[{"article_type":"original","oa":1,"abstract":[{"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.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2022-08-08T07:42:09Z","doi":"10.1073/pnas.2121058119","file":[{"file_id":"11747","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","relation":"main_file","file_size":2506262,"date_created":"2022-08-08T07:42:09Z","creator":"dernst","access_level":"open_access","file_name":"2022_PNAS_Li.pdf","success":1,"date_updated":"2022-08-08T07:42:09Z","content_type":"application/pdf"}],"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"_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","grant_number":"25351"}],"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.","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.","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","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","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."},"date_created":"2022-08-04T20:06:49Z","title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"status":"public","keyword":["Multidisciplinary"],"publication_status":"published","year":"2022","issue":"31","intvolume":" 119","publication":"Proceedings of the National Academy of Sciences","publisher":"Proceedings of the National Academy of Sciences","author":[{"first_name":"Lanxin","orcid":"0000-0002-5607-272X","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang"},{"first_name":"Saqer S.","full_name":"Alotaibi, Saqer S.","last_name":"Alotaibi"},{"last_name":"Pěnčík","full_name":"Pěnčík, Aleš","first_name":"Aleš"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257","first_name":"Maciek"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"volume":119,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","article_processing_charge":"No","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).”","pmid":1,"quality_controlled":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"_id":"11723","ddc":["580"],"article_number":"e2121058119","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","day":"25","date_updated":"2023-08-03T12:43:53Z","language":[{"iso":"eng"}],"date_published":"2022-07-25T00:00:00Z","external_id":{"isi":["000881496900002"],"pmid":["35878023"]},"isi":1,"month":"07"},{"author":[{"first_name":"Z","last_name":"Tian","full_name":"Tian, Z"},{"first_name":"Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"L","full_name":"Zhu, L","last_name":"Zhu"},{"last_name":"Jiang","full_name":"Jiang, B","first_name":"B"},{"first_name":"H","full_name":"Wang, H","last_name":"Wang"},{"last_name":"Gao","full_name":"Gao, R","first_name":"R"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Xiao","full_name":"Xiao, G","first_name":"G"}],"publisher":"Oxford University Press","scopus_import":"1","type":"journal_article","has_accepted_license":"1","volume":34,"quality_controlled":"1","pmid":1,"article_processing_charge":"No","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).","ddc":["580"],"_id":"12053","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"day":"01","date_updated":"2023-08-03T13:41:06Z","external_id":{"isi":["000852753000001"],"pmid":["36040191"]},"date_published":"2022-12-01T00:00:00Z","language":[{"iso":"eng"}],"month":"12","isi":1,"page":"4816-4839","oa":1,"article_type":"original","project":[{"call_identifier":"FWF","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"file":[{"creator":"dernst","access_level":"open_access","file_name":"2022_PlantCell_Tian.pdf","relation":"main_file","date_created":"2023-01-20T08:29:12Z","file_size":3282540,"checksum":"1c606d9545f29dfca15235f69ad27b58","file_id":"12318","content_type":"application/pdf","success":1,"date_updated":"2023-01-20T08:29:12Z"}],"file_date_updated":"2023-01-20T08:29:12Z","doi":"10.1093/plcell/koac270","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"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum)","date_created":"2022-09-07T14:19:39Z","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","short":"Z. Tian, Y. Zhang, L. Zhu, B. Jiang, H. Wang, R. Gao, J. Friml, G. Xiao, The Plant Cell 34 (2022) 4816–4839.","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.","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.","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"},"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"related_material":{"link":[{"url":"https://doi.org/10.1093/plcell/koac342","relation":"erratum"}]},"publication_status":"published","department":[{"_id":"JiFr"}],"status":"public","year":"2022","issue":"12","publication":"The Plant Cell","intvolume":" 34"},{"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-33198-9"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"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","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.","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.","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"},"title":"WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions","date_created":"2022-09-07T14:19:26Z","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"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-022-32888-8","file_date_updated":"2022-09-08T07:46:16Z","project":[{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"file":[{"success":1,"date_updated":"2022-09-08T07:46:16Z","content_type":"application/pdf","file_id":"12063","checksum":"43336758c89cd6c045839089af070afe","relation":"main_file","file_size":6678579,"date_created":"2022-09-08T07:46:16Z","creator":"dernst","access_level":"open_access","file_name":"2022_NatureCommunications_Konstantinova.pdf"}],"article_type":"original","oa":1,"intvolume":" 13","publication":"Nature Communications","year":"2022","status":"public","department":[{"_id":"JiFr"}],"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"_id":"12052","ddc":["580"],"article_number":"5147","article_processing_charge":"No","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).","pmid":1,"quality_controlled":"1","has_accepted_license":"1","volume":13,"type":"journal_article","publisher":"Springer Nature","author":[{"full_name":"Konstantinova, N","last_name":"Konstantinova","first_name":"N"},{"first_name":"Lukas","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer"},{"orcid":"0000-0003-0619-7783","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","last_name":"Glanc"},{"first_name":"R","full_name":"Keshkeih, R","last_name":"Keshkeih"},{"orcid":"0000-0002-0471-8285","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","last_name":"Tan"},{"first_name":"M","last_name":"Di Donato","full_name":"Di Donato, M"},{"last_name":"Retzer","full_name":"Retzer, K","first_name":"K"},{"first_name":"J","last_name":"Moulinier-Anzola","full_name":"Moulinier-Anzola, J"},{"first_name":"M","last_name":"Schwihla","full_name":"Schwihla, M"},{"first_name":"B","last_name":"Korbei","full_name":"Korbei, B"},{"first_name":"M","full_name":"Geisler, M","last_name":"Geisler"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"full_name":"Luschnig, C","last_name":"Luschnig","first_name":"C"}],"isi":1,"month":"09","language":[{"iso":"eng"}],"date_published":"2022-09-01T00:00:00Z","external_id":{"isi":["000848744900004"],"pmid":["36050482"]},"date_updated":"2023-08-03T13:40:32Z","license":"https://creativecommons.org/licenses/by/4.0/","day":"01"},{"intvolume":" 609","publication":"Nature","issue":"7927","year":"2022","status":"public","department":[{"_id":"JiFr"}],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"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.","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","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","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.","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.","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."},"title":"Structural insights into auxin recognition and efflux by Arabidopsis PIN1","date_created":"2022-09-07T14:19:52Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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."}],"doi":"10.1038/s41586-022-05143-9","file_date_updated":"2022-09-08T08:02:54Z","file":[{"date_created":"2022-09-08T08:02:54Z","file_size":32344580,"relation":"main_file","access_level":"open_access","file_name":"2022_Nature_Yang.pdf","creator":"dernst","file_id":"12064","checksum":"3136a585f8e1c7e73b5e1418b3d01898","content_type":"application/pdf","date_updated":"2022-09-08T08:02:54Z","success":1}],"article_type":"original","oa":1,"page":"611-615","isi":1,"month":"08","language":[{"iso":"eng"}],"date_published":"2022-08-02T00:00:00Z","external_id":{"pmid":["35917925"],"isi":["000848082900002"]},"date_updated":"2023-08-03T13:41:44Z","day":"02","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"_id":"12054","ddc":["580"],"article_processing_charge":"No","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.","pmid":1,"quality_controlled":"1","volume":609,"has_accepted_license":"1","scopus_import":"1","type":"journal_article","publisher":"Springer Nature","author":[{"first_name":"Z","last_name":"Yang","full_name":"Yang, Z"},{"last_name":"Xia","full_name":"Xia, J","first_name":"J"},{"first_name":"J","full_name":"Hong, J","last_name":"Hong"},{"first_name":"C","full_name":"Zhang, C","last_name":"Zhang"},{"last_name":"Wei","full_name":"Wei, H","first_name":"H"},{"first_name":"W","last_name":"Ying","full_name":"Ying, W"},{"full_name":"Sun, C","last_name":"Sun","first_name":"C"},{"first_name":"L","last_name":"Sun","full_name":"Sun, L"},{"full_name":"Mao, Y","last_name":"Mao","first_name":"Y"},{"first_name":"Y","full_name":"Gao, Y","last_name":"Gao"},{"last_name":"Tan","full_name":"Tan, S","first_name":"S"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Li","full_name":"Li, D","first_name":"D"},{"last_name":"Liu","full_name":"Liu, X","first_name":"X"},{"last_name":"Sun","full_name":"Sun, L","first_name":"L"}]},{"intvolume":" 221","publication":"Journal of Cell Biology","issue":"12","year":"2022","status":"public","department":[{"_id":"JiFr"}],"keyword":["Cell Biology"],"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"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.","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.","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.","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","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)."},"date_created":"2023-01-12T11:57:10Z","title":"Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2023-01-23T10:30:11Z","doi":"10.1083/jcb.202203139","file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-01-23T10:30:11Z","relation":"main_file","date_created":"2023-01-23T10:30:11Z","file_size":10365777,"creator":"dernst","access_level":"open_access","file_name":"2022_JCB_Zhao.pdf","file_id":"12342","checksum":"050b5cc4b25e6b94fe3e3cbfe0f5c06b"}],"oa":1,"article_type":"original","isi":1,"month":"12","language":[{"iso":"eng"}],"date_published":"2022-12-01T00:00:00Z","external_id":{"isi":["000932958800001"],"pmid":["36260289"]},"date_updated":"2023-08-03T14:20:15Z","day":"01","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"_id":"12121","ddc":["580"],"article_number":"e202203139","article_processing_charge":"No","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.","pmid":1,"quality_controlled":"1","volume":221,"has_accepted_license":"1","type":"journal_article","scopus_import":"1","publisher":"Rockefeller University Press","author":[{"first_name":"Jierui","full_name":"Zhao, Jierui","last_name":"Zhao"},{"first_name":"Mai Thu","full_name":"Bui, Mai Thu","last_name":"Bui"},{"first_name":"Juncai","last_name":"Ma","full_name":"Ma, Juncai"},{"first_name":"Fabian","last_name":"Künzl","full_name":"Künzl, Fabian"},{"first_name":"Lorenzo","full_name":"Picchianti, Lorenzo","last_name":"Picchianti"},{"first_name":"Juan Carlos","last_name":"De La Concepcion","full_name":"De La Concepcion, Juan Carlos"},{"first_name":"Yixuan","last_name":"Chen","full_name":"Chen, Yixuan"},{"full_name":"Petsangouraki, Sofia","last_name":"Petsangouraki","first_name":"Sofia"},{"first_name":"Azadeh","full_name":"Mohseni, Azadeh","last_name":"Mohseni"},{"first_name":"Marta","last_name":"García-Leon","full_name":"García-Leon, Marta"},{"first_name":"Marta Salas","last_name":"Gomez","full_name":"Gomez, Marta Salas"},{"first_name":"Caterina","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","last_name":"Giannini"},{"last_name":"Gwennogan","full_name":"Gwennogan, Dubois","first_name":"Dubois"},{"first_name":"Roksolana","last_name":"Kobylinska","full_name":"Kobylinska, Roksolana"},{"last_name":"Clavel","full_name":"Clavel, Marion","first_name":"Marion"},{"last_name":"Schellmann","full_name":"Schellmann, Swen","first_name":"Swen"},{"first_name":"Yvon","full_name":"Jaillais, Yvon","last_name":"Jaillais"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Byung-Ho","last_name":"Kang","full_name":"Kang, Byung-Ho"},{"first_name":"Yasin","last_name":"Dagdas","full_name":"Dagdas, Yasin"}]},{"publication_status":"published","department":[{"_id":"JiFr"}],"status":"public","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"year":"2022","publication":"Nature Communications","intvolume":" 13","article_type":"original","oa":1,"file":[{"file_name":"2022_NatureCommunications_Huang.pdf","access_level":"open_access","creator":"dernst","file_size":3375249,"date_created":"2023-01-23T11:17:33Z","relation":"main_file","checksum":"233922a7b9507d9d48591e6799e4526e","file_id":"12346","content_type":"application/pdf","date_updated":"2023-01-23T11:17:33Z","success":1}],"abstract":[{"lang":"eng","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-022-34723-6","file_date_updated":"2023-01-23T11:17:33Z","title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","date_created":"2023-01-12T12:02:41Z","citation":{"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","ieee":"J. Huang et al., “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” Nature Communications, vol. 13. Springer Nature, 2022.","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.","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.","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.","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).","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"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","day":"15","date_updated":"2023-08-04T08:52:01Z","date_published":"2022-11-15T00:00:00Z","external_id":{"isi":["000884426700001"],"pmid":["36379956"]},"language":[{"iso":"eng"}],"month":"11","isi":1,"publisher":"Springer Nature","author":[{"full_name":"Huang, Jian","last_name":"Huang","first_name":"Jian"},{"full_name":"Zhao, Lei","last_name":"Zhao","first_name":"Lei"},{"first_name":"Shikha","full_name":"Malik, Shikha","last_name":"Malik"},{"last_name":"Gentile","full_name":"Gentile, Benjamin R.","first_name":"Benjamin R."},{"last_name":"Xiong","full_name":"Xiong, Va","first_name":"Va"},{"first_name":"Tzahi","last_name":"Arazi","full_name":"Arazi, Tzahi"},{"full_name":"Owen, Heather A.","last_name":"Owen","first_name":"Heather A."},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Dazhong","last_name":"Zhao","full_name":"Zhao, Dazhong"}],"type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":13,"quality_controlled":"1","article_processing_charge":"No","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.","pmid":1,"article_number":"6960","ddc":["580"],"publication_identifier":{"issn":["2041-1723"]},"_id":"12130"},{"author":[{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M"},{"orcid":"0000-0001-9732-3815","first_name":"Tommaso","full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo"},{"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","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"publisher":"Elsevier","has_accepted_license":"1","volume":15,"type":"journal_article","scopus_import":"1","pmid":1,"article_processing_charge":"Yes (via OA deal)","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.","quality_controlled":"1","_id":"12239","publication_identifier":{"issn":["1674-2052"]},"ddc":["580"],"day":"03","date_updated":"2023-08-04T09:39:24Z","language":[{"iso":"eng"}],"external_id":{"pmid":["36081349"],"isi":["000882769800009"]},"date_published":"2022-10-03T00:00:00Z","isi":1,"month":"10","oa":1,"article_type":"original","page":"1533-1542","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.1016/j.molp.2022.09.003","file_date_updated":"2023-01-30T07:46:51Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","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."}],"file":[{"date_created":"2023-01-30T07:46:51Z","file_size":2307251,"relation":"main_file","file_name":"2022_MolecularPlant_Johnson.pdf","access_level":"open_access","creator":"dernst","file_id":"12435","checksum":"04d5c12490052d03e4dc4412338a43dd","content_type":"application/pdf","date_updated":"2023-01-30T07:46:51Z","success":1}],"project":[{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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","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.","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","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.","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."},"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","date_created":"2023-01-16T09:51:49Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["Plant Science","Molecular Biology"],"department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"status":"public","publication_status":"published","year":"2022","issue":"10","intvolume":" 15","publication":"Molecular Plant"},{"day":"06","date_updated":"2023-08-09T10:13:57Z","date_published":"2022-06-06T00:00:00Z","external_id":{"pmid":["35683031"],"isi":["000808733300001"]},"language":[{"iso":"eng"}],"month":"06","isi":1,"publisher":"MDPI","author":[{"last_name":"Bilanovičová","full_name":"Bilanovičová, V","first_name":"V"},{"full_name":"Rýdza, N","last_name":"Rýdza","first_name":"N"},{"last_name":"Koczka","full_name":"Koczka, L","first_name":"L"},{"last_name":"Hess","full_name":"Hess, M","first_name":"M"},{"full_name":"Feraru, E","last_name":"Feraru","first_name":"E"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nodzyński","full_name":"Nodzyński, T","first_name":"T"}],"type":"journal_article","has_accepted_license":"1","volume":23,"quality_controlled":"1","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).","article_processing_charge":"Yes","pmid":1,"ddc":["570"],"publication_identifier":{"issn":["1422-0067"]},"_id":"11489","publication_status":"published","department":[{"_id":"JiFr"}],"status":"public","year":"2022","issue":"11","publication":"International Journal of Molecular Sciences","intvolume":" 23","page":"6352","article_type":"original","oa":1,"file":[{"success":1,"date_updated":"2022-07-06T07:36:59Z","content_type":"application/pdf","checksum":"e997a57a928ec9d51fad8ce824a05935","file_id":"11492","creator":"cchlebak","access_level":"open_access","file_name":"2022_IntJMolSci_Bilanovicova.pdf","relation":"main_file","file_size":2324542,"date_created":"2022-07-06T07:36:59Z"}],"project":[{"call_identifier":"FWF","grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"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."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2022-07-06T07:36:59Z","doi":"10.3390/ijms23116352","date_created":"2022-07-05T15:14:34Z","title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","citation":{"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.","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.","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","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.","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","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."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version"},{"day":"03","date_updated":"2023-10-03T11:04:53Z","date_published":"2022-11-03T00:00:00Z","external_id":{"isi":["000875061600013"],"pmid":["36289340"]},"language":[{"iso":"eng"}],"month":"11","isi":1,"publisher":"Springer Nature","author":[{"first_name":"Linlin","orcid":"0000-0001-5187-8401","last_name":"Qi","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","full_name":"Qi, Linlin"},{"first_name":"Mateusz","full_name":"Kwiatkowski, Mateusz","last_name":"Kwiatkowski"},{"full_name":"Chen, Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","last_name":"Chen","first_name":"Huihuang"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","first_name":"Lukas"},{"first_name":"Scott A","orcid":"0000-0002-4566-0593","last_name":"Sinclair","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","full_name":"Sinclair, Scott A"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia","last_name":"Zou","first_name":"Minxia"},{"full_name":"del Genio, Charo I.","last_name":"del Genio","first_name":"Charo I."},{"first_name":"Martin F.","full_name":"Kubeš, Martin F.","last_name":"Kubeš"},{"first_name":"Richard","full_name":"Napier, Richard","last_name":"Napier"},{"last_name":"Jaworski","full_name":"Jaworski, Krzysztof","first_name":"Krzysztof"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"type":"journal_article","scopus_import":"1","volume":611,"quality_controlled":"1","article_processing_charge":"No","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_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"_id":"12144","publication_status":"published","department":[{"_id":"JiFr"}],"status":"public","year":"2022","issue":"7934","publication":"Nature","intvolume":" 611","page":"133-138","oa":1,"article_type":"original","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.1038/s41586-022-05369-7","date_created":"2023-01-12T12:06:05Z","title":"Adenylate cyclase activity of TIR1/AFB auxin receptors in plants","citation":{"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.","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.","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","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","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.","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."},"oa_version":"Submitted Version","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"}]},{"issue":"23","intvolume":" 57","publication":"Developmental Cell","department":[{"_id":"JiFr"}],"status":"public","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"publication_status":"published","year":"2022","citation":{"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","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.","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.","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.","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.","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"},"date_created":"2023-01-12T11:57:00Z","title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","oa_version":"None","article_type":"original","page":"2638-2651.e6","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.devcel.2022.11.006","language":[{"iso":"eng"}],"date_published":"2022-12-05T00:00:00Z","external_id":{"pmid":["36473460"],"isi":["000919603800005"]},"isi":1,"month":"12","day":"05","date_updated":"2023-10-04T08:23:20Z","article_processing_charge":"No","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).","pmid":1,"quality_controlled":"1","publication_identifier":{"issn":["1534-5807"]},"_id":"12120","publisher":"Elsevier","author":[{"first_name":"Huixin","full_name":"Xiao, Huixin","last_name":"Xiao"},{"first_name":"Yumei","full_name":"Hu, Yumei","last_name":"Hu"},{"full_name":"Wang, Yaping","last_name":"Wang","first_name":"Yaping"},{"first_name":"Jinkui","last_name":"Cheng","full_name":"Cheng, Jinkui"},{"first_name":"Jinyi","full_name":"Wang, Jinyi","last_name":"Wang"},{"full_name":"Chen, Guojingwei","last_name":"Chen","first_name":"Guojingwei"},{"first_name":"Qian","last_name":"Li","full_name":"Li, Qian"},{"last_name":"Wang","full_name":"Wang, Shuwei","first_name":"Shuwei"},{"first_name":"Yalu","full_name":"Wang, Yalu","last_name":"Wang"},{"last_name":"Wang","full_name":"Wang, Shao-Shuai","first_name":"Shao-Shuai"},{"full_name":"Wang, Yi","last_name":"Wang","first_name":"Yi"},{"last_name":"Xuan","full_name":"Xuan, Wei","first_name":"Wei"},{"first_name":"Zhen","full_name":"Li, Zhen","last_name":"Li"},{"last_name":"Guo","full_name":"Guo, Yan","first_name":"Yan"},{"last_name":"Gong","full_name":"Gong, Zhizhong","first_name":"Zhizhong"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Jing","full_name":"Zhang, Jing","last_name":"Zhang"}],"volume":57,"scopus_import":"1","type":"journal_article"}]