[{"abstract":[{"text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.","lang":"eng"}],"_id":"10841","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).","date_published":"2022-06-01T00:00:00Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","issue":"6","isi":1,"scopus_import":"1","date_created":"2022-03-08T13:47:51Z","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.” <i>Plant Cell</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>.","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>","ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford University Press, 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. <i>Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","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.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>."},"type":"journal_article","author":[{"full_name":"Dahhan, DA","first_name":"DA","last_name":"Dahhan"},{"last_name":"Reynolds","first_name":"GD","full_name":"Reynolds, GD"},{"first_name":"JJ","last_name":"Cárdenas","full_name":"Cárdenas, JJ"},{"first_name":"D","last_name":"Eeckhout","full_name":"Eeckhout, D"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J"},{"full_name":"Yperman, K","last_name":"Yperman","first_name":"K"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vang","first_name":"N","full_name":"Vang, N"},{"first_name":"X","last_name":"Yan","full_name":"Yan, X"},{"full_name":"Hwang, I","first_name":"I","last_name":"Hwang"},{"full_name":"Heese, A","first_name":"A","last_name":"Heese"},{"last_name":"De Jaeger","first_name":"G","full_name":"De Jaeger, G"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Van Damme, D","first_name":"D","last_name":"Van Damme"},{"full_name":"Pan, J","first_name":"J","last_name":"Pan"},{"full_name":"Bednarek, SY","first_name":"SY","last_name":"Bednarek"}],"language":[{"iso":"eng"}],"project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publication_status":"published","article_type":"original","intvolume":"        34","month":"06","acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1093/plcell/koac071","article_processing_charge":"No","fulldoi":"https://doi.org/10.1093/plcell/koac071","oa":1,"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"pmid":1,"publication":"Plant Cell","publisher":"Oxford University Press","oa_version":"Preprint","date_updated":"2025-05-14T11:06:15Z","quality_controlled":"1","external_id":{"pmid":["35218346"],"isi":["000767438800001"]},"volume":34,"page":"2150-2173","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.09.16.460678"}],"year":"2022"},{"pmid":1,"oa":1,"publication_identifier":{"eissn":["1091-6490"]},"fulldoi":"https://doi.org/10.1073/pnas.2118220119","article_processing_charge":"No","doi":"10.1073/pnas.2118220119","article_type":"original","month":"03","intvolume":"       119","publication_status":"published","ddc":["580"],"language":[{"iso":"eng"}],"author":[{"full_name":"Lu, Qing","first_name":"Qing","last_name":"Lu"},{"first_name":"Yonghong","last_name":"Zhang","full_name":"Zhang, Yonghong"},{"full_name":"Hellner, Joakim","last_name":"Hellner","first_name":"Joakim"},{"full_name":"Giannini, Caterina","last_name":"Giannini","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"first_name":"Xiangyu","last_name":"Xu","full_name":"Xu, Xiangyu"},{"full_name":"Pauwels, Jarne","last_name":"Pauwels","first_name":"Jarne"},{"full_name":"Ma, Qian","last_name":"Ma","first_name":"Qian"},{"full_name":"Dejonghe, Wim","first_name":"Wim","last_name":"Dejonghe"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin"},{"full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte","first_name":"Brigitte"},{"full_name":"Impens, Francis","last_name":"Impens","first_name":"Francis"},{"first_name":"Kris","last_name":"Gevaert","full_name":"Gevaert, Kris"},{"full_name":"De Smet, Ive","first_name":"Ive","last_name":"De Smet"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Molina, Daniel Martinez","last_name":"Molina","first_name":"Daniel Martinez"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"year":"2022","external_id":{"isi":["000771756300008"],"pmid":["35254915"]},"volume":119,"file":[{"date_created":"2022-03-21T09:19:47Z","file_name":"2022_PNAS_Lu.pdf","access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_id":"10910","checksum":"83e0fea7919570d0b519b41193342571","success":1,"file_size":2169534,"date_updated":"2022-03-21T09:19:47Z"}],"date_updated":"2025-05-14T11:01:45Z","quality_controlled":"1","oa_version":"Published Version","publication":"Proceedings of the National Academy of Sciences of the United States of America","publisher":"National Academy of Sciences","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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"},"status":"public","article_number":"e2118220119","department":[{"_id":"JiFr"}],"date_published":"2022-03-07T00:00:00Z","file_date_updated":"2022-03-21T09:19:47Z","has_accepted_license":"1","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.).","abstract":[{"lang":"eng","text":"Despite the growing interest in using chemical genetics in plant research, small molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or posttranslational modifications, allows the discovery of drug targets or the study of protein–metabolite and protein–protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf, thus revealing cross-talk between brassinosteroid and auxin signaling."}],"_id":"10888","type":"journal_article","citation":{"ama":"Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(11). doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>","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.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>.","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.","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).","ieee":"Q. Lu <i>et al.</i>, “Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11. 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. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>","mla":"Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11, e2118220119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>."},"date_created":"2022-03-20T23:01:39Z","scopus_import":"1","isi":1,"issue":"11","title":"Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling","day":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","department":[{"_id":"JiFr"}],"date_published":"2022-06-06T00:00:00Z","has_accepted_license":"1","file_date_updated":"2022-07-06T07:36:59Z","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).","abstract":[{"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.","lang":"eng"}],"_id":"11489","type":"journal_article","citation":{"apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &#38; Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>","short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","ieee":"V. Bilanovičová <i>et al.</i>, “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11. MDPI, p. 6352, 2022.","mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>.","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.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>.","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. <i>International Journal of Molecular Sciences</i>. 2022;23(11):6352. doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>","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."},"date_created":"2022-07-05T15:14:34Z","isi":1,"scopus_import":"1","issue":"11","day":"06","title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1422-0067"]},"oa":1,"pmid":1,"article_processing_charge":"Yes","corr_author":"1","fulldoi":"https://doi.org/10.3390/ijms23116352","doi":"10.3390/ijms23116352","month":"06","ddc":["570"],"intvolume":"        23","article_type":"original","publication_status":"published","language":[{"iso":"eng"}],"project":[{"name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"full_name":"Bilanovičová, V","first_name":"V","last_name":"Bilanovičová"},{"last_name":"Rýdza","first_name":"N","full_name":"Rýdza, N"},{"full_name":"Koczka, L","last_name":"Koczka","first_name":"L"},{"last_name":"Hess","first_name":"M","full_name":"Hess, M"},{"last_name":"Feraru","first_name":"E","full_name":"Feraru, E"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"T","last_name":"Nodzyński","full_name":"Nodzyński, T"}],"year":"2022","external_id":{"pmid":["35683031"],"isi":["000808733300001"]},"page":"6352","file":[{"file_size":2324542,"file_id":"11492","checksum":"e997a57a928ec9d51fad8ce824a05935","success":1,"date_updated":"2022-07-06T07:36:59Z","date_created":"2022-07-06T07:36:59Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"cchlebak","file_name":"2022_IntJMolSci_Bilanovicova.pdf"}],"volume":23,"oa_version":"Published Version","quality_controlled":"1","date_updated":"2025-04-15T08:12:07Z","publication":"International Journal of Molecular Sciences","publisher":"MDPI","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"}},{"fulldoi":"https://doi.org/10.3389/fpls.2022.862398","article_processing_charge":"No","pmid":1,"oa":1,"publication_identifier":{"eissn":["1664-462X"]},"doi":"10.3389/fpls.2022.862398","intvolume":"        13","publication_status":"published","month":"06","ddc":["580"],"article_type":"original","author":[{"first_name":"Ren","last_name":"Wang","full_name":"Wang, Ren"},{"full_name":"Himschoot, Ellie","first_name":"Ellie","last_name":"Himschoot"},{"last_name":"Chen","first_name":"Jian","full_name":"Chen, Jian"},{"full_name":"Boudsocq, Marie","first_name":"Marie","last_name":"Boudsocq"},{"full_name":"Geelen, Danny","last_name":"Geelen","first_name":"Danny"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"}],"language":[{"iso":"eng"}],"year":"2022","external_id":{"isi":["000819250500001"],"pmid":["35783951"]},"volume":13,"file":[{"date_created":"2022-07-18T08:05:15Z","access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_name":"2022_FrontiersPlantScience_Wang.pdf","file_size":5040638,"checksum":"95313515637c0f84de591d204375d764","file_id":"11596","success":1,"date_updated":"2022-07-18T08:05:15Z"}],"quality_controlled":"1","date_updated":"2023-08-03T12:01:47Z","oa_version":"Published Version","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"},"related_material":{"link":[{"url":"https://doi.org/10.3389/fpls.2022.1100792","relation":"erratum"}]},"publication":"Frontiers in Plant Science","publisher":"Frontiers","article_number":"862398","status":"public","date_published":"2022-06-16T00:00:00Z","department":[{"_id":"JiFr"}],"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.","file_date_updated":"2022-07-18T08:05:15Z","has_accepted_license":"1","_id":"11589","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_created":"2022-07-17T22:01:54Z","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.” <i>Frontiers in Plant Science</i>. Frontiers, 2022. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>.","ama":"Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. 2022;13. doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>","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.","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022).","apa":"Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste, S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>","ieee":"R. Wang <i>et al.</i>, “Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana,” <i>Frontiers in Plant Science</i>, vol. 13. Frontiers, 2022.","mla":"Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>, vol. 13, 862398, Frontiers, 2022, doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>."},"scopus_import":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","day":"16"},{"date_updated":"2026-06-18T19:02:05Z","OA_place":"publisher","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"id":"8138","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"7142","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10411","status":"public"},{"id":"8931","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7465"},{"id":"9287","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"6260","status":"public"}]},"year":"2022","page":"248","file":[{"access_level":"open_access","content_type":"application/pdf","creator":"mgallei","relation":"main_file","file_name":"Thesis_Gallei.pdf","date_created":"2022-07-25T09:08:47Z","date_updated":"2022-07-25T09:08:47Z","file_size":9730864,"checksum":"bd7ac35403cf5b4b2607287d2a104b3a","file_id":"11645"},{"file_name":"Thesis_Gallei_source.docx","creator":"mgallei","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","date_created":"2022-07-25T09:09:09Z","date_updated":"2022-07-25T09:39:58Z","file_id":"11646","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","file_size":19560720},{"date_updated":"2022-07-25T09:39:58Z","checksum":"3994f7f20058941b5bb8a16886b21e71","file_id":"11647","file_size":24542837,"description":"This is the print version of the thesis including the full appendix","file_name":"Thesis_Gallei_to_print.pdf","access_level":"closed","relation":"source_file","content_type":"application/pdf","creator":"mgallei","date_created":"2022-07-25T09:09:32Z"},{"access_level":"open_access","creator":"mgallei","content_type":"application/pdf","relation":"main_file","file_name":"Thesis_Gallei_Appendix.pdf","date_created":"2022-07-25T11:48:45Z","date_updated":"2022-07-25T11:48:45Z","file_size":15435966,"file_id":"11650","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b"}],"ddc":["575"],"month":"07","publication_status":"published","author":[{"full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"ec_funded":1,"language":[{"iso":"eng"}],"corr_author":"1","fulldoi":"https://doi.org/10.15479/at:ista:11626","degree_awarded":"PhD","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"oa":1,"publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:11626","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","day":"20","type":"dissertation","supervisor":[{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739"},{"full_name":"Shani, Eilon","last_name":"Shani","first_name":"Eilon"}],"date_created":"2022-07-20T11:21:53Z","citation":{"ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>.","mla":"Gallei, Michelle C. <i>Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>.","apa":"Gallei, M. C. (2022). <i>Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022."},"file_date_updated":"2022-07-25T11:48:45Z","has_accepted_license":"1","_id":"11626","abstract":[{"lang":"eng","text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth."}],"status":"public","date_published":"2022-07-20T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}]},{"date_published":"2022-07-25T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"article_number":"e2121058119","status":"public","keyword":["Multidisciplinary"],"_id":"11723","abstract":[{"lang":"eng","text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term."}],"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).”","has_accepted_license":"1","file_date_updated":"2022-08-08T07:42:09Z","date_created":"2022-08-04T20:06:49Z","citation":{"mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2121058119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., &#38; Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>","ieee":"L. Li <i>et al.</i>, “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. National Academy of Sciences, 2022.","short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2121058119\">10.1073/pnas.2121058119</a>","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.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2121058119\">https://doi.org/10.1073/pnas.2121058119</a>.","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 of the United States of America. 119(31), e2121058119."},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","day":"25","issue":"31","scopus_import":"1","isi":1,"doi":"10.1073/pnas.2121058119","corr_author":"1","fulldoi":"https://doi.org/10.1073/pnas.2121058119","article_processing_charge":"No","pmid":1,"oa":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li","full_name":"Li, Lanxin"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","last_name":"Chen","first_name":"Huihuang","full_name":"Chen, Huihuang"},{"last_name":"Alotaibi","first_name":"Saqer S.","full_name":"Alotaibi, Saqer S."},{"full_name":"Pěnčík, Aleš","first_name":"Aleš","last_name":"Pěnčík"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"intvolume":"       119","article_type":"original","month":"07","ddc":["580"],"publication_status":"published","volume":119,"file":[{"file_size":2506262,"file_id":"11747","checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","success":1,"date_updated":"2022-08-08T07:42:09Z","date_created":"2022-08-08T07:42:09Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","relation":"main_file","file_name":"2022_PNAS_Li.pdf"}],"external_id":{"isi":["000881496900002"],"pmid":["35878023"]},"year":"2022","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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"},"publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_updated":"2025-05-14T11:01:00Z","quality_controlled":"1","oa_version":"Published Version"},{"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"},"publisher":"Springer Nature","publication":"Nature Communications","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-33198-9"}]},"quality_controlled":"1","date_updated":"2025-04-15T07:32:09Z","oa_version":"Published Version","file":[{"file_name":"2022_NatureCommunications_Konstantinova.pdf","content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2022-09-08T07:46:16Z","date_updated":"2022-09-08T07:46:16Z","success":1,"checksum":"43336758c89cd6c045839089af070afe","file_id":"12063","file_size":6678579}],"volume":13,"external_id":{"isi":["000848744900004"],"pmid":["36050482"]},"year":"2022","author":[{"full_name":"Konstantinova, N","first_name":"N","last_name":"Konstantinova"},{"full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","last_name":"Glanc","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"full_name":"Keshkeih, R","first_name":"R","last_name":"Keshkeih"},{"orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"full_name":"Di Donato, M","last_name":"Di Donato","first_name":"M"},{"first_name":"K","last_name":"Retzer","full_name":"Retzer, K"},{"first_name":"J","last_name":"Moulinier-Anzola","full_name":"Moulinier-Anzola, J"},{"full_name":"Schwihla, M","first_name":"M","last_name":"Schwihla"},{"full_name":"Korbei, B","last_name":"Korbei","first_name":"B"},{"full_name":"Geisler, M","last_name":"Geisler","first_name":"M"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"last_name":"Luschnig","first_name":"C","full_name":"Luschnig, C"}],"project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"month":"09","intvolume":"        13","article_type":"original","publication_status":"published","ddc":["580"],"doi":"10.1038/s41467-022-32888-8","fulldoi":"https://doi.org/10.1038/s41467-022-32888-8","article_processing_charge":"No","pmid":1,"publication_identifier":{"issn":["2041-1723"]},"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions","day":"01","scopus_import":"1","isi":1,"citation":{"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.","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.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32888-8\">https://doi.org/10.1038/s41467-022-32888-8</a>.","ama":"Konstantinova N, Hörmayer L, Glanc M, et al. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32888-8\">10.1038/s41467-022-32888-8</a>","mla":"Konstantinova, N., et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” <i>Nature Communications</i>, vol. 13, 5147, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32888-8\">10.1038/s41467-022-32888-8</a>.","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).","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32888-8\">https://doi.org/10.1038/s41467-022-32888-8</a>","ieee":"N. Konstantinova <i>et al.</i>, “WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022."},"date_created":"2022-09-07T14:19:26Z","type":"journal_article","_id":"12052","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"}],"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).","file_date_updated":"2022-09-08T07:46:16Z","has_accepted_license":"1","date_published":"2022-09-01T00:00:00Z","department":[{"_id":"JiFr"}],"article_number":"5147","status":"public"},{"oa_version":"Published Version","quality_controlled":"1","date_updated":"2025-04-15T08:12:07Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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"},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/plcell/koac342"}]},"publisher":"Oxford University Press","publication":"The Plant Cell","year":"2022","page":"4816-4839","file":[{"date_updated":"2023-01-20T08:29:12Z","success":1,"file_id":"12318","checksum":"1c606d9545f29dfca15235f69ad27b58","file_size":3282540,"file_name":"2022_PlantCell_Tian.pdf","content_type":"application/pdf","creator":"dernst","relation":"main_file","access_level":"open_access","date_created":"2023-01-20T08:29:12Z"}],"volume":34,"external_id":{"isi":["000852753000001"],"pmid":["36040191"]},"ddc":["580"],"month":"12","intvolume":"        34","publication_status":"published","article_type":"original","author":[{"full_name":"Tian, Z","first_name":"Z","last_name":"Tian"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhu, L","first_name":"L","last_name":"Zhu"},{"first_name":"B","last_name":"Jiang","full_name":"Jiang, B"},{"full_name":"Wang, H","first_name":"H","last_name":"Wang"},{"first_name":"R","last_name":"Gao","full_name":"Gao, R"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"first_name":"G","last_name":"Xiao","full_name":"Xiao, G"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_processing_charge":"No","fulldoi":"https://doi.org/10.1093/plcell/koac270","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"oa":1,"pmid":1,"doi":"10.1093/plcell/koac270","issue":"12","isi":1,"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","title":"Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum)","type":"journal_article","citation":{"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.","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). <i>The Plant Cell</i>. 2022;34(12):4816-4839. doi:<a href=\"https://doi.org/10.1093/plcell/koac270\">10.1093/plcell/koac270</a>","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).” <i>The Plant Cell</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/plcell/koac270\">https://doi.org/10.1093/plcell/koac270</a>.","mla":"Tian, Z., et al. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” <i>The Plant Cell</i>, vol. 34, no. 12, Oxford University Press, 2022, pp. 4816–39, doi:<a href=\"https://doi.org/10.1093/plcell/koac270\">10.1093/plcell/koac270</a>.","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). <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac270\">https://doi.org/10.1093/plcell/koac270</a>","short":"Z. Tian, Y. Zhang, L. Zhu, B. Jiang, H. Wang, R. Gao, J. Friml, G. Xiao, The Plant Cell 34 (2022) 4816–4839.","ieee":"Z. Tian <i>et al.</i>, “Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum),” <i>The Plant Cell</i>, vol. 34, no. 12. Oxford University Press, pp. 4816–4839, 2022."},"date_created":"2022-09-07T14:19:39Z","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).","file_date_updated":"2023-01-20T08:29:12Z","has_accepted_license":"1","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"}],"_id":"12053","status":"public","date_published":"2022-12-01T00:00:00Z","department":[{"_id":"JiFr"}]},{"title":"Structural insights into auxin recognition and efflux by Arabidopsis PIN1","day":"02","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","isi":1,"issue":"7927","citation":{"mla":"Yang, Z., et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 611–15, doi:<a href=\"https://doi.org/10.1038/s41586-022-05143-9\">10.1038/s41586-022-05143-9</a>.","ieee":"Z. Yang <i>et al.</i>, “Structural insights into auxin recognition and efflux by Arabidopsis PIN1,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 611–615, 2022.","apa":"Yang, Z., Xia, J., Hong, J., Zhang, C., Wei, H., Ying, W., … Sun, L. (2022). Structural insights into auxin recognition and efflux by Arabidopsis PIN1. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05143-9\">https://doi.org/10.1038/s41586-022-05143-9</a>","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. <i>Nature</i>. 2022;609(7927):611-615. doi:<a href=\"https://doi.org/10.1038/s41586-022-05143-9\">10.1038/s41586-022-05143-9</a>","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.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05143-9\">https://doi.org/10.1038/s41586-022-05143-9</a>.","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."},"date_created":"2022-09-07T14:19:52Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"_id":"12054","file_date_updated":"2022-09-08T08:02:54Z","has_accepted_license":"1","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.","department":[{"_id":"JiFr"}],"date_published":"2022-08-02T00:00:00Z","status":"public","publisher":"Springer Nature","publication":"Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","date_updated":"2023-08-03T13:41:44Z","oa_version":"Published Version","external_id":{"pmid":["35917925"],"isi":["000848082900002"]},"volume":609,"file":[{"success":1,"checksum":"3136a585f8e1c7e73b5e1418b3d01898","file_id":"12064","file_size":32344580,"date_updated":"2022-09-08T08:02:54Z","date_created":"2022-09-08T08:02:54Z","file_name":"2022_Nature_Yang.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst","access_level":"open_access"}],"page":"611-615","year":"2022","language":[{"iso":"eng"}],"author":[{"full_name":"Yang, Z","first_name":"Z","last_name":"Yang"},{"full_name":"Xia, J","first_name":"J","last_name":"Xia"},{"full_name":"Hong, J","first_name":"J","last_name":"Hong"},{"full_name":"Zhang, C","first_name":"C","last_name":"Zhang"},{"first_name":"H","last_name":"Wei","full_name":"Wei, H"},{"full_name":"Ying, W","last_name":"Ying","first_name":"W"},{"last_name":"Sun","first_name":"C","full_name":"Sun, C"},{"last_name":"Sun","first_name":"L","full_name":"Sun, L"},{"full_name":"Mao, Y","last_name":"Mao","first_name":"Y"},{"last_name":"Gao","first_name":"Y","full_name":"Gao, Y"},{"full_name":"Tan, S","last_name":"Tan","first_name":"S"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"},{"full_name":"Li, D","last_name":"Li","first_name":"D"},{"full_name":"Liu, X","first_name":"X","last_name":"Liu"},{"full_name":"Sun, L","last_name":"Sun","first_name":"L"}],"intvolume":"       609","publication_status":"published","month":"08","article_type":"original","ddc":["580"],"doi":"10.1038/s41586-022-05143-9","pmid":1,"oa":1,"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"fulldoi":"https://doi.org/10.1038/s41586-022-05143-9","article_processing_charge":"No"},{"date_published":"2022-12-05T00:00:00Z","department":[{"_id":"JiFr"}],"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"status":"public","abstract":[{"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.","lang":"eng"}],"_id":"12120","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).","citation":{"mla":"Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” <i>Developmental Cell</i>, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>.","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. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>","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.","ieee":"H. Xiao <i>et al.</i>, “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” <i>Developmental Cell</i>, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022.","ista":"Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6.","ama":"Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. <i>Developmental Cell</i>. 2022;57(23):2638-2651.e6. doi:<a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">10.1016/j.devcel.2022.11.006</a>","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.” <i>Developmental Cell</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.devcel.2022.11.006\">https://doi.org/10.1016/j.devcel.2022.11.006</a>."},"date_created":"2023-01-12T11:57:00Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05","title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","issue":"23","isi":1,"scopus_import":"1","doi":"10.1016/j.devcel.2022.11.006","article_processing_charge":"No","fulldoi":"https://doi.org/10.1016/j.devcel.2022.11.006","oa":1,"publication_identifier":{"issn":["1534-5807"]},"pmid":1,"author":[{"full_name":"Xiao, Huixin","last_name":"Xiao","first_name":"Huixin"},{"full_name":"Hu, Yumei","last_name":"Hu","first_name":"Yumei"},{"full_name":"Wang, Yaping","first_name":"Yaping","last_name":"Wang"},{"last_name":"Cheng","first_name":"Jinkui","full_name":"Cheng, Jinkui"},{"full_name":"Wang, Jinyi","first_name":"Jinyi","last_name":"Wang"},{"last_name":"Chen","first_name":"Guojingwei","full_name":"Chen, Guojingwei"},{"full_name":"Li, Qian","first_name":"Qian","last_name":"Li"},{"last_name":"Wang","first_name":"Shuwei","full_name":"Wang, Shuwei"},{"full_name":"Wang, Yalu","last_name":"Wang","first_name":"Yalu"},{"full_name":"Wang, Shao-Shuai","last_name":"Wang","first_name":"Shao-Shuai"},{"last_name":"Wang","first_name":"Yi","full_name":"Wang, Yi"},{"last_name":"Xuan","first_name":"Wei","full_name":"Xuan, Wei"},{"last_name":"Li","first_name":"Zhen","full_name":"Li, Zhen"},{"full_name":"Guo, Yan","first_name":"Yan","last_name":"Guo"},{"last_name":"Gong","first_name":"Zhizhong","full_name":"Gong, Zhizhong"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"last_name":"Zhang","first_name":"Jing","full_name":"Zhang, Jing"}],"language":[{"iso":"eng"}],"publication_status":"published","article_type":"original","ddc":["580"],"intvolume":"        57","month":"12","OA_type":"free access","external_id":{"pmid":["36473460"],"isi":["000919603800005"]},"page":"2638-2651.e6","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2022.11.006","open_access":"1"}],"volume":57,"year":"2022","publisher":"Elsevier","publication":"Developmental Cell","oa_version":"Published Version","date_updated":"2026-06-18T17:23:10Z","quality_controlled":"1","OA_place":"publisher"},{"abstract":[{"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.","lang":"eng"}],"_id":"12121","file_date_updated":"2023-01-23T10:30:11Z","has_accepted_license":"1","acknowledgement":"We thank Suayip Ustün, Karin Schumacher, Erika Isono, Gerd Juergens, Takashi Ueda, Daniel Hofius, and Liwen Jiang for sharing published materials.\r\nWe acknowledge funding from Austrian Academy of Sciences, Austrian Science Fund (FWF, P 32355, P 34944), Austrian Science Fund (FWF-SFB F79), Vienna Science and Technology\r\nFund (WWTF, LS17-047) to Y. Dagdas; Austrian Academy of Sciences DOC Fellowship to J. Zhao, Marie Curie VIP2 Fellowship to J.C. De La Concepcion and M. Clavel; Hong Kong Research Grant Council (GRF14121019, 14113921, AoE/M-05/12, C4002-17G) to B.-H. Kang. We thank Vienna Biocenter Core Facilities (VBCF) Protein Chemistry, Biooptics, Plant Sciences, Molecular Biology, and Protein Technologies. We thank J. Matthew Watson\r\nand members of the Dagdas lab for the critical reading and editing of the manuscript.","department":[{"_id":"JiFr"}],"date_published":"2022-12-01T00:00:00Z","status":"public","keyword":["Cell Biology"],"article_number":"e202203139","title":"Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole","day":"01","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","isi":1,"issue":"12","citation":{"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).","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. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202203139\">https://doi.org/10.1083/jcb.202203139</a>","ieee":"J. Zhao <i>et al.</i>, “Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole,” <i>Journal of Cell Biology</i>, vol. 221, no. 12. Rockefeller University Press, 2022.","mla":"Zhao, Jierui, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” <i>Journal of Cell Biology</i>, vol. 221, no. 12, e202203139, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202203139\">10.1083/jcb.202203139</a>.","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.","ama":"Zhao J, Bui MT, Ma J, et al. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. <i>Journal of Cell Biology</i>. 2022;221(12). doi:<a href=\"https://doi.org/10.1083/jcb.202203139\">10.1083/jcb.202203139</a>","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.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202203139\">https://doi.org/10.1083/jcb.202203139</a>."},"date_created":"2023-01-12T11:57:10Z","type":"journal_article","language":[{"iso":"eng"}],"author":[{"last_name":"Zhao","first_name":"Jierui","full_name":"Zhao, Jierui"},{"full_name":"Bui, Mai Thu","last_name":"Bui","first_name":"Mai Thu"},{"last_name":"Ma","first_name":"Juncai","full_name":"Ma, Juncai"},{"full_name":"Künzl, Fabian","last_name":"Künzl","first_name":"Fabian"},{"last_name":"Picchianti","first_name":"Lorenzo","full_name":"Picchianti, Lorenzo"},{"first_name":"Juan Carlos","last_name":"De La Concepcion","full_name":"De La Concepcion, Juan Carlos"},{"full_name":"Chen, Yixuan","last_name":"Chen","first_name":"Yixuan"},{"full_name":"Petsangouraki, Sofia","last_name":"Petsangouraki","first_name":"Sofia"},{"first_name":"Azadeh","last_name":"Mohseni","full_name":"Mohseni, Azadeh"},{"last_name":"García-Leon","first_name":"Marta","full_name":"García-Leon, Marta"},{"full_name":"Gomez, Marta Salas","first_name":"Marta Salas","last_name":"Gomez"},{"full_name":"Giannini, Caterina","first_name":"Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"full_name":"Gwennogan, Dubois","last_name":"Gwennogan","first_name":"Dubois"},{"first_name":"Roksolana","last_name":"Kobylinska","full_name":"Kobylinska, Roksolana"},{"last_name":"Clavel","first_name":"Marion","full_name":"Clavel, Marion"},{"full_name":"Schellmann, Swen","last_name":"Schellmann","first_name":"Swen"},{"full_name":"Jaillais, Yvon","first_name":"Yvon","last_name":"Jaillais"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Kang","first_name":"Byung-Ho","full_name":"Kang, Byung-Ho"},{"full_name":"Dagdas, Yasin","first_name":"Yasin","last_name":"Dagdas"}],"intvolume":"       221","month":"12","ddc":["580"],"publication_status":"published","article_type":"original","doi":"10.1083/jcb.202203139","pmid":1,"oa":1,"publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"fulldoi":"https://doi.org/10.1083/jcb.202203139","article_processing_charge":"No","publisher":"Rockefeller University Press","publication":"Journal of Cell Biology","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","date_updated":"2023-08-03T14:20:15Z","oa_version":"Published Version","external_id":{"pmid":["36260289"],"isi":["000932958800001"]},"volume":221,"file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_name":"2022_JCB_Zhao.pdf","date_created":"2023-01-23T10:30:11Z","date_updated":"2023-01-23T10:30:11Z","file_size":10365777,"checksum":"050b5cc4b25e6b94fe3e3cbfe0f5c06b","file_id":"12342","success":1}],"year":"2022"},{"quality_controlled":"1","date_updated":"2025-07-08T09:01:02Z","oa_version":"Published Version","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"},"publisher":"Springer Nature","publication":"Nature Communications","year":"2022","external_id":{"isi":["000884426700001"],"pmid":["36379956"]},"file":[{"file_size":3375249,"success":1,"file_id":"12346","checksum":"233922a7b9507d9d48591e6799e4526e","date_updated":"2023-01-23T11:17:33Z","date_created":"2023-01-23T11:17:33Z","creator":"dernst","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2022_NatureCommunications_Huang.pdf"}],"volume":13,"article_type":"original","publication_status":"published","intvolume":"        13","month":"11","ddc":["580"],"author":[{"full_name":"Huang, Jian","first_name":"Jian","last_name":"Huang"},{"first_name":"Lei","last_name":"Zhao","full_name":"Zhao, Lei"},{"first_name":"Shikha","last_name":"Malik","full_name":"Malik, Shikha"},{"full_name":"Gentile, Benjamin R.","first_name":"Benjamin R.","last_name":"Gentile"},{"last_name":"Xiong","first_name":"Va","full_name":"Xiong, Va"},{"full_name":"Arazi, Tzahi","first_name":"Tzahi","last_name":"Arazi"},{"first_name":"Heather A.","last_name":"Owen","full_name":"Owen, Heather A."},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"first_name":"Dazhong","last_name":"Zhao","full_name":"Zhao, Dazhong"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41467-022-34723-6","article_processing_charge":"No","pmid":1,"oa":1,"publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-022-34723-6","scopus_import":"1","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","day":"15","type":"journal_article","date_created":"2023-01-12T12:02:41Z","citation":{"mla":"Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” <i>Nature Communications</i>, vol. 13, 6960, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>.","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).","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>","ieee":"J. Huang <i>et al.</i>, “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” <i>Nature Communications</i>, 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.","ama":"Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-34723-6\">10.1038/s41467-022-34723-6</a>","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.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-34723-6\">https://doi.org/10.1038/s41467-022-34723-6</a>."},"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.","file_date_updated":"2023-01-23T11:17:33Z","has_accepted_license":"1","_id":"12130","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."}],"article_number":"6960","status":"public","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"date_published":"2022-11-15T00:00:00Z","department":[{"_id":"JiFr"}]},{"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"month":"11","publication_status":"published","intvolume":"       611","article_type":"original","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ec_funded":1,"language":[{"iso":"eng"}],"author":[{"full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","last_name":"Qi","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"full_name":"Kwiatkowski, Mateusz","last_name":"Kwiatkowski","first_name":"Mateusz"},{"full_name":"Chen, Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","last_name":"Chen","first_name":"Huihuang"},{"first_name":"Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas"},{"orcid":"0000-0002-4566-0593","last_name":"Sinclair","first_name":"Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","full_name":"Sinclair, Scott A"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou","first_name":"Minxia","full_name":"Zou, Minxia"},{"first_name":"Charo I.","last_name":"del Genio","full_name":"del Genio, Charo I."},{"first_name":"Martin F.","last_name":"Kubeš","full_name":"Kubeš, Martin F."},{"full_name":"Napier, Richard","last_name":"Napier","first_name":"Richard"},{"first_name":"Krzysztof","last_name":"Jaworski","full_name":"Jaworski, Krzysztof"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"oa":1,"corr_author":"1","fulldoi":"https://doi.org/10.1038/s41586-022-05369-7","article_processing_charge":"No","doi":"10.1038/s41586-022-05369-7","quality_controlled":"1","date_updated":"2025-04-14T07:45:02Z","oa_version":"Submitted Version","publication":"Nature","publisher":"Springer Nature","year":"2022","volume":611,"page":"133-138","external_id":{"isi":["000875061600013"],"pmid":["36289340"]},"main_file_link":[{"open_access":"1","url":"http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf"}],"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.","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"}],"_id":"12144","status":"public","department":[{"_id":"JiFr"}],"date_published":"2022-11-03T00:00:00Z","scopus_import":"1","isi":1,"issue":"7934","title":"Adenylate cyclase activity of TIR1/AFB auxin receptors in plants","day":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","citation":{"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.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05369-7\">https://doi.org/10.1038/s41586-022-05369-7</a>.","ama":"Qi L, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. <i>Nature</i>. 2022;611(7934):133-138. doi:<a href=\"https://doi.org/10.1038/s41586-022-05369-7\">10.1038/s41586-022-05369-7</a>","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.","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.","ieee":"L. Qi <i>et al.</i>, “Adenylate cyclase activity of TIR1/AFB auxin receptors in plants,” <i>Nature</i>, 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. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05369-7\">https://doi.org/10.1038/s41586-022-05369-7</a>","mla":"Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” <i>Nature</i>, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38, doi:<a href=\"https://doi.org/10.1038/s41586-022-05369-7\">10.1038/s41586-022-05369-7</a>."},"date_created":"2023-01-12T12:06:05Z"},{"oa_version":"Published Version","date_updated":"2025-04-15T07:32:09Z","quality_controlled":"1","publication":"Molecular Plant","publisher":"Elsevier","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"},"year":"2022","external_id":{"pmid":["36081349"],"isi":["000882769800009"]},"file":[{"content_type":"application/pdf","relation":"main_file","creator":"dernst","access_level":"open_access","file_name":"2022_MolecularPlant_Johnson.pdf","date_created":"2023-01-30T07:46:51Z","date_updated":"2023-01-30T07:46:51Z","file_size":2307251,"success":1,"file_id":"12435","checksum":"04d5c12490052d03e4dc4412338a43dd"}],"volume":15,"page":"1533-1542","publication_status":"published","intvolume":"        15","article_type":"original","month":"10","ddc":["580"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J"},{"first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Costanzo, Tommaso","orcid":"0000-0001-9732-3815","first_name":"Tommaso","last_name":"Costanzo","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"first_name":"Dana A.","last_name":"Dahhan","full_name":"Dahhan, Dana A."},{"full_name":"Bednarek, Sebastian Y.","last_name":"Bednarek","first_name":"Sebastian Y."},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"oa":1,"publication_identifier":{"issn":["1674-2052"]},"pmid":1,"article_processing_charge":"Yes (via OA deal)","fulldoi":"https://doi.org/10.1016/j.molp.2022.09.003","corr_author":"1","doi":"10.1016/j.molp.2022.09.003","isi":1,"scopus_import":"1","issue":"10","day":"03","title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","citation":{"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.","ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, 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., &#38; Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>","mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>","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.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>.","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."},"date_created":"2023-01-16T09:51:49Z","file_date_updated":"2023-01-30T07:46:51Z","has_accepted_license":"1","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.","abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"_id":"12239","keyword":["Plant Science","Molecular Biology"],"status":"public","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"date_published":"2022-10-03T00:00:00Z"},{"file":[{"date_created":"2023-07-17T11:46:34Z","file_name":"2023_FrontiersFungalBio_Ingole.pdf","access_level":"open_access","content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13242","checksum":"2254e0119c0749d6f7237084fefcece6","success":1,"file_size":27966699,"date_updated":"2023-07-17T11:46:34Z"}],"volume":3,"year":"2022","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"},"publication":"Frontiers in Fungal Biology","publisher":"Frontiers Media","oa_version":"Published Version","date_updated":"2024-03-06T14:01:57Z","quality_controlled":"1","doi":"10.3389/ffunb.2022.1029114","article_processing_charge":"Yes","fulldoi":"https://doi.org/10.3389/ffunb.2022.1029114","publication_identifier":{"eissn":["2673-6128"]},"oa":1,"author":[{"last_name":"Ingole","first_name":"Kishor D.","full_name":"Ingole, Kishor D."},{"full_name":"Nagarajan, Nithya","last_name":"Nagarajan","first_name":"Nithya"},{"full_name":"Uhse, Simon","last_name":"Uhse","first_name":"Simon"},{"first_name":"Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina"},{"full_name":"Djamei, Armin","first_name":"Armin","last_name":"Djamei"}],"language":[{"iso":"eng"}],"article_type":"original","intvolume":"         3","publication_status":"published","ddc":["579"],"month":"10","citation":{"ama":"Ingole KD, Nagarajan N, Uhse S, Giannini C, Djamei A. Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. <i>Frontiers in Fungal Biology</i>. 2022;3. doi:<a href=\"https://doi.org/10.3389/ffunb.2022.1029114\">10.3389/ffunb.2022.1029114</a>","chicago":"Ingole, Kishor D., Nithya Nagarajan, Simon Uhse, Caterina Giannini, and Armin Djamei. “Tetracycline-Controlled (TetON) Gene Expression System for the Smut Fungus Ustilago Maydis.” <i>Frontiers in Fungal Biology</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/ffunb.2022.1029114\">https://doi.org/10.3389/ffunb.2022.1029114</a>.","ista":"Ingole KD, Nagarajan N, Uhse S, Giannini C, Djamei A. 2022. Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. 3, 1029114.","mla":"Ingole, Kishor D., et al. “Tetracycline-Controlled (TetON) Gene Expression System for the Smut Fungus Ustilago Maydis.” <i>Frontiers in Fungal Biology</i>, vol. 3, 1029114, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/ffunb.2022.1029114\">10.3389/ffunb.2022.1029114</a>.","apa":"Ingole, K. D., Nagarajan, N., Uhse, S., Giannini, C., &#38; Djamei, A. (2022). Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. <i>Frontiers in Fungal Biology</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/ffunb.2022.1029114\">https://doi.org/10.3389/ffunb.2022.1029114</a>","ieee":"K. D. Ingole, N. Nagarajan, S. Uhse, C. Giannini, and A. Djamei, “Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis,” <i>Frontiers in Fungal Biology</i>, vol. 3. Frontiers Media, 2022.","short":"K.D. Ingole, N. Nagarajan, S. Uhse, C. Giannini, A. Djamei, Frontiers in Fungal Biology 3 (2022)."},"date_created":"2023-07-16T22:01:12Z","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"19","title":"Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis","scopus_import":"1","date_published":"2022-10-19T00:00:00Z","department":[{"_id":"JiFr"}],"article_number":"1029114","status":"public","_id":"13240","abstract":[{"lang":"eng","text":"Ustilago maydis is a biotrophic phytopathogenic fungus that causes corn smut disease. As a well-established model system, U. maydis is genetically fully accessible with large omics datasets available and subject to various biological questions ranging from DNA-repair, RNA-transport, and protein secretion to disease biology. For many genetic approaches, tight control of transgene regulation is important. Here we established an optimised version of the Tetracycline-ON (TetON) system for U. maydis. We demonstrate the Tetracycline concentration-dependent expression of fluorescent protein transgenes and the system’s suitability for the induced expression of the toxic protein BCL2 Associated X-1 (Bax1). The Golden Gate compatible vector system contains a native minimal promoter from the mating factor a-1 encoding gene, mfa with ten copies of the tet-regulated operator (tetO) and a codon optimised Tet-repressor (tetR*) which is translationally fused to the native transcriptional corepressor Mql1 (UMAG_05501). The metabolism-independent transcriptional regulator system is functional both, in liquid culture as well as on solid media in the presence of the inducer and can become a useful tool for toxin-antitoxin studies, identification of antifungal proteins, and to study functions of toxic gene products in Ustilago maydis."}],"acknowledgement":"The research leading to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme ERC-2013-STG (grant agreement: 335691), the Austrian Science Fund (I 3033-B22), the Austrian Academy of Sciences, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy EXC-2070-390732324 (PhenoRob) and DFG grant (DJ 64/5-1).\r\nWe would like to thank the GMI/IMBA/IMP core facilities for their excellent technical support. We would like to acknowledge Dr. Sinéad A. O’Sullivan from DZNE, University of Bonn for providing anti-GFP antibodies. The authors are thankful to the Excellence University of Bonn for providing infrastructure and instrumentation facilities at the INRES-Plant Pathology department.","has_accepted_license":"1","file_date_updated":"2023-07-17T11:46:34Z"},{"abstract":[{"text":"In plants, the antagonism between growth and defense is hardwired by hormonal signaling. The perception of pathogen-associated molecular patterns (PAMPs) from invading microorganisms inhibits auxin signaling and plant growth. Conversely, pathogens manipulate auxin signaling to promote disease, but how this hormone inhibits immunity is not fully understood. Ustilago maydis is a maize pathogen that induces auxin signaling in its host. We characterized a U. maydis effector protein, Naked1 (Nkd1), that is translocated into the host nucleus. Through its native ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif, Nkd1 binds to the transcriptional co-repressors TOPLESS/TOPLESS-related (TPL/TPRs) and prevents the recruitment of a transcriptional repressor involved in hormonal signaling, leading to the de-repression of auxin and jasmonate signaling and thereby promoting susceptibility to (hemi)biotrophic pathogens. A moderate upregulation of auxin signaling inhibits the PAMP-triggered reactive oxygen species (ROS) burst, an early defense response. Thus, our findings establish a clear mechanism for auxin-induced pathogen susceptibility. Engineered Nkd1 variants with increased expression or increased EAR-mediated TPL/TPR binding trigger typical salicylic-acid-mediated defense reactions, leading to pathogen resistance. This implies that moderate binding of Nkd1 to TPL is a result of a balancing evolutionary selection process to enable TPL manipulation while avoiding host recognition.","lang":"eng"}],"_id":"17068","acknowledgement":"The research leading to these results received funding from the European Research Council under the European Union Seventh Framework Programme ERC-2013-STG grant agreement \r\n335691; the Austrian Science Fund (FWF) P27818-B22,I 3033-B22; the Austrian Academy of Sciences (OEAW); and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2070-390732324.\r\nWe would like to thank the GMI/IMBA/IMP core facilities for excellent technical support, especially the BioOptics and Molecular Biology Services. We thank the Plant Sciences and Next Generation Sequencing Facilities at the Vienna BioCenter Core Facilities GmbH (VBCF). We are grateful to the Jirí Friml and Jürgen Kleine-Vehn laboratories for providing useful A. thaliana lines. We thank Mathias Madalinski for peptide synthesis and Dr. J. Matthew Watson for proofreading and valuable feedback on the manuscript. The authors declare no competing interests.","file_date_updated":"2024-08-05T10:26:29Z","has_accepted_license":"1","date_published":"2022-03-14T00:00:00Z","department":[{"_id":"JiFr"}],"article_number":"100269","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1","day":"14","issue":"2","scopus_import":"1","date_created":"2024-05-29T06:10:22Z","citation":{"short":"F. Navarrete, M.C. Gallei, A.E. Kornienko, I. Saado, M. Khan, K.-S. Chia, M.A. Darino, J. Bindics, A. Djamei, Plant Communications 3 (2022).","ieee":"F. Navarrete <i>et al.</i>, “TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1,” <i>Plant Communications</i>, vol. 3, no. 2. Elsevier, 2022.","apa":"Navarrete, F., Gallei, M. C., Kornienko, A. E., Saado, I., Khan, M., Chia, K.-S., … Djamei, A. (2022). TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2021.100269\">https://doi.org/10.1016/j.xplc.2021.100269</a>","mla":"Navarrete, Fernando, et al. “TOPLESS Promotes Plant Immunity by Repressing Auxin Signaling and Is Targeted by the Fungal Effector Naked1.” <i>Plant Communications</i>, vol. 3, no. 2, 100269, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.xplc.2021.100269\">10.1016/j.xplc.2021.100269</a>.","chicago":"Navarrete, Fernando, Michelle C Gallei, Aleksandra E. Kornienko, Indira Saado, Mamoona Khan, Khong-Sam Chia, Martin A. Darino, Janos Bindics, and Armin Djamei. “TOPLESS Promotes Plant Immunity by Repressing Auxin Signaling and Is Targeted by the Fungal Effector Naked1.” <i>Plant Communications</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.xplc.2021.100269\">https://doi.org/10.1016/j.xplc.2021.100269</a>.","ama":"Navarrete F, Gallei MC, Kornienko AE, et al. TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. <i>Plant Communications</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1016/j.xplc.2021.100269\">10.1016/j.xplc.2021.100269</a>","ista":"Navarrete F, Gallei MC, Kornienko AE, Saado I, Khan M, Chia K-S, Darino MA, Bindics J, Djamei A. 2022. TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1. Plant Communications. 3(2), 100269."},"type":"journal_article","author":[{"full_name":"Navarrete, Fernando","first_name":"Fernando","last_name":"Navarrete"},{"full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","last_name":"Gallei","first_name":"Michelle C"},{"full_name":"Kornienko, Aleksandra E.","first_name":"Aleksandra E.","last_name":"Kornienko"},{"last_name":"Saado","first_name":"Indira","full_name":"Saado, Indira"},{"first_name":"Mamoona","last_name":"Khan","full_name":"Khan, Mamoona"},{"full_name":"Chia, Khong-Sam","first_name":"Khong-Sam","last_name":"Chia"},{"full_name":"Darino, Martin A.","first_name":"Martin A.","last_name":"Darino"},{"first_name":"Janos","last_name":"Bindics","full_name":"Bindics, Janos"},{"full_name":"Djamei, Armin","last_name":"Djamei","first_name":"Armin"}],"language":[{"iso":"eng"}],"month":"03","ddc":["580"],"intvolume":"         3","publication_status":"published","article_type":"original","doi":"10.1016/j.xplc.2021.100269","fulldoi":"https://doi.org/10.1016/j.xplc.2021.100269","article_processing_charge":"Yes","pmid":1,"oa":1,"publication_identifier":{"issn":["2590-3462"]},"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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"},"publisher":"Elsevier","publication":"Plant Communications","quality_controlled":"1","date_updated":"2024-08-05T10:27:03Z","oa_version":"Published Version","volume":3,"file":[{"date_created":"2024-08-05T10:26:29Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_name":"2022_PlantComm_Navarrete.pdf","file_size":3216686,"file_id":"17393","checksum":"1eeb6ee65419e4aa34627fea6857f343","success":1,"date_updated":"2024-08-05T10:26:29Z"}],"external_id":{"pmid":["35529945"]},"year":"2022"},{"pmid":1,"oa":1,"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"fulldoi":"https://doi.org/10.1126/science.abl4683","article_processing_charge":"No","doi":"10.1126/science.abl4683","OA_type":"green","article_type":"original","publication_status":"published","month":"01","intvolume":"       375","language":[{"iso":"eng"}],"author":[{"last_name":"Zhong","first_name":"Sheng","full_name":"Zhong, Sheng"},{"full_name":"Li, Ling","first_name":"Ling","last_name":"Li"},{"first_name":"Zhijuan","last_name":"Wang","full_name":"Wang, Zhijuan"},{"id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","last_name":"Ge","first_name":"Zengxiang","orcid":"0000-0001-9381-3577","full_name":"Ge, Zengxiang"},{"first_name":"Qiyun","last_name":"Li","full_name":"Li, Qiyun"},{"full_name":"Bleckmann, Andrea","last_name":"Bleckmann","first_name":"Andrea"},{"last_name":"Wang","first_name":"Jizong","full_name":"Wang, Jizong"},{"first_name":"Zihan","last_name":"Song","full_name":"Song, Zihan"},{"last_name":"Shi","first_name":"Yihao","full_name":"Shi, Yihao"},{"full_name":"Liu, Tianxu","last_name":"Liu","first_name":"Tianxu"},{"full_name":"Li, Luhan","first_name":"Luhan","last_name":"Li"},{"full_name":"Zhou, Huabin","last_name":"Zhou","first_name":"Huabin"},{"first_name":"Yanyan","last_name":"Wang","full_name":"Wang, Yanyan"},{"full_name":"Zhang, Li","last_name":"Zhang","first_name":"Li"},{"full_name":"Wu, Hen-Ming","first_name":"Hen-Ming","last_name":"Wu"},{"full_name":"Lai, Luhua","first_name":"Luhua","last_name":"Lai"},{"full_name":"Gu, Hongya","first_name":"Hongya","last_name":"Gu"},{"full_name":"Dong, Juan","last_name":"Dong","first_name":"Juan"},{"last_name":"Cheung","first_name":"Alice Y.","full_name":"Cheung, Alice Y."},{"full_name":"Dresselhaus, Thomas","last_name":"Dresselhaus","first_name":"Thomas"},{"full_name":"Qu, Li-Jia","first_name":"Li-Jia","last_name":"Qu"}],"year":"2022","external_id":{"pmid":["35050671"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9040003"}],"volume":375,"page":"290-296","date_updated":"2025-04-24T11:39:46Z","quality_controlled":"1","OA_place":"repository","oa_version":"Submitted Version","publisher":"American Association for the Advancement of Science","publication":"Science","status":"public","department":[{"_id":"JiFr"}],"date_published":"2022-01-20T00:00:00Z","acknowledgement":"We thank D. Ye for providing fer-4 and myb97 myb101 myb120 mutant seeds; L. Smith for sharing anj, herk1, anj herk1, and fer anj herk1 mutant seeds; J. F. Harper for providing aca9 mutant seeds; and C. Li and Q. Duan for sharing fer+/− mutant seeds.\r\nL.-J.Q. was funded by the National Natural Science Foundation of China (grant nos. 31991202, 31830004, 31620103903, and 31621001), S.Z. was supported by the Young Elite Scientists Sponsorship Program by the China Association of Science and Technology (2019QNRC001), Z.G. was supported by a NSFC Young Scientists Fund (31900161), A.Y.C. was funded by the US Natural Science Foundation (IOS-1645854, MCB-1715764, and MCB-0955910), J.D. was funded by the National Institute of Health (R01GM109080), and T.D. was supported by the German Research Foundation DFG (SFB924).","_id":"17069","abstract":[{"lang":"eng","text":"Fertilization of an egg by multiple sperm (polyspermy) leads to lethal genome imbalance and chromosome segregation defects. In Arabidopsis thaliana, the block to polyspermy is facilitated by a mechanism that prevents polytubey (the arrival of multiple pollen tubes to one ovule). We show here that FERONIA, ANJEA, and HERCULES RECEPTOR KINASE 1 receptor-like kinases located at the septum interact with pollen tube–specific RALF6, 7, 16, 36, and 37 peptide ligands to establish this polytubey block. The same combination of RALF (rapid alkalinization factor) peptides and receptor complexes controls pollen tube reception and rupture inside the targeted ovule. Pollen tube rupture releases the polytubey block at the septum, which allows the emergence of secondary pollen tubes upon fertilization failure. Thus, orchestrated steps in the fertilization process in Arabidopsis are coordinated by the same signaling components to guarantee and optimize reproductive success."}],"type":"journal_article","date_created":"2024-05-29T06:11:10Z","citation":{"ista":"Zhong S, Li L, Wang Z, Ge Z, Li Q, Bleckmann A, Wang J, Song Z, Shi Y, Liu T, Li L, Zhou H, Wang Y, Zhang L, Wu H-M, Lai L, Gu H, Dong J, Cheung AY, Dresselhaus T, Qu L-J. 2022. RALF peptide signaling controls the polytubey block in Arabidopsis. Science. 375(6578), 290–296.","chicago":"Zhong, Sheng, Ling Li, Zhijuan Wang, Zengxiang Ge, Qiyun Li, Andrea Bleckmann, Jizong Wang, et al. “RALF Peptide Signaling Controls the Polytubey Block in Arabidopsis.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.abl4683\">https://doi.org/10.1126/science.abl4683</a>.","ama":"Zhong S, Li L, Wang Z, et al. RALF peptide signaling controls the polytubey block in Arabidopsis. <i>Science</i>. 2022;375(6578):290-296. doi:<a href=\"https://doi.org/10.1126/science.abl4683\">10.1126/science.abl4683</a>","mla":"Zhong, Sheng, et al. “RALF Peptide Signaling Controls the Polytubey Block in Arabidopsis.” <i>Science</i>, vol. 375, no. 6578, American Association for the Advancement of Science, 2022, pp. 290–96, doi:<a href=\"https://doi.org/10.1126/science.abl4683\">10.1126/science.abl4683</a>.","short":"S. Zhong, L. Li, Z. Wang, Z. Ge, Q. Li, A. Bleckmann, J. Wang, Z. Song, Y. Shi, T. Liu, L. Li, H. Zhou, Y. Wang, L. Zhang, H.-M. Wu, L. Lai, H. Gu, J. Dong, A.Y. Cheung, T. Dresselhaus, L.-J. Qu, Science 375 (2022) 290–296.","ieee":"S. Zhong <i>et al.</i>, “RALF peptide signaling controls the polytubey block in Arabidopsis,” <i>Science</i>, vol. 375, no. 6578. American Association for the Advancement of Science, pp. 290–296, 2022.","apa":"Zhong, S., Li, L., Wang, Z., Ge, Z., Li, Q., Bleckmann, A., … Qu, L.-J. (2022). RALF peptide signaling controls the polytubey block in Arabidopsis. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abl4683\">https://doi.org/10.1126/science.abl4683</a>"},"scopus_import":"1","issue":"6578","title":"RALF peptide signaling controls the polytubey block in Arabidopsis","day":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"doi":"10.5772/intechopen.100535","publication_identifier":{"isbn":["9781839697500"]},"oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.5772/intechopen.100535","ec_funded":1,"language":[{"iso":"eng"}],"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Floriach-Clark, Jordi","first_name":"Jordi","last_name":"Floriach-Clark"},{"full_name":"Tang, Han","last_name":"Tang","first_name":"Han","orcid":"0000-0001-6152-6637","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E"},{"first_name":"Viola","last_name":"Willemsen","full_name":"Willemsen, Viola"}],"month":"06","ddc":["580"],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5772/intechopen.100535"}],"year":"2022","publisher":"IntechOpen","publication":"Model Organisms in Plant Genetics","editor":[{"first_name":"Ibrokhim Y.","last_name":"Abdurakhmonov","full_name":"Abdurakhmonov, Ibrokhim Y."}],"oa_version":"Published Version","quality_controlled":"1","date_updated":"2026-06-18T17:52:59Z","department":[{"_id":"JiFr"}],"date_published":"2022-06-23T00:00:00Z","status":"public","_id":"17085","abstract":[{"lang":"eng","text":"Mosses are a cosmopolitan group of land plants, sister to vascular plants, with a high potential for molecular and cell biological research. The species Physcomitrium patens has helped gaining better understanding of the biological processes of the plant cell, and it has become a central system to understand water-to-land plant transition through 2D-to-3D growth transition, regulation of asymmetric cell division, shoot apical cell establishment and maintenance, phyllotaxis and regeneration. P. patens was the first fully sequenced moss in 2008, with the latest annotated release in 2018. It has been shown that many gene functions and networks are conserved in mosses when compared to angiosperms. Importantly, this model organism has a simplified and accessible body structure that facilitates close tracking in time and space with the support of live cell imaging set-ups and multiple reporter lines. This has become possible thanks to its fully established molecular toolkit, with highly efficient PEG-assisted, CRISPR/Cas9 and RNAi transformation and silencing protocols, among others. Here we provide examples on how mosses exhibit advantages over vascular plants to study several processes and their future potential to answer some other outstanding questions in plant cell biology."}],"acknowledgement":"The authors would like to thank Dr. Jeroen de Keijzer and Dr. Tijs Ketelaar for their thoughtful and detailed review of the manuscript. Also, the funding agencies Technology, Knowledge and Innovation, division Horticulture and Propagating Material (TKI T&U) and the Dutch Research Council (NWO) (reference number: TKILWV20.390) for funding JFC and the ERC grant to Prof. J. Friml (reference number: PR1023ERC02) for funding HT. The authors would like to sincerely apologise for the literature not cited that may be relevant for this chapter and is not present due to space constraints.","citation":{"ista":"Floriach-Clark J, Tang H, Willemsen V. 2022.Mosses: Accessible Systems for Plant Development Studies. In: Model Organisms in Plant Genetics. .","chicago":"Floriach-Clark, Jordi, Han Tang, and Viola Willemsen. “Mosses: Accessible Systems for Plant Development Studies.” In <i>Model Organisms in Plant Genetics</i>, edited by Ibrokhim Y. Abdurakhmonov. IntechOpen, 2022. <a href=\"https://doi.org/10.5772/intechopen.100535\">https://doi.org/10.5772/intechopen.100535</a>.","ama":"Floriach-Clark J, Tang H, Willemsen V. Mosses: Accessible Systems for Plant Development Studies. In: Abdurakhmonov IY, ed. <i>Model Organisms in Plant Genetics</i>. IntechOpen; 2022. doi:<a href=\"https://doi.org/10.5772/intechopen.100535\">10.5772/intechopen.100535</a>","mla":"Floriach-Clark, Jordi, et al. “Mosses: Accessible Systems for Plant Development Studies.” <i>Model Organisms in Plant Genetics</i>, edited by Ibrokhim Y. Abdurakhmonov, IntechOpen, 2022, doi:<a href=\"https://doi.org/10.5772/intechopen.100535\">10.5772/intechopen.100535</a>.","ieee":"J. Floriach-Clark, H. Tang, and V. Willemsen, “Mosses: Accessible Systems for Plant Development Studies,” in <i>Model Organisms in Plant Genetics</i>, I. Y. Abdurakhmonov, Ed. IntechOpen, 2022.","apa":"Floriach-Clark, J., Tang, H., &#38; Willemsen, V. (2022). Mosses: Accessible Systems for Plant Development Studies. In I. Y. Abdurakhmonov (Ed.), <i>Model Organisms in Plant Genetics</i>. IntechOpen. <a href=\"https://doi.org/10.5772/intechopen.100535\">https://doi.org/10.5772/intechopen.100535</a>","short":"J. Floriach-Clark, H. Tang, V. Willemsen, in:, I.Y. Abdurakhmonov (Ed.), Model Organisms in Plant Genetics, IntechOpen, 2022."},"date_created":"2024-05-29T06:35:13Z","type":"book_chapter","day":"23","title":"Mosses: Accessible Systems for Plant Development Studies","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"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.","_id":"10016","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. "}],"status":"public","article_number":"a039859","department":[{"_id":"JiFr"}],"date_published":"2022-05-27T00:00:00Z","scopus_import":"1","isi":1,"issue":"5","title":"Fourteen stations of auxin","day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_created":"2021-09-14T11:36:53Z","citation":{"mla":"Friml, Jiří. “Fourteen Stations of Auxin.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 14, no. 5, a039859, Cold Spring Harbor Laboratory Press, 2022, doi:<a href=\"https://doi.org/10.1101/cshperspect.a039859\">10.1101/cshperspect.a039859</a>.","short":"J. Friml, Cold Spring Harbor Perspectives in Biology 14 (2022).","apa":"Friml, J. (2022). Fourteen stations of auxin. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a039859\">https://doi.org/10.1101/cshperspect.a039859</a>","ieee":"J. Friml, “Fourteen stations of auxin,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 14, no. 5. Cold Spring Harbor Laboratory Press, 2022.","chicago":"Friml, Jiří. “Fourteen Stations of Auxin.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2022. <a href=\"https://doi.org/10.1101/cshperspect.a039859\">https://doi.org/10.1101/cshperspect.a039859</a>.","ama":"Friml J. Fourteen stations of auxin. <i>Cold Spring Harbor Perspectives in Biology</i>. 2022;14(5). doi:<a href=\"https://doi.org/10.1101/cshperspect.a039859\">10.1101/cshperspect.a039859</a>","ista":"Friml J. 2022. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 14(5), a039859."},"article_type":"review","publication_status":"published","month":"05","intvolume":"        14","ddc":["580"],"language":[{"iso":"eng"}],"author":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"publication_identifier":{"issn":["1943-0264"]},"oa":1,"corr_author":"1","fulldoi":"https://doi.org/10.1101/cshperspect.a039859","article_processing_charge":"No","doi":"10.1101/cshperspect.a039859","date_updated":"2026-06-18T08:35:48Z","quality_controlled":"1","oa_version":"Published Version","publisher":"Cold Spring Harbor Laboratory Press","publication":"Cold Spring Harbor Perspectives in Biology","year":"2022","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a039859 "}],"volume":14,"external_id":{"isi":["000806563000003"],"pmid":["34400554"]}},{"doi":"10.1016/j.tplants.2021.11.006","article_processing_charge":"No","corr_author":"1","fulldoi":"https://doi.org/10.1016/j.tplants.2021.11.006","publication_identifier":{"issn":["1360-1385"]},"oa":1,"pmid":1,"author":[{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X"},{"full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"_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"}],"month":"05","intvolume":"        27","publication_status":"published","article_type":"original","ddc":["580"],"page":"440-449","file":[{"file_size":805779,"success":1,"file_id":"14480","checksum":"3d94980ee1ff6bec100dd813f6a921a6","date_updated":"2023-11-02T17:00:03Z","date_created":"2023-11-02T17:00:03Z","creator":"amally","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"Li Plants 2021_accepted.pdf"}],"volume":27,"external_id":{"isi":["000793707900005"],"pmid":["34848141"]},"year":"2022","publisher":"Cell Press","related_material":{"record":[{"status":"public","id":"11626","relation":"dissertation_contains"}]},"publication":"Trends in Plant Science","oa_version":"Submitted Version","quality_controlled":"1","date_updated":"2026-04-07T14:18:57Z","date_published":"2022-05-01T00:00:00Z","department":[{"_id":"JiFr"}],"status":"public","abstract":[{"lang":"eng","text":"The phytohormone auxin is the major growth regulator governing tropic responses including gravitropism. Auxin build-up at the lower side of stimulated shoots promotes cell expansion, whereas in roots it inhibits growth, leading to upward shoot bending and downward root bending, respectively. Yet it remains an enigma how the same signal can trigger such opposite cellular responses. In this review, we discuss several recent unexpected insights into the mechanisms underlying auxin regulation of growth, challenging several existing models. We focus on the divergent mechanisms of apoplastic pH regulation in shoots and roots revisiting the classical Acid Growth Theory and discuss coordinated involvement of multiple auxin signaling pathways. From this emerges a more comprehensive, updated picture how auxin regulates growth."}],"_id":"10411","acknowledgement":"The authors thank Alexandra Mally for editing the text. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 to Jiří Friml and the DOC Fellowship of the Austrian Academy of Sciences to Lanxin Li. All figures were created with BioRender.com.","has_accepted_license":"1","file_date_updated":"2023-11-02T17:00:03Z","citation":{"mla":"Li, Lanxin, et al. “Bending to Auxin: Fast Acid Growth for Tropisms.” <i>Trends in Plant Science</i>, vol. 27, no. 5, Cell Press, 2022, pp. 440–49, doi:<a href=\"https://doi.org/10.1016/j.tplants.2021.11.006\">10.1016/j.tplants.2021.11.006</a>.","apa":"Li, L., Gallei, M. C., &#38; Friml, J. (2022). Bending to auxin: Fast acid growth for tropisms. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2021.11.006\">https://doi.org/10.1016/j.tplants.2021.11.006</a>","short":"L. Li, M.C. Gallei, J. Friml, Trends in Plant Science 27 (2022) 440–449.","ieee":"L. Li, M. C. Gallei, and J. Friml, “Bending to auxin: Fast acid growth for tropisms,” <i>Trends in Plant Science</i>, vol. 27, no. 5. Cell Press, pp. 440–449, 2022.","ista":"Li L, Gallei MC, Friml J. 2022. Bending to auxin: Fast acid growth for tropisms. Trends in Plant Science. 27(5), 440–449.","chicago":"Li, Lanxin, Michelle C Gallei, and Jiří Friml. “Bending to Auxin: Fast Acid Growth for Tropisms.” <i>Trends in Plant Science</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.tplants.2021.11.006\">https://doi.org/10.1016/j.tplants.2021.11.006</a>.","ama":"Li L, Gallei MC, Friml J. Bending to auxin: Fast acid growth for tropisms. <i>Trends in Plant Science</i>. 2022;27(5):440-449. doi:<a href=\"https://doi.org/10.1016/j.tplants.2021.11.006\">10.1016/j.tplants.2021.11.006</a>"},"date_created":"2021-12-05T23:01:43Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","title":"Bending to auxin: Fast acid growth for tropisms","issue":"5","isi":1,"scopus_import":"1"}]