[{"article_processing_charge":"Yes (via OA deal)","isi":1,"month":"10","issue":"2","page":"510-522","file_date_updated":"2021-10-07T13:42:47Z","quality_controlled":"1","ddc":["580"],"year":"2021","language":[{"iso":"eng"}],"volume":232,"publication_status":"published","type":"journal_article","publisher":"Wiley","corr_author":"1","has_accepted_license":"1","intvolume":"       232","scopus_import":"1","doi":"10.1111/nph.17617","citation":{"mla":"Han, Huibin, et al. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>, vol. 232, no. 2, Wiley, 2021, pp. 510–22, doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>.","apa":"Han, H., Adamowski, M., Qi, L., Alotaibi, S., &#38; Friml, J. (2021). PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>","ista":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. 2021. PIN-mediated polar auxin transport regulations in plant tropic responses. New Phytologist. 232(2), 510–522.","chicago":"Han, Huibin, Maciek Adamowski, Linlin Qi, SS Alotaibi, and Jiří Friml. “PIN-Mediated Polar Auxin Transport Regulations in Plant Tropic Responses.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.17617\">https://doi.org/10.1111/nph.17617</a>.","ieee":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, and J. Friml, “PIN-mediated polar auxin transport regulations in plant tropic responses,” <i>New Phytologist</i>, vol. 232, no. 2. Wiley, pp. 510–522, 2021.","short":"H. Han, M. Adamowski, L. Qi, S. Alotaibi, J. Friml, New Phytologist 232 (2021) 510–522.","ama":"Han H, Adamowski M, Qi L, Alotaibi S, Friml J. PIN-mediated polar auxin transport regulations in plant tropic responses. <i>New Phytologist</i>. 2021;232(2):510-522. doi:<a href=\"https://doi.org/10.1111/nph.17617\">10.1111/nph.17617</a>"},"abstract":[{"text":"Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment.","lang":"eng"}],"title":"PIN-mediated polar auxin transport regulations in plant tropic responses","author":[{"first_name":"Huibin","last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Adamowski","first_name":"Maciek","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Linlin","last_name":"Qi","full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425"},{"full_name":"Alotaibi, SS","last_name":"Alotaibi","first_name":"SS"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"}],"article_type":"original","acknowledgement":"We are grateful to Lukas Fiedler, Alexandra Mally (IST Austria) and Dr. Bartel Vanholme (VIB, Ghent) for their critical comments on the manuscript. We apologize to those researchers whose great work was not cited. This work is supported by the European Research Council under the European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to JF. HH is supported by the China Scholarship Council (CSC scholarship, 201506870018) and a starting grant from Jiangxi Agriculture University (9232308314).","day":"01","department":[{"_id":"JiFr"}],"ec_funded":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2025-04-14T07:45:00Z","oa_version":"Published Version","date_created":"2021-07-14T15:29:14Z","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"pmid":1,"_id":"9656","publication":"New Phytologist","file":[{"file_id":"10105","access_level":"open_access","date_updated":"2021-10-07T13:42:47Z","success":1,"content_type":"application/pdf","date_created":"2021-10-07T13:42:47Z","checksum":"6422a6eb329b52d96279daaee0fcf189","file_size":1939800,"relation":"main_file","file_name":"2021_NewPhytologist_Han.pdf","creator":"kschuh"}],"date_published":"2021-10-01T00:00:00Z","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"external_id":{"isi":["000680587100001"],"pmid":["34254313"]},"oa":1},{"article_type":"original","day":"07","department":[{"_id":"JiFr"}],"author":[{"full_name":"Gao, Z","first_name":"Z","last_name":"Gao"},{"full_name":"Chen, Z","first_name":"Z","last_name":"Chen"},{"full_name":"Cui, Y","first_name":"Y","last_name":"Cui"},{"full_name":"Ke, M","last_name":"Ke","first_name":"M"},{"full_name":"Xu, H","first_name":"H","last_name":"Xu"},{"full_name":"Xu, Q","last_name":"Xu","first_name":"Q"},{"last_name":"Chen","first_name":"J","full_name":"Chen, J"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"last_name":"Huang","first_name":"L","full_name":"Huang, L"},{"full_name":"Zhao, H","first_name":"H","last_name":"Zhao"},{"full_name":"Huang, D","first_name":"D","last_name":"Huang"},{"last_name":"Mai","first_name":"S","full_name":"Mai, S"},{"full_name":"Xu, T","first_name":"T","last_name":"Xu"},{"last_name":"Liu","first_name":"X","full_name":"Liu, X"},{"first_name":"S","last_name":"Li","full_name":"Li, S"},{"last_name":"Guan","first_name":"Y","full_name":"Guan, Y"},{"full_name":"Yang, W","last_name":"Yang","first_name":"W"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Petrášek, J","last_name":"Petrášek","first_name":"J"},{"full_name":"Zhang, J","first_name":"J","last_name":"Zhang"},{"full_name":"Chen, X","first_name":"X","last_name":"Chen"}],"title":"GmPIN-dependent polar auxin transport is involved in soybean nodule development","status":"public","date_updated":"2024-10-21T06:02:03Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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)"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Plant Cell","file":[{"relation":"main_file","checksum":"6715712ec306c321f0204c817b7f8ae7","date_created":"2021-07-19T12:13:34Z","file_size":10566921,"creator":"cziletti","file_name":"2021_PlantCell_Gao.pdf","file_id":"9691","date_updated":"2021-07-19T12:13:34Z","success":1,"content_type":"application/pdf","access_level":"open_access"}],"date_created":"2021-07-14T15:32:43Z","oa_version":"Published Version","_id":"9657","pmid":1,"oa":1,"external_id":{"isi":["000702165300012"],"pmid":["34240197"]},"date_published":"2021-07-07T00:00:00Z","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"month":"07","file_date_updated":"2021-07-19T12:13:34Z","issue":"9","page":"2981–3003","article_processing_charge":"No","isi":1,"language":[{"iso":"eng"}],"volume":33,"quality_controlled":"1","year":"2021","ddc":["580"],"has_accepted_license":"1","intvolume":"        33","publication_status":"published","type":"journal_article","publisher":"American Society of Plant Biologists","citation":{"ista":"Gao Z, Chen Z, Cui Y, Ke M, Xu H, Xu Q, Chen J, Li Y, Huang L, Zhao H, Huang D, Mai S, Xu T, Liu X, Li S, Guan Y, Yang W, Friml J, Petrášek J, Zhang J, Chen X. 2021. GmPIN-dependent polar auxin transport is involved in soybean nodule development. Plant Cell. 33(9), 2981–3003.","chicago":"Gao, Z, Z Chen, Y Cui, M Ke, H Xu, Q Xu, J Chen, et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>.","ieee":"Z. Gao <i>et al.</i>, “GmPIN-dependent polar auxin transport is involved in soybean nodule development,” <i>Plant Cell</i>, vol. 33, no. 9. American Society of Plant Biologists, pp. 2981–3003, 2021.","ama":"Gao Z, Chen Z, Cui Y, et al. GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. 2021;33(9):2981–3003. doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>","short":"Z. Gao, Z. Chen, Y. Cui, M. Ke, H. Xu, Q. Xu, J. Chen, Y. Li, L. Huang, H. Zhao, D. Huang, S. Mai, T. Xu, X. Liu, S. Li, Y. Guan, W. Yang, J. Friml, J. Petrášek, J. Zhang, X. Chen, Plant Cell 33 (2021) 2981–3003.","apa":"Gao, Z., Chen, Z., Cui, Y., Ke, M., Xu, H., Xu, Q., … Chen, X. (2021). GmPIN-dependent polar auxin transport is involved in soybean nodule development. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plcell/koab183\">https://doi.org/10.1093/plcell/koab183</a>","mla":"Gao, Z., et al. “GmPIN-Dependent Polar Auxin Transport Is Involved in Soybean Nodule Development.” <i>Plant Cell</i>, vol. 33, no. 9, American Society of Plant Biologists, 2021, pp. 2981–3003, doi:<a href=\"https://doi.org/10.1093/plcell/koab183\">10.1093/plcell/koab183</a>."},"abstract":[{"lang":"eng","text":"To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia."}],"scopus_import":"1","doi":"10.1093/plcell/koab183"},{"publication":"Genes","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2021-08-16T09:02:40Z","file_id":"9919","file_name":"2021_Genes_Zeng.pdf","creator":"asandaue","file_size":1340305,"checksum":"3d99535618cf9a5b14d264408fa52e97","date_created":"2021-08-16T09:02:40Z","relation":"main_file"}],"date_created":"2021-08-15T22:01:28Z","article_number":"1141","oa_version":"Published Version","_id":"9909","oa":1,"external_id":{"isi":["000690558000001"]},"date_published":"2021-07-27T00:00:00Z","publication_identifier":{"eissn":["2073-4425"]},"acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","article_type":"original","department":[{"_id":"JiFr"}],"day":"27","title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","author":[{"full_name":"Zeng, Yinwei","last_name":"Zeng","first_name":"Yinwei"},{"full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Trinh","first_name":"Hoang Khai","full_name":"Trinh, Hoang Khai"},{"full_name":"Heugebaert, Thomas","last_name":"Heugebaert","first_name":"Thomas"},{"full_name":"Stevens, Christian V.","first_name":"Christian V.","last_name":"Stevens"},{"full_name":"Garcia-Maquilon, Irene","first_name":"Irene","last_name":"Garcia-Maquilon"},{"full_name":"Rodriguez, Pedro L.","last_name":"Rodriguez","first_name":"Pedro L."},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Geelen, Danny","last_name":"Geelen","first_name":"Danny"}],"status":"public","date_updated":"2026-04-02T13:57:06Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","intvolume":"        12","publication_status":"published","publisher":"MDPI","type":"journal_article","citation":{"apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>, vol. 12, no. 8, 1141, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>.","ieee":"Y. Zeng <i>et al.</i>, “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>.","short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>"},"abstract":[{"text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.","lang":"eng"}],"scopus_import":"1","doi":"10.3390/genes12081141","month":"07","file_date_updated":"2021-08-16T09:02:40Z","issue":"8","article_processing_charge":"Yes","isi":1,"language":[{"iso":"eng"}],"volume":12,"quality_controlled":"1","year":"2021","ddc":["580","570"]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-28T12:37:19Z","status":"public","title":"Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)","main_file_link":[{"url":"https://doi.org/10.1080/15548627.2020.1797280","open_access":"1"}],"author":[{"last_name":"Klionsky","first_name":"Daniel J.","full_name":"Klionsky, Daniel J."},{"full_name":"Abdel-Aziz, Amal Kamal","first_name":"Amal Kamal","last_name":"Abdel-Aziz"},{"last_name":"Abdelfatah","first_name":"Sara","full_name":"Abdelfatah, Sara"},{"full_name":"Abdellatif, Mahmoud","first_name":"Mahmoud","last_name":"Abdellatif"},{"last_name":"Abdoli","first_name":"Asghar","full_name":"Abdoli, Asghar"},{"first_name":"Steffen","last_name":"Abel","full_name":"Abel, Steffen"},{"full_name":"Abeliovich, Hagai","last_name":"Abeliovich","first_name":"Hagai"},{"last_name":"Abildgaard","first_name":"Marie H.","full_name":"Abildgaard, Marie H."},{"full_name":"Abudu, Yakubu Princely","last_name":"Abudu","first_name":"Yakubu Princely"},{"first_name":"Abraham","last_name":"Acevedo-Arozena","full_name":"Acevedo-Arozena, Abraham"},{"full_name":"Adamopoulos, Iannis E.","first_name":"Iannis E.","last_name":"Adamopoulos"},{"full_name":"Adeli, Khosrow","first_name":"Khosrow","last_name":"Adeli"},{"last_name":"Adolph","first_name":"Timon E.","full_name":"Adolph, Timon E."},{"last_name":"Adornetto","first_name":"Annagrazia","full_name":"Adornetto, Annagrazia"},{"full_name":"Aflaki, Elma","first_name":"Elma","last_name":"Aflaki"},{"last_name":"Agam","first_name":"Galila","full_name":"Agam, Galila"},{"first_name":"Anupam","last_name":"Agarwal","full_name":"Agarwal, Anupam"},{"full_name":"Aggarwal, Bharat B.","last_name":"Aggarwal","first_name":"Bharat B."},{"first_name":"Maria","last_name":"Agnello","full_name":"Agnello, Maria"},{"full_name":"Agostinis, Patrizia","first_name":"Patrizia","last_name":"Agostinis"},{"last_name":"Agrewala","first_name":"Javed N.","full_name":"Agrewala, Javed N."},{"full_name":"Agrotis, Alexander","first_name":"Alexander","last_name":"Agrotis"},{"full_name":"Aguilar, Patricia V.","last_name":"Aguilar","first_name":"Patricia V."},{"full_name":"Ahmad, S. Tariq","first_name":"S. Tariq","last_name":"Ahmad"},{"full_name":"Ahmed, Zubair M.","first_name":"Zubair M.","last_name":"Ahmed"},{"full_name":"Ahumada-Castro, Ulises","last_name":"Ahumada-Castro","first_name":"Ulises"},{"first_name":"Sonja","last_name":"Aits","full_name":"Aits, Sonja"},{"first_name":"Shu","last_name":"Aizawa","full_name":"Aizawa, Shu"},{"last_name":"Akkoc","first_name":"Yunus","full_name":"Akkoc, Yunus"},{"full_name":"Akoumianaki, Tonia","last_name":"Akoumianaki","first_name":"Tonia"},{"full_name":"Akpinar, Hafize Aysin","last_name":"Akpinar","first_name":"Hafize Aysin"},{"last_name":"Al-Abd","first_name":"Ahmed M.","full_name":"Al-Abd, Ahmed M."},{"first_name":"Lina","last_name":"Al-Akra","full_name":"Al-Akra, Lina"},{"full_name":"Al-Gharaibeh, Abeer","last_name":"Al-Gharaibeh","first_name":"Abeer"},{"full_name":"Alaoui-Jamali, Moulay A.","last_name":"Alaoui-Jamali","first_name":"Moulay A."},{"last_name":"Alberti","first_name":"Simon","full_name":"Alberti, Simon"},{"first_name":"Elísabet","last_name":"Alcocer-Gómez","full_name":"Alcocer-Gómez, Elísabet"},{"full_name":"Alessandri, Cristiano","last_name":"Alessandri","first_name":"Cristiano"},{"first_name":"Muhammad","last_name":"Ali","full_name":"Ali, Muhammad"},{"first_name":"M. Abdul","last_name":"Alim Al-Bari","full_name":"Alim Al-Bari, M. Abdul"},{"full_name":"Aliwaini, Saeb","last_name":"Aliwaini","first_name":"Saeb"},{"full_name":"Alizadeh, Javad","first_name":"Javad","last_name":"Alizadeh"},{"first_name":"Eugènia","last_name":"Almacellas","full_name":"Almacellas, Eugènia"},{"full_name":"Almasan, Alexandru","last_name":"Almasan","first_name":"Alexandru"},{"full_name":"Alonso, Alicia","last_name":"Alonso","first_name":"Alicia"},{"last_name":"Alonso","first_name":"Guillermo D.","full_name":"Alonso, Guillermo D."},{"last_name":"Altan-Bonnet","first_name":"Nihal","full_name":"Altan-Bonnet, Nihal"},{"full_name":"Altieri, Dario C.","first_name":"Dario C.","last_name":"Altieri"},{"full_name":"Álvarez, Élida M.C.","first_name":"Élida M.C.","last_name":"Álvarez"},{"last_name":"Alves","first_name":"Sara","full_name":"Alves, Sara"},{"first_name":"Cristine","last_name":"Alves Da Costa","full_name":"Alves Da Costa, Cristine"},{"full_name":"Alzaharna, Mazen M.","first_name":"Mazen 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M.","first_name":"Christine M.","last_name":"Zimmermann"},{"full_name":"Ziviani, Elena","last_name":"Ziviani","first_name":"Elena"},{"first_name":"Teresa","last_name":"Zoladek","full_name":"Zoladek, Teresa"},{"last_name":"Zong","first_name":"Wei Xing","full_name":"Zong, Wei Xing"},{"first_name":"Dmitry B.","last_name":"Zorov","full_name":"Zorov, Dmitry B."},{"full_name":"Zorzano, Antonio","last_name":"Zorzano","first_name":"Antonio"},{"full_name":"Zou, Weiping","last_name":"Zou","first_name":"Weiping"},{"last_name":"Zou","first_name":"Zhen","full_name":"Zou, Zhen"},{"full_name":"Zou, Zhengzhi","first_name":"Zhengzhi","last_name":"Zou"},{"last_name":"Zuryn","first_name":"Steven","full_name":"Zuryn, Steven"},{"full_name":"Zwerschke, Werner","last_name":"Zwerschke","first_name":"Werner"},{"last_name":"Brand-Saberi","first_name":"Beate","full_name":"Brand-Saberi, Beate"},{"last_name":"Dong","first_name":"X. Charlie","full_name":"Dong, X. Charlie"},{"full_name":"Kenchappa, Chandra Shekar","first_name":"Chandra Shekar","last_name":"Kenchappa"},{"last_name":"Li","first_name":"Zuguo","full_name":"Li, Zuguo"},{"last_name":"Lin","first_name":"Yong","full_name":"Lin, Yong"},{"full_name":"Oshima, Shigeru","first_name":"Shigeru","last_name":"Oshima"},{"full_name":"Rong, Yueguang","first_name":"Yueguang","last_name":"Rong"},{"full_name":"Sluimer, Judith C.","last_name":"Sluimer","first_name":"Judith C."},{"full_name":"Stallings, Christina L.","first_name":"Christina L.","last_name":"Stallings"},{"full_name":"Tong, Chun Kit","first_name":"Chun Kit","last_name":"Tong"}],"day":"08","department":[{"_id":"JiFr"},{"_id":"CaHe"}],"article_type":"review","acknowledgement":"This work was supported by the National Institute of General Medical Sciences [GM131919]. Due to space and other limitations, it is not possible to include all other sources of financial support.","publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"OA_type":"free access","date_published":"2021-02-08T00:00:00Z","external_id":{"isi":["000636121800001"],"pmid":["33634751"]},"oa":1,"pmid":1,"_id":"9298","oa_version":"Published Version","date_created":"2021-03-28T22:01:44Z","publication":"Autophagy","ddc":["580","570"],"year":"2021","quality_controlled":"1","volume":17,"language":[{"iso":"eng"}],"isi":1,"article_processing_charge":"No","page":"1-382","issue":"1","month":"02","doi":"10.1080/15548627.2020.1797280","scopus_import":"1","abstract":[{"text":"In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field. ","lang":"eng"}],"citation":{"ama":"Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). <i>Autophagy</i>. 2021;17(1):1-382. doi:<a href=\"https://doi.org/10.1080/15548627.2020.1797280\">10.1080/15548627.2020.1797280</a>","short":"D.J. Klionsky, A.K. Abdel-Aziz, S. Abdelfatah, M. Abdellatif, A. Abdoli, S. Abel, H. Abeliovich, M.H. Abildgaard, Y.P. Abudu, A. Acevedo-Arozena, I.E. Adamopoulos, K. Adeli, T.E. Adolph, A. Adornetto, E. Aflaki, G. Agam, A. Agarwal, B.B. Aggarwal, M. Agnello, P. Agostinis, J.N. Agrewala, A. Agrotis, P.V. Aguilar, S.T. Ahmad, Z.M. Ahmed, U. Ahumada-Castro, S. Aits, S. Aizawa, Y. Akkoc, T. Akoumianaki, H.A. Akpinar, A.M. Al-Abd, L. Al-Akra, A. Al-Gharaibeh, M.A. Alaoui-Jamali, S. Alberti, E. Alcocer-Gómez, C. Alessandri, M. Ali, M.A. Alim Al-Bari, S. Aliwaini, J. Alizadeh, E. Almacellas, A. Almasan, A. Alonso, G.D. Alonso, N. Altan-Bonnet, D.C. Altieri, É.M.C. Álvarez, S. Alves, C. Alves Da Costa, M.M. Alzaharna, M. Amadio, C. Amantini, C. Amaral, S. Ambrosio, A.O. Amer, V. Ammanathan, Z. An, S.U. Andersen, S.A. Andrabi, M. Andrade-Silva, A.M. Andres, S. Angelini, D. Ann, U.C. Anozie, M.Y. Ansari, P. Antas, A. Antebi, Z. Antón, T. Anwar, L. Apetoh, N. Apostolova, T. Araki, Y. Araki, K. Arasaki, W.L. Araújo, J. Araya, C. Arden, M.A. Arévalo, S. Arguelles, E. Arias, J. Arikkath, H. Arimoto, A.R. Ariosa, D. Armstrong-James, L. Arnauné-Pelloquin, A. Aroca, D.S. Arroyo, I. Arsov, R. Artero, D.M.L. Asaro, M. Aschner, M. Ashrafizadeh, O. Ashur-Fabian, A.G. Atanasov, A.K. Au, P. Auberger, H.W. Auner, L. Aurelian, R. Autelli, L. Avagliano, Y. Ávalos, S. Aveic, C.A. Aveleira, T. Avin-Wittenberg, Y. Aydin, S. Ayton, S. Ayyadevara, M. Azzopardi, M. Baba, J.M. Backer, S.K. Backues, D.H. Bae, O.N. Bae, S.H. Bae, E.H. Baehrecke, A. Baek, S.H. Baek, S.H. Baek, G. Bagetta, A. Bagniewska-Zadworna, H. Bai, J. Bai, X. Bai, Y. Bai, N. Bairagi, S. Baksi, T. Balbi, C.T. Baldari, W. Balduini, A. Ballabio, M. Ballester, S. Balazadeh, R. Balzan, R. Bandopadhyay, S. Banerjee, S. Banerjee, Á. Bánréti, Y. Bao, M.S. Baptista, A. Baracca, C. Barbati, A. Bargiela, D. Barilà, P.G. Barlow, S.J. Barmada, E. Barreiro, G.E. Barreto, J. Bartek, B. Bartel, A. Bartolome, G.R. Barve, S.H. Basagoudanavar, D.C. Bassham, R.C. Bast, A. Basu, H. Batoko, I. Batten, E.E. Baulieu, B.L. Baumgarner, J. Bayry, R. Beale, I. Beau, F. Beaumatin, L.R.G. Bechara, G.R. Beck, M.F. Beers, J. Begun, C. Behrends, G.M.N. Behrens, R. Bei, E. Bejarano, S. Bel, C. Behl, A. Belaid, N. Belgareh-Touzé, C. Bellarosa, F. Belleudi, M. Belló Pérez, R. Bello-Morales, J.S.D.O. Beltran, S. Beltran, D.M. Benbrook, M. Bendorius, B.A. Benitez, I. Benito-Cuesta, J. Bensalem, M.W. Berchtold, S. Berezowska, D. Bergamaschi, M. Bergami, A. Bergmann, L. Berliocchi, C. Berlioz-Torrent, A. Bernard, L. Berthoux, C.G. Besirli, S. Besteiro, V.M. Betin, R. Beyaert, J.S. Bezbradica, K. Bhaskar, I. Bhatia-Kissova, R. Bhattacharya, S. Bhattacharya, S. Bhattacharyya, M.S. Bhuiyan, S.K. Bhutia, L. Bi, X. Bi, T.J. Biden, K. Bijian, V.A. Billes, N. Binart, C. Bincoletto, A.B. Birgisdottir, G. Bjorkoy, G. Blanco, A. Blas-Garcia, J. Blasiak, R. Blomgran, K. Blomgren, J.S. Blum, E. Boada-Romero, M. Boban, K. Boesze-Battaglia, P. Boeuf, B. Boland, P. Bomont, P. Bonaldo, S.R. Bonam, L. Bonfili, J.S. Bonifacino, B.A. Boone, M.D. Bootman, M. Bordi, C. Borner, B.C. Bornhauser, G. Borthakur, J. Bosch, S. Bose, L.M. Botana, J. Botas, C.M. Boulanger, M.E. Boulton, M. Bourdenx, B. Bourgeois, N.M. Bourke, G. Bousquet, P. Boya, P.V. Bozhkov, L.H.M. Bozi, T.O. Bozkurt, D.E. Brackney, C.H. Brandts, R.J. Braun, G.H. Braus, R. Bravo-Sagua, J.M. Bravo-San Pedro, P. Brest, M.A. Bringer, A. Briones-Herrera, V.C. Broaddus, P. Brodersen, J.L. Brodsky, S.L. Brody, P.G. Bronson, J.M. Bronstein, C.N. Brown, R.E. Brown, P.C. Brum, J.H. Brumell, N. Brunetti-Pierri, D. Bruno, R.J. Bryson-Richardson, C. Bucci, C. Buchrieser, M. Bueno, L.E. Buitrago-Molina, S. Buraschi, S. Buch, J.R. Buchan, E.M. Buckingham, H. Budak, M. Budini, G. Bultynck, F. Burada, J.R. Burgoyne, M.I. Burón, V. Bustos, S. Büttner, E. Butturini, A. Byrd, I. Cabas, S. Cabrera-Benitez, K. Cadwell, J. Cai, L. Cai, Q. Cai, M. Cairó, J.A. Calbet, G.A. Caldwell, K.A. Caldwell, J.A. Call, R. Calvani, A.C. Calvo, M. Calvo-Rubio Barrera, N.O.S. Camara, J.H. Camonis, N. Camougrand, M. Campanella, E.M. Campbell, F.X. Campbell-Valois, S. Campello, I. Campesi, J.C. Campos, O. Camuzard, J. Cancino, D. Candido De Almeida, L. Canesi, I. Caniggia, B. Canonico, C. Cantí, B. Cao, M. Caraglia, B. Caramés, E.H. Carchman, E. Cardenal-Muñoz, C. Cardenas, L. Cardenas, S.M. Cardoso, J.S. Carew, G.F. Carle, G. Carleton, S. Carloni, D. Carmona-Gutierrez, L.A. Carneiro, O. Carnevali, J.M. Carosi, S. Carra, A. Carrier, L. Carrier, B. Carroll, A.B. Carter, A.N. Carvalho, M. Casanova, C. Casas, J. Casas, C. Cassioli, E.F. Castillo, K. Castillo, S. Castillo-Lluva, F. Castoldi, M. Castori, A.F. Castro, M. Castro-Caldas, J. Castro-Hernandez, S. Castro-Obregon, S.D. Catz, C. Cavadas, F. Cavaliere, G. Cavallini, M. Cavinato, M.L. Cayuela, P. Cebollada Rica, V. Cecarini, F. Cecconi, M. Cechowska-Pasko, S. Cenci, V. Ceperuelo-Mallafré, J.J. Cerqueira, J.M. Cerutti, D. Cervia, V.B. Cetintas, S. Cetrullo, H.J. Chae, A.S. Chagin, C.Y. Chai, G. Chakrabarti, O. Chakrabarti, T. Chakraborty, T. Chakraborty, M. Chami, G. Chamilos, D.W. Chan, E.Y.W. Chan, E.D. Chan, H.Y.E. Chan, H.H. Chan, H. Chan, M.T.V. Chan, Y.S. Chan, P.K. Chandra, C.P. Chang, C. Chang, H.C. Chang, K. Chang, J. Chao, T. Chapman, N. Charlet-Berguerand, S. Chatterjee, S.K. Chaube, A. Chaudhary, S. Chauhan, E. Chaum, F. Checler, M.E. Cheetham, C.S. Chen, G.C. Chen, J.F. Chen, L.L. Chen, L. Chen, L. Chen, M. Chen, M.K. Chen, N. Chen, Q. Chen, R.H. Chen, S. Chen, W. Chen, W. Chen, X.M. Chen, X.W. Chen, X. Chen, Y. Chen, Y.G. Chen, Y. Chen, Y. Chen, Y.J. Chen, Y.Q. Chen, Z.S. Chen, Z. Chen, Z.H. Chen, Z.J. Chen, Z. Chen, H. Cheng, J. Cheng, S.Y. Cheng, W. Cheng, X. Cheng, X.T. Cheng, Y. Cheng, Z. Cheng, Z. Chen, H. Cheong, J.K. Cheong, B.V. Chernyak, S. Cherry, C.F.R. Cheung, C.H.A. Cheung, K.H. Cheung, E. Chevet, R.J. Chi, A.K.S. Chiang, F. Chiaradonna, R. Chiarelli, M. Chiariello, N. Chica, S. Chiocca, M. Chiong, S.H. Chiou, A.I. Chiramel, V. Chiurchiù, D.H. Cho, S.K. Choe, A.M.K. Choi, M.E. Choi, K.R. Choudhury, N.S. Chow, C.T. Chu, J.P. Chua, J.J.E. Chua, H. Chung, K.P. Chung, S. Chung, S.H. Chung, Y.L. Chung, V. Cianfanelli, I.A. Ciechomska, M. Cifuentes, L. Cinque, S. Cirak, M. Cirone, M.J. Clague, R. Clarke, E. Clementi, E.M. Coccia, P. Codogno, E. Cohen, M.M. Cohen, T. Colasanti, F. Colasuonno, R.A. Colbert, A. Colell, M. Čolić, N.S. Coll, M.O. Collins, M.I. Colombo, D.A. Colón-Ramos, L. Combaret, S. Comincini, M.R. Cominetti, A. Consiglio, A. Conte, F. Conti, V.R. Contu, M.R. Cookson, K.M. Coombs, I. Coppens, M.T. Corasaniti, D.P. Corkery, N. Cordes, K. Cortese, M.D.C. Costa, S. Costantino, P. Costelli, A. 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Yu, J. Yuan, L.Q. Yuan, S. Yuan, S.S.F. Yuan, Y. Yuan, Z. Yuan, J. Yue, Z. Yue, J. Yun, R.L. Yung, D.N. Zacks, G. Zaffagnini, V.O. Zambelli, I. Zanella, Q.S. Zang, S. Zanivan, S. Zappavigna, P. Zaragoza, K.S. Zarbalis, A. Zarebkohan, A. Zarrouk, S.O. Zeitlin, J. Zeng, J.D. Zeng, E. Žerovnik, L. Zhan, B. Zhang, D.D. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H. Zhang, H.L. Zhang, J. Zhang, J. Zhang, J.P. Zhang, K.Y.B. Zhang, L.W. Zhang, L. Zhang, L. Zhang, L. Zhang, L. Zhang, M. Zhang, P. Zhang, S. Zhang, W. Zhang, X. Zhang, X.W. Zhang, X. Zhang, X. Zhang, X. Zhang, X. Zhang, X.D. Zhang, Y. Zhang, Y. Zhang, Y. Zhang, Y.D. Zhang, Y. Zhang, Y.Y. Zhang, Y. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, Z. Zhang, H. Zhao, L. Zhao, S. Zhao, T. Zhao, X.F. Zhao, Y. Zhao, Y. Zhao, Y. Zhao, Y. Zhao, G. Zheng, K. Zheng, L. Zheng, S. Zheng, X.L. Zheng, Y. Zheng, Z.G. Zheng, B. Zhivotovsky, Q. Zhong, A. Zhou, B. Zhou, C. Zhou, G. Zhou, H. Zhou, H. Zhou, H. Zhou, J. Zhou, J. Zhou, J. Zhou, J. Zhou, K. Zhou, R. Zhou, X.J. Zhou, Y. Zhou, Y. Zhou, Y. Zhou, Z.Y. Zhou, Z. Zhou, B. Zhu, C. Zhu, G.Q. Zhu, H. Zhu, H. Zhu, H. Zhu, W.G. Zhu, Y. Zhu, Y. Zhu, H. Zhuang, X. Zhuang, K. Zientara-Rytter, C.M. Zimmermann, E. Ziviani, T. Zoladek, W.X. Zong, D.B. Zorov, A. Zorzano, W. Zou, Z. Zou, Z. Zou, S. Zuryn, W. Zwerschke, B. Brand-Saberi, X.C. Dong, C.S. Kenchappa, Z. Li, Y. Lin, S. Oshima, Y. Rong, J.C. Sluimer, C.L. Stallings, C.K. Tong, Autophagy 17 (2021) 1–382.","ieee":"D. J. Klionsky <i>et al.</i>, “Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition),” <i>Autophagy</i>, vol. 17, no. 1. Taylor &#38; Francis, pp. 1–382, 2021.","ista":"Klionsky DJ et al. 2021. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. 17(1), 1–382.","chicago":"Klionsky, Daniel J., Amal Kamal Abdel-Aziz, Sara Abdelfatah, Mahmoud Abdellatif, Asghar Abdoli, Steffen Abel, Hagai Abeliovich, et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” <i>Autophagy</i>. Taylor &#38; Francis, 2021. <a href=\"https://doi.org/10.1080/15548627.2020.1797280\">https://doi.org/10.1080/15548627.2020.1797280</a>.","mla":"Klionsky, Daniel J., et al. “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th Edition).” <i>Autophagy</i>, vol. 17, no. 1, Taylor &#38; Francis, 2021, pp. 1–382, doi:<a href=\"https://doi.org/10.1080/15548627.2020.1797280\">10.1080/15548627.2020.1797280</a>.","apa":"Klionsky, D. J., Abdel-Aziz, A. K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., … Tong, C. K. (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2020.1797280\">https://doi.org/10.1080/15548627.2020.1797280</a>"},"type":"journal_article","publisher":"Taylor & Francis","publication_status":"published","intvolume":"        17"},{"_id":"9992","project":[{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development"},{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"date_created":"2021-09-09T07:37:20Z","oa_version":"Published Version","file":[{"relation":"source_file","file_size":25179004,"checksum":"c763064adaa720e16066c1a4f9682bbb","date_created":"2021-09-09T07:29:48Z","embargo_to":"open_access","creator":"lhoermaye","file_name":"Thesis_vupload.docx","file_id":"9993","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2021-09-15T22:30:26Z","access_level":"closed"},{"file_name":"Thesis_vfinal_pdfa.pdf","embargo":"2021-09-09","creator":"lhoermaye","file_size":6246900,"date_created":"2021-09-09T14:25:08Z","checksum":"53911b06e93d7cdbbf4c7f4c162fa70f","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-09-15T22:30:26Z","file_id":"9996"}],"publication_identifier":{"issn":["2663-337X"]},"date_published":"2021-09-13T00:00:00Z","oa":1,"title":"Wound healing in the Arabidopsis root meristem","author":[{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","last_name":"Hörmayer","first_name":"Lukas"}],"alternative_title":["ISTA Thesis"],"ec_funded":1,"day":"13","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"degree_awarded":"PhD","OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-08T07:11:47Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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)"},"status":"public","publisher":"Institute of Science and Technology Austria","type":"dissertation","corr_author":"1","supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","has_accepted_license":"1","doi":"10.15479/at:ista:9992","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6943"},{"id":"8002","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6351"}]},"abstract":[{"lang":"eng","text":"Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells.\r\nFor answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally,\r\nthe major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation\r\nand this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. "}],"citation":{"short":"L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of Science and Technology Austria, 2021.","ama":"Hörmayer L. Wound healing in the Arabidopsis root meristem. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>","ista":"Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute of Science and Technology Austria.","chicago":"Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>.","ieee":"L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of Science and Technology Austria, 2021.","mla":"Hörmayer, Lukas. <i>Wound Healing in the Arabidopsis Root Meristem</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:9992\">10.15479/at:ista:9992</a>.","apa":"Hörmayer, L. (2021). <i>Wound healing in the Arabidopsis root meristem</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:9992\">https://doi.org/10.15479/at:ista:9992</a>"},"article_processing_charge":"No","file_date_updated":"2021-09-15T22:30:26Z","page":"168","month":"09","ddc":["575"],"year":"2021","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}]},{"has_accepted_license":"1","intvolume":"       303","publication_status":"published","publisher":"Elsevier","type":"journal_article","corr_author":"1","citation":{"apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>.","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>.","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750."},"abstract":[{"lang":"eng","text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy."}],"scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"11626","status":"public"},{"relation":"dissertation_contains","id":"10083","status":"public"}]},"doi":"10.1016/j.plantsci.2020.110750","month":"02","file_date_updated":"2021-02-04T07:49:25Z","article_processing_charge":"Yes (via OA deal)","isi":1,"language":[{"iso":"eng"}],"volume":303,"quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"year":"2021","ddc":["580"],"publication":"Plant Science","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2021-02-04T07:49:25Z","file_id":"9083","file_name":"2021_PlantScience_Gelova.pdf","creator":"dernst","file_size":12563728,"checksum":"a7f2562bdca62d67dfa88e271b62a629","date_created":"2021-02-04T07:49:25Z","relation":"main_file"}],"article_number":"110750","oa_version":"Published Version","date_created":"2020-12-09T14:48:28Z","pmid":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"_id":"8931","external_id":{"isi":["000614154500001"],"pmid":["33487339"]},"oa":1,"date_published":"2021-02-01T00:00:00Z","publication_identifier":{"issn":["0168-9452"]},"article_type":"original","acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","day":"01","department":[{"_id":"JiFr"},{"_id":"Bio"}],"ec_funded":1,"author":[{"id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","first_name":"Zuzana","last_name":"Gelová"},{"last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pernisová, Markéta","first_name":"Markéta","last_name":"Pernisová"},{"first_name":"Géraldine","last_name":"Brunoud","full_name":"Brunoud, Géraldine"},{"first_name":"Xixi","last_name":"Zhang","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Michalko","first_name":"Jaroslav","full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zlata","last_name":"Pavlovicova","full_name":"Pavlovicova, Zlata"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin"},{"last_name":"Hajny","first_name":"Jakub","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"last_name":"Čovanová","first_name":"Milada","full_name":"Čovanová, Milada"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xu, Tongda","first_name":"Tongda","last_name":"Xu"},{"full_name":"Vernoux, Teva","first_name":"Teva","last_name":"Vernoux"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"}],"title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-08-12T22:30:43Z","keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","last_name":"Narasimhan","first_name":"Madhumitha"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","first_name":"Lesia"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin","full_name":"Han, Huibin"},{"last_name":"Himschoot","first_name":"E","full_name":"Himschoot, E"},{"full_name":"Wang, R","first_name":"R","last_name":"Wang"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"last_name":"Sánchez-Simarro","first_name":"J","full_name":"Sánchez-Simarro, J"},{"last_name":"Aniento","first_name":"F","full_name":"Aniento, F"},{"last_name":"Adamowski","first_name":"Maciek","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking","department":[{"_id":"JiFr"}],"day":"01","ec_funded":1,"article_type":"original","acknowledgement":"We thank Ivan Kulik for developing the Chip’n’Dale apparatus with Lanxin Li; the IST machine shop and the Bioimaging facility for their excellent support; Matouš Glanc and Matyáš Fendrych for their valuable discussions and help; Barbara Casillas-Perez for her help with statistics. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 742985). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. ","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-08-12T22:30:44Z","status":"public","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"pmid":1,"_id":"9287","oa_version":"Published Version","date_created":"2021-03-26T12:08:38Z","file":[{"file_id":"10273","content_type":"application/pdf","success":1,"date_updated":"2021-11-11T15:07:51Z","access_level":"open_access","relation":"main_file","file_size":2289127,"date_created":"2021-11-11T15:07:51Z","checksum":"532bb9469d3b665907f06df8c383eade","creator":"cziletti","file_name":"2021_PlantPhysio_Narasimhan.pdf"}],"publication":"Plant Physiology","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"date_published":"2021-06-01T00:00:00Z","external_id":{"pmid":["33734402"],"isi":["000671555900031"]},"oa":1,"isi":1,"article_processing_charge":"Yes (in subscription journal)","issue":"2","page":"1122–1142","file_date_updated":"2021-11-11T15:07:51Z","month":"06","year":"2021","ddc":["580"],"quality_controlled":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"volume":186,"language":[{"iso":"eng"}],"type":"journal_article","corr_author":"1","publisher":"Oxford University Press","publication_status":"published","intvolume":"       186","has_accepted_license":"1","related_material":{"link":[{"url":"https://doi.org/10.1093/plphys/kiab380","relation":"erratum"}],"record":[{"relation":"dissertation_contains","id":"11626","status":"public"},{"status":"public","id":"10083","relation":"dissertation_contains"}]},"doi":"10.1093/plphys/kiab134","scopus_import":"1","abstract":[{"text":"The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the\r\nauxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural (IAA) and synthetic (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network (EE/TGN), rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using Total Internal Reflection Fluorescence (TIRF) microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus contributing to its\r\npolarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments. ","lang":"eng"}],"citation":{"chicago":"Narasimhan, Madhumitha, Michelle C Gallei, Shutang Tan, Alexander J Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez Solovey, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>.","ista":"Narasimhan M, Gallei MC, Tan S, Johnson AJ, Verstraeten I, Li L, Rodriguez Solovey L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. 2021. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. Plant Physiology. 186(2), 1122–1142.","ieee":"M. Narasimhan <i>et al.</i>, “Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking,” <i>Plant Physiology</i>, vol. 186, no. 2. Oxford University Press, pp. 1122–1142, 2021.","short":"M. Narasimhan, M.C. Gallei, S. Tan, A.J. Johnson, I. Verstraeten, L. Li, L. Rodriguez Solovey, H. Han, E. Himschoot, R. Wang, S. Vanneste, J. Sánchez-Simarro, F. Aniento, M. Adamowski, J. Friml, Plant Physiology 186 (2021) 1122–1142.","ama":"Narasimhan M, Gallei MC, Tan S, et al. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. 2021;186(2):1122–1142. doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>","mla":"Narasimhan, Madhumitha, et al. “Systematic Analysis of Specific and Nonspecific Auxin Effects on Endocytosis and Trafficking.” <i>Plant Physiology</i>, vol. 186, no. 2, Oxford University Press, 2021, pp. 1122–1142, doi:<a href=\"https://doi.org/10.1093/plphys/kiab134\">10.1093/plphys/kiab134</a>.","apa":"Narasimhan, M., Gallei, M. C., Tan, S., Johnson, A. J., Verstraeten, I., Li, L., … Friml, J. (2021). Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiab134\">https://doi.org/10.1093/plphys/kiab134</a>"}},{"doi":"10.15479/at:ista:10083","related_material":{"record":[{"status":"public","id":"442","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6627","status":"public"},{"relation":"part_of_dissertation","id":"8931","status":"public"},{"relation":"part_of_dissertation","id":"8986","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10095"},{"id":"8283","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"9287","relation":"part_of_dissertation"},{"id":"10015","relation":"part_of_dissertation","status":"public"}]},"citation":{"apa":"Li, L. (2021). <i>Rapid cell growth regulation in Arabidopsis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>","mla":"Li, Lanxin. <i>Rapid Cell Growth Regulation in Arabidopsis</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>.","short":"L. Li, Rapid Cell Growth Regulation in Arabidopsis, Institute of Science and Technology Austria, 2021.","ama":"Li L. Rapid cell growth regulation in Arabidopsis. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10083\">10.15479/at:ista:10083</a>","ieee":"L. Li, “Rapid cell growth regulation in Arabidopsis,” Institute of Science and Technology Austria, 2021.","chicago":"Li, Lanxin. “Rapid Cell Growth Regulation in Arabidopsis.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10083\">https://doi.org/10.15479/at:ista:10083</a>.","ista":"Li L. 2021. Rapid cell growth regulation in Arabidopsis. Institute of Science and Technology Austria."},"abstract":[{"lang":"eng","text":"Plant motions occur across a wide spectrum of timescales, ranging from seed dispersal through bursting (milliseconds) and stomatal opening (minutes) to long-term adaptation of gross architecture. Relatively fast motions include water-driven growth as exemplified by root cell expansion under abiotic/biotic stresses or during gravitropism. A showcase is a root growth inhibition in 30 seconds triggered by the phytohormone auxin. However, the cellular and molecular mechanisms are still largely unknown. This thesis covers the studies about this topic as follows. By taking advantage of microfluidics combined with live imaging, pharmaceutical tools, and transgenic lines, we examined the kinetics of and causal relationship among various auxininduced rapid cellular changes in root growth, apoplastic pH, cytosolic Ca2+, cortical microtubule (CMT) orientation, and vacuolar morphology. We revealed that CMT reorientation and vacuolar constriction are the consequence of growth itself instead of responding directly to auxin. In contrast, auxin induces apoplast alkalinization to rapidly inhibit root growth in 30 seconds. This auxin-triggered apoplast alkalinization results from rapid H+- influx that is contributed by Ca2+ inward channel CYCLIC NUCLEOTIDE-GATED CHANNEL 14 (CNGC14)-dependent Ca2+ signaling. To dissect which auxin signaling mediates the rapid apoplast alkalinization, we\r\ncombined microfluidics and genetic engineering to verify that TIR1/AFB receptors conduct a non-transcriptional regulation on Ca2+ and H+ -influx. This non-canonical pathway is mostly mediated by the cytosolic portion of TIR1/AFB. On the other hand, we uncovered, using biochemical and phospho-proteomic analysis, that auxin cell surface signaling component TRANSMEMBRANE KINASE 1 (TMK1) plays a negative role during auxin-trigger apoplast\r\nalkalinization and root growth inhibition through directly activating PM H+ -ATPases. Therefore, we discovered that PM H+ -ATPases counteract instead of mediate the auxintriggered rapid H+ -influx, and that TIR1/AFB and TMK1 regulate root growth antagonistically. This opposite effect of TIR1/AFB and TMK1 is consistent during auxin-induced hypocotyl elongation, leading us to explore the relation of two signaling pathways. Assisted with biochemistry and fluorescent imaging, we verified for the first time that TIR1/AFB and TMK1 can interact with each other. The ability of TIR1/AFB binding to membrane lipid provides a basis for the interaction of plasma membrane- and cytosol-localized proteins.\r\nBesides, transgenic analysis combined with genetic engineering and biochemistry showed that  vi\r\nthey do function in the same pathway. Particularly, auxin-induced TMK1 increase is TIR1/AFB dependent, suggesting TIR1/AFB regulation on TMK1. Conversely, TMK1 also regulates TIR1/AFB protein levels and thus auxin canonical signaling. To follow the study of rapid growth regulation, we analyzed another rapid growth regulator, signaling peptide RALF1. We showed that RALF1 also triggers a rapid and reversible growth inhibition caused by H + influx, highly resembling but not dependent on auxin. Besides, RALF1 promotes auxin biosynthesis by increasing expression of auxin biosynthesis enzyme YUCCAs and thus induces auxin signaling in ca. 1 hour, contributing to the sustained RALF1-triggered growth inhibition. These studies collectively contribute to understanding rapid regulation on plant cell\r\ngrowth, novel auxin signaling pathway as well as auxin-peptide crosstalk. "}],"publication_status":"published","type":"dissertation","publisher":"Institute of Science and Technology Austria","corr_author":"1","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"has_accepted_license":"1","ddc":["575"],"year":"2021","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"10","file_date_updated":"2022-12-20T23:30:03Z","date_published":"2021-10-06T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"oa":1,"date_created":"2021-10-04T13:33:10Z","oa_version":"Published Version","_id":"10083","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"file":[{"file_size":8616142,"checksum":"3b2f55b3b8ae05337a0dcc1cd8595b10","date_created":"2021-10-14T08:00:07Z","relation":"main_file","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014_pdftron.pdf","embargo":"2022-10-14","creator":"cchlebak","file_id":"10138","access_level":"open_access","content_type":"application/pdf","date_updated":"2022-12-20T23:30:03Z"},{"date_updated":"2022-12-20T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"10139","creator":"cchlebak","embargo_to":"open_access","file_name":"0._IST_Austria_Thesis_Lanxin_Li_1014.docx","relation":"source_file","date_created":"2021-10-14T08:00:13Z","checksum":"f23ed258ca894f6aabf58b0c128bf242","file_size":15058499}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_updated":"2026-04-16T12:20:41Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","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)"},"title":"Rapid cell growth regulation in Arabidopsis","author":[{"last_name":"Li","first_name":"Lanxin","full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","OA_place":"publisher","ec_funded":1,"day":"06","department":[{"_id":"GradSch"},{"_id":"JiFr"}]},{"oa":1,"external_id":{"isi":["000676604700001"],"pmid":["34359847"]},"publication_identifier":{"issn":["2073-4409"]},"date_published":"2021-07-02T00:00:00Z","file":[{"access_level":"open_access","date_updated":"2021-09-16T09:07:06Z","content_type":"application/pdf","success":1,"file_id":"10021","file_name":"2021_Cells_Nikonorova.pdf","creator":"cchlebak","date_created":"2021-09-16T09:07:06Z","checksum":"2a9f534b9c2200e72e2cde95afaf4eed","file_size":2667848,"relation":"main_file"}],"publication":"Cells","_id":"10015","pmid":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"}],"date_created":"2021-09-14T11:36:20Z","oa_version":"Published Version","article_number":"1665 ","date_updated":"2026-08-12T22:30:44Z","keyword":["primary root","(phospho)proteomics","auxin","(receptor) kinase"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"department":[{"_id":"JiFr"}],"day":"02","acknowledgement":"We thank the Nottingham Stock Centre for seeds, Frank Van Breusegem for the phb3 mutant, and Herman Höfte for the the1 mutant. Open Access Funding by the Austrian Science Fund (FWF).","article_type":"original","title":"The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators","author":[{"first_name":"N","last_name":"Nikonorova","full_name":"Nikonorova, N"},{"full_name":"Murphy, E","first_name":"E","last_name":"Murphy"},{"last_name":"Fonseca de Lima","first_name":"CF","full_name":"Fonseca de Lima, CF"},{"last_name":"Zhu","first_name":"S","full_name":"Zhu, S"},{"full_name":"van de Cotte, B","first_name":"B","last_name":"van de Cotte"},{"full_name":"Vu, LD","last_name":"Vu","first_name":"LD"},{"full_name":"Balcerowicz, D","last_name":"Balcerowicz","first_name":"D"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"X","last_name":"Kong","full_name":"Kong, X"},{"last_name":"De Rop","first_name":"G","full_name":"De Rop, G"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vissenberg","first_name":"K","full_name":"Vissenberg, K"},{"full_name":"Morris, PC","last_name":"Morris","first_name":"PC"},{"first_name":"Z","last_name":"Ding","full_name":"Ding, Z"},{"full_name":"De Smet, I","first_name":"I","last_name":"De Smet"}],"alternative_title":["Protein Phosphorylation and Cell Signaling in Plants"],"abstract":[{"text":"Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxincontrolled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2\r\nThr31 phosphorylation site for growth regulation in the Arabidopsis root tip.","lang":"eng"}],"citation":{"apa":"Nikonorova, N., Murphy, E., Fonseca de Lima, C., Zhu, S., van de Cotte, B., Vu, L., … De Smet, I. (2021). The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071665\">https://doi.org/10.3390/cells10071665</a>","mla":"Nikonorova, N., et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” <i>Cells</i>, vol. 10, 1665, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071665\">10.3390/cells10071665</a>.","ama":"Nikonorova N, Murphy E, Fonseca de Lima C, et al. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. <i>Cells</i>. 2021;10. doi:<a href=\"https://doi.org/10.3390/cells10071665\">10.3390/cells10071665</a>","short":"N. Nikonorova, E. Murphy, C. Fonseca de Lima, S. Zhu, B. van de Cotte, L. Vu, D. Balcerowicz, L. Li, X. Kong, G. De Rop, T. Beeckman, J. Friml, K. Vissenberg, P. Morris, Z. Ding, I. De Smet, Cells 10 (2021).","ieee":"N. Nikonorova <i>et al.</i>, “The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators,” <i>Cells</i>, vol. 10. MDPI, 2021.","chicago":"Nikonorova, N, E Murphy, CF Fonseca de Lima, S Zhu, B van de Cotte, LD Vu, D Balcerowicz, et al. “The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071665\">https://doi.org/10.3390/cells10071665</a>.","ista":"Nikonorova N, Murphy E, Fonseca de Lima C, Zhu S, van de Cotte B, Vu L, Balcerowicz D, Li L, Kong X, De Rop G, Beeckman T, Friml J, Vissenberg K, Morris P, Ding Z, De Smet I. 2021. The Arabidopsis root tip (phospho)proteomes at growth-promoting versus growth-repressing conditions reveal novel root growth regulators. Cells. 10, 1665."},"doi":"10.3390/cells10071665","related_material":{"record":[{"status":"public","id":"10083","relation":"dissertation_contains"}]},"scopus_import":"1","intvolume":"        10","has_accepted_license":"1","publisher":"MDPI","type":"journal_article","publication_status":"published","volume":10,"language":[{"iso":"eng"}],"ddc":["575"],"year":"2021","quality_controlled":"1","file_date_updated":"2021-09-16T09:07:06Z","month":"07","isi":1,"article_processing_charge":"Yes"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-08-12T22:30:43Z","author":[{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Roosjen","first_name":"Mark","full_name":"Roosjen, Mark"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"orcid":"0000-0002-7244-7237","full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jian","last_name":"Chen","full_name":"Chen, Jian"},{"first_name":"Lana","last_name":"Shabala","full_name":"Shabala, Lana"},{"full_name":"Smet, Wouter","last_name":"Smet","first_name":"Wouter"},{"last_name":"Ren","first_name":"Hong","full_name":"Ren, Hong"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"last_name":"Shabala","first_name":"Sergey","full_name":"Shabala, Sergey"},{"full_name":"De Rybel, Bert","first_name":"Bert","last_name":"De Rybel"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"first_name":"William M.","last_name":"Gray","full_name":"Gray, William M."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"title":"Cell surface and intracellular auxin signalling for H+-fluxes in root growth","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"acknowledgement":"We thank Nataliia Gnyliukh and Lukas Hörmayer for technical assistance and Nadine Paris for sharing PM-Cyto seeds. We gratefully acknowledge Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001.), the Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910),  the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., the China Scholarship Council to J.C.","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"day":"09","ec_funded":1,"date_published":"2021-09-09T00:00:00Z","publication_identifier":{"issn":["2693-5015"]},"oa":1,"article_number":"266395","oa_version":"Preprint","date_created":"2021-10-06T08:56:22Z","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root"}],"_id":"10095","publication":"Research Square","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"year":"2021","language":[{"iso":"eng"}],"article_processing_charge":"No","month":"09","related_material":{"record":[{"id":"10223","relation":"later_version","status":"public"},{"id":"10083","relation":"dissertation_contains","status":"public"}]},"doi":"10.21203/rs.3.rs-266395/v3","citation":{"mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, 266395, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (n.d.). Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Research Square (n.d.).","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">10.21203/rs.3.rs-266395/v3</a>","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H+-fluxes in root growth,” <i>Research Square</i>. .","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H+-fluxes in root growth. Research Square, 266395.","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+-Fluxes in Root Growth.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-266395/v3\">https://doi.org/10.21203/rs.3.rs-266395/v3</a>."},"abstract":[{"text":"Growth regulation tailors plant development to its environment. A showcase is response to gravity, where shoots bend up and roots down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots, while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phospho-proteomics in Arabidopsis thaliana, we advance our understanding how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on the rapid regulation of the apoplastic pH, a causative growth determinant. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+-influx, causing apoplast alkalinisation. The simultaneous activation of these two counteracting mechanisms poises the root for a rapid, fine-tuned growth modulation while navigating complex soil environment.","lang":"eng"}],"publication_status":"draft","corr_author":"1","type":"preprint"},{"volume":40,"language":[{"iso":"eng"}],"ddc":["580"],"year":"2021","acknowledged_ssus":[{"_id":"Bio"}],"quality_controlled":"1","file_date_updated":"2021-02-11T12:28:29Z","issue":"3","month":"02","isi":1,"article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.","lang":"eng"}],"citation":{"apa":"Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R., … Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>","mla":"Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>, vol. 40, no. 3, e106862, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>.","short":"K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli, J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A. Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).","ama":"Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. <i>EMBO Journal</i>. 2021;40(3). doi:<a href=\"https://doi.org/10.15252/embj.2020106862\">10.15252/embj.2020106862</a>","ista":"Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L, Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO Journal. 40(3), e106862.","chicago":"Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2020106862\">https://doi.org/10.15252/embj.2020106862</a>.","ieee":"K. Ötvös <i>et al.</i>, “Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport,” <i>EMBO Journal</i>, vol. 40, no. 3. Embo Press, 2021."},"doi":"10.15252/embj.2020106862","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/","description":"News on IST Homepage"}],"record":[{"id":"10303","relation":"dissertation_contains","status":"public"}]},"scopus_import":"1","intvolume":"        40","has_accepted_license":"1","publisher":"Embo Press","type":"journal_article","corr_author":"1","publication_status":"published","date_updated":"2026-08-12T22:30:48Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"01","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"acknowledgement":"We acknowledge Gergely Molnar for critical reading of the manuscript, Alexander Johnson for language editing and Yulija Salanenka for technical assistance. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund (FWF): I03630 to J.F","article_type":"original","author":[{"last_name":"Ötvös","first_name":"Krisztina","full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marconi, Marco","last_name":"Marconi","first_name":"Marco"},{"full_name":"Vega, Andrea","first_name":"Andrea","last_name":"Vega"},{"last_name":"O’Brien","first_name":"Jose","full_name":"O’Brien, Jose"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson"},{"id":"4827E134-F248-11E8-B48F-1D18A9856A87","first_name":"Rashed","last_name":"Abualia","full_name":"Abualia, Rashed","orcid":"0000-0002-9357-9415"},{"first_name":"Livio","last_name":"Antonielli","full_name":"Antonielli, Livio"},{"orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C","first_name":"Juan C","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","last_name":"Cuesta","first_name":"Candela"},{"last_name":"Artner","first_name":"Christina","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bouguyon","first_name":"Eleonore","full_name":"Bouguyon, Eleonore"},{"full_name":"Gojon, Alain","first_name":"Alain","last_name":"Gojon"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Gutiérrez","first_name":"Rodrigo A.","full_name":"Gutiérrez, Rodrigo A."},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","last_name":"Wabnik","first_name":"Krzysztof T"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport","oa":1,"external_id":{"isi":["000604645600001"],"pmid":[" 33399250"]},"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"date_published":"2021-02-01T00:00:00Z","file":[{"relation":"main_file","checksum":"dc55c900f3b061d6c2790b8813d759a3","date_created":"2021-02-11T12:28:29Z","file_size":2358617,"creator":"dernst","file_name":"2021_Embo_Otvos.pdf","file_id":"9110","date_updated":"2021-02-11T12:28:29Z","success":1,"content_type":"application/pdf","access_level":"open_access"}],"publication":"EMBO Journal","_id":"9010","pmid":1,"project":[{"_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"},{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"date_created":"2021-01-17T23:01:12Z","article_number":"e106862","oa_version":"Published Version"},{"acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","article_type":"original","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"day":"14","title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","author":[{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","last_name":"Johnson","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"last_name":"Dahhan","first_name":"Dana A","full_name":"Dahhan, Dana A"},{"first_name":"Nataliia","last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9438-4783","full_name":"Zheden, Vanessa","first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tommaso","last_name":"Costanzo","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425"},{"first_name":"Pierre","last_name":"Mahou","full_name":"Mahou, Pierre"},{"full_name":"Hrtyan, Mónika","last_name":"Hrtyan","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jie","last_name":"Wang","full_name":"Wang, Jie"},{"full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","last_name":"Aguilera Servin","first_name":"Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87"},{"last_name":"van Damme","first_name":"Daniël","full_name":"van Damme, Daniël"},{"first_name":"Emmanuel","last_name":"Beaurepaire","full_name":"Beaurepaire, Emmanuel"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose"},{"full_name":"Bednarek, Sebastian Y","first_name":"Sebastian Y","last_name":"Bednarek"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"}],"status":"public","date_updated":"2026-08-12T22:30:51Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the National Academy of Sciences of the United States of America","file":[{"file_id":"10546","access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2021-12-15T08:59:40Z","file_size":2757340,"date_created":"2021-12-15T08:59:40Z","checksum":"8d01e72e22c4fb1584e72d8601947069","relation":"main_file","file_name":"2021_PNAS_Johnson.pdf","creator":"cchlebak"}],"date_created":"2021-08-11T14:11:43Z","article_number":"e2113046118","oa_version":"Published Version","_id":"9887","pmid":1,"project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"date_published":"2021-12-14T00:00:00Z","publication_identifier":{"eissn":["1091-6490"]},"month":"12","file_date_updated":"2021-12-15T08:59:40Z","issue":"51","article_processing_charge":"No","isi":1,"language":[{"iso":"eng"}],"volume":118,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"quality_controlled":"1","ddc":["580"],"year":"2021","has_accepted_license":"1","intvolume":"       118","publication_status":"published","type":"journal_article","corr_author":"1","publisher":"National Academy of Sciences","citation":{"chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences of the United States of America. 118(51), e2113046118.","ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51. National Academy of Sciences, 2021.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>."},"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells."}],"scopus_import":"1","doi":"10.1073/pnas.2113046118","related_material":{"record":[{"status":"public","relation":"research_data","id":"14988"},{"status":"public","relation":"dissertation_contains","id":"14510"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.04.26.441441"}]}},{"publication":"Plants","file":[{"creator":"dernst","file_name":"2020_Plants_Moturu.pdf","relation":"main_file","date_created":"2020-03-23T13:37:00Z","checksum":"6d5af3e17266a48996b4af4e67e88a85","file_size":2373484,"date_updated":"2020-07-14T12:48:00Z","content_type":"application/pdf","access_level":"open_access","file_id":"7614"}],"oa_version":"Published Version","article_number":"299","date_created":"2020-03-15T23:00:52Z","pmid":1,"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"_id":"7582","external_id":{"isi":["000525315000035"],"pmid":["32121542"]},"oa":1,"date_published":"2020-03-01T00:00:00Z","publication_identifier":{"eissn":["2223-7747"]},"article_type":"original","department":[{"_id":"JiFr"}],"day":"01","ec_funded":1,"title":"Molecular evolution and diversification of proteins involved in miRNA maturation pathway","author":[{"last_name":"Moturu","first_name":"Taraka Ramji","full_name":"Moturu, Taraka Ramji"},{"full_name":"Sinha, Sansrity","first_name":"Sansrity","last_name":"Sinha"},{"full_name":"Salava, Hymavathi","first_name":"Hymavathi","last_name":"Salava"},{"first_name":"Sravankumar","last_name":"Thula","full_name":"Thula, Sravankumar"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"full_name":"Vařeková, Radka Svobodová","last_name":"Vařeková","first_name":"Radka Svobodová"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"}],"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-02T14:35:47Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","intvolume":"         9","publication_status":"published","type":"journal_article","publisher":"MDPI","corr_author":"1","citation":{"mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” <i>Plants</i>, vol. 9, no. 3, 299, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/plants9030299\">10.3390/plants9030299</a>.","apa":"Moturu, T. R., Sinha, S., Salava, H., Thula, S., Nodzyński, T., Vařeková, R. S., … Simon, S. (2020). Molecular evolution and diversification of proteins involved in miRNA maturation pathway. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants9030299\">https://doi.org/10.3390/plants9030299</a>","ista":"Moturu TR, Sinha S, Salava H, Thula S, Nodzyński T, Vařeková RS, Friml J, Simon S. 2020. Molecular evolution and diversification of proteins involved in miRNA maturation pathway. Plants. 9(3), 299.","ieee":"T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of proteins involved in miRNA maturation pathway,” <i>Plants</i>, vol. 9, no. 3. MDPI, 2020.","chicago":"Moturu, Taraka Ramji, Sansrity Sinha, Hymavathi Salava, Sravankumar Thula, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” <i>Plants</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/plants9030299\">https://doi.org/10.3390/plants9030299</a>.","short":"T.R. Moturu, S. Sinha, H. Salava, S. Thula, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Plants 9 (2020).","ama":"Moturu TR, Sinha S, Salava H, et al. Molecular evolution and diversification of proteins involved in miRNA maturation pathway. <i>Plants</i>. 2020;9(3). doi:<a href=\"https://doi.org/10.3390/plants9030299\">10.3390/plants9030299</a>"},"abstract":[{"text":"Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase II, regulate the expression of genes involved in a multitude of processes in eukaryotes. miRNA biogenesis and the proteins involved in the biogenesis pathway differ across plant and animal lineages. The major proteins constituting the biogenesis pathway, namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied. However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH)) of the pathway that differs across the two lineages remain largely uncharacterized. We present the first detailed report on the molecular evolution and divergence of these proteins across eukaryotes. Although DDL is present in eukaryotes and prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which correlates with the differences in miRNA length across the two lineages. Our data enhance the current understanding of the structure–function relationship of these proteins and reveals previous unexplored crucial residues in the three proteins that can be used as a basis for further functional characterization. The data presented here on the number of miRNAs in crown eukaryotic lineages are consistent with the notion of the expansion of the number of miRNA-coding genes in animal and plant lineages correlating with organismal complexity. Whether this difference in functionally correlates with the diversification (or presence/absence) of the three proteins studied here or the miRNA signaling in the plant and animal lineages is unclear. Based on our results of the three proteins studied here and previously available data concerning the evolution of miRNA genes in the plant and animal lineages, we believe that miRNAs probably evolved once in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes.","lang":"eng"}],"scopus_import":"1","doi":"10.3390/plants9030299","month":"03","issue":"3","file_date_updated":"2020-07-14T12:48:00Z","article_processing_charge":"No","isi":1,"language":[{"iso":"eng"}],"volume":9,"quality_controlled":"1","ddc":["580"],"year":"2020"},{"scopus_import":"1","related_material":{"link":[{"url":"https://doi.org/10.1038/s41477-020-0719-y","relation":"erratum"}]},"doi":"10.1038/s41477-020-0648-9","citation":{"chicago":"Tan, Shutang, Xixi Zhang, Wei Kong, Xiao-Li Yang, Gergely Molnar, Zuzana Vondráková, Roberta Filepová, Jan Petrášek, Jiří Friml, and Hong-Wei Xue. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux in Arabidopsis.” <i>Nature Plants</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41477-020-0648-9\">https://doi.org/10.1038/s41477-020-0648-9</a>.","ieee":"S. Tan <i>et al.</i>, “The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis,” <i>Nature Plants</i>, vol. 6. Springer Nature, pp. 556–569, 2020.","ista":"Tan S, Zhang X, Kong W, Yang X-L, Molnar G, Vondráková Z, Filepová R, Petrášek J, Friml J, Xue H-W. 2020. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. Nature Plants. 6, 556–569.","short":"S. Tan, X. Zhang, W. Kong, X.-L. Yang, G. Molnar, Z. Vondráková, R. Filepová, J. Petrášek, J. Friml, H.-W. Xue, Nature Plants 6 (2020) 556–569.","ama":"Tan S, Zhang X, Kong W, et al. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. <i>Nature Plants</i>. 2020;6:556-569. doi:<a href=\"https://doi.org/10.1038/s41477-020-0648-9\">10.1038/s41477-020-0648-9</a>","apa":"Tan, S., Zhang, X., Kong, W., Yang, X.-L., Molnar, G., Vondráková, Z., … Xue, H.-W. (2020). The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-020-0648-9\">https://doi.org/10.1038/s41477-020-0648-9</a>","mla":"Tan, Shutang, et al. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux in Arabidopsis.” <i>Nature Plants</i>, vol. 6, Springer Nature, 2020, pp. 556–69, doi:<a href=\"https://doi.org/10.1038/s41477-020-0648-9\">10.1038/s41477-020-0648-9</a>."},"abstract":[{"lang":"eng","text":"Directional intercellular transport of the phytohormone auxin mediated by PIN FORMED (PIN) efflux carriers plays essential roles in both coordinating patterning processes and integrating multiple external cues by rapidly redirecting auxin fluxes. Multilevel regulations of PIN activity under internal and external cues are complicated; however, the underlying molecular mechanism remains elusive. Here we demonstrate that 3’-Phosphoinositide-Dependent Protein Kinase1 (PDK1), which is conserved in plants and mammals, functions as a molecular hub integrating the upstream lipid signalling and the downstream substrate activity through phosphorylation. Genetic analysis uncovers that loss-of-function Arabidopsis mutant pdk1.1 pdk1.2 exhibits a plethora of abnormalities in organogenesis and growth, due to the defective PIN-dependent auxin transport. Further cellular and biochemical analyses reveal that PDK1 phosphorylates D6 Protein Kinase to facilitate its activity towards PIN proteins. Our studies establish a lipid-dependent phosphorylation cascade connecting membrane composition-based cellular signalling with plant growth and patterning by regulating morphogenetic auxin fluxes."}],"publication_status":"published","publisher":"Springer Nature","type":"journal_article","intvolume":"         6","quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"year":"2020","language":[{"iso":"eng"}],"volume":6,"article_processing_charge":"No","isi":1,"month":"05","page":"556-569","date_published":"2020-05-01T00:00:00Z","publication_identifier":{"eissn":["2055-0278"]},"external_id":{"isi":["000531787500006"],"pmid":["32393881"]},"oa":1,"oa_version":"Preprint","date_created":"2020-03-21T16:34:16Z","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis","grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425"}],"pmid":1,"_id":"7600","publication":"Nature Plants","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_updated":"2026-04-02T11:50:26Z","author":[{"last_name":"Tan","first_name":"Shutang","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","last_name":"Zhang","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi"},{"last_name":"Kong","first_name":"Wei","full_name":"Kong, Wei"},{"full_name":"Yang, Xiao-Li","last_name":"Yang","first_name":"Xiao-Li"},{"full_name":"Molnar, Gergely","first_name":"Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vondráková, Zuzana","last_name":"Vondráková","first_name":"Zuzana"},{"full_name":"Filepová, Roberta","first_name":"Roberta","last_name":"Filepová"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"},{"first_name":"Hong-Wei","last_name":"Xue","full_name":"Xue, Hong-Wei"}],"title":"The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis","main_file_link":[{"url":"https://doi.org/10.1101/755504","open_access":"1"}],"article_type":"original","department":[{"_id":"JiFr"}],"day":"01","ec_funded":1},{"article_type":"original","ec_funded":1,"department":[{"_id":"JiFr"}],"day":"01","author":[{"first_name":"Xixi","last_name":"Zhang","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A"},{"last_name":"Adamowski","first_name":"Maciek","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marhavá","first_name":"Petra","full_name":"Marhavá, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"},{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","last_name":"Zhang","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"last_name":"Pukyšová","first_name":"Vendula","full_name":"Pukyšová, Vendula"},{"last_name":"Sánchez","first_name":"Adrià Sans","full_name":"Sánchez, Adrià Sans"},{"full_name":"Raxwal, Vivek Kumar","last_name":"Raxwal","first_name":"Vivek Kumar"},{"full_name":"Hardtke, Christian S.","first_name":"Christian S.","last_name":"Hardtke"},{"last_name":"Nodzynski","first_name":"Tomasz","full_name":"Nodzynski, Tomasz"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"main_file_link":[{"url":"https://doi.org/10.1105/tpc.19.00869","open_access":"1"}],"title":"Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters","status":"public","date_updated":"2026-06-18T19:24:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"The Plant Cell","date_created":"2020-03-28T07:39:22Z","oa_version":"Published Version","_id":"7619","pmid":1,"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"oa":1,"external_id":{"isi":["000545741500030"],"pmid":["32193204"]},"date_published":"2020-05-01T00:00:00Z","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"month":"05","issue":"5","page":"1644-1664","article_processing_charge":"No","isi":1,"language":[{"iso":"eng"}],"volume":32,"acknowledged_ssus":[{"_id":"Bio"}],"quality_controlled":"1","ddc":["580"],"year":"2020","intvolume":"        32","publication_status":"published","type":"journal_article","publisher":"American Society of Plant Biologists","corr_author":"1","citation":{"ama":"Zhang X, Adamowski M, Marhavá P, et al. Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. <i>The Plant Cell</i>. 2020;32(5):1644-1664. doi:<a href=\"https://doi.org/10.1105/tpc.19.00869\">10.1105/tpc.19.00869</a>","short":"X. Zhang, M. Adamowski, P. Marhavá, S. Tan, Y. Zhang, L. Rodriguez Solovey, M. Zwiewka, V. Pukyšová, A.S. Sánchez, V.K. Raxwal, C.S. Hardtke, T. Nodzynski, J. Friml, The Plant Cell 32 (2020) 1644–1664.","ieee":"X. Zhang <i>et al.</i>, “Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters,” <i>The Plant Cell</i>, vol. 32, no. 5. American Society of Plant Biologists, pp. 1644–1664, 2020.","chicago":"Zhang, Xixi, Maciek Adamowski, Petra Marhavá, Shutang Tan, Yuzhou Zhang, Lesia Rodriguez Solovey, Marta Zwiewka, et al. “Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters.” <i>The Plant Cell</i>. American Society of Plant Biologists, 2020. <a href=\"https://doi.org/10.1105/tpc.19.00869\">https://doi.org/10.1105/tpc.19.00869</a>.","ista":"Zhang X, Adamowski M, Marhavá P, Tan S, Zhang Y, Rodriguez Solovey L, Zwiewka M, Pukyšová V, Sánchez AS, Raxwal VK, Hardtke CS, Nodzynski T, Friml J. 2020. Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. 32(5), 1644–1664.","apa":"Zhang, X., Adamowski, M., Marhavá, P., Tan, S., Zhang, Y., Rodriguez Solovey, L., … Friml, J. (2020). Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. <i>The Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.19.00869\">https://doi.org/10.1105/tpc.19.00869</a>","mla":"Zhang, Xixi, et al. “Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters.” <i>The Plant Cell</i>, vol. 32, no. 5, American Society of Plant Biologists, 2020, pp. 1644–64, doi:<a href=\"https://doi.org/10.1105/tpc.19.00869\">10.1105/tpc.19.00869</a>."},"abstract":[{"lang":"eng","text":"Cell polarity is a fundamental feature of all multicellular organisms. In plants, prominent cell polarity markers are PIN auxin transporters crucial for plant development. To identify novel components involved in cell polarity establishment and maintenance, we carried out a forward genetic screening with PIN2:PIN1-HA;pin2 Arabidopsis plants, which ectopically express predominantly basally localized PIN1 in the root epidermal cells leading to agravitropic root growth. From the screen, we identified the regulator of PIN polarity 12 (repp12) mutation, which restored gravitropic root growth and caused PIN1-HA polarity switch from basal to apical side of root epidermal cells. Complementation experiments established the repp12 causative mutation as an amino acid substitution in Aminophospholipid ATPase3 (ALA3), a phospholipid flippase with predicted function in vesicle formation. ala3 T-DNA mutants show defects in many auxin-regulated processes, in asymmetric auxin distribution and in PIN trafficking. Analysis of quintuple and sextuple mutants confirmed a crucial role of ALA proteins in regulating plant development and in PIN trafficking and polarity. Genetic and physical interaction studies revealed that ALA3 functions together with GNOM and BIG3 ARF GEFs. Taken together, our results identified ALA3 flippase as an important interactor and regulator of ARF GEF functioning in PIN polarity, trafficking and auxin-mediated development."}],"scopus_import":"1","doi":"10.1105/tpc.19.00869"},{"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2024-10-21T06:02:26Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","day":"06","department":[{"_id":"JiFr"}],"author":[{"full_name":"Lee, E","last_name":"Lee","first_name":"E"},{"full_name":"Vila Nova Santana, B","last_name":"Vila Nova Santana","first_name":"B"},{"first_name":"E","last_name":"Samuels","full_name":"Samuels, E"},{"last_name":"Benitez-Fuente","first_name":"F","full_name":"Benitez-Fuente, F"},{"full_name":"Corsi, E","last_name":"Corsi","first_name":"E"},{"full_name":"Botella, MA","first_name":"MA","last_name":"Botella"},{"first_name":"J","last_name":"Perez-Sancho","full_name":"Perez-Sancho, J"},{"full_name":"Vanneste, S","first_name":"S","last_name":"Vanneste"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Macho, A","last_name":"Macho","first_name":"A"},{"last_name":"Alves Azevedo","first_name":"A","full_name":"Alves Azevedo, A"},{"last_name":"Rosado","first_name":"A","full_name":"Rosado, A"}],"title":"Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis","external_id":{"pmid":["32179893"],"isi":["000553125400007"]},"oa":1,"date_published":"2020-07-06T00:00:00Z","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"publication":"Journal of Experimental Botany","file":[{"file_name":"2020_JourExperimBotany_Lee.pdf","creator":"dernst","file_size":1916031,"checksum":"b06aaaa93dc41896da805fe4b75cf3a1","date_created":"2020-10-06T07:41:35Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2020-10-06T07:41:35Z","file_id":"8613"}],"oa_version":"Published Version","date_created":"2020-04-06T10:57:08Z","pmid":1,"_id":"7646","language":[{"iso":"eng"}],"volume":71,"quality_controlled":"1","ddc":["580"],"year":"2020","month":"07","issue":"14","page":"3986–3998","file_date_updated":"2020-10-06T07:41:35Z","article_processing_charge":"No","isi":1,"citation":{"apa":"Lee, E., Vila Nova Santana, B., Samuels, E., Benitez-Fuente, F., Corsi, E., Botella, M., … Rosado, A. (2020). Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/eraa138\">https://doi.org/10.1093/jxb/eraa138</a>","mla":"Lee, E., et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” <i>Journal of Experimental Botany</i>, vol. 71, no. 14, Oxford University Press, 2020, pp. 3986–3998, doi:<a href=\"https://doi.org/10.1093/jxb/eraa138\">10.1093/jxb/eraa138</a>.","ieee":"E. Lee <i>et al.</i>, “Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis,” <i>Journal of Experimental Botany</i>, vol. 71, no. 14. Oxford University Press, pp. 3986–3998, 2020.","chicago":"Lee, E, B Vila Nova Santana, E Samuels, F Benitez-Fuente, E Corsi, MA Botella, J Perez-Sancho, et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/jxb/eraa138\">https://doi.org/10.1093/jxb/eraa138</a>.","ista":"Lee E, Vila Nova Santana B, Samuels E, Benitez-Fuente F, Corsi E, Botella M, Perez-Sancho J, Vanneste S, Friml J, Macho A, Alves Azevedo A, Rosado A. 2020. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental Botany. 71(14), 3986–3998.","ama":"Lee E, Vila Nova Santana B, Samuels E, et al. Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. <i>Journal of Experimental Botany</i>. 2020;71(14):3986–3998. doi:<a href=\"https://doi.org/10.1093/jxb/eraa138\">10.1093/jxb/eraa138</a>","short":"E. Lee, B. Vila Nova Santana, E. Samuels, F. Benitez-Fuente, E. Corsi, M. Botella, J. Perez-Sancho, S. Vanneste, J. Friml, A. Macho, A. Alves Azevedo, A. Rosado, Journal of Experimental Botany 71 (2020) 3986–3998."},"abstract":[{"text":"In plant cells, environmental stressors promote changes in connectivity between the cortical ER and the PM. Although this process is tightly regulated in space and time, the molecular signals and structural components mediating these changes in inter-organelle communication are only starting to be characterized. In this report, we confirm the presence of a putative tethering complex containing the synaptotagmins 1 and 5 (SYT1 and SYT5) and the Ca2+ and lipid binding protein 1 (CLB1/SYT7). This complex is enriched at ER-PM contact sites (EPCS), have slow responses to changes in extracellular Ca2+, and display severe cytoskeleton-dependent rearrangements in response to the trivalent lanthanum (La3+) and gadolinium (Gd3+) rare earth elements (REEs). Although REEs are generally used as non-selective cation channel blockers at the PM, here we show that the slow internalization of REEs into the cytosol underlies the activation of the Ca2+/Calmodulin intracellular signaling, the accumulation of phosphatidylinositol-4-phosphate (PI4P) at the PM, and the cytoskeleton-dependent rearrangement of the SYT1/SYT5 EPCS complexes. We propose that the observed EPCS rearrangements act as a slow adaptive response to sustained stress conditions, and that this process involves the accumulation of stress-specific phosphoinositides species at the PM.","lang":"eng"}],"scopus_import":"1","doi":"10.1093/jxb/eraa138","has_accepted_license":"1","intvolume":"        71","publication_status":"published","type":"journal_article","publisher":"Oxford University Press"},{"day":"01","department":[{"_id":"JiFr"}],"article_type":"original","title":"Neo-gibberellin signaling: Guiding the next generation of the green revolution","author":[{"first_name":"Huidan","last_name":"Xue","full_name":"Xue, Huidan"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","first_name":"Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xiao, Guanghui","last_name":"Xiao","first_name":"Guanghui"}],"date_updated":"2025-06-25T10:59:39Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Trends in Plant Science","pmid":1,"_id":"7686","oa_version":"None","date_created":"2020-04-26T22:00:46Z","external_id":{"pmid":["32407691"],"isi":["000533518400003"]},"publication_identifier":{"issn":["1360-1385"]},"date_published":"2020-06-01T00:00:00Z","page":"520-522","issue":"6","month":"06","isi":1,"article_processing_charge":"No","volume":25,"language":[{"iso":"eng"}],"year":"2020","quality_controlled":"1","intvolume":"        25","type":"journal_article","publisher":"Elsevier","publication_status":"published","abstract":[{"text":"The agricultural green revolution spectacularly enhanced crop yield and lodging resistance with modified DELLA-mediated gibberellin signaling. However, this was achieved at the expense of reduced nitrogen-use efficiency (NUE). Recently, Wu et al. revealed novel gibberellin signaling that provides a blueprint for improving tillering and NUE in Green Revolution varieties (GRVs). ","lang":"eng"}],"citation":{"apa":"Xue, H., Zhang, Y., &#38; Xiao, G. (2020). Neo-gibberellin signaling: Guiding the next generation of the green revolution. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2020.04.001\">https://doi.org/10.1016/j.tplants.2020.04.001</a>","mla":"Xue, Huidan, et al. “Neo-Gibberellin Signaling: Guiding the next Generation of the Green Revolution.” <i>Trends in Plant Science</i>, vol. 25, no. 6, Elsevier, 2020, pp. 520–22, doi:<a href=\"https://doi.org/10.1016/j.tplants.2020.04.001\">10.1016/j.tplants.2020.04.001</a>.","ista":"Xue H, Zhang Y, Xiao G. 2020. Neo-gibberellin signaling: Guiding the next generation of the green revolution. Trends in Plant Science. 25(6), 520–522.","ieee":"H. Xue, Y. Zhang, and G. Xiao, “Neo-gibberellin signaling: Guiding the next generation of the green revolution,” <i>Trends in Plant Science</i>, vol. 25, no. 6. Elsevier, pp. 520–522, 2020.","chicago":"Xue, Huidan, Yuzhou Zhang, and Guanghui Xiao. “Neo-Gibberellin Signaling: Guiding the next Generation of the Green Revolution.” <i>Trends in Plant Science</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.tplants.2020.04.001\">https://doi.org/10.1016/j.tplants.2020.04.001</a>.","ama":"Xue H, Zhang Y, Xiao G. Neo-gibberellin signaling: Guiding the next generation of the green revolution. <i>Trends in Plant Science</i>. 2020;25(6):520-522. doi:<a href=\"https://doi.org/10.1016/j.tplants.2020.04.001\">10.1016/j.tplants.2020.04.001</a>","short":"H. Xue, Y. Zhang, G. Xiao, Trends in Plant Science 25 (2020) 520–522."},"doi":"10.1016/j.tplants.2020.04.001","scopus_import":"1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","date_updated":"2025-04-15T07:32:09Z","author":[{"first_name":"J","last_name":"Wang","full_name":"Wang, J"},{"full_name":"Mylle, E","last_name":"Mylle","first_name":"E"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843"},{"full_name":"Besbrugge, N","first_name":"N","last_name":"Besbrugge"},{"last_name":"De Jaeger","first_name":"G","full_name":"De Jaeger, G"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Pleskot, R","last_name":"Pleskot","first_name":"R"},{"full_name":"van Damme, D","first_name":"D","last_name":"van Damme"}],"title":"High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.13.948109"}],"article_type":"original","department":[{"_id":"JiFr"}],"day":"01","date_published":"2020-07-01T00:00:00Z","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"oa":1,"external_id":{"pmid":["32321842"],"isi":["000550682000018"]},"date_created":"2020-04-29T15:23:00Z","oa_version":"Preprint","_id":"7695","pmid":1,"project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"publication":"Plant Physiology","quality_controlled":"1","year":"2020","language":[{"iso":"eng"}],"volume":183,"article_processing_charge":"No","isi":1,"month":"07","issue":"3","page":"986-997","scopus_import":"1","doi":"10.1104/pp.20.00178","citation":{"mla":"Wang, J., et al. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” <i>Plant Physiology</i>, vol. 183, no. 3, American Society of Plant Biologists, 2020, pp. 986–97, doi:<a href=\"https://doi.org/10.1104/pp.20.00178\">10.1104/pp.20.00178</a>.","apa":"Wang, J., Mylle, E., Johnson, A. J., Besbrugge, N., De Jaeger, G., Friml, J., … van Damme, D. (2020). High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.20.00178\">https://doi.org/10.1104/pp.20.00178</a>","ama":"Wang J, Mylle E, Johnson AJ, et al. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. <i>Plant Physiology</i>. 2020;183(3):986-997. doi:<a href=\"https://doi.org/10.1104/pp.20.00178\">10.1104/pp.20.00178</a>","short":"J. Wang, E. Mylle, A.J. Johnson, N. Besbrugge, G. De Jaeger, J. Friml, R. Pleskot, D. van Damme, Plant Physiology 183 (2020) 986–997.","chicago":"Wang, J, E Mylle, Alexander J Johnson, N Besbrugge, G De Jaeger, Jiří Friml, R Pleskot, and D van Damme. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2020. <a href=\"https://doi.org/10.1104/pp.20.00178\">https://doi.org/10.1104/pp.20.00178</a>.","ieee":"J. Wang <i>et al.</i>, “High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits,” <i>Plant Physiology</i>, vol. 183, no. 3. American Society of Plant Biologists, pp. 986–997, 2020.","ista":"Wang J, Mylle E, Johnson AJ, Besbrugge N, De Jaeger G, Friml J, Pleskot R, van Damme D. 2020. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 183(3), 986–997."},"abstract":[{"lang":"eng","text":"The TPLATE complex (TPC) is a key endocytic adaptor protein complex in plants. TPC in Arabidopsis (Arabidopsis thaliana) contains six evolutionarily conserved subunits and two plant-specific subunits, AtEH1/Pan1 and AtEH2/Pan1, although cytoplasmic proteins are not associated with the hexameric subcomplex in the cytoplasm. To investigate the dynamic assembly of the octameric TPC at the plasma membrane (PM), we performed state-of-the-art dual-color live cell imaging at physiological and lowered temperatures. Lowering the temperature slowed down endocytosis, thereby enhancing the temporal resolution of the differential recruitment of endocytic components. Under both normal and lowered temperature conditions, the core TPC subunit TPLATE and the AtEH/Pan1 proteins exhibited simultaneous recruitment at the PM. These results, together with co-localization analysis of different TPC subunits, allow us to conclude that TPC in plant cells is not recruited to the PM sequentially but as an octameric complex."}],"publication_status":"published","type":"journal_article","publisher":"American Society of Plant Biologists","intvolume":"       183"},{"publication":"New Phytologist","file":[{"file_name":"2020_09_NewPhytologist_Zhang.pdf","creator":"dernst","file_size":3643395,"checksum":"8e8150dbbba8cb65b72f81d1f0864b8b","date_created":"2020-11-24T12:19:38Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2020-11-24T12:19:38Z","file_id":"8799"}],"date_created":"2020-04-30T08:43:29Z","oa_version":"Published Version","_id":"7697","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"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"external_id":{"pmid":["32350870"],"isi":["000534092400001"]},"date_published":"2020-09-01T00:00:00Z","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"article_type":"original","ec_funded":1,"day":"01","department":[{"_id":"JiFr"}],"title":"Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters","author":[{"orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1618-2737","full_name":"Hartinger, Corinna","last_name":"Hartinger","first_name":"Corinna","id":"AEFB2266-8ABF-11EA-AA39-812C3623CBE4"},{"last_name":"Wang","first_name":"Xiaojuan","full_name":"Wang, Xiaojuan"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"status":"public","date_updated":"2025-04-14T07:45:03Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","intvolume":"       227","publication_status":"published","corr_author":"1","publisher":"Wiley","type":"journal_article","citation":{"ama":"Zhang Y, Hartinger C, Wang X, Friml J. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. <i>New Phytologist</i>. 2020;227(5):1406-1416. doi:<a href=\"https://doi.org/10.1111/nph.16629\">10.1111/nph.16629</a>","short":"Y. Zhang, C. Hartinger, X. Wang, J. Friml, New Phytologist 227 (2020) 1406–1416.","chicago":"Zhang, Yuzhou, Corinna Hartinger, Xiaojuan Wang, and Jiří Friml. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” <i>New Phytologist</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/nph.16629\">https://doi.org/10.1111/nph.16629</a>.","ista":"Zhang Y, Hartinger C, Wang X, Friml J. 2020. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 227(5), 1406–1416.","ieee":"Y. Zhang, C. Hartinger, X. Wang, and J. Friml, “Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters,” <i>New Phytologist</i>, vol. 227, no. 5. Wiley, pp. 1406–1416, 2020.","mla":"Zhang, Yuzhou, et al. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” <i>New Phytologist</i>, vol. 227, no. 5, Wiley, 2020, pp. 1406–16, doi:<a href=\"https://doi.org/10.1111/nph.16629\">10.1111/nph.16629</a>.","apa":"Zhang, Y., Hartinger, C., Wang, X., &#38; Friml, J. (2020). Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16629\">https://doi.org/10.1111/nph.16629</a>"},"abstract":[{"lang":"eng","text":"* Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane‐based PIN‐FORMED (PIN) auxin transporters. PINs localize to a particular side of the plasma membrane (PM) or to the endoplasmic reticulum (ER) to directionally transport auxin and maintain intercellular and intracellular auxin homeostasis, respectively. However, the molecular cues that confer their diverse cellular localizations remain largely unknown.\r\n* In this study, we systematically swapped the domains between ER‐ and PM‐localized PIN proteins, as well as between apical and basal PM‐localized PINs from Arabidopsis thaliana , to shed light on why PIN family members with similar topological structures reside at different membrane compartments within cells.\r\n* Our results show that not only do the N‐ and C‐terminal transmembrane domains (TMDs) and central hydrophilic loop contribute to their differential subcellular localizations and cellular polarity, but that the pairwise‐matched N‐ and C‐terminal TMDs resulting from intramolecular domain–domain coevolution are also crucial for their divergent patterns of localization.\r\n* These findings illustrate the complexity of the evolutionary path of PIN proteins in acquiring their plethora of developmental functions and adaptive growth in plants."}],"scopus_import":"1","doi":"10.1111/nph.16629","month":"09","file_date_updated":"2020-11-24T12:19:38Z","issue":"5","page":"1406-1416","article_processing_charge":"Yes (via OA deal)","isi":1,"language":[{"iso":"eng"}],"volume":227,"quality_controlled":"1","year":"2020","ddc":["580"]},{"publication_status":"published","publisher":"eLife Sciences Publications","type":"journal_article","has_accepted_license":"1","intvolume":"         9","scopus_import":"1","doi":"10.7554/elife.51787","citation":{"short":"A. Kuhn, S. Ramans Harborough, H.M. McLaughlin, B. Natarajan, I. Verstraeten, J. Friml, S. Kepinski, L. Østergaard, ELife 9 (2020).","ama":"Kuhn A, Ramans Harborough S, McLaughlin HM, et al. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.51787\">10.7554/elife.51787</a>","ista":"Kuhn A, Ramans Harborough S, McLaughlin HM, Natarajan B, Verstraeten I, Friml J, Kepinski S, Østergaard L. 2020. Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. eLife. 9, e51787.","ieee":"A. Kuhn <i>et al.</i>, “Direct ETTIN-auxin interaction controls chromatin states in gynoecium development,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","chicago":"Kuhn, André, Sigurd Ramans Harborough, Heather M McLaughlin, Bhavani Natarajan, Inge Verstraeten, Jiří Friml, Stefan Kepinski, and Lars Østergaard. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.51787\">https://doi.org/10.7554/elife.51787</a>.","apa":"Kuhn, A., Ramans Harborough, S., McLaughlin, H. M., Natarajan, B., Verstraeten, I., Friml, J., … Østergaard, L. (2020). Direct ETTIN-auxin interaction controls chromatin states in gynoecium development. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.51787\">https://doi.org/10.7554/elife.51787</a>","mla":"Kuhn, André, et al. “Direct ETTIN-Auxin Interaction Controls Chromatin States in Gynoecium Development.” <i>ELife</i>, vol. 9, e51787, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.51787\">10.7554/elife.51787</a>."},"abstract":[{"lang":"eng","text":"Hormonal signalling in animals often involves direct transcription factor-hormone interactions that modulate gene expression. In contrast, plant hormone signalling is most commonly based on de-repression via the degradation of transcriptional repressors. Recently, we uncovered a non-canonical signalling mechanism for the plant hormone auxin whereby auxin directly affects the activity of the atypical auxin response factor (ARF), ETTIN towards target genes without the requirement for protein degradation. Here we show that ETTIN directly binds auxin, leading to dissociation from co-repressor proteins of the TOPLESS/TOPLESS-RELATED family followed by histone acetylation and induction of gene expression. This mechanism is reminiscent of animal hormone signalling as it affects the activity towards regulation of target genes and provides the first example of a DNA-bound hormone receptor in plants. Whilst auxin affects canonical ARFs indirectly by facilitating degradation of Aux/IAA repressors, direct ETTIN-auxin interactions allow switching between repressive and de-repressive chromatin states in an instantly-reversible manner."}],"article_processing_charge":"No","isi":1,"month":"04","file_date_updated":"2020-07-14T12:48:03Z","quality_controlled":"1","ddc":["580"],"year":"2020","language":[{"iso":"eng"}],"volume":9,"date_created":"2020-05-04T08:50:47Z","oa_version":"Published Version","article_number":"e51787","_id":"7793","pmid":1,"publication":"eLife","file":[{"date_updated":"2020-07-14T12:48:03Z","content_type":"application/pdf","access_level":"open_access","file_id":"7794","creator":"dernst","file_name":"2020_eLife_Kuhn.pdf","relation":"main_file","date_created":"2020-05-04T09:06:43Z","checksum":"15d740de1a741fdcc6ec128c48eed017","file_size":2893082}],"date_published":"2020-04-08T00:00:00Z","publication_identifier":{"issn":["2050-084X"]},"oa":1,"external_id":{"isi":["000527752200001"],"pmid":["32267233"]},"author":[{"full_name":"Kuhn, André","first_name":"André","last_name":"Kuhn"},{"last_name":"Ramans Harborough","first_name":"Sigurd","full_name":"Ramans Harborough, Sigurd"},{"full_name":"McLaughlin, Heather M","last_name":"McLaughlin","first_name":"Heather M"},{"full_name":"Natarajan, Bhavani","last_name":"Natarajan","first_name":"Bhavani"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kepinski, Stefan","first_name":"Stefan","last_name":"Kepinski"},{"full_name":"Østergaard, Lars","last_name":"Østergaard","first_name":"Lars"}],"title":"Direct ETTIN-auxin interaction controls chromatin states in gynoecium development","article_type":"original","department":[{"_id":"JiFr"}],"day":"08","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_updated":"2023-08-21T06:17:12Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}}]