"],"eissn":["1365-3040"]},"month":"06","file":[{"date_created":"2023-11-02T17:02:11Z","date_updated":"2023-11-02T17:02:11Z","success":1,"checksum":"a812418fede076741c9c4dc07f317068","file_id":"14481","relation":"main_file","creator":"amally","content_type":"application/pdf","file_size":8437528,"file_name":"Zhao PlantCellEnv 2021_accepted.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","intvolume":" 44","title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","status":"public","ddc":["580"],"_id":"9189","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","abstract":[{"text":"Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses.","lang":"eng"}],"type":"journal_article","date_published":"2021-06-01T00:00:00Z","page":"1846-1857","article_type":"original","citation":{"ama":"Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 2021;44(6):1846-1857. doi:10.1111/pce.14029","apa":"Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. Wiley. https://doi.org/10.1111/pce.14029","ieee":"Y. Zhao et al., “INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance,” Plant, Cell & Environment, vol. 44, no. 6. Wiley, pp. 1846–1857, 2021.","ista":"Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 44(6), 1846–1857.","short":"Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian, X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X. Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo, C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell & Environment 44 (2021) 1846–1857.","mla":"Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment, vol. 44, no. 6, Wiley, 2021, pp. 1846–57, doi:10.1111/pce.14029.","chicago":"Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment. Wiley, 2021. https://doi.org/10.1111/pce.14029."},"publication":"Plant, Cell & Environment","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"}]