[{"citation":{"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).","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.","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.","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","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.","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","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."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_type":"original","date_published":"2023-06-12T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"12","_id":"13201","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 120","title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"relation":"main_file","embargo":"2023-12-12","file_id":"13204","checksum":"d800e06252eaefba28531fa9440f23f0","date_created":"2023-07-10T08:48:40Z","date_updated":"2023-12-13T23:30:03Z","access_level":"open_access","file_name":"2023_PNAS_Wang.pdf","file_size":5244581,"content_type":"application/pdf","creator":"alisjak"}],"type":"journal_article","issue":"25","abstract":[{"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.","lang":"eng"}],"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"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1073/pnas.2221313120","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"06","pmid":1,"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).","year":"2023","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publication_status":"published","author":[{"last_name":"Wang","first_name":"Yalu","full_name":"Wang, Yalu"},{"first_name":"Zhi","last_name":"Yuan","full_name":"Yuan, Zhi"},{"full_name":"Wang, Jinyi","last_name":"Wang","first_name":"Jinyi"},{"full_name":"Xiao, Huixin","last_name":"Xiao","first_name":"Huixin"},{"first_name":"Lu","last_name":"Wan","full_name":"Wan, Lu"},{"full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X"},{"first_name":"Yan","last_name":"Guo","full_name":"Guo, Yan"},{"full_name":"Gong, Zhizhong","last_name":"Gong","first_name":"Zhizhong"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Jing","last_name":"Zhang","first_name":"Jing"}],"volume":120,"date_updated":"2023-12-13T23:30:04Z","date_created":"2023-07-09T22:01:12Z","article_number":"e2221313120","file_date_updated":"2023-12-13T23:30:03Z"},{"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":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"doi":"10.15479/at:ista:14510","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"month":"11","year":"2023","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"14591","relation":"part_of_dissertation","status":"public"},{"id":"9887","status":"public","relation":"part_of_dissertation"},{"id":"8139","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Nataliia","last_name":"Gnyliukh","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia"}],"date_updated":"2024-03-28T23:30:46Z","date_created":"2023-11-10T09:10:06Z","ec_funded":1,"file_date_updated":"2023-11-23T13:10:55Z","citation":{"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.","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.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria.","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","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510"},"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"],"has_accepted_license":"1","article_processing_charge":"No","day":"10","_id":"14510","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","ddc":["570"],"title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","oa_version":"Published Version","file":[{"creator":"ngnyliuk","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":20824903,"file_name":"Thesis_Gnyliukh_final_08_11_23.docx","access_level":"closed","date_updated":"2023-11-20T09:18:51Z","date_created":"2023-11-20T09:18:51Z","checksum":"3d5e680bfc61f98e308c434f45cc9bd6","file_id":"14567","relation":"source_file"},{"access_level":"closed","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","embargo_to":"open_access","creator":"ngnyliuk","content_type":"application/pdf","file_size":24871844,"file_id":"14568","embargo":"2024-11-23","relation":"main_file","checksum":"bfc96d47fc4e7e857dd71656097214a4","date_created":"2023-11-20T09:23:11Z","date_updated":"2023-11-23T13:10:55Z"}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"publication_identifier":{"issn":["1943-0264"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1101/cshperspect.a039859 ","isi":1,"quality_controlled":"1","oa":1,"external_id":{"pmid":["34400554"],"isi":["000806563000003"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a039859 "}],"article_number":"a039859","volume":14,"date_created":"2021-09-14T11:36:53Z","date_updated":"2023-08-02T06:54:42Z","author":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"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.","year":"2022","article_processing_charge":"No","day":"27","scopus_import":"1","date_published":"2022-05-27T00:00:00Z","article_type":"review","citation":{"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 .","short":"J. Friml, Cold Spring Harbor Perspectives in Biology 14 (2022).","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 .","ama":"Friml J. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 2022;14(5). doi:10.1101/cshperspect.a039859 ","ista":"Friml J. 2022. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 14(5), 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 "},"publication":"Cold Spring Harbor Perspectives in Biology","issue":"5","abstract":[{"lang":"eng","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. "}],"type":"journal_article","oa_version":"Published Version","intvolume":" 14","title":"Fourteen stations of auxin","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10016"},{"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"},{"last_name":"Vangheluwe","first_name":"Nick","full_name":"Vangheluwe, Nick"},{"first_name":"Stan","last_name":"Van Praet","full_name":"Van Praet, Stan"},{"first_name":"Lingxiang","last_name":"Jiang","full_name":"Jiang, Lingxiang"},{"full_name":"Baster, Pawel","first_name":"Pawel","last_name":"Baster","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Cuyper, Carolien","first_name":"Carolien","last_name":"De Cuyper"},{"last_name":"Boyer","first_name":"Francois-Didier","full_name":"Boyer, Francois-Didier"},{"first_name":"Elisabeth","last_name":"Stes","full_name":"Stes, Elisabeth"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"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","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","doi":"10.1093/pcp/pcab149","language":[{"iso":"eng"}],"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,"publication_identifier":{"issn":["0032-0781"],"eissn":["1471-9053"]},"month":"01","oa_version":"Published Version","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","issue":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2022-01-21T00:00:00Z","citation":{"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.","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"},"publication":"Plant & Cell Physiology","page":"104-119","article_type":"original","article_processing_charge":"No","day":"21","scopus_import":"1","keyword":["flavonols","MAX2","rac-Gr24","RNA-seq","root development","transcriptional regulation"]},{"language":[{"iso":"eng"}],"doi":"10.1093/jxb/erac019","quality_controlled":"1","isi":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"main_file_link":[{"open_access":"1","url":"https://biblio.ugent.be/publication/8738721"}],"oa":1,"external_id":{"pmid":["35085386"],"isi":["000764220900001"]},"month":"04","publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"date_updated":"2023-08-02T14:07:58Z","date_created":"2022-02-03T09:19:01Z","volume":73,"author":[{"first_name":"R","last_name":"Wang","full_name":"Wang, R"},{"last_name":"Himschoot","first_name":"E","full_name":"Himschoot, E"},{"full_name":"Grenzi, M","last_name":"Grenzi","first_name":"M"},{"full_name":"Chen, J","first_name":"J","last_name":"Chen"},{"full_name":"Safi, A","first_name":"A","last_name":"Safi"},{"first_name":"M","last_name":"Krebs","full_name":"Krebs, M"},{"full_name":"Schumacher, K","last_name":"Schumacher","first_name":"K"},{"first_name":"MK","last_name":"Nowack","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"},{"last_name":"De Smet","first_name":"I","full_name":"De Smet, I"},{"full_name":"Geelen, D","last_name":"Geelen","first_name":"D"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"first_name":"A","last_name":"Costa","full_name":"Costa, A"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"}],"publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"JiFr"}],"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,"ec_funded":1,"article_number":"erac019","date_published":"2022-04-18T00:00:00Z","article_type":"original","publication":"Journal of Experimental Botany","citation":{"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.","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."},"day":"18","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","title":"Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots","status":"public","intvolume":" 73","_id":"10717","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"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.","lang":"eng"}],"issue":"8","type":"journal_article"},{"doi":"10.1111/jipb.13225","language":[{"iso":"eng"}],"external_id":{"pmid":["35018726"],"isi":["000761281200011"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1111/jipb.13225","open_access":"1"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"month":"02","author":[{"first_name":"Z","last_name":"Yu","full_name":"Yu, Z"},{"first_name":"F","last_name":"Zhang","full_name":"Zhang, F"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Z","last_name":"Ding","full_name":"Ding, 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","date_published":"2022-02-01T00:00:00Z","citation":{"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.","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.","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","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.","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.","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"},"publication":"Journal of Integrative Plant Biology","page":"371-392","article_type":"review","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Published Version","_id":"10719","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 64","status":"public","title":"Auxin signaling: Research advances over the past 30 years","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"},{"article_number":"102174","file_date_updated":"2022-03-10T13:34:09Z","pmid":1,"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).","year":"2022","publisher":"Elsevier","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","first_name":"Jakub","last_name":"Hajny","full_name":"Hajny, Jakub"},{"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","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"volume":65,"date_updated":"2023-08-02T14:29:12Z","date_created":"2022-02-20T23:01:32Z","publication_identifier":{"issn":["1369-5266"]},"month":"02","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":["35123880"],"isi":["000758724700004"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.pbi.2022.102174","language":[{"iso":"eng"}],"type":"journal_article","issue":"2","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."}],"_id":"10768","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 65","title":"Auxin canalization: From speculative models toward molecular players","status":"public","ddc":["580"],"file":[{"file_name":"2022_CurrentOpPlantBiology_Hajny.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":820322,"file_id":"10844","relation":"main_file","date_updated":"2022-03-10T13:34:09Z","date_created":"2022-03-10T13:34:09Z","success":1,"checksum":"f1ee02b6fb4200934eeb31fa69120885"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","citation":{"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.","ista":"Hajny J, Tan S, Friml J. 2022. Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. 65(2), 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","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.","short":"J. Hajny, S. Tan, J. Friml, Current Opinion in Plant Biology 65 (2022).","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."},"publication":"Current Opinion in Plant Biology","article_type":"original","date_published":"2022-02-01T00:00:00Z"},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2022-06-01T00:00:00Z","page":"2150-2173","article_type":"original","citation":{"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.","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.","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.","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","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.","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"},"publication":"Plant Cell","issue":"6","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 34","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","status":"public","_id":"10841","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"month":"06","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1093/plcell/koac071","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,"main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"oa":1,"external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"volume":34,"date_created":"2022-03-08T13:47:51Z","date_updated":"2023-08-02T14:46:48Z","author":[{"first_name":"DA","last_name":"Dahhan","full_name":"Dahhan, DA"},{"first_name":"GD","last_name":"Reynolds","full_name":"Reynolds, GD"},{"full_name":"Cárdenas, JJ","last_name":"Cárdenas","first_name":"JJ"},{"full_name":"Eeckhout, D","first_name":"D","last_name":"Eeckhout"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson"},{"first_name":"K","last_name":"Yperman","full_name":"Yperman, K"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann"},{"first_name":"N","last_name":"Vang","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"},{"first_name":"G","last_name":"De Jaeger","full_name":"De Jaeger, G"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Van Damme, D","first_name":"D","last_name":"Van Damme"},{"full_name":"Pan, J","first_name":"J","last_name":"Pan"},{"last_name":"Bednarek","first_name":"SY","full_name":"Bednarek, SY"}],"publisher":"Oxford Academic","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publication_status":"published","pmid":1,"year":"2022","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)."},{"author":[{"first_name":"Qing","last_name":"Lu","full_name":"Lu, Qing"},{"full_name":"Zhang, Yonghong","last_name":"Zhang","first_name":"Yonghong"},{"last_name":"Hellner","first_name":"Joakim","full_name":"Hellner, Joakim"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini","first_name":"Caterina","full_name":"Giannini, Caterina"},{"full_name":"Xu, Xiangyu","last_name":"Xu","first_name":"Xiangyu"},{"first_name":"Jarne","last_name":"Pauwels","full_name":"Pauwels, Jarne"},{"full_name":"Ma, Qian","first_name":"Qian","last_name":"Ma"},{"last_name":"Dejonghe","first_name":"Wim","full_name":"Dejonghe, Wim"},{"full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","last_name":"Han"},{"first_name":"Brigitte","last_name":"Van De Cotte","full_name":"Van De Cotte, Brigitte"},{"last_name":"Impens","first_name":"Francis","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","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Molina, Daniel Martinez","first_name":"Daniel Martinez","last_name":"Molina"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"date_created":"2022-03-20T23:01:39Z","date_updated":"2023-08-03T06:06:27Z","volume":119,"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,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Proceedings of the National Academy of Sciences","file_date_updated":"2022-03-21T09:19:47Z","article_number":"e2118220119","doi":"10.1073/pnas.2118220119","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":{"pmid":["35254915"],"isi":["000771756300008"]},"isi":1,"quality_controlled":"1","month":"03","publication_identifier":{"eissn":["1091-6490"]},"oa_version":"Published Version","file":[{"creator":"dernst","file_size":2169534,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_PNAS_Lu.pdf","success":1,"checksum":"83e0fea7919570d0b519b41193342571","date_updated":"2022-03-21T09:19:47Z","date_created":"2022-03-21T09:19:47Z","file_id":"10910","relation":"main_file"}],"_id":"10888","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["580"],"title":"Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling","intvolume":" 119","abstract":[{"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.","lang":"eng"}],"issue":"11","type":"journal_article","date_published":"2022-03-07T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"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.","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).","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.","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","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.","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"},"article_type":"original","day":"07","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"file_date_updated":"2022-07-18T08:05:15Z","article_number":"862398","author":[{"last_name":"Wang","first_name":"Ren","full_name":"Wang, Ren"},{"full_name":"Himschoot, Ellie","last_name":"Himschoot","first_name":"Ellie"},{"full_name":"Chen, Jian","first_name":"Jian","last_name":"Chen"},{"full_name":"Boudsocq, Marie","last_name":"Boudsocq","first_name":"Marie"},{"first_name":"Danny","last_name":"Geelen","full_name":"Geelen, Danny"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, 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_created":"2022-07-17T22:01:54Z","date_updated":"2023-08-03T12:01:47Z","volume":13,"year":"2022","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.","pmid":1,"publication_status":"published","publisher":"Frontiers","department":[{"_id":"JiFr"}],"month":"06","publication_identifier":{"eissn":["1664-462X"]},"doi":"10.3389/fpls.2022.862398","language":[{"iso":"eng"}],"external_id":{"pmid":["35783951"],"isi":["000819250500001"]},"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,"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","oa_version":"Published Version","file":[{"date_updated":"2022-07-18T08:05:15Z","date_created":"2022-07-18T08:05:15Z","success":1,"checksum":"95313515637c0f84de591d204375d764","file_id":"11596","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":5040638,"file_name":"2022_FrontiersPlantScience_Wang.pdf","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11589","ddc":["580"],"title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","status":"public","intvolume":" 13","day":"16","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2022-06-16T00:00:00Z","publication":"Frontiers in Plant Science","citation":{"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.","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022).","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.","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","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.","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.","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"},"article_type":"original"}]