[{"scopus_import":"1","citation":{"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>.","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.","short":"Z. Tian, Y. Zhang, L. Zhu, B. Jiang, H. Wang, R. Gao, J. Friml, G. Xiao, The Plant Cell 34 (2022) 4816–4839.","chicago":"Tian, Z, Yuzhou Zhang, L Zhu, B Jiang, H Wang, R Gao, Jiří Friml, and G Xiao. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” <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>.","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>","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>","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."},"intvolume":"        34","month":"12","ddc":["580"],"issue":"12","file_date_updated":"2023-01-20T08:29:12Z","status":"public","publisher":"Oxford University Press","date_created":"2022-09-07T14:19:39Z","language":[{"iso":"eng"}],"type":"journal_article","has_accepted_license":"1","file":[{"file_id":"12318","date_updated":"2023-01-20T08:29:12Z","file_size":3282540,"relation":"main_file","file_name":"2022_PlantCell_Tian.pdf","access_level":"open_access","date_created":"2023-01-20T08:29:12Z","success":1,"creator":"dernst","checksum":"1c606d9545f29dfca15235f69ad27b58","content_type":"application/pdf"}],"doi":"10.1093/plcell/koac270","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"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).","title":"Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum)","page":"4816-4839","day":"01","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"volume":34,"fulldoi":"https://doi.org/10.1093/plcell/koac270","article_processing_charge":"No","oa":1,"project":[{"name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","pmid":1,"date_updated":"2025-04-15T08:12:07Z","date_published":"2022-12-01T00:00:00Z","external_id":{"isi":["000852753000001"],"pmid":["36040191"]},"isi":1,"_id":"12053","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2022","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/plcell/koac342"}]},"article_type":"original","author":[{"full_name":"Tian, Z","last_name":"Tian","first_name":"Z"},{"last_name":"Zhang","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956"},{"full_name":"Zhu, L","last_name":"Zhu","first_name":"L"},{"full_name":"Jiang, B","last_name":"Jiang","first_name":"B"},{"full_name":"Wang, H","last_name":"Wang","first_name":"H"},{"last_name":"Gao","full_name":"Gao, R","first_name":"R"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"G","full_name":"Xiao, G","last_name":"Xiao"}],"publication":"The Plant Cell","quality_controlled":"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"}]},{"date_published":"2022-08-02T00:00:00Z","date_updated":"2023-08-03T13:41:44Z","pmid":1,"publication_status":"published","article_type":"original","author":[{"first_name":"Z","full_name":"Yang, Z","last_name":"Yang"},{"first_name":"J","full_name":"Xia, J","last_name":"Xia"},{"first_name":"J","full_name":"Hong, J","last_name":"Hong"},{"full_name":"Zhang, C","last_name":"Zhang","first_name":"C"},{"first_name":"H","last_name":"Wei","full_name":"Wei, H"},{"last_name":"Ying","full_name":"Ying, W","first_name":"W"},{"first_name":"C","last_name":"Sun","full_name":"Sun, C"},{"first_name":"L","full_name":"Sun, L","last_name":"Sun"},{"first_name":"Y","last_name":"Mao","full_name":"Mao, Y"},{"first_name":"Y","full_name":"Gao, Y","last_name":"Gao"},{"last_name":"Tan","full_name":"Tan, S","first_name":"S"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Li, D","last_name":"Li","first_name":"D"},{"first_name":"X","full_name":"Liu, X","last_name":"Liu"},{"first_name":"L","full_name":"Sun, L","last_name":"Sun"}],"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"}],"quality_controlled":"1","publication":"Nature","_id":"12054","isi":1,"external_id":{"pmid":["35917925"],"isi":["000848082900002"]},"year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":609,"fulldoi":"https://doi.org/10.1038/s41586-022-05143-9","license":"https://creativecommons.org/licenses/by/4.0/","department":[{"_id":"JiFr"}],"doi":"10.1038/s41586-022-05143-9","file":[{"success":1,"creator":"dernst","checksum":"3136a585f8e1c7e73b5e1418b3d01898","content_type":"application/pdf","access_level":"open_access","date_created":"2022-09-08T08:02:54Z","file_id":"12064","file_size":32344580,"date_updated":"2022-09-08T08:02:54Z","relation":"main_file","file_name":"2022_Nature_Yang.pdf"}],"date_created":"2022-09-07T14:19:52Z","has_accepted_license":"1","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","acknowledgement":"We thank the Cryo-EM Center of the University of Science and Technology of China (USTC) and the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science, for the EM facility support; we thank B. Zhu, X. Huang and all the other staff members for their technical support on cryo-EM data collection. We thank J. Ren for his technical support with the transport assays and M. Seeger for providing the sybody libraries. This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB 37020204 to D.L. and XDB37020103 to Linfeng Sun), National Natural Science Foundation of China (82151215 and 31870726 to D.L., 31900885 to X.L., and 31870732 to Linfeng Sun), Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun), the Fundamental Research Funds for the Central Universities (WK9100000031 to Linfeng Sun), and the USTC Research Funds of the Double First-Class Initiative (YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation, and a Young Scholar Award from the Cyrus Tang Foundation.","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"day":"02","page":"611-615","title":"Structural insights into auxin recognition and efflux by Arabidopsis PIN1","month":"08","citation":{"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>","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>","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.","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>.","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.","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."},"scopus_import":"1","intvolume":"       609","publisher":"Springer Nature","issue":"7927","ddc":["580"],"status":"public","file_date_updated":"2022-09-08T08:02:54Z"},{"intvolume":"        57","citation":{"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.","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>","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>.","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>","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.","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>."},"scopus_import":"1","month":"12","status":"public","issue":"23","ddc":["580"],"publisher":"Elsevier","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"type":"journal_article","language":[{"iso":"eng"}],"date_created":"2023-01-12T11:57:00Z","doi":"10.1016/j.devcel.2022.11.006","department":[{"_id":"JiFr"}],"day":"05","title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","page":"2638-2651.e6","acknowledgement":"The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu Jiang for helpful discussions. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153).","publication_identifier":{"issn":["1534-5807"]},"oa_version":"Published Version","fulldoi":"https://doi.org/10.1016/j.devcel.2022.11.006","volume":57,"article_processing_charge":"No","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2022.11.006","open_access":"1"}],"pmid":1,"publication_status":"published","date_published":"2022-12-05T00:00:00Z","date_updated":"2026-06-18T17:23:10Z","OA_type":"free access","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","isi":1,"_id":"12120","external_id":{"pmid":["36473460"],"isi":["000919603800005"]},"abstract":[{"lang":"eng","text":"Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth."}],"quality_controlled":"1","publication":"Developmental Cell","article_type":"original","author":[{"first_name":"Huixin","full_name":"Xiao, Huixin","last_name":"Xiao"},{"first_name":"Yumei","full_name":"Hu, Yumei","last_name":"Hu"},{"first_name":"Yaping","last_name":"Wang","full_name":"Wang, Yaping"},{"first_name":"Jinkui","full_name":"Cheng, Jinkui","last_name":"Cheng"},{"full_name":"Wang, Jinyi","last_name":"Wang","first_name":"Jinyi"},{"first_name":"Guojingwei","full_name":"Chen, Guojingwei","last_name":"Chen"},{"full_name":"Li, Qian","last_name":"Li","first_name":"Qian"},{"first_name":"Shuwei","last_name":"Wang","full_name":"Wang, Shuwei"},{"last_name":"Wang","full_name":"Wang, Yalu","first_name":"Yalu"},{"full_name":"Wang, Shao-Shuai","last_name":"Wang","first_name":"Shao-Shuai"},{"first_name":"Yi","full_name":"Wang, Yi","last_name":"Wang"},{"first_name":"Wei","full_name":"Xuan, Wei","last_name":"Xuan"},{"first_name":"Zhen","last_name":"Li","full_name":"Li, Zhen"},{"first_name":"Yan","full_name":"Guo, Yan","last_name":"Guo"},{"full_name":"Gong, Zhizhong","last_name":"Gong","first_name":"Zhizhong"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"last_name":"Zhang","full_name":"Zhang, Jing","first_name":"Jing"}]},{"intvolume":"       221","citation":{"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>.","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).","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.","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>.","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>","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>","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."},"scopus_import":"1","month":"12","status":"public","file_date_updated":"2023-01-23T10:30:11Z","article_number":"e202203139","issue":"12","ddc":["580"],"publisher":"Rockefeller University Press","keyword":["Cell Biology"],"has_accepted_license":"1","type":"journal_article","language":[{"iso":"eng"}],"date_created":"2023-01-12T11:57:10Z","department":[{"_id":"JiFr"}],"doi":"10.1083/jcb.202203139","file":[{"file_id":"12342","file_size":10365777,"relation":"main_file","date_updated":"2023-01-23T10:30:11Z","file_name":"2022_JCB_Zhao.pdf","access_level":"open_access","date_created":"2023-01-23T10:30:11Z","success":1,"creator":"dernst","content_type":"application/pdf","checksum":"050b5cc4b25e6b94fe3e3cbfe0f5c06b"}],"day":"01","title":"Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole","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.","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"oa_version":"Published Version","fulldoi":"https://doi.org/10.1083/jcb.202203139","volume":221,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"article_processing_charge":"No","pmid":1,"publication_status":"published","date_published":"2022-12-01T00:00:00Z","date_updated":"2023-08-03T14:20:15Z","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"_id":"12121","external_id":{"isi":["000932958800001"],"pmid":["36260289"]},"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"}],"publication":"Journal of Cell Biology","quality_controlled":"1","author":[{"first_name":"Jierui","last_name":"Zhao","full_name":"Zhao, Jierui"},{"first_name":"Mai Thu","full_name":"Bui, Mai Thu","last_name":"Bui"},{"full_name":"Ma, Juncai","last_name":"Ma","first_name":"Juncai"},{"first_name":"Fabian","full_name":"Künzl, Fabian","last_name":"Künzl"},{"full_name":"Picchianti, Lorenzo","last_name":"Picchianti","first_name":"Lorenzo"},{"first_name":"Juan Carlos","last_name":"De La Concepcion","full_name":"De La Concepcion, Juan Carlos"},{"last_name":"Chen","full_name":"Chen, Yixuan","first_name":"Yixuan"},{"first_name":"Sofia","last_name":"Petsangouraki","full_name":"Petsangouraki, Sofia"},{"full_name":"Mohseni, Azadeh","last_name":"Mohseni","first_name":"Azadeh"},{"full_name":"García-Leon, Marta","last_name":"García-Leon","first_name":"Marta"},{"last_name":"Gomez","full_name":"Gomez, Marta Salas","first_name":"Marta Salas"},{"full_name":"Giannini, Caterina","last_name":"Giannini","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"first_name":"Dubois","full_name":"Gwennogan, Dubois","last_name":"Gwennogan"},{"first_name":"Roksolana","last_name":"Kobylinska","full_name":"Kobylinska, Roksolana"},{"last_name":"Clavel","full_name":"Clavel, Marion","first_name":"Marion"},{"first_name":"Swen","last_name":"Schellmann","full_name":"Schellmann, Swen"},{"full_name":"Jaillais, Yvon","last_name":"Jaillais","first_name":"Yvon"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Kang, Byung-Ho","last_name":"Kang","first_name":"Byung-Ho"},{"first_name":"Yasin","last_name":"Dagdas","full_name":"Dagdas, Yasin"}],"article_type":"original"},{"oa":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1038/s41467-022-34723-6","volume":13,"date_updated":"2025-07-08T09:01:02Z","date_published":"2022-11-15T00:00:00Z","publication_status":"published","pmid":1,"author":[{"last_name":"Huang","full_name":"Huang, Jian","first_name":"Jian"},{"first_name":"Lei","last_name":"Zhao","full_name":"Zhao, Lei"},{"first_name":"Shikha","last_name":"Malik","full_name":"Malik, Shikha"},{"first_name":"Benjamin R.","last_name":"Gentile","full_name":"Gentile, Benjamin R."},{"first_name":"Va","full_name":"Xiong, Va","last_name":"Xiong"},{"full_name":"Arazi, Tzahi","last_name":"Arazi","first_name":"Tzahi"},{"full_name":"Owen, Heather A.","last_name":"Owen","first_name":"Heather A."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"first_name":"Dazhong","full_name":"Zhao, Dazhong","last_name":"Zhao"}],"article_type":"original","publication":"Nature Communications","quality_controlled":"1","abstract":[{"text":"Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants.","lang":"eng"}],"external_id":{"pmid":["36379956"],"isi":["000884426700001"]},"isi":1,"_id":"12130","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","month":"11","scopus_import":"1","citation":{"apa":"Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. <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>","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>.","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>","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.","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).","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."},"intvolume":"        13","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"publisher":"Springer Nature","ddc":["580"],"article_number":"6960","file_date_updated":"2023-01-23T11:17:33Z","status":"public","file":[{"content_type":"application/pdf","checksum":"233922a7b9507d9d48591e6799e4526e","success":1,"creator":"dernst","file_size":3375249,"date_updated":"2023-01-23T11:17:33Z","relation":"main_file","file_name":"2022_NatureCommunications_Huang.pdf","file_id":"12346","date_created":"2023-01-23T11:17:33Z","access_level":"open_access"}],"doi":"10.1038/s41467-022-34723-6","department":[{"_id":"JiFr"}],"date_created":"2023-01-12T12:02:41Z","language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","oa_version":"Published Version","publication_identifier":{"eissn":["2041-1723"]},"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.","title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","day":"15"},{"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"fulldoi":"https://doi.org/10.1038/s41586-022-05369-7","volume":611,"article_processing_charge":"No","oa":1,"main_file_link":[{"url":"http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","external_id":{"isi":["000875061600013"],"pmid":["36289340"]},"isi":1,"_id":"12144","quality_controlled":"1","publication":"Nature","abstract":[{"lang":"eng","text":"The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants."}],"author":[{"last_name":"Qi","full_name":"Qi, Linlin","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401"},{"first_name":"Mateusz","full_name":"Kwiatkowski, Mateusz","last_name":"Kwiatkowski"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang"},{"orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas"},{"last_name":"Sinclair","full_name":"Sinclair, Scott A","first_name":"Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4566-0593"},{"id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","first_name":"Minxia","last_name":"Zou","full_name":"Zou, Minxia"},{"last_name":"del Genio","full_name":"del Genio, Charo I.","first_name":"Charo I."},{"full_name":"Kubeš, Martin F.","last_name":"Kubeš","first_name":"Martin F."},{"full_name":"Napier, Richard","last_name":"Napier","first_name":"Richard"},{"first_name":"Krzysztof","full_name":"Jaworski, Krzysztof","last_name":"Jaworski"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","publication_status":"published","pmid":1,"ec_funded":1,"date_updated":"2025-04-14T07:45:02Z","date_published":"2022-11-03T00:00:00Z","status":"public","issue":"7934","publisher":"Springer Nature","intvolume":"       611","scopus_import":"1","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>","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>","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.","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>.","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.","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."},"month":"11","corr_author":"1","page":"133-138","title":"Adenylate cyclase activity of TIR1/AFB auxin receptors in plants","day":"03","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"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.","oa_version":"Submitted Version","language":[{"iso":"eng"}],"type":"journal_article","date_created":"2023-01-12T12:06:05Z","department":[{"_id":"JiFr"}],"doi":"10.1038/s41586-022-05369-7"},{"status":"public","file_date_updated":"2023-01-30T07:46:51Z","issue":"10","ddc":["580"],"publisher":"Elsevier","keyword":["Plant Science","Molecular Biology"],"intvolume":"        15","citation":{"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>.","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.","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.","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>.","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>","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>","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."},"scopus_import":"1","corr_author":"1","month":"10","day":"03","title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","page":"1533-1542","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.","publication_identifier":{"issn":["1674-2052"]},"oa_version":"Published Version","type":"journal_article","has_accepted_license":"1","language":[{"iso":"eng"}],"date_created":"2023-01-16T09:51:49Z","doi":"10.1016/j.molp.2022.09.003","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"file":[{"creator":"dernst","success":1,"content_type":"application/pdf","checksum":"04d5c12490052d03e4dc4412338a43dd","file_id":"12435","file_name":"2022_MolecularPlant_Johnson.pdf","relation":"main_file","file_size":2307251,"date_updated":"2023-01-30T07:46:51Z","date_created":"2023-01-30T07:46:51Z","access_level":"open_access"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"project":[{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"fulldoi":"https://doi.org/10.1016/j.molp.2022.09.003","volume":15,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"article_processing_charge":"Yes (via OA deal)","year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"_id":"12239","external_id":{"isi":["000882769800009"],"pmid":["36081349"]},"abstract":[{"lang":"eng","text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs."}],"publication":"Molecular Plant","quality_controlled":"1","article_type":"original","author":[{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","full_name":"Johnson, Alexander J","last_name":"Johnson"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","last_name":"Costanzo","full_name":"Costanzo, Tommaso"},{"first_name":"Dana A.","last_name":"Dahhan","full_name":"Dahhan, Dana A."},{"first_name":"Sebastian Y.","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y."},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"}],"pmid":1,"publication_status":"published","date_published":"2022-10-03T00:00:00Z","date_updated":"2025-04-15T07:32:09Z"},{"publication":"Frontiers in Fungal Biology","quality_controlled":"1","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."}],"author":[{"last_name":"Ingole","full_name":"Ingole, Kishor D.","first_name":"Kishor D."},{"first_name":"Nithya","last_name":"Nagarajan","full_name":"Nagarajan, Nithya"},{"last_name":"Uhse","full_name":"Uhse, Simon","first_name":"Simon"},{"full_name":"Giannini, Caterina","last_name":"Giannini","first_name":"Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"first_name":"Armin","full_name":"Djamei, Armin","last_name":"Djamei"}],"article_type":"original","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2022","_id":"13240","date_updated":"2024-03-06T14:01:57Z","date_published":"2022-10-19T00:00:00Z","publication_status":"published","article_processing_charge":"Yes","oa":1,"fulldoi":"https://doi.org/10.3389/ffunb.2022.1029114","volume":3,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","title":"Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis","day":"19","publication_identifier":{"eissn":["2673-6128"]},"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.","file":[{"success":1,"creator":"dernst","content_type":"application/pdf","checksum":"2254e0119c0749d6f7237084fefcece6","date_created":"2023-07-17T11:46:34Z","access_level":"open_access","file_id":"13242","date_updated":"2023-07-17T11:46:34Z","file_size":27966699,"relation":"main_file","file_name":"2023_FrontiersFungalBio_Ingole.pdf"}],"doi":"10.3389/ffunb.2022.1029114","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","date_created":"2023-07-16T22:01:12Z","publisher":"Frontiers Media","file_date_updated":"2023-07-17T11:46:34Z","article_number":"1029114","status":"public","ddc":["579"],"month":"10","intvolume":"         3","scopus_import":"1","citation":{"short":"K.D. Ingole, N. Nagarajan, S. Uhse, C. Giannini, A. Djamei, Frontiers in Fungal Biology 3 (2022).","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.","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>.","ista":"Ingole KD, Nagarajan N, Uhse S, Giannini C, Djamei A. 2022. Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. 3, 1029114.","apa":"Ingole, K. D., Nagarajan, N., Uhse, S., Giannini, C., &#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>","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>."}},{"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"volume":3,"fulldoi":"https://doi.org/10.1016/j.xplc.2021.100269","article_processing_charge":"Yes","oa":1,"publication_status":"published","pmid":1,"date_updated":"2024-08-05T10:27:03Z","date_published":"2022-03-14T00:00:00Z","external_id":{"pmid":["35529945"]},"_id":"17068","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","author":[{"full_name":"Navarrete, Fernando","last_name":"Navarrete","first_name":"Fernando"},{"first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kornienko","full_name":"Kornienko, Aleksandra E.","first_name":"Aleksandra E."},{"full_name":"Saado, Indira","last_name":"Saado","first_name":"Indira"},{"full_name":"Khan, Mamoona","last_name":"Khan","first_name":"Mamoona"},{"last_name":"Chia","full_name":"Chia, Khong-Sam","first_name":"Khong-Sam"},{"last_name":"Darino","full_name":"Darino, Martin A.","first_name":"Martin A."},{"full_name":"Bindics, Janos","last_name":"Bindics","first_name":"Janos"},{"first_name":"Armin","last_name":"Djamei","full_name":"Djamei, Armin"}],"article_type":"original","quality_controlled":"1","publication":"Plant Communications","abstract":[{"lang":"eng","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."}],"scopus_import":"1","citation":{"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>.","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.","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).","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>","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>.","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>","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."},"intvolume":"         3","month":"03","ddc":["580"],"issue":"2","file_date_updated":"2024-08-05T10:26:29Z","article_number":"100269","status":"public","publisher":"Elsevier","date_created":"2024-05-29T06:10:22Z","language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","file":[{"content_type":"application/pdf","checksum":"1eeb6ee65419e4aa34627fea6857f343","creator":"dernst","success":1,"file_name":"2022_PlantComm_Navarrete.pdf","relation":"main_file","file_size":3216686,"date_updated":"2024-08-05T10:26:29Z","file_id":"17393","access_level":"open_access","date_created":"2024-08-05T10:26:29Z"}],"doi":"10.1016/j.xplc.2021.100269","department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["2590-3462"]},"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.","title":"TOPLESS promotes plant immunity by repressing auxin signaling and is targeted by the fungal effector Naked1","day":"14","oa_version":"Published Version"},{"fulldoi":"https://doi.org/10.1126/science.abl4683","volume":375,"article_processing_charge":"No","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9040003","open_access":"1"}],"pmid":1,"publication_status":"published","date_published":"2022-01-20T00:00:00Z","date_updated":"2025-04-24T11:39:46Z","OA_type":"green","year":"2022","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"17069","external_id":{"pmid":["35050671"]},"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."}],"publication":"Science","quality_controlled":"1","author":[{"last_name":"Zhong","full_name":"Zhong, Sheng","first_name":"Sheng"},{"first_name":"Ling","full_name":"Li, Ling","last_name":"Li"},{"first_name":"Zhijuan","full_name":"Wang, Zhijuan","last_name":"Wang"},{"id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","orcid":"0000-0001-9381-3577","last_name":"Ge","full_name":"Ge, Zengxiang","first_name":"Zengxiang"},{"full_name":"Li, Qiyun","last_name":"Li","first_name":"Qiyun"},{"first_name":"Andrea","last_name":"Bleckmann","full_name":"Bleckmann, Andrea"},{"full_name":"Wang, Jizong","last_name":"Wang","first_name":"Jizong"},{"last_name":"Song","full_name":"Song, Zihan","first_name":"Zihan"},{"first_name":"Yihao","last_name":"Shi","full_name":"Shi, Yihao"},{"first_name":"Tianxu","full_name":"Liu, Tianxu","last_name":"Liu"},{"first_name":"Luhan","last_name":"Li","full_name":"Li, Luhan"},{"full_name":"Zhou, Huabin","last_name":"Zhou","first_name":"Huabin"},{"first_name":"Yanyan","full_name":"Wang, Yanyan","last_name":"Wang"},{"first_name":"Li","last_name":"Zhang","full_name":"Zhang, Li"},{"last_name":"Wu","full_name":"Wu, Hen-Ming","first_name":"Hen-Ming"},{"first_name":"Luhua","full_name":"Lai, Luhua","last_name":"Lai"},{"first_name":"Hongya","last_name":"Gu","full_name":"Gu, Hongya"},{"first_name":"Juan","full_name":"Dong, Juan","last_name":"Dong"},{"last_name":"Cheung","full_name":"Cheung, Alice Y.","first_name":"Alice Y."},{"first_name":"Thomas","full_name":"Dresselhaus, Thomas","last_name":"Dresselhaus"},{"first_name":"Li-Jia","full_name":"Qu, Li-Jia","last_name":"Qu"}],"article_type":"original","intvolume":"       375","citation":{"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>","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>","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."},"scopus_import":"1","month":"01","status":"public","issue":"6578","publisher":"American Association for the Advancement of Science","type":"journal_article","language":[{"iso":"eng"}],"date_created":"2024-05-29T06:11:10Z","department":[{"_id":"JiFr"}],"doi":"10.1126/science.abl4683","day":"20","title":"RALF peptide signaling controls the polytubey block in Arabidopsis","page":"290-296","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).","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"oa_version":"Submitted Version"},{"citation":{"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>","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>","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>.","ista":"Floriach-Clark J, Tang H, Willemsen V. 2022.Mosses: Accessible Systems for Plant Development Studies. In: Model Organisms in Plant Genetics. .","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.","short":"J. Floriach-Clark, H. Tang, V. Willemsen, in:, I.Y. Abdurakhmonov (Ed.), Model Organisms in Plant Genetics, IntechOpen, 2022."},"month":"06","ddc":["580"],"status":"public","publisher":"IntechOpen","date_created":"2024-05-29T06:35:13Z","type":"book_chapter","language":[{"iso":"eng"}],"doi":"10.5772/intechopen.100535","department":[{"_id":"JiFr"}],"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.","publication_identifier":{"isbn":["9781839697500"]},"day":"23","title":"Mosses: Accessible Systems for Plant Development Studies","oa_version":"Published Version","fulldoi":"https://doi.org/10.5772/intechopen.100535","editor":[{"last_name":"Abdurakhmonov","full_name":"Abdurakhmonov, Ibrokhim Y.","first_name":"Ibrokhim Y."}],"main_file_link":[{"url":"https://doi.org/10.5772/intechopen.100535","open_access":"1"}],"oa":1,"article_processing_charge":"No","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"publication_status":"published","date_published":"2022-06-23T00:00:00Z","ec_funded":1,"date_updated":"2026-06-18T17:52:59Z","_id":"17085","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jordi","full_name":"Floriach-Clark, Jordi","last_name":"Floriach-Clark"},{"first_name":"Han","last_name":"Tang","full_name":"Tang, Han","orcid":"0000-0001-6152-6637","id":"19BDF720-25A0-11EA-AC6E-928F3DDC885E"},{"last_name":"Willemsen","full_name":"Willemsen, Viola","first_name":"Viola"}],"abstract":[{"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.","lang":"eng"}],"publication":"Model Organisms in Plant Genetics","quality_controlled":"1"},{"publication_identifier":{"issn":["1943-0264"]},"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.","title":"Fourteen stations of auxin","day":"27","oa_version":"Published Version","date_created":"2021-09-14T11:36:53Z","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"JiFr"}],"doi":"10.1101/cshperspect.a039859","ddc":["580"],"issue":"5","article_number":"a039859","status":"public","publisher":"Cold Spring Harbor Laboratory Press","scopus_import":"1","citation":{"ista":"Friml J. 2022. Fourteen stations of auxin. Cold Spring Harbor Perspectives in Biology. 14(5), a039859.","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>","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>","short":"J. Friml, Cold Spring Harbor Perspectives in Biology 14 (2022).","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.","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>."},"intvolume":"        14","month":"05","corr_author":"1","external_id":{"isi":["000806563000003"],"pmid":["34400554"]},"isi":1,"_id":"10016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","author":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"}],"article_type":"review","publication":"Cold Spring Harbor Perspectives in Biology","quality_controlled":"1","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. "}],"publication_status":"published","pmid":1,"date_updated":"2026-06-18T08:35:48Z","date_published":"2022-05-27T00:00:00Z","fulldoi":"https://doi.org/10.1101/cshperspect.a039859","volume":14,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a039859 "}],"oa":1,"article_processing_charge":"No"},{"month":"05","corr_author":"1","intvolume":"        27","scopus_import":"1","citation":{"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.","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>.","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>.","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>","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>"},"publisher":"Cell Press","file_date_updated":"2023-11-02T17:00:03Z","status":"public","ddc":["580"],"issue":"5","file":[{"file_name":"Li Plants 2021_accepted.pdf","file_size":805779,"relation":"main_file","date_updated":"2023-11-02T17:00:03Z","file_id":"14480","access_level":"open_access","date_created":"2023-11-02T17:00:03Z","content_type":"application/pdf","checksum":"3d94980ee1ff6bec100dd813f6a921a6","creator":"amally","success":1}],"doi":"10.1016/j.tplants.2021.11.006","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","date_created":"2021-12-05T23:01:43Z","oa_version":"Submitted Version","title":"Bending to auxin: Fast acid growth for tropisms","page":"440-449","day":"01","publication_identifier":{"issn":["1360-1385"]},"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.","oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.1016/j.tplants.2021.11.006","volume":27,"project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-04-07T14:18:57Z","date_published":"2022-05-01T00:00:00Z","publication_status":"published","pmid":1,"publication":"Trends in Plant Science","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"}]},"article_type":"original","author":[{"last_name":"Li","full_name":"Li, Lanxin","first_name":"Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","external_id":{"pmid":["34848141"],"isi":["000793707900005"]},"isi":1,"_id":"10411"},{"title":"Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots","day":"18","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"acknowledgement":"We thank Joerg Kudla (WWU Munster, Germany), Petra Dietrich (F.A. University of Erlangen-Nurnberg, Germany) for sharing published materials, and NASC for providing seeds. We thank Veronique Storme for help with the statistical analyses. Part of the imaging analysis was carried out at NOLIMITS, an advanced imaging facility established by the University of Milan.\r\nThis work was supported by grants of the China Scholarship Council (CSC) to RW and JC; Fonds Wetenschappelijk Onderzoek (FWO) to TB and (G002220N) SV; the special research fund of Ghent University to EH; the Deutsche Forschungsgemeinschaft (DFG) through Grants within FOR964 (MK and KS); Piano di Sviluppo di Ateneo 2019 (University of Milan) to AC; the European Research Council (ERC) T-Rex project 682436 to DVD; the ERC ETAP project 742985 to JF, and by a PhD fellowship from the University of Milan to MG.","oa_version":"Submitted Version","language":[{"iso":"eng"}],"type":"journal_article","date_created":"2022-02-03T09:19:01Z","doi":"10.1093/jxb/erac019","department":[{"_id":"JiFr"}],"article_number":"erac019","status":"public","issue":"8","publisher":"Oxford University Press","intvolume":"        73","scopus_import":"1","citation":{"ista":"Wang R, Himschoot E, Grenzi M, Chen J, Safi A, Krebs M, Schumacher K, Nowack M, Moeder W, Yoshioka K, Van Damme D, De Smet I, Geelen D, Beeckman T, Friml J, Costa A, Vanneste S. 2022. Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. Journal of Experimental Botany. 73(8), erac019.","apa":"Wang, R., Himschoot, E., Grenzi, M., Chen, J., Safi, A., Krebs, M., … Vanneste, S. (2022). Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erac019\">https://doi.org/10.1093/jxb/erac019</a>","chicago":"Wang, R, E Himschoot, M Grenzi, J Chen, A Safi, M Krebs, K Schumacher, et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jxb/erac019\">https://doi.org/10.1093/jxb/erac019</a>.","ama":"Wang R, Himschoot E, Grenzi M, et al. Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots. <i>Journal of Experimental Botany</i>. 2022;73(8). doi:<a href=\"https://doi.org/10.1093/jxb/erac019\">10.1093/jxb/erac019</a>","short":"R. Wang, E. Himschoot, M. Grenzi, J. Chen, A. Safi, M. Krebs, K. Schumacher, M. Nowack, W. Moeder, K. Yoshioka, D. Van Damme, I. De Smet, D. Geelen, T. Beeckman, J. Friml, A. Costa, S. Vanneste, Journal of Experimental Botany 73 (2022).","ieee":"R. Wang <i>et al.</i>, “Auxin analog-induced Ca2+ signaling is independent of inhibition of endosomal aggregation in Arabidopsis roots,” <i>Journal of Experimental Botany</i>, vol. 73, no. 8. Oxford University Press, 2022.","mla":"Wang, R., et al. “Auxin Analog-Induced Ca2+ Signaling Is Independent of Inhibition of Endosomal Aggregation in Arabidopsis Roots.” <i>Journal of Experimental Botany</i>, vol. 73, no. 8, erac019, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/jxb/erac019\">10.1093/jxb/erac019</a>."},"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","external_id":{"pmid":["35085386"],"isi":["000764220900001"]},"_id":"10717","isi":1,"publication":"Journal of Experimental Botany","quality_controlled":"1","abstract":[{"text":"Much of what we know about the role of auxin in plant development derives from exogenous manipulations of auxin distribution and signaling, using inhibitors, auxins and auxin analogs. In this context, synthetic auxin analogs, such as 1-Naphtalene Acetic Acid (1-NAA), are often favored over the endogenous auxin indole-3-acetic acid (IAA), in part due to their higher stability. While such auxin analogs have proven to be instrumental to reveal the various faces of auxin, they display in some cases distinct bioactivities compared to IAA. Here, we focused on the effect of auxin analogs on the accumulation of PIN proteins in Brefeldin A-sensitive endosomal aggregations (BFA bodies), and the correlation with the ability to elicit Ca 2+ responses. For a set of commonly used auxin analogs, we evaluated if auxin-analog induced Ca 2+ signaling inhibits PIN accumulation. Not all auxin analogs elicited a Ca 2+ response, and their differential ability to elicit Ca 2+ responses correlated partially with their ability to inhibit BFA-body formation. However, in tir1/afb and cngc14, 1-NAA-induced Ca 2+ signaling was strongly impaired, yet 1-NAA still could inhibit PIN accumulation in BFA bodies. This demonstrates that TIR1/AFB-CNGC14-dependent Ca 2+ signaling does not inhibit BFA body formation in Arabidopsis roots.","lang":"eng"}],"article_type":"original","author":[{"first_name":"R","last_name":"Wang","full_name":"Wang, R"},{"first_name":"E","full_name":"Himschoot, E","last_name":"Himschoot"},{"first_name":"M","last_name":"Grenzi","full_name":"Grenzi, M"},{"last_name":"Chen","full_name":"Chen, J","first_name":"J"},{"last_name":"Safi","full_name":"Safi, A","first_name":"A"},{"first_name":"M","full_name":"Krebs, M","last_name":"Krebs"},{"last_name":"Schumacher","full_name":"Schumacher, K","first_name":"K"},{"first_name":"MK","full_name":"Nowack, MK","last_name":"Nowack"},{"full_name":"Moeder, W","last_name":"Moeder","first_name":"W"},{"first_name":"K","last_name":"Yoshioka","full_name":"Yoshioka, K"},{"last_name":"Van Damme","full_name":"Van Damme, D","first_name":"D"},{"full_name":"De Smet, I","last_name":"De Smet","first_name":"I"},{"last_name":"Geelen","full_name":"Geelen, D","first_name":"D"},{"first_name":"T","full_name":"Beeckman, T","last_name":"Beeckman"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Costa, A","last_name":"Costa","first_name":"A"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"}],"publication_status":"published","pmid":1,"ec_funded":1,"date_updated":"2025-05-14T11:06:37Z","date_published":"2022-04-18T00:00:00Z","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"volume":73,"fulldoi":"https://doi.org/10.1093/jxb/erac019","article_processing_charge":"No","oa":1,"main_file_link":[{"open_access":"1","url":"https://biblio.ugent.be/publication/8738721"}]},{"quality_controlled":"1","publication":"Journal of Integrative Plant Biology","abstract":[{"text":"Auxin, one of the first identified and most widely studied phytohormones, has been and will remain a hot topic in plant biology. After more than a century of passionate exploration, the mysteries of its synthesis, transport, signaling, and metabolism have largely been unlocked. Due to the rapid development of new technologies, new methods, and new genetic materials, the study of auxin has entered the fast lane over the past 30 years. Here, we highlight advances in understanding auxin signaling, including auxin perception, rapid auxin responses, TRANSPORT INHIBITOR RESPONSE 1 and AUXIN SIGNALING F-boxes (TIR1/AFBs)-mediated transcriptional and non-transcriptional branches, and the epigenetic regulation of auxin signaling. We also focus on feedback inhibition mechanisms that prevent the over-amplification of auxin signals. In addition, we cover the TRANSMEMBRANE KINASEs (TMKs)-mediated non-canonical signaling, which converges with TIR1/AFBs-mediated transcriptional regulation to coordinate plant growth and development. The identification of additional auxin signaling components and their regulation will continue to open new avenues of research in this field, leading to an increasingly deeper, more comprehensive understanding of how auxin signals are interpreted at the cellular level to regulate plant growth and development.","lang":"eng"}],"article_type":"review","author":[{"last_name":"Yu","full_name":"Yu, Z","first_name":"Z"},{"first_name":"F","last_name":"Zhang","full_name":"Zhang, F"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"first_name":"Z","full_name":"Ding, Z","last_name":"Ding"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","external_id":{"isi":["000761281200011"],"pmid":["35018726"]},"_id":"10719","isi":1,"date_updated":"2026-06-18T08:47:21Z","date_published":"2022-02-01T00:00:00Z","publication_status":"published","pmid":1,"oa":1,"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1111/jipb.13225","open_access":"1"}],"fulldoi":"https://doi.org/10.1111/jipb.13225","volume":64,"oa_version":"Published Version","page":"371-392","title":"Auxin signaling: Research advances over the past 30 years","day":"01","publication_identifier":{"eissn":["1744-7909"],"issn":["1672-9072"]},"acknowledgement":"This research was financially supported by the National Natural Science Foundation of China and the Israel Science Foundation (NSFC-ISF; 32061143005), National Natural Science Foundation of China (32000225), Natural Science Foundation of Shandong Province (ZR2020QC036), and China Postdoctoral Science Foundation (2020M682165).\r\n","doi":"10.1111/jipb.13225","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"type":"journal_article","date_created":"2022-02-03T09:52:59Z","publisher":"Wiley","status":"public","ddc":["580"],"issue":"2","month":"02","corr_author":"1","intvolume":"        64","scopus_import":"1","citation":{"mla":"Yu, Z., et al. “Auxin Signaling: Research Advances over the Past 30 Years.” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 2, Wiley, 2022, pp. 371–92, doi:<a href=\"https://doi.org/10.1111/jipb.13225\">10.1111/jipb.13225</a>.","ieee":"Z. Yu, F. Zhang, J. Friml, and Z. Ding, “Auxin signaling: Research advances over the past 30 years,” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 2. Wiley, pp. 371–392, 2022.","short":"Z. Yu, F. Zhang, J. Friml, Z. Ding, Journal of Integrative Plant Biology 64 (2022) 371–392.","ama":"Yu Z, Zhang F, Friml J, Ding Z. Auxin signaling: Research advances over the past 30 years. <i>Journal of Integrative Plant Biology</i>. 2022;64(2):371-392. doi:<a href=\"https://doi.org/10.1111/jipb.13225\">10.1111/jipb.13225</a>","chicago":"Yu, Z, F Zhang, Jiří Friml, and Z Ding. “Auxin Signaling: Research Advances over the Past 30 Years.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jipb.13225\">https://doi.org/10.1111/jipb.13225</a>.","apa":"Yu, Z., Zhang, F., Friml, J., &#38; Ding, Z. (2022). Auxin signaling: Research advances over the past 30 years. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.13225\">https://doi.org/10.1111/jipb.13225</a>","ista":"Yu Z, Zhang F, Friml J, Ding Z. 2022. Auxin signaling: Research advances over the past 30 years. Journal of Integrative Plant Biology. 64(2), 371–392."}},{"author":[{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub","last_name":"Hajny","first_name":"Jakub"},{"full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"}],"article_type":"original","abstract":[{"lang":"eng","text":"Among the most fascinated properties of the plant hormone auxin is its ability to promote formation of its own directional transport routes. These gradually narrowing auxin channels form from the auxin source toward the sink and involve coordinated, collective polarization of individual cells. Once established, the channels provide positional information, along which new vascular strands form, for example, during organogenesis, regeneration, or leave venation. The main prerequisite of this still mysterious auxin canalization mechanism is a feedback between auxin signaling and its directional transport. This is manifested by auxin-induced re-arrangements of polar, subcellular localization of PIN-FORMED (PIN) auxin exporters. Immanent open questions relate to how position of auxin source and sink as well as tissue context are sensed and translated into tissue polarization and how cells communicate to polarize coordinately. Recently, identification of the first molecular players opens new avenues into molecular studies of this intriguing example of self-organizing plant development."}],"publication":"Current Opinion in Plant Biology","quality_controlled":"1","_id":"10768","isi":1,"external_id":{"pmid":["35123880"],"isi":["000758724700004"]},"year":"2022","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-02-01T00:00:00Z","date_updated":"2024-10-09T21:01:37Z","pmid":1,"publication_status":"published","oa":1,"article_processing_charge":"Yes (via OA deal)","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1016/j.pbi.2022.102174","volume":65,"oa_version":"Published Version","acknowledgement":"The authors apologize to those researchers whose work was not cited. In addition, exciting topics such as PIN polarization in context of phyllotaxis, shoot branching and termination of gravitropic bending, or role of additional auxin transporters could not have been included owing to lack of space. This work was supported by the Czech Science Foundation GAČR (GA18-26981S). The authors also acknowledge the EMBO for supporting J.H. with a long-term fellowship (ALTF217-2021).","publication_identifier":{"issn":["1369-5266"]},"day":"01","title":"Auxin canalization: From speculative models toward molecular players","department":[{"_id":"JiFr"}],"doi":"10.1016/j.pbi.2022.102174","file":[{"creator":"dernst","success":1,"content_type":"application/pdf","checksum":"f1ee02b6fb4200934eeb31fa69120885","access_level":"open_access","date_created":"2022-03-10T13:34:09Z","file_id":"10844","file_name":"2022_CurrentOpPlantBiology_Hajny.pdf","relation":"main_file","date_updated":"2022-03-10T13:34:09Z","file_size":820322}],"date_created":"2022-02-20T23:01:32Z","type":"journal_article","has_accepted_license":"1","language":[{"iso":"eng"}],"publisher":"Elsevier","issue":"2","ddc":["580"],"status":"public","file_date_updated":"2022-03-10T13:34:09Z","article_number":"102174","corr_author":"1","month":"02","citation":{"mla":"Hajny, Jakub, et al. “Auxin Canalization: From Speculative Models toward Molecular Players.” <i>Current Opinion in Plant Biology</i>, vol. 65, no. 2, 102174, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">10.1016/j.pbi.2022.102174</a>.","ieee":"J. Hajny, S. Tan, and J. Friml, “Auxin canalization: From speculative models toward molecular players,” <i>Current Opinion in Plant Biology</i>, vol. 65, no. 2. Elsevier, 2022.","short":"J. Hajny, S. Tan, J. Friml, Current Opinion in Plant Biology 65 (2022).","apa":"Hajny, J., Tan, S., &#38; Friml, J. (2022). Auxin canalization: From speculative models toward molecular players. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">https://doi.org/10.1016/j.pbi.2022.102174</a>","chicago":"Hajny, Jakub, Shutang Tan, and Jiří Friml. “Auxin Canalization: From Speculative Models toward Molecular Players.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">https://doi.org/10.1016/j.pbi.2022.102174</a>.","ama":"Hajny J, Tan S, Friml J. Auxin canalization: From speculative models toward molecular players. <i>Current Opinion in Plant Biology</i>. 2022;65(2). doi:<a href=\"https://doi.org/10.1016/j.pbi.2022.102174\">10.1016/j.pbi.2022.102174</a>","ista":"Hajny J, Tan S, Friml J. 2022. Auxin canalization: From speculative models toward molecular players. Current Opinion in Plant Biology. 65(2), 102174."},"scopus_import":"1","intvolume":"        65"},{"volume":63,"fulldoi":"https://doi.org/10.1093/pcp/pcab149","main_file_link":[{"url":"https://doi.org/10.1093/pcp/pcab149","open_access":"1"}],"oa":1,"article_processing_charge":"No","external_id":{"pmid":["34791413"],"isi":["000877899400009"]},"isi":1,"_id":"10583","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","article_type":"original","author":[{"first_name":"Sylwia","last_name":"Struk","full_name":"Struk, Sylwia"},{"first_name":"Lukas","last_name":"Braem","full_name":"Braem, Lukas"},{"first_name":"Cedrick","full_name":"Matthys, Cedrick","last_name":"Matthys"},{"first_name":"Alan","full_name":"Walton, Alan","last_name":"Walton"},{"first_name":"Nick","last_name":"Vangheluwe","full_name":"Vangheluwe, Nick"},{"first_name":"Stan","full_name":"Van Praet, Stan","last_name":"Van Praet"},{"last_name":"Jiang","full_name":"Jiang, Lingxiang","first_name":"Lingxiang"},{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Baster","full_name":"Baster, Pawel"},{"first_name":"Carolien","full_name":"De Cuyper, Carolien","last_name":"De Cuyper"},{"first_name":"Francois-Didier","full_name":"Boyer, Francois-Didier","last_name":"Boyer"},{"last_name":"Stes","full_name":"Stes, Elisabeth","first_name":"Elisabeth"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Gevaert, Kris","last_name":"Gevaert","first_name":"Kris"},{"full_name":"Goormachtig, Sofie","last_name":"Goormachtig","first_name":"Sofie"}],"publication":"Plant & Cell Physiology","quality_controlled":"1","abstract":[{"lang":"eng","text":"The synthetic strigolactone (SL) analog, rac-GR24, has been instrumental in studying the role of SLs as well as karrikins because it activates the receptors DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2) of their signaling pathways, respectively. Treatment with rac-GR24 modifies the root architecture at different levels, such as decreasing the lateral root density (LRD), while promoting root hair elongation or flavonol accumulation. Previously, we have shown that the flavonol biosynthesis is transcriptionally activated in the root by rac-GR24 treatment, but, thus far, the molecular players involved in that response have remained unknown. To get an in-depth insight into the changes that occur after the compound is perceived by the roots, we compared the root transcriptomes of the wild type and the more axillary growth2 (max2) mutant, affected in both SL and karrikin signaling pathways, with and without rac-GR24 treatment. Quantitative reverse transcription (qRT)-PCR, reporter line analysis and mutant phenotyping indicated that the flavonol response and the root hair elongation are controlled by the ELONGATED HYPOCOTYL 5 (HY5) and MYB12 transcription factors, but HY5, in contrast to MYB12, affects the LRD as well. Furthermore, we identified the transcription factors TARGET OF MONOPTEROS 5 (TMO5) and TMO5 LIKE1 as negative and the Mediator complex as positive regulators of the rac-GR24 effect on LRD. Altogether, hereby, we get closer toward understanding the molecular mechanisms that underlay the rac-GR24 responses in the root."}],"publication_status":"published","pmid":1,"date_updated":"2026-07-28T12:02:02Z","OA_type":"free access","date_published":"2022-01-21T00:00:00Z","ddc":["580"],"issue":"1","status":"public","keyword":["flavonols","MAX2","rac-Gr24","RNA-seq","root development","transcriptional regulation"],"publisher":"Oxford University Press","scopus_import":"1","citation":{"mla":"Struk, Sylwia, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density.” <i>Plant &#38; Cell Physiology</i>, vol. 63, no. 1, Oxford University Press, 2022, pp. 104–19, doi:<a href=\"https://doi.org/10.1093/pcp/pcab149\">10.1093/pcp/pcab149</a>.","ieee":"S. Struk <i>et al.</i>, “Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density,” <i>Plant &#38; Cell Physiology</i>, vol. 63, no. 1. Oxford University Press, pp. 104–119, 2022.","short":"S. Struk, L. Braem, C. Matthys, A. Walton, N. Vangheluwe, S. Van Praet, L. Jiang, P. Baster, C. De Cuyper, F.-D. Boyer, E. Stes, T. Beeckman, J. Friml, K. Gevaert, S. Goormachtig, Plant &#38; Cell Physiology 63 (2022) 104–119.","chicago":"Struk, Sylwia, Lukas Braem, Cedrick Matthys, Alan Walton, Nick Vangheluwe, Stan Van Praet, Lingxiang Jiang, et al. “Transcriptional Analysis in the Arabidopsis Roots Reveals New Regulators That Link Rac-GR24 Treatment with Changes in Flavonol Accumulation, Root Hair Elongation and Lateral Root Density.” <i>Plant &#38; Cell Physiology</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/pcp/pcab149\">https://doi.org/10.1093/pcp/pcab149</a>.","apa":"Struk, S., Braem, L., Matthys, C., Walton, A., Vangheluwe, N., Van Praet, S., … Goormachtig, S. (2022). Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. <i>Plant &#38; Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcab149\">https://doi.org/10.1093/pcp/pcab149</a>","ama":"Struk S, Braem L, Matthys C, et al. Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. <i>Plant &#38; Cell Physiology</i>. 2022;63(1):104-119. doi:<a href=\"https://doi.org/10.1093/pcp/pcab149\">10.1093/pcp/pcab149</a>","ista":"Struk S, Braem L, Matthys C, Walton A, Vangheluwe N, Van Praet S, Jiang L, Baster P, De Cuyper C, Boyer F-D, Stes E, Beeckman T, Friml J, Gevaert K, Goormachtig S. 2022. Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density. Plant &#38; Cell Physiology. 63(1), 104–119."},"intvolume":"        63","month":"01","publication_identifier":{"issn":["0032-0781"],"eissn":["1471-9053"]},"acknowledgement":"The authors thank Ralf Stracke (Bielefeld University, Bielefeld, Germany) for providing the myb mutants and their colleagues Bert De Rybel for the tmo5t;mo5l1 double mutant, Boris Parizot for tips on the RNA-seq analysis, Veronique Storme for statistical help on both the RNA-seq and lateral root density, and Martine De Cock for help in preparing the manuscript.","title":"Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density","page":"104-119","day":"21","oa_version":"Published Version","date_created":"2021-12-28T11:44:18Z","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1093/pcp/pcab149","department":[{"_id":"JiFr"}]},{"volume":233,"fulldoi":"https://doi.org/10.1111/nph.17792","oa":1,"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1111/nph.17792","open_access":"1"}],"pmid":1,"publication_status":"published","date_published":"2022-01-01T00:00:00Z","date_updated":"2026-07-28T12:06:20Z","OA_type":"free access","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","_id":"10282","isi":1,"external_id":{"isi":["000714678100001"],"biorxivid":["10.1101/2020.05.02.074070"],"pmid":["34637542"]},"abstract":[{"lang":"eng","text":"Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development."}],"publication":"New Phytologist","quality_controlled":"1","article_type":"original","author":[{"full_name":"Kashkan, Ivan","last_name":"Kashkan","first_name":"Ivan"},{"full_name":"Hrtyan, Mónika","last_name":"Hrtyan","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Retzer, Katarzyna","last_name":"Retzer","first_name":"Katarzyna"},{"last_name":"Humpolíčková","full_name":"Humpolíčková, Jana","first_name":"Jana"},{"last_name":"Jayasree","full_name":"Jayasree, Aswathy","first_name":"Aswathy"},{"full_name":"Filepová, Roberta","last_name":"Filepová","first_name":"Roberta"},{"first_name":"Zuzana","full_name":"Vondráková, Zuzana","last_name":"Vondráková"},{"orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu"},{"first_name":"Debbie","full_name":"Rombaut, Debbie","last_name":"Rombaut"},{"first_name":"Thomas B.","full_name":"Jacobs, Thomas B.","last_name":"Jacobs"},{"first_name":"Mikko J.","full_name":"Frilander, Mikko J.","last_name":"Frilander"},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"first_name":"Kamil","full_name":"Růžička, Kamil","last_name":"Růžička"}],"intvolume":"       233","citation":{"short":"I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2022) 329–343.","ieee":"I. Kashkan <i>et al.</i>, “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 233, no. 1. Wiley, pp. 329–343, 2022.","mla":"Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 233, no. 1, Wiley, 2022, pp. 329–43, doi:<a href=\"https://doi.org/10.1111/nph.17792\">10.1111/nph.17792</a>.","ista":"Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2022. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233(1), 329–343.","ama":"Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. <i>New Phytologist</i>. 2022;233(1):329-343. doi:<a href=\"https://doi.org/10.1111/nph.17792\">10.1111/nph.17792</a>","chicago":"Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/nph.17792\">https://doi.org/10.1111/nph.17792</a>.","apa":"Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2022). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17792\">https://doi.org/10.1111/nph.17792</a>"},"scopus_import":"1","month":"01","status":"public","issue":"1","publisher":"Wiley","type":"journal_article","language":[{"iso":"eng"}],"date_created":"2021-11-14T23:01:24Z","department":[{"_id":"JiFr"}],"doi":"10.1111/nph.17792","day":"01","biorxivid":1,"title":"Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana","page":"329-343","acknowledgement":"We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests.","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"oa_version":"Published Version"},{"oa_version":"Submitted Version","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","page":"575-581","day":"15","file":[{"success":1,"creator":"amally","content_type":"application/pdf","checksum":"a6055c606aefb900bf62ae3e7d15f921","file_id":"14483","file_size":79774945,"relation":"main_file","date_updated":"2023-11-02T17:12:37Z","file_name":"Friml Nature 2022_merged.pdf","access_level":"open_access","date_created":"2023-11-02T17:12:37Z"}],"department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"doi":"10.1038/s41586-022-05187-x","date_created":"2023-01-16T10:04:48Z","language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","publisher":"Springer Nature","ddc":["580"],"issue":"7927","file_date_updated":"2023-11-02T17:12:37Z","status":"public","month":"09","corr_author":"1","scopus_import":"1","citation":{"mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581."},"intvolume":"       609","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19395"},{"relation":"dissertation_contains","status":"public","id":"23145"},{"relation":"dissertation_contains","id":"20364","status":"public"}]},"article_type":"original","author":[{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","last_name":"Gallei","full_name":"Gallei, Michelle C","first_name":"Michelle C"},{"last_name":"Gelová","full_name":"Gelová, Zuzana","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752"},{"first_name":"Alexander J","full_name":"Johnson, Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"first_name":"Aline","full_name":"Monzer, Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark","full_name":"Roosjen, Mark","last_name":"Roosjen"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","last_name":"Verstraeten","full_name":"Verstraeten, Inge","first_name":"Inge"},{"first_name":"Branka D.","last_name":"Živanović","full_name":"Živanović, Branka D."},{"last_name":"Zou","full_name":"Zou, Minxia","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"last_name":"Fiedler","full_name":"Fiedler, Lukas","first_name":"Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina"},{"first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"first_name":"Mónika","last_name":"Hrtyan","full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Andre","full_name":"Kuhn, Andre","last_name":"Kuhn"},{"last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","last_name":"Randuch","full_name":"Randuch, Marek"},{"first_name":"Nikola","full_name":"Rýdza, Nikola","last_name":"Rýdza"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"first_name":"Shutang","full_name":"Tan, Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anastasiia","full_name":"Teplova, Anastasiia","last_name":"Teplova","id":"e3736151-106c-11ec-b916-c2558e2762c6"},{"first_name":"Toshinori","full_name":"Kinoshita, Toshinori","last_name":"Kinoshita"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"last_name":"Rakusová","full_name":"Rakusová, Hana","first_name":"Hana"}],"quality_controlled":"1","publication":"Nature","abstract":[{"lang":"eng","text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization."}],"external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"isi":1,"_id":"12291","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","ec_funded":1,"date_updated":"2026-10-31T23:31:11Z","date_published":"2022-09-15T00:00:00Z","publication_status":"published","pmid":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"oa":1,"article_processing_charge":"No","fulldoi":"https://doi.org/10.1038/s41586-022-05187-x","volume":609},{"citation":{"ista":"Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5747100\">10.5281/ZENODO.5747100</a>.","ama":"Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:<a href=\"https://doi.org/10.5281/ZENODO.5747100\">10.5281/ZENODO.5747100</a>","chicago":"Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo, 2021. <a href=\"https://doi.org/10.5281/ZENODO.5747100\">https://doi.org/10.5281/ZENODO.5747100</a>.","apa":"Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5747100\">https://doi.org/10.5281/ZENODO.5747100</a>","short":"A.J. Johnson, (2021).","ieee":"A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021.","mla":"Johnson, Alexander J. <i>Raw Data from Johnson et Al, PNAS, 2021</i>. Zenodo, 2021, doi:<a href=\"https://doi.org/10.5281/ZENODO.5747100\">10.5281/ZENODO.5747100</a>."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.5281/ZENODO.5747100","corr_author":"1","month":"12","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5747100","open_access":"1"}],"article_processing_charge":"No","oa":1,"ddc":["580"],"status":"public","publisher":"Zenodo","date_created":"2024-02-14T14:13:48Z","has_accepted_license":"1","type":"research_data_reference","date_published":"2021-12-01T00:00:00Z","date_updated":"2025-05-14T09:25:33Z","doi":"10.5281/ZENODO.5747100","department":[{"_id":"JiFr"}],"_id":"14988","year":"2021","day":"01","title":"Raw data from Johnson et al, PNAS, 2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","full_name":"Johnson, Alexander J","last_name":"Johnson"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9887"}]},"abstract":[{"lang":"eng","text":"Raw data generated from the publication - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In PNAS"}]}]