[{"day":"01","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"citation":{"ieee":"M. Del Bianco, J. Friml, L. Strader, and S. Kepinski, “Auxin research: Creating tools for a greener future,” Journal of Experimental Botany, vol. 74, no. 22. Oxford University Press, pp. 6889–6892, 2023.","short":"M. Del Bianco, J. Friml, L. Strader, S. Kepinski, Journal of Experimental Botany 74 (2023) 6889–6892.","ista":"Del Bianco M, Friml J, Strader L, Kepinski S. 2023. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 74(22), 6889–6892.","ama":"Del Bianco M, Friml J, Strader L, Kepinski S. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 2023;74(22):6889-6892. doi:10.1093/jxb/erad420","apa":"Del Bianco, M., Friml, J., Strader, L., & Kepinski, S. (2023). Auxin research: Creating tools for a greener future. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erad420","chicago":"Del Bianco, Marta, Jiří Friml, Lucia Strader, and Stefan Kepinski. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany. Oxford University Press, 2023. https://doi.org/10.1093/jxb/erad420.","mla":"Del Bianco, Marta, et al. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany, vol. 74, no. 22, Oxford University Press, 2023, pp. 6889–92, doi:10.1093/jxb/erad420."},"_id":"14709","scopus_import":"1","article_type":"original","oa_version":"Published Version","intvolume":" 74","type":"journal_article","month":"12","language":[{"iso":"eng"}],"date_published":"2023-12-01T00:00:00Z","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","date_updated":"2025-09-09T14:06:39Z","isi":1,"oa":1,"file_date_updated":"2024-01-02T09:23:57Z","issue":"22","publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"doi":"10.1093/jxb/erad420","publication":"Journal of Experimental Botany","year":"2023","date_created":"2023-12-24T23:00:53Z","has_accepted_license":"1","ddc":["580"],"quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"2023_JourExperimentalBotany_DelBianco.pdf","date_created":"2024-01-02T09:23:57Z","creator":"dernst","success":1,"file_id":"14724","file_size":425194,"date_updated":"2024-01-02T09:23:57Z","checksum":"f66fb960fd791dea53fd0e087f2fbbe8","relation":"main_file","access_level":"open_access"}],"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Del Bianco","first_name":"Marta","full_name":"Del Bianco, Marta"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"full_name":"Strader, Lucia","last_name":"Strader","first_name":"Lucia"},{"full_name":"Kepinski, Stefan","last_name":"Kepinski","first_name":"Stefan"}],"volume":74,"title":"Auxin research: Creating tools for a greener future","page":"6889-6892","license":"https://creativecommons.org/licenses/by/4.0/","article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"Amid the delays due to the global pandemic, in early October 2022, the auxin community gathered in the idyllic peninsula of Cavtat, Croatia. More than 170 scientists from across the world converged to discuss the latest advancements in fundamental and applied research in the field. The topics, from signalling and transport to plant architecture and response to the environment, show how auxin research must bridge from the molecular realm to macroscopic developmental responses. This is mirrored in this collection of reviews, contributed by participants of the Auxin 2022 meeting.","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001145889700001"],"pmid":["38038239"]}},{"citation":{"chicago":"Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms242216527.","apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., & Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms242216527","mla":"Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal of Molecular Sciences, vol. 24, no. 22, 16527, MDPI, 2023, doi:10.3390/ijms242216527.","ieee":"A. Teplova et al., “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” International Journal of Molecular Sciences, vol. 24, no. 22. MDPI, 2023.","short":"A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina, N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences 24 (2023).","ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527.","ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 2023;24(22). doi:10.3390/ijms242216527"},"tmp":{"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)","short":"CC BY (4.0)"},"day":"01","status":"public","file_date_updated":"2024-01-10T13:39:42Z","oa":1,"isi":1,"date_updated":"2024-10-09T21:07:49Z","publisher":"MDPI","department":[{"_id":"JiFr"}],"date_published":"2023-11-01T00:00:00Z","language":[{"iso":"eng"}],"month":"11","type":"journal_article","acknowledgement":"We thank C.U.T. Hellen for critically reading the manuscript. The MALDI MS facility and CLSM became available to us in the framework of Moscow State University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071.","intvolume":" 24","oa_version":"Published Version","article_type":"original","_id":"14776","file":[{"relation":"main_file","checksum":"4df7d206ba022b7f54eff1f0aec1659a","access_level":"open_access","date_updated":"2024-01-10T13:39:42Z","file_size":2637784,"file_id":"14791","creator":"dernst","success":1,"date_created":"2024-01-10T13:39:42Z","content_type":"application/pdf","file_name":"2023_IJMS_Teplova.pdf"}],"quality_controlled":"1","corr_author":"1","ddc":["580"],"has_accepted_license":"1","article_number":"16527","date_created":"2024-01-10T09:24:35Z","year":"2023","publication":"International Journal of Molecular Sciences","doi":"10.3390/ijms242216527","publication_identifier":{"issn":["1422-0067"]},"issue":"22","external_id":{"isi":["001113792600001"],"pmid":["38003717"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident."}],"article_processing_charge":"Yes","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","volume":24,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia","last_name":"Teplova","first_name":"Anastasiia"},{"last_name":"Pigidanov","first_name":"Artemii A.","full_name":"Pigidanov, Artemii A."},{"full_name":"Serebryakova, Marina V.","first_name":"Marina V.","last_name":"Serebryakova"},{"first_name":"Sergei A.","last_name":"Golyshev","full_name":"Golyshev, Sergei A."},{"full_name":"Galiullina, Raisa A.","last_name":"Galiullina","first_name":"Raisa A."},{"first_name":"Nina V.","last_name":"Chichkova","full_name":"Chichkova, Nina V."},{"first_name":"Andrey B.","last_name":"Vartapetian","full_name":"Vartapetian, Andrey B."}],"pmid":1},{"_id":"13212","scopus_import":"1","article_type":"letter_note","oa_version":"Published Version","intvolume":" 16","type":"journal_article","acknowledgement":"We thank all the authors for sharing the published materials. This research was supported by the Lab Support Facility and the Imaging and Optics Facility of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This project was funded by the European Research Council Advanced Grant (ETAP-742985).","month":"07","language":[{"iso":"eng"}],"date_published":"2023-07-01T00:00:00Z","department":[{"_id":"JiFr"}],"publisher":"Elsevier","date_updated":"2026-07-06T12:58:58Z","isi":1,"oa":1,"file_date_updated":"2024-01-29T10:37:05Z","day":"01","status":"public","ec_funded":1,"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"citation":{"apa":"Chen, H., Li, L., Zou, M., Qi, L., & Friml, J. (2023). Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2023.06.007","chicago":"Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant. Elsevier, 2023. https://doi.org/10.1016/j.molp.2023.06.007.","mla":"Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant, vol. 16, no. 7, Elsevier, 2023, pp. 1117–19, doi:10.1016/j.molp.2023.06.007.","short":"H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.","ieee":"H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and AFB1 receptors in auxin signalling.,” Molecular Plant, vol. 16, no. 7. Elsevier, pp. 1117–1119, 2023.","ama":"Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 2023;16(7):1117-1119. doi:10.1016/j.molp.2023.06.007","ista":"Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119."},"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"related_material":{"record":[{"id":"19478","relation":"dissertation_contains","status":"public"}]},"pmid":1,"author":[{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","first_name":"Huihuang","last_name":"Chen"},{"last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","last_name":"Zou","first_name":"Minxia"},{"last_name":"Qi","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":16,"title":"Distinct functions of TIR1 and AFB1 receptors in auxin signalling.","page":"1117-1119","article_processing_charge":"Yes (via OA deal)","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"lang":"eng","text":"Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast."}],"publication_status":"published","external_id":{"pmid":["37393433"],"isi":["001044410900001"]},"issue":"7","publication_identifier":{"issn":["1752-9867"],"eissn":["1674-2052"]},"doi":"10.1016/j.molp.2023.06.007","publication":"Molecular Plant","das_tickbox":"1","year":"2023","date_created":"2023-07-12T07:32:46Z","has_accepted_license":"1","ddc":["580"],"corr_author":"1","quality_controlled":"1","file":[{"file_id":"14894","relation":"main_file","checksum":"6012b7e4a2f680ee6c1f84001e2b945f","access_level":"open_access","date_updated":"2024-01-29T10:37:05Z","file_size":1000871,"date_created":"2024-01-29T10:37:05Z","file_name":"2023_MolecularPlant_Chen.pdf","content_type":"application/pdf","creator":"dernst","success":1}]},{"publication":"Plant Communications","das_tickbox":"1","issue":"6","publication_identifier":{"eissn":["2590-3462"]},"doi":"10.1016/j.xplc.2023.100632","article_number":"100632","year":"2023","date_created":"2023-07-12T07:32:00Z","ddc":["580"],"has_accepted_license":"1","quality_controlled":"1","file":[{"success":1,"creator":"dernst","date_created":"2024-01-30T10:54:40Z","content_type":"application/pdf","file_name":"2023_PlantCommunications_Xia.pdf","access_level":"open_access","checksum":"f8ef92af6096834f91ce38587fb1db9f","relation":"main_file","date_updated":"2024-01-30T10:54:40Z","file_size":1434862,"file_id":"14900"}],"pmid":1,"volume":4,"author":[{"full_name":"Xia, Jing","last_name":"Xia","first_name":"Jing"},{"full_name":"Kong, Mengjuan","first_name":"Mengjuan","last_name":"Kong"},{"last_name":"Yang","first_name":"Zhisen","full_name":"Yang, Zhisen"},{"last_name":"Sun","first_name":"Lianghanxiao","full_name":"Sun, Lianghanxiao"},{"last_name":"Peng","first_name":"Yakun","full_name":"Peng, Yakun"},{"full_name":"Mao, Yanbo","last_name":"Mao","first_name":"Yanbo"},{"full_name":"Wei, Hong","last_name":"Wei","first_name":"Hong"},{"full_name":"Ying, Wei","last_name":"Ying","first_name":"Wei"},{"first_name":"Yongxiao","last_name":"Gao","full_name":"Gao, Yongxiao"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"full_name":"Weng, Jianping","first_name":"Jianping","last_name":"Weng"},{"full_name":"Liu, Xin","first_name":"Xin","last_name":"Liu"},{"first_name":"Linfeng","last_name":"Sun","full_name":"Sun, Linfeng"},{"last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen","abstract":[{"text":"The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we reveal that naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated developmental processes. Additional cellular and biochemical evidence indicates that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analyses confirm that naproxen binds directly to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate. Thus, by combining cellular, biochemical, and structural approaches, this study clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of this compound may advance our understanding of the molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in auxin biology and agriculture.","lang":"eng"}],"external_id":{"pmid":["37254481"],"isi":["001113003000001"]},"publication_status":"published","article_processing_charge":"Yes","day":"13","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"citation":{"ama":"Xia J, Kong M, Yang Z, et al. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. 2023;4(6). doi:10.1016/j.xplc.2023.100632","ista":"Xia J, Kong M, Yang Z, Sun L, Peng Y, Mao Y, Wei H, Ying W, Gao Y, Friml J, Weng J, Liu X, Sun L, Tan S. 2023. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. 4(6), 100632.","short":"J. Xia, M. Kong, Z. Yang, L. Sun, Y. Peng, Y. Mao, H. Wei, W. Ying, Y. Gao, J. Friml, J. Weng, X. Liu, L. Sun, S. Tan, Plant Communications 4 (2023).","ieee":"J. Xia et al., “Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen,” Plant Communications, vol. 4, no. 6. Elsevier, 2023.","mla":"Xia, Jing, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” Plant Communications, vol. 4, no. 6, 100632, Elsevier, 2023, doi:10.1016/j.xplc.2023.100632.","chicago":"Xia, Jing, Mengjuan Kong, Zhisen Yang, Lianghanxiao Sun, Yakun Peng, Yanbo Mao, Hong Wei, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” Plant Communications. Elsevier, 2023. https://doi.org/10.1016/j.xplc.2023.100632.","apa":"Xia, J., Kong, M., Yang, Z., Sun, L., Peng, Y., Mao, Y., … Tan, S. (2023). Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2023.100632"},"_id":"13209","scopus_import":"1","acknowledgement":"This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB37020103 to Linfeng Sun); research funds from the Center for Advanced Interdisciplinary Science\r\nand Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China (QYPY20220012 to S.T.); start-up funding from the University of Science and Technology of China and the\r\nChinese Academy of Sciences (GG9100007007, KY9100000026,KY9100000051, and KJ2070000079 to S.T.); the National Natural Science Foundation of China (31900885 to X.L. and 31870732 to Linfeng Sun); the Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun); the Fundamental Research Funds for the Central Universities (WK9100000021 to S.T. and WK9100000031 to Linfeng Sun); and the USTC Research Funds of the Double First-Class Initiative (YD9100002016 to S.T. and YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation.We thank Dr. Yang Zhao for sharing published materials (Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences) and the Cryo-EM Center of the University of Science and Technology of China for the EM facility support. We are grateful to Y. Gao and all other staff members for their technical support on cryo-EM data collection. ","type":"journal_article","article_type":"original","intvolume":" 4","oa_version":"Published Version","department":[{"_id":"JiFr"}],"publisher":"Elsevier","date_updated":"2026-07-06T12:59:25Z","month":"11","language":[{"iso":"eng"}],"date_published":"2023-11-13T00:00:00Z","oa":1,"file_date_updated":"2024-01-30T10:54:40Z","isi":1},{"_id":"13201","scopus_import":"1","acknowledgement":"We are grateful to Caifu Jiang for providing ethyl metha-nesulfonate- mutagenized population, Yi Wang for providing Xenopus oocytes, Jun Fan and Zhaosheng Kong for providing tobacco BY- 2 cells, and Claus Schwechheimer, Alain Gojon, and Shutang Tan for helpful discussions. This work was supported by the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), Hainan Provincial Natural Science Foundation of China (323CXTD379), Chinese Universities Scientific Fund (2023TC019), Beijing Municipal Natural Science Foundation (5192011), Beijing Outstanding University Discipline Program, and China Postdoctoral Science Foundation (BH2020259460).","type":"journal_article","article_type":"original","oa_version":"Published Version","intvolume":" 120","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","date_updated":"2023-12-13T23:30:04Z","language":[{"iso":"eng"}],"month":"06","date_published":"2023-06-12T00:00:00Z","oa":1,"file_date_updated":"2023-12-13T23:30:03Z","isi":1,"day":"12","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"citation":{"ama":"Wang Y, Yuan Z, Wang J, et al. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(25). doi:10.1073/pnas.2221313120","ista":"Wang Y, Yuan Z, Wang J, Xiao H, Wan L, Li L, Guo Y, Gong Z, Friml J, Zhang J. 2023. The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. 120(25), e2221313120.","short":"Y. Wang, Z. Yuan, J. Wang, H. Xiao, L. Wan, L. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","ieee":"Y. Wang et al., “The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25. National Academy of Sciences, 2023.","mla":"Wang, Yalu, et al. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 25, e2221313120, National Academy of Sciences, 2023, doi:10.1073/pnas.2221313120.","apa":"Wang, Y., Yuan, Z., Wang, J., Xiao, H., Wan, L., Li, L., … Zhang, J. (2023). The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2221313120","chicago":"Wang, Yalu, Zhi Yuan, Jinyi Wang, Huixin Xiao, Lu Wan, Lanxin Li, Yan Guo, Zhizhong Gong, Jiří Friml, and Jing Zhang. “The Nitrate Transporter NRT2.1 Directly Antagonizes PIN7-Mediated Auxin Transport for Root Growth Adaptation.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2221313120."},"pmid":1,"volume":120,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Wang, Yalu","first_name":"Yalu","last_name":"Wang"},{"last_name":"Yuan","first_name":"Zhi","full_name":"Yuan, Zhi"},{"first_name":"Jinyi","last_name":"Wang","full_name":"Wang, Jinyi"},{"first_name":"Huixin","last_name":"Xiao","full_name":"Xiao, Huixin"},{"full_name":"Wan, Lu","first_name":"Lu","last_name":"Wan"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin"},{"first_name":"Yan","last_name":"Guo","full_name":"Guo, Yan"},{"full_name":"Gong, Zhizhong","first_name":"Zhizhong","last_name":"Gong"},{"last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Zhang, Jing","first_name":"Jing","last_name":"Zhang"}],"title":"The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation","abstract":[{"lang":"eng","text":"As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability."}],"publication_status":"published","external_id":{"pmid":["37307446"],"isi":["001030689600003"]},"article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"25","doi":"10.1073/pnas.2221313120","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_number":"e2221313120","year":"2023","date_created":"2023-07-09T22:01:12Z","ddc":["570"],"has_accepted_license":"1","file":[{"file_id":"13204","embargo":"2023-12-12","access_level":"open_access","checksum":"d800e06252eaefba28531fa9440f23f0","relation":"main_file","date_updated":"2023-12-13T23:30:03Z","file_size":5244581,"date_created":"2023-07-10T08:48:40Z","content_type":"application/pdf","file_name":"2023_PNAS_Wang.pdf","creator":"alisjak"}],"quality_controlled":"1"},{"month":"11","language":[{"iso":"eng"}],"date_published":"2023-11-10T00:00:00Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"date_updated":"2026-09-04T22:30:56Z","oa":1,"file_date_updated":"2024-11-23T23:30:38Z","_id":"14510","oa_version":"Published Version","type":"dissertation","citation":{"apa":"Gnyliukh, N. (2023). Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14510","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14510.","mla":"Gnyliukh, Nataliia. Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14510.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. 2023. doi:10.15479/at:ista:14510","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle formation during endocytosis in plants. Institute of Science and Technology Austria."},"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"alternative_title":["ISTA Thesis"],"day":"10","status":"public","ec_funded":1,"tmp":{"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)","short":"CC BY (4.0)"},"title":"Mechanism of clathrin-coated vesicle formation during endocytosis in plants","degree_awarded":"PhD","keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"supervisor":[{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"page":"180","article_processing_charge":"No","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and\r\ndevelopment by controlling plasma membrane protein composition and cargo uptake. CME\r\nrelies on the precise recruitment control of protein regulators for vesicle maturation and\r\nrelease. During the early stages of endocytosis, an area of flat membrane is remodelled by\r\nproteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated\r\nvesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane,\r\nand cargo proceeds for recycling or degradation through early endosomes / Trans Golgi\r\nnetwork. Protein machineries that mediate membrane bending and vesicle release in plants\r\nare unknown. However, studies show, that plant endocytosis is actin independent, thus\r\nindicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced\r\nlive microscopy approaches we investigate the TPLATE complex, a plant-specific\r\nendocytosis protein complex. We found that TPLATE is peripherally associated with\r\nclathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of\r\nplant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a\r\nrole in vesicle release, shows the recruitment of the protein already at the early stages of\r\nendocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to\r\ninduce membrane deformation and tubulation, suggesting its role also in membrane bending\r\nduring early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle\r\nscission machinery; however, their precise role in plant CME has not been yet elucidated.\r\nHere, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution\r\nimaging of endocytic events in vivo and protein characterisation. Although DRP2s and\r\nSH3P2 arrive together during late CME and physically interact, genetic analysis using\r\n∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest\r\nthat SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our\r\nresearch, these observations provide new important insights into the mechanism of plant\r\nCME and show that, despite plants posses many homologues of mammalian and yeast CME\r\ncomponents, they do not necessarily act in the same manner. ","lang":"eng"}],"publication_status":"published","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}],"related_material":{"record":[{"id":"14591","relation":"part_of_dissertation","status":"public"},{"id":"9887","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"8139","status":"public"}]},"author":[{"first_name":"Nataliia","last_name":"Gnyliukh","full_name":"Gnyliukh, Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","has_accepted_license":"1","ddc":["570"],"corr_author":"1","file":[{"checksum":"3d5e680bfc61f98e308c434f45cc9bd6","relation":"source_file","access_level":"closed","file_size":20824903,"date_updated":"2024-11-23T23:30:38Z","embargo_to":"open_access","file_id":"14567","creator":"ngnyliuk","date_created":"2023-11-20T09:18:51Z","file_name":"Thesis_Gnyliukh_final_08_11_23.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"date_created":"2023-11-20T09:23:11Z","content_type":"application/pdf","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","creator":"ngnyliuk","file_id":"14568","embargo":"2024-11-23","access_level":"open_access","relation":"main_file","checksum":"bfc96d47fc4e7e857dd71656097214a4","file_size":24871844,"date_updated":"2024-11-23T23:30:38Z"}],"publication_identifier":{"isbn":["978-3-99078-037-4"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:14510","year":"2023","date_created":"2023-11-10T09:10:06Z"},{"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"corr_author":"1","citation":{"chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523.","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.10.09.561523"}],"ec_funded":1,"year":"2023","date_created":"2023-11-22T10:17:49Z","status":"public","day":"10","publication":"bioRxiv","doi":"10.1101/2023.10.09.561523","oa":1,"abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.","lang":"eng"}],"publication_status":"draft","article_processing_charge":"No","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"date_updated":"2026-09-04T22:30:55Z","month":"10","language":[{"iso":"eng"}],"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","date_published":"2023-10-10T00:00:00Z","OA_place":"repository","type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","author":[{"orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J"},{"last_name":"Nagel","first_name":"Marie-Kristin","full_name":"Nagel, Marie-Kristin"},{"last_name":"Monzer","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"last_name":"Hlavata","first_name":"Annamaria","full_name":"Hlavata, Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Isono","first_name":"Erika","full_name":"Isono, Erika"},{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"}],"related_material":{"record":[{"id":"15330","relation":"later_version","status":"public"},{"relation":"dissertation_contains","id":"14510","status":"public"}]},"_id":"14591","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}]},{"main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"quality_controlled":"1","issue":"6","doi":"10.1093/plcell/koac071","publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"publication":"Plant Cell","year":"2022","date_created":"2022-03-08T13:47:51Z","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","page":"2150-2173","article_processing_charge":"No","abstract":[{"text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.","lang":"eng"}],"external_id":{"pmid":["35218346"],"isi":["000767438800001"]},"publication_status":"published","acknowledged_ssus":[{"_id":"EM-Fac"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Dahhan, DA","last_name":"Dahhan","first_name":"DA"},{"first_name":"GD","last_name":"Reynolds","full_name":"Reynolds, GD"},{"first_name":"JJ","last_name":"Cárdenas","full_name":"Cárdenas, JJ"},{"last_name":"Eeckhout","first_name":"D","full_name":"Eeckhout, D"},{"last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843"},{"first_name":"K","last_name":"Yperman","full_name":"Yperman, K"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"last_name":"Vang","first_name":"N","full_name":"Vang, N"},{"last_name":"Yan","first_name":"X","full_name":"Yan, X"},{"full_name":"Hwang, I","last_name":"Hwang","first_name":"I"},{"full_name":"Heese, A","first_name":"A","last_name":"Heese"},{"first_name":"G","last_name":"De Jaeger","full_name":"De Jaeger, G"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"first_name":"D","last_name":"Van Damme","full_name":"Van Damme, D"},{"full_name":"Pan, J","first_name":"J","last_name":"Pan"},{"first_name":"SY","last_name":"Bednarek","full_name":"Bednarek, SY"}],"volume":34,"citation":{"ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 2022;34(6):2150-2173. doi:10.1093/plcell/koac071","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","ieee":"D. Dahhan et al., “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” Plant Cell, vol. 34, no. 6. Oxford University Press, pp. 2150–2173, 2022.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:10.1093/plcell/koac071.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac071","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell. Oxford University Press, 2022. https://doi.org/10.1093/plcell/koac071."},"project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"day":"01","status":"public","language":[{"iso":"eng"}],"month":"06","date_published":"2022-06-01T00:00:00Z","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publisher":"Oxford University Press","date_updated":"2025-05-14T11:06:15Z","isi":1,"oa":1,"_id":"10841","scopus_import":"1","article_type":"original","oa_version":"Preprint","intvolume":" 34","acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","type":"journal_article"},{"citation":{"ieee":"Q. Lu et al., “Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 11. National Academy of Sciences, 2022.","short":"Q. Lu, Y. Zhang, J. Hellner, C. Giannini, X. Xu, J. Pauwels, Q. Ma, W. Dejonghe, H. Han, B. Van De Cotte, F. Impens, K. Gevaert, I. De Smet, J. Friml, D.M. Molina, E. Russinova, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ama":"Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(11). doi:10.1073/pnas.2118220119","ista":"Lu Q, Zhang Y, Hellner J, Giannini C, Xu X, Pauwels J, Ma Q, Dejonghe W, Han H, Van De Cotte B, Impens F, Gevaert K, De Smet I, Friml J, Molina DM, Russinova E. 2022. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 119(11), e2118220119.","chicago":"Lu, Qing, Yonghong Zhang, Joakim Hellner, Caterina Giannini, Xiangyu Xu, Jarne Pauwels, Qian Ma, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2118220119.","apa":"Lu, Q., Zhang, Y., Hellner, J., Giannini, C., Xu, X., Pauwels, J., … Russinova, E. (2022). Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2118220119","mla":"Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 11, e2118220119, National Academy of Sciences, 2022, doi:10.1073/pnas.2118220119."},"status":"public","day":"07","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"month":"03","language":[{"iso":"eng"}],"date_published":"2022-03-07T00:00:00Z","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"date_updated":"2025-05-14T11:01:45Z","isi":1,"oa":1,"file_date_updated":"2022-03-21T09:19:47Z","_id":"10888","scopus_import":"1","article_type":"original","intvolume":" 119","oa_version":"Published Version","acknowledgement":"We thank Yanhai Yin for providing the anti-BES1 antibody, Johan Winne and Brenda Callebaut for synthesizing bikinin, Yuki Kondo and Hiroo Fukuda for published materials, Tomasz Nodzy\u0003nski for useful advice, and Martine De Cock for help in preparing the manuscript. This\r\nwork was supported by the China Scholarship Council for predoctoral (Q.L. and X.X.) and postdoctoral (Y.Z.) fellowships; the Agency for Innovation by Science and Technology for a predoctoral fellowship (W.D.); the Research Foundation-Flanders, Projects G009018N and G002121N (E.R.); and the VIB TechWatch Fund (E.R.).","type":"journal_article","has_accepted_license":"1","ddc":["580"],"file":[{"file_size":2169534,"date_updated":"2022-03-21T09:19:47Z","checksum":"83e0fea7919570d0b519b41193342571","relation":"main_file","access_level":"open_access","file_id":"10910","creator":"dernst","success":1,"file_name":"2022_PNAS_Lu.pdf","content_type":"application/pdf","date_created":"2022-03-21T09:19:47Z"}],"quality_controlled":"1","issue":"11","publication_identifier":{"eissn":["1091-6490"]},"doi":"10.1073/pnas.2118220119","publication":"Proceedings of the National Academy of Sciences of the United States of America","year":"2022","date_created":"2022-03-20T23:01:39Z","article_number":"e2118220119","title":"Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Despite the growing interest in using chemical genetics in plant research, small molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or posttranslational modifications, allows the discovery of drug targets or the study of protein–metabolite and protein–protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf, thus revealing cross-talk between brassinosteroid and auxin signaling."}],"external_id":{"isi":["000771756300008"],"pmid":["35254915"]},"publication_status":"published","pmid":1,"author":[{"first_name":"Qing","last_name":"Lu","full_name":"Lu, Qing"},{"full_name":"Zhang, Yonghong","last_name":"Zhang","first_name":"Yonghong"},{"full_name":"Hellner, Joakim","last_name":"Hellner","first_name":"Joakim"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina","last_name":"Giannini","first_name":"Caterina"},{"full_name":"Xu, Xiangyu","first_name":"Xiangyu","last_name":"Xu"},{"full_name":"Pauwels, Jarne","first_name":"Jarne","last_name":"Pauwels"},{"full_name":"Ma, Qian","last_name":"Ma","first_name":"Qian"},{"full_name":"Dejonghe, Wim","first_name":"Wim","last_name":"Dejonghe"},{"first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"first_name":"Brigitte","last_name":"Van De Cotte","full_name":"Van De Cotte, Brigitte"},{"full_name":"Impens, Francis","last_name":"Impens","first_name":"Francis"},{"full_name":"Gevaert, Kris","first_name":"Kris","last_name":"Gevaert"},{"full_name":"De Smet, Ive","first_name":"Ive","last_name":"De Smet"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"},{"full_name":"Molina, Daniel Martinez","last_name":"Molina","first_name":"Daniel Martinez"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":119},{"year":"2022","date_created":"2022-07-05T15:14:34Z","publication":"International Journal of Molecular Sciences","issue":"11","publication_identifier":{"issn":["1422-0067"]},"doi":"10.3390/ijms23116352","quality_controlled":"1","file":[{"creator":"cchlebak","success":1,"content_type":"application/pdf","file_name":"2022_IntJMolSci_Bilanovicova.pdf","date_created":"2022-07-06T07:36:59Z","date_updated":"2022-07-06T07:36:59Z","file_size":2324542,"relation":"main_file","checksum":"e997a57a928ec9d51fad8ce824a05935","access_level":"open_access","file_id":"11492"}],"corr_author":"1","ddc":["570"],"has_accepted_license":"1","volume":23,"author":[{"full_name":"Bilanovičová, V","last_name":"Bilanovičová","first_name":"V"},{"full_name":"Rýdza, N","first_name":"N","last_name":"Rýdza"},{"full_name":"Koczka, L","first_name":"L","last_name":"Koczka"},{"first_name":"M","last_name":"Hess","full_name":"Hess, M"},{"first_name":"E","last_name":"Feraru","full_name":"Feraru, E"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"},{"last_name":"Nodzyński","first_name":"T","full_name":"Nodzyński, T"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"abstract":[{"text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.","lang":"eng"}],"external_id":{"isi":["000808733300001"],"pmid":["35683031"]},"publication_status":"published","page":"6352","article_processing_charge":"Yes","title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","day":"06","project":[{"call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988"}],"citation":{"ieee":"V. Bilanovičová et al., “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” International Journal of Molecular Sciences, vol. 23, no. 11. MDPI, p. 6352, 2022.","short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 2022;23(11):6352. doi:10.3390/ijms23116352","chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” International Journal of Molecular Sciences. MDPI, 2022. https://doi.org/10.3390/ijms23116352.","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., & Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms23116352","mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” International Journal of Molecular Sciences, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:10.3390/ijms23116352."},"type":"journal_article","acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","article_type":"original","oa_version":"Published Version","intvolume":" 23","_id":"11489","scopus_import":"1","oa":1,"file_date_updated":"2022-07-06T07:36:59Z","isi":1,"publisher":"MDPI","department":[{"_id":"JiFr"}],"date_updated":"2025-04-15T08:12:07Z","language":[{"iso":"eng"}],"month":"06","date_published":"2022-06-06T00:00:00Z"},{"citation":{"apa":"Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste, S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2022.862398","chicago":"Wang, Ren, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří Friml, Tom Beeckman, and Steffen Vanneste. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” Frontiers in Plant Science. Frontiers, 2022. https://doi.org/10.3389/fpls.2022.862398.","mla":"Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” Frontiers in Plant Science, vol. 13, 862398, Frontiers, 2022, doi:10.3389/fpls.2022.862398.","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022).","ieee":"R. Wang et al., “Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana,” Frontiers in Plant Science, vol. 13. Frontiers, 2022.","ama":"Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 2022;13. doi:10.3389/fpls.2022.862398","ista":"Wang R, Himschoot E, Chen J, Boudsocq M, Geelen D, Friml J, Beeckman T, Vanneste S. 2022. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 13, 862398."},"tmp":{"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)","short":"CC BY (4.0)"},"status":"public","day":"16","isi":1,"oa":1,"file_date_updated":"2022-07-18T08:05:15Z","language":[{"iso":"eng"}],"month":"06","date_published":"2022-06-16T00:00:00Z","publisher":"Frontiers","department":[{"_id":"JiFr"}],"date_updated":"2023-08-03T12:01:47Z","article_type":"original","oa_version":"Published Version","intvolume":" 13","type":"journal_article","acknowledgement":"RW and JC predoctoral fellows that were supported by the Chinese Science Counsil. The IPS2 benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).\r\nWe thank Jen Sheen for establishing and generously sharing the CKP family clone sets, and for providing useful feedback on the manuscript.","_id":"11589","scopus_import":"1","quality_controlled":"1","file":[{"success":1,"creator":"dernst","file_name":"2022_FrontiersPlantScience_Wang.pdf","content_type":"application/pdf","date_created":"2022-07-18T08:05:15Z","file_size":5040638,"date_updated":"2022-07-18T08:05:15Z","access_level":"open_access","relation":"main_file","checksum":"95313515637c0f84de591d204375d764","file_id":"11596"}],"has_accepted_license":"1","ddc":["580"],"year":"2022","date_created":"2022-07-17T22:01:54Z","article_number":"862398","publication_identifier":{"eissn":["1664-462X"]},"doi":"10.3389/fpls.2022.862398","publication":"Frontiers in Plant Science","article_processing_charge":"No","abstract":[{"text":"Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana.","lang":"eng"}],"publication_status":"published","external_id":{"pmid":["35783951"],"isi":["000819250500001"]},"title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Wang","first_name":"Ren","full_name":"Wang, Ren"},{"full_name":"Himschoot, Ellie","last_name":"Himschoot","first_name":"Ellie"},{"first_name":"Jian","last_name":"Chen","full_name":"Chen, Jian"},{"last_name":"Boudsocq","first_name":"Marie","full_name":"Boudsocq, Marie"},{"first_name":"Danny","last_name":"Geelen","full_name":"Geelen, Danny"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"}],"volume":13,"related_material":{"link":[{"url":"https://doi.org/10.3389/fpls.2022.1100792","relation":"erratum"}]},"pmid":1},{"has_accepted_license":"1","ddc":["575"],"corr_author":"1","file":[{"date_created":"2022-07-25T09:08:47Z","file_name":"Thesis_Gallei.pdf","content_type":"application/pdf","creator":"mgallei","file_id":"11645","access_level":"open_access","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","relation":"main_file","file_size":9730864,"date_updated":"2022-07-25T09:08:47Z"},{"creator":"mgallei","file_name":"Thesis_Gallei_source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2022-07-25T09:09:09Z","file_size":19560720,"date_updated":"2022-07-25T09:39:58Z","access_level":"closed","relation":"source_file","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","file_id":"11646"},{"date_updated":"2022-07-25T09:39:58Z","file_size":24542837,"checksum":"3994f7f20058941b5bb8a16886b21e71","relation":"source_file","access_level":"closed","file_id":"11647","description":"This is the print version of the thesis including the full appendix","creator":"mgallei","file_name":"Thesis_Gallei_to_print.pdf","content_type":"application/pdf","date_created":"2022-07-25T09:09:32Z"},{"creator":"mgallei","date_created":"2022-07-25T11:48:45Z","file_name":"Thesis_Gallei_Appendix.pdf","content_type":"application/pdf","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","relation":"main_file","access_level":"open_access","file_size":15435966,"date_updated":"2022-07-25T11:48:45Z","file_id":"11650"}],"doi":"10.15479/at:ista:11626","publication_identifier":{"isbn":["978-3-99078-019-0"],"issn":["2663-337X"]},"date_created":"2022-07-20T11:21:53Z","year":"2022","supervisor":[{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"},{"first_name":"Eilon","last_name":"Shani","full_name":"Shani, Eilon"}],"degree_awarded":"PhD","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","article_processing_charge":"No","page":"248","publication_status":"published","abstract":[{"text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.","lang":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"8138","status":"public"},{"id":"7142","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"10411","relation":"part_of_dissertation"},{"status":"public","id":"8931","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7465","status":"public"},{"relation":"part_of_dissertation","id":"9287","status":"public"},{"relation":"part_of_dissertation","id":"6260","status":"public"}]},"author":[{"full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C","last_name":"Gallei"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","citation":{"ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:10.15479/at:ista:11626","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","mla":"Gallei, Michelle C. Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11626.","apa":"Gallei, M. C. (2022). Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11626","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11626."},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"alternative_title":["ISTA Thesis"],"day":"20","status":"public","ec_funded":1,"date_published":"2022-07-20T00:00:00Z","language":[{"iso":"eng"}],"month":"07","date_updated":"2026-06-18T19:02:05Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"file_date_updated":"2022-07-25T11:48:45Z","oa":1,"_id":"11626","oa_version":"Published Version","type":"dissertation"},{"status":"public","day":"25","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"citation":{"short":"L. Li, H. Chen, S.S. Alotaibi, A. Pěnčík, M. Adamowski, O. Novák, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ieee":"L. Li et al., “RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31. National Academy of Sciences, 2022.","ista":"Li L, Chen H, Alotaibi SS, Pěnčík A, Adamowski M, Novák O, Friml J. 2022. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2121058119.","ama":"Li L, Chen H, Alotaibi SS, et al. RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(31). doi:10.1073/pnas.2121058119","chicago":"Li, Lanxin, Huihuang Chen, Saqer S. Alotaibi, Aleš Pěnčík, Maciek Adamowski, Ondřej Novák, and Jiří Friml. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2121058119.","apa":"Li, L., Chen, H., Alotaibi, S. S., Pěnčík, A., Adamowski, M., Novák, O., & Friml, J. (2022). RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2121058119","mla":"Li, Lanxin, et al. “RALF1 Peptide Triggers Biphasic Root Growth Inhibition Upstream of Auxin Biosynthesis.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31, e2121058119, National Academy of Sciences, 2022, doi:10.1073/pnas.2121058119."},"project":[{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","_id":"11723","oa_version":"Published Version","intvolume":" 119","article_type":"original","acknowledgement":"We thank Sarah M. Assmann, Kris Vissenberg, and Nadine Paris for kindly sharing seeds; Matyáš Fendrych for initiating this project and providing constant support; Lukas Fiedler for revising the manuscript; and Huibin Han and Arseny Savin for contributing to genotyping. This work was supported by the Austrian Science Fund (FWF) I 3630-B25 (to J.F.) and the Doctoral Fellowship Progrmme of the Austrian Academy of Sciences (to L.L.) We also acknowledge Taif University Researchers Supporting Project TURSP-HC2021/02 and funding “Plants as a tool for sustainable global development (no. CZ.02.1.01/0.0/0.0/16_019/0000827).”","type":"journal_article","date_published":"2022-07-25T00:00:00Z","language":[{"iso":"eng"}],"month":"07","date_updated":"2025-05-14T11:01:00Z","publisher":"National Academy of Sciences","department":[{"_id":"GradSch"},{"_id":"JiFr"}],"isi":1,"file_date_updated":"2022-08-08T07:42:09Z","oa":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.2121058119","issue":"31","publication":"Proceedings of the National Academy of Sciences of the United States of America","date_created":"2022-08-04T20:06:49Z","year":"2022","article_number":"e2121058119","has_accepted_license":"1","ddc":["580"],"corr_author":"1","file":[{"creator":"dernst","success":1,"content_type":"application/pdf","file_name":"2022_PNAS_Li.pdf","date_created":"2022-08-08T07:42:09Z","date_updated":"2022-08-08T07:42:09Z","file_size":2506262,"checksum":"ae6f19b0d9efba6687f9e4dc1bab1d6e","relation":"main_file","access_level":"open_access","file_id":"11747"}],"quality_controlled":"1","pmid":1,"author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li"},{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang","last_name":"Chen","first_name":"Huihuang"},{"full_name":"Alotaibi, Saqer S.","last_name":"Alotaibi","first_name":"Saqer S."},{"full_name":"Pěnčík, Aleš","last_name":"Pěnčík","first_name":"Aleš"},{"last_name":"Adamowski","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":119,"keyword":["Multidisciplinary"],"title":"RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis","article_processing_charge":"No","publication_status":"published","external_id":{"pmid":["35878023"],"isi":["000881496900002"]},"abstract":[{"lang":"eng","text":"Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term."}]},{"article_number":"5147","year":"2022","date_created":"2022-09-07T14:19:26Z","publication":"Nature Communications","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-022-32888-8","quality_controlled":"1","file":[{"success":1,"creator":"dernst","file_name":"2022_NatureCommunications_Konstantinova.pdf","content_type":"application/pdf","date_created":"2022-09-08T07:46:16Z","date_updated":"2022-09-08T07:46:16Z","file_size":6678579,"access_level":"open_access","relation":"main_file","checksum":"43336758c89cd6c045839089af070afe","file_id":"12063"}],"ddc":["580"],"has_accepted_license":"1","volume":13,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Konstantinova, N","last_name":"Konstantinova","first_name":"N"},{"last_name":"Hörmayer","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas"},{"first_name":"Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"full_name":"Keshkeih, R","first_name":"R","last_name":"Keshkeih"},{"orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","first_name":"Shutang","last_name":"Tan"},{"last_name":"Di Donato","first_name":"M","full_name":"Di Donato, M"},{"last_name":"Retzer","first_name":"K","full_name":"Retzer, K"},{"full_name":"Moulinier-Anzola, J","last_name":"Moulinier-Anzola","first_name":"J"},{"last_name":"Schwihla","first_name":"M","full_name":"Schwihla, M"},{"full_name":"Korbei, B","first_name":"B","last_name":"Korbei"},{"full_name":"Geisler, M","last_name":"Geisler","first_name":"M"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Luschnig","first_name":"C","full_name":"Luschnig, C"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-022-33198-9","relation":"erratum"}]},"pmid":1,"abstract":[{"text":"Directionality in the intercellular transport of the plant hormone auxin is determined by polar plasma membrane localization of PIN-FORMED (PIN) auxin transport proteins. However, apart from PIN phosphorylation at conserved motifs, no further determinants explicitly controlling polar PIN sorting decisions have been identified. Here we present Arabidopsis WAVY GROWTH 3 (WAV3) and closely related RING-finger E3 ubiquitin ligases, whose loss-of-function mutants show a striking apical-to-basal polarity switch in PIN2 localization in root meristem cells. WAV3 E3 ligases function as essential determinants for PIN polarity, acting independently from PINOID/WAG-dependent PIN phosphorylation. They antagonize ectopic deposition of de novo synthesized PIN proteins already immediately following completion of cell division, presumably via preventing PIN sorting into basal, ARF GEF-mediated trafficking. Our findings reveal an involvement of E3 ligases in the selective targeting of apically localized PINs in higher plants.","lang":"eng"}],"external_id":{"pmid":["36050482"],"isi":["000848744900004"]},"publication_status":"published","article_processing_charge":"No","title":"WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions","tmp":{"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)","short":"CC BY (4.0)"},"day":"01","status":"public","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Konstantinova, N., et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” Nature Communications, vol. 13, 5147, Springer Nature, 2022, doi:10.1038/s41467-022-32888-8.","apa":"Konstantinova, N., Hörmayer, L., Glanc, M., Keshkeih, R., Tan, S., Di Donato, M., … Luschnig, C. (2022). WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-32888-8","chicago":"Konstantinova, N, Lukas Hörmayer, Matous Glanc, R Keshkeih, Shutang Tan, M Di Donato, K Retzer, et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-32888-8.","ista":"Konstantinova N, Hörmayer L, Glanc M, Keshkeih R, Tan S, Di Donato M, Retzer K, Moulinier-Anzola J, Schwihla M, Korbei B, Geisler M, Friml J, Luschnig C. 2022. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. 13, 5147.","ama":"Konstantinova N, Hörmayer L, Glanc M, et al. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. 2022;13. doi:10.1038/s41467-022-32888-8","short":"N. Konstantinova, L. Hörmayer, M. Glanc, R. Keshkeih, S. Tan, M. Di Donato, K. Retzer, J. Moulinier-Anzola, M. Schwihla, B. Korbei, M. Geisler, J. Friml, C. Luschnig, Nature Communications 13 (2022).","ieee":"N. Konstantinova et al., “WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions,” Nature Communications, vol. 13. Springer Nature, 2022."},"type":"journal_article","acknowledgement":"We would like to thank Tatsuo Sakai, Marcus Heisler, Toru Fujiwara, Lucia Strader, Christian Hardtke, Malcolm Bennett, Claus Schwechheimer, Gerd Jürgens and Remko Offringa for sharing published materials and Alba Grau Gimeno for support. We are greatly indebted to Bert de Rybel for supporting N.K. and M.G. to work on the final stages of manuscript preparation as postdocs in his laboratory. A full-length SOR1 cDNA clone (J090099M14) was obtained from the National Agriculture and Food Research Organization (NARO, Japan). Support by the Multiscale Imaging Core Facility at the BOKU is greatly acknowledged. This work has been supported by grants from the Austrian Science Fund (FWF P25931-B16; P31493-B25 to Christian Luschnig; I3630-B25 to Jiří Friml; P30850-B32 to Barbara Korbei) and from the Swiss National Funds (31003A-165877/1 to Markus Geisler) and the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant agreement No 885979 to Matouš Glanc).","article_type":"original","oa_version":"Published Version","intvolume":" 13","_id":"12052","scopus_import":"1","oa":1,"file_date_updated":"2022-09-08T07:46:16Z","isi":1,"publisher":"Springer Nature","department":[{"_id":"JiFr"}],"date_updated":"2025-04-15T07:32:09Z","month":"09","language":[{"iso":"eng"}],"date_published":"2022-09-01T00:00:00Z"},{"issue":"12","doi":"10.1093/plcell/koac270","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"publication":"The Plant Cell","year":"2022","date_created":"2022-09-07T14:19:39Z","has_accepted_license":"1","ddc":["580"],"quality_controlled":"1","file":[{"file_name":"2022_PlantCell_Tian.pdf","content_type":"application/pdf","date_created":"2023-01-20T08:29:12Z","success":1,"creator":"dernst","file_id":"12318","date_updated":"2023-01-20T08:29:12Z","file_size":3282540,"access_level":"open_access","checksum":"1c606d9545f29dfca15235f69ad27b58","relation":"main_file"}],"related_material":{"link":[{"url":"https://doi.org/10.1093/plcell/koac342","relation":"erratum"}]},"pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Z","last_name":"Tian","full_name":"Tian, Z"},{"full_name":"Zhang, Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","last_name":"Zhang"},{"full_name":"Zhu, L","first_name":"L","last_name":"Zhu"},{"full_name":"Jiang, B","last_name":"Jiang","first_name":"B"},{"last_name":"Wang","first_name":"H","full_name":"Wang, H"},{"last_name":"Gao","first_name":"R","full_name":"Gao, R"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"G","last_name":"Xiao","full_name":"Xiao, G"}],"volume":34,"title":"Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum)","page":"4816-4839","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Strigolactones (SLs) are a class of phytohormones that regulate plant shoot branching and adventitious root development. However, little is known regarding the role of SLs in controlling the behavior of the smallest unit of the organism, the single cell. Here, taking advantage of a classic single-cell model offered by the cotton (Gossypium hirsutum) fiber cell, we show that SLs, whose biosynthesis is fine-tuned by gibberellins (GAs), positively regulate cell elongation and cell wall thickness by promoting the biosynthesis of very-long-chain fatty acids (VLCFAs) and cellulose, respectively. Furthermore, we identified two layers of transcription factors (TFs) involved in the hierarchical regulation of this GA-SL crosstalk. The top-layer TF GROWTH-REGULATING FACTOR 4 (GhGRF4) directly activates expression of the SL biosynthetic gene DWARF27 (D27) to increase SL accumulation in fiber cells and GAs induce GhGRF4 expression. SLs induce the expression of four second-layer TF genes (GhNAC100-2, GhBLH51, GhGT2, and GhB9SHZ1), which transmit SL signals downstream to two ketoacyl-CoA synthase genes (KCS) and three cellulose synthase (CesA) genes by directly activating their transcription. Finally, the KCS and CesA enzymes catalyze the biosynthesis of very long chain fatty acids and cellulose, respectively, to regulate development of high-grade cotton fibers. In addition to providing a theoretical basis for cotton fiber improvement, our results shed light on SL signaling in plant development at the single-cell level."}],"publication_status":"published","external_id":{"pmid":["36040191"],"isi":["000852753000001"]},"day":"01","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"citation":{"apa":"Tian, Z., Zhang, Y., Zhu, L., Jiang, B., Wang, H., Gao, R., … Xiao, G. (2022). Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac270","chicago":"Tian, Z, Yuzhou Zhang, L Zhu, B Jiang, H Wang, R Gao, Jiří Friml, and G Xiao. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” The Plant Cell. Oxford University Press, 2022. https://doi.org/10.1093/plcell/koac270.","mla":"Tian, Z., et al. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” The Plant Cell, vol. 34, no. 12, Oxford University Press, 2022, pp. 4816–39, doi:10.1093/plcell/koac270.","short":"Z. Tian, Y. Zhang, L. Zhu, B. Jiang, H. Wang, R. Gao, J. Friml, G. Xiao, The Plant Cell 34 (2022) 4816–4839.","ieee":"Z. Tian et al., “Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum),” The Plant Cell, vol. 34, no. 12. Oxford University Press, pp. 4816–4839, 2022.","ista":"Tian Z, Zhang Y, Zhu L, Jiang B, Wang H, Gao R, Friml J, Xiao G. 2022. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. 34(12), 4816–4839.","ama":"Tian Z, Zhang Y, Zhu L, et al. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. 2022;34(12):4816-4839. doi:10.1093/plcell/koac270"},"project":[{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","grant_number":"P29988","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development"}],"_id":"12053","scopus_import":"1","article_type":"original","oa_version":"Published Version","intvolume":" 34","acknowledgement":"This work was supported by the National Natural Science Foundation of China (32070549), Shaanxi Youth Entrusted Talent Program (20190205), Fundamental Research Funds for the Central Universities (GK202002005 and GK202201017), Young Elite Scientists Sponsorship Program by China Association for Science and Technology (CAST) (2019-2021QNRC001), State Key Laboratory of Cotton Biology Open Fund (CB2020A12 and CB2021A21) and FWF Stand-alone Project (P29988).","type":"journal_article","language":[{"iso":"eng"}],"month":"12","date_published":"2022-12-01T00:00:00Z","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","date_updated":"2025-04-15T08:12:07Z","isi":1,"oa":1,"file_date_updated":"2023-01-20T08:29:12Z"},{"_id":"12054","scopus_import":"1","acknowledgement":"We thank the Cryo-EM Center of the University of Science and Technology of China (USTC) and the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science, for the EM facility support; we thank B. Zhu, X. Huang and all the other staff members for their technical support on cryo-EM data collection. We thank J. Ren for his technical support with the transport assays and M. Seeger for providing the sybody libraries. This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB 37020204 to D.L. and XDB37020103 to Linfeng Sun), National Natural Science Foundation of China (82151215 and 31870726 to D.L., 31900885 to X.L., and 31870732 to Linfeng Sun), Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun), the Fundamental Research Funds for the Central Universities (WK9100000031 to Linfeng Sun), and the USTC Research Funds of the Double First-Class Initiative (YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation, and a Young Scholar Award from the Cyrus Tang Foundation.","type":"journal_article","article_type":"original","intvolume":" 609","oa_version":"Published Version","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"date_updated":"2023-08-03T13:41:44Z","month":"08","language":[{"iso":"eng"}],"date_published":"2022-08-02T00:00:00Z","oa":1,"file_date_updated":"2022-09-08T08:02:54Z","isi":1,"status":"public","day":"02","tmp":{"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)","short":"CC BY (4.0)"},"citation":{"apa":"Yang, Z., Xia, J., Hong, J., Zhang, C., Wei, H., Ying, W., … Sun, L. (2022). Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05143-9","chicago":"Yang, Z, J Xia, J Hong, C Zhang, H Wei, W Ying, C Sun, et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05143-9.","mla":"Yang, Z., et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” Nature, vol. 609, no. 7927, Springer Nature, 2022, pp. 611–15, doi:10.1038/s41586-022-05143-9.","ieee":"Z. Yang et al., “Structural insights into auxin recognition and efflux by Arabidopsis PIN1,” Nature, vol. 609, no. 7927. Springer Nature, pp. 611–615, 2022.","short":"Z. Yang, J. Xia, J. Hong, C. Zhang, H. Wei, W. Ying, C. Sun, L. Sun, Y. Mao, Y. Gao, S. Tan, J. Friml, D. Li, X. Liu, L. Sun, Nature 609 (2022) 611–615.","ista":"Yang Z, Xia J, Hong J, Zhang C, Wei H, Ying W, Sun C, Sun L, Mao Y, Gao Y, Tan S, Friml J, Li D, Liu X, Sun L. 2022. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. 609(7927), 611–615.","ama":"Yang Z, Xia J, Hong J, et al. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. 2022;609(7927):611-615. doi:10.1038/s41586-022-05143-9"},"pmid":1,"volume":609,"author":[{"full_name":"Yang, Z","last_name":"Yang","first_name":"Z"},{"first_name":"J","last_name":"Xia","full_name":"Xia, J"},{"full_name":"Hong, J","first_name":"J","last_name":"Hong"},{"last_name":"Zhang","first_name":"C","full_name":"Zhang, C"},{"first_name":"H","last_name":"Wei","full_name":"Wei, H"},{"last_name":"Ying","first_name":"W","full_name":"Ying, W"},{"full_name":"Sun, C","first_name":"C","last_name":"Sun"},{"full_name":"Sun, L","first_name":"L","last_name":"Sun"},{"last_name":"Mao","first_name":"Y","full_name":"Mao, Y"},{"last_name":"Gao","first_name":"Y","full_name":"Gao, Y"},{"full_name":"Tan, S","first_name":"S","last_name":"Tan"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"D","last_name":"Li","full_name":"Li, D"},{"full_name":"Liu, X","last_name":"Liu","first_name":"X"},{"last_name":"Sun","first_name":"L","full_name":"Sun, L"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Structural insights into auxin recognition and efflux by Arabidopsis PIN1","abstract":[{"lang":"eng","text":"Polar auxin transport is unique to plants and coordinates their growth and development1,2. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and drive polar auxin transport3,4; however, their structures and transport mechanisms remain largely unknown. Here, we report three inward-facing conformation structures of Arabidopsis thaliana PIN1: the apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The transmembrane domain of PIN1 shares a conserved NhaA fold5. In the substrate-bound structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding. NPA competes with IAA for the same site at the intracellular pocket, but with a much higher affinity. These findings inform our understanding of the substrate recognition and transport mechanisms of PINs and set up a framework for future research on directional auxin transport, one of the most crucial processes underlying plant development."}],"publication_status":"published","external_id":{"pmid":["35917925"],"isi":["000848082900002"]},"page":"611-615","article_processing_charge":"No","publication":"Nature","issue":"7927","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"doi":"10.1038/s41586-022-05143-9","year":"2022","date_created":"2022-09-07T14:19:52Z","ddc":["580"],"has_accepted_license":"1","file":[{"file_id":"12064","relation":"main_file","checksum":"3136a585f8e1c7e73b5e1418b3d01898","access_level":"open_access","file_size":32344580,"date_updated":"2022-09-08T08:02:54Z","date_created":"2022-09-08T08:02:54Z","content_type":"application/pdf","file_name":"2022_Nature_Yang.pdf","creator":"dernst","success":1}],"quality_controlled":"1"},{"ddc":["580"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2022.11.006"}],"quality_controlled":"1","publication":"Developmental Cell","issue":"23","publication_identifier":{"issn":["1534-5807"]},"doi":"10.1016/j.devcel.2022.11.006","year":"2022","date_created":"2023-01-12T11:57:00Z","title":"Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"abstract":[{"text":"Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.","lang":"eng"}],"external_id":{"pmid":["36473460"],"isi":["000919603800005"]},"publication_status":"published","page":"2638-2651.e6","article_processing_charge":"No","pmid":1,"volume":57,"OA_place":"publisher","author":[{"full_name":"Xiao, Huixin","first_name":"Huixin","last_name":"Xiao"},{"full_name":"Hu, Yumei","last_name":"Hu","first_name":"Yumei"},{"first_name":"Yaping","last_name":"Wang","full_name":"Wang, Yaping"},{"last_name":"Cheng","first_name":"Jinkui","full_name":"Cheng, Jinkui"},{"full_name":"Wang, Jinyi","first_name":"Jinyi","last_name":"Wang"},{"full_name":"Chen, Guojingwei","first_name":"Guojingwei","last_name":"Chen"},{"last_name":"Li","first_name":"Qian","full_name":"Li, Qian"},{"full_name":"Wang, Shuwei","first_name":"Shuwei","last_name":"Wang"},{"last_name":"Wang","first_name":"Yalu","full_name":"Wang, Yalu"},{"full_name":"Wang, Shao-Shuai","last_name":"Wang","first_name":"Shao-Shuai"},{"last_name":"Wang","first_name":"Yi","full_name":"Wang, Yi"},{"first_name":"Wei","last_name":"Xuan","full_name":"Xuan, Wei"},{"full_name":"Li, Zhen","last_name":"Li","first_name":"Zhen"},{"first_name":"Yan","last_name":"Guo","full_name":"Guo, Yan"},{"first_name":"Zhizhong","last_name":"Gong","full_name":"Gong, Zhizhong"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"full_name":"Zhang, Jing","first_name":"Jing","last_name":"Zhang"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Xiao, Huixin, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental Cell, vol. 57, no. 23, Elsevier, 2022, p. 2638–2651.e6, doi:10.1016/j.devcel.2022.11.006.","chicago":"Xiao, Huixin, Yumei Hu, Yaping Wang, Jinkui Cheng, Jinyi Wang, Guojingwei Chen, Qian Li, et al. “Nitrate Availability Controls Translocation of the Transcription Factor NAC075 for Cell-Type-Specific Reprogramming of Root Growth.” Developmental Cell. Elsevier, 2022. https://doi.org/10.1016/j.devcel.2022.11.006.","apa":"Xiao, H., Hu, Y., Wang, Y., Cheng, J., Wang, J., Chen, G., … Zhang, J. (2022). Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2022.11.006","ama":"Xiao H, Hu Y, Wang Y, et al. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 2022;57(23):2638-2651.e6. doi:10.1016/j.devcel.2022.11.006","ista":"Xiao H, Hu Y, Wang Y, Cheng J, Wang J, Chen G, Li Q, Wang S, Wang Y, Wang S-S, Wang Y, Xuan W, Li Z, Guo Y, Gong Z, Friml J, Zhang J. 2022. Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth. Developmental Cell. 57(23), 2638–2651.e6.","short":"H. Xiao, Y. Hu, Y. Wang, J. Cheng, J. Wang, G. Chen, Q. Li, S. Wang, Y. Wang, S.-S. Wang, Y. Wang, W. Xuan, Z. Li, Y. Guo, Z. Gong, J. Friml, J. Zhang, Developmental Cell 57 (2022) 2638–2651.e6.","ieee":"H. Xiao et al., “Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth,” Developmental Cell, vol. 57, no. 23. Elsevier, p. 2638–2651.e6, 2022."},"status":"public","day":"05","OA_type":"free access","publisher":"Elsevier","department":[{"_id":"JiFr"}],"date_updated":"2026-06-18T17:23:10Z","month":"12","language":[{"iso":"eng"}],"date_published":"2022-12-05T00:00:00Z","oa":1,"isi":1,"_id":"12120","scopus_import":"1","acknowledgement":"The authors are grateful to Jörg Kudla, Ying Miao, Yu Zheng, Gang Li, and Jun Zheng for providing published materials and to Wenkun Zhou and Caifu Jiang for helpful discussions. This work was supported by grants from the National Key Research and Development Program of China (2021YFF1000500), the National Natural Science Foundation of China (32170265 and 32022007), the Beijing Municipal Natural Science Foundation (5192011), and the Chinese Universities Scientific Fund (2022TC153).","type":"journal_article","article_type":"original","intvolume":" 57","oa_version":"Published Version"},{"volume":221,"author":[{"full_name":"Zhao, Jierui","last_name":"Zhao","first_name":"Jierui"},{"full_name":"Bui, Mai Thu","first_name":"Mai Thu","last_name":"Bui"},{"last_name":"Ma","first_name":"Juncai","full_name":"Ma, Juncai"},{"last_name":"Künzl","first_name":"Fabian","full_name":"Künzl, Fabian"},{"full_name":"Picchianti, Lorenzo","last_name":"Picchianti","first_name":"Lorenzo"},{"full_name":"De La Concepcion, Juan Carlos","last_name":"De La Concepcion","first_name":"Juan Carlos"},{"first_name":"Yixuan","last_name":"Chen","full_name":"Chen, Yixuan"},{"first_name":"Sofia","last_name":"Petsangouraki","full_name":"Petsangouraki, Sofia"},{"full_name":"Mohseni, Azadeh","first_name":"Azadeh","last_name":"Mohseni"},{"first_name":"Marta","last_name":"García-Leon","full_name":"García-Leon, Marta"},{"first_name":"Marta Salas","last_name":"Gomez","full_name":"Gomez, Marta Salas"},{"first_name":"Caterina","last_name":"Giannini","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"first_name":"Dubois","last_name":"Gwennogan","full_name":"Gwennogan, Dubois"},{"first_name":"Roksolana","last_name":"Kobylinska","full_name":"Kobylinska, Roksolana"},{"full_name":"Clavel, Marion","last_name":"Clavel","first_name":"Marion"},{"first_name":"Swen","last_name":"Schellmann","full_name":"Schellmann, Swen"},{"full_name":"Jaillais, Yvon","last_name":"Jaillais","first_name":"Yvon"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kang","first_name":"Byung-Ho","full_name":"Kang, Byung-Ho"},{"full_name":"Dagdas, Yasin","first_name":"Yasin","last_name":"Dagdas"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"abstract":[{"lang":"eng","text":"Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants."}],"external_id":{"isi":["000932958800001"],"pmid":["36260289"]},"publication_status":"published","article_processing_charge":"No","title":"Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole","keyword":["Cell Biology"],"article_number":"e202203139","year":"2022","date_created":"2023-01-12T11:57:10Z","publication":"Journal of Cell Biology","issue":"12","doi":"10.1083/jcb.202203139","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"file":[{"creator":"dernst","success":1,"file_name":"2022_JCB_Zhao.pdf","content_type":"application/pdf","date_created":"2023-01-23T10:30:11Z","date_updated":"2023-01-23T10:30:11Z","file_size":10365777,"checksum":"050b5cc4b25e6b94fe3e3cbfe0f5c06b","relation":"main_file","access_level":"open_access","file_id":"12342"}],"quality_controlled":"1","ddc":["580"],"has_accepted_license":"1","type":"journal_article","acknowledgement":"We thank Suayip Ustün, Karin Schumacher, Erika Isono, Gerd Juergens, Takashi Ueda, Daniel Hofius, and Liwen Jiang for sharing published materials.\r\nWe acknowledge funding from Austrian Academy of Sciences, Austrian Science Fund (FWF, P 32355, P 34944), Austrian Science Fund (FWF-SFB F79), Vienna Science and Technology\r\nFund (WWTF, LS17-047) to Y. Dagdas; Austrian Academy of Sciences DOC Fellowship to J. Zhao, Marie Curie VIP2 Fellowship to J.C. De La Concepcion and M. Clavel; Hong Kong Research Grant Council (GRF14121019, 14113921, AoE/M-05/12, C4002-17G) to B.-H. Kang. We thank Vienna Biocenter Core Facilities (VBCF) Protein Chemistry, Biooptics, Plant Sciences, Molecular Biology, and Protein Technologies. We thank J. Matthew Watson\r\nand members of the Dagdas lab for the critical reading and editing of the manuscript.","article_type":"original","intvolume":" 221","oa_version":"Published Version","_id":"12121","scopus_import":"1","oa":1,"file_date_updated":"2023-01-23T10:30:11Z","isi":1,"publisher":"Rockefeller University Press","department":[{"_id":"JiFr"}],"date_updated":"2023-08-03T14:20:15Z","language":[{"iso":"eng"}],"month":"12","date_published":"2022-12-01T00:00:00Z","tmp":{"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)","short":"CC BY (4.0)"},"day":"01","status":"public","citation":{"chicago":"Zhao, Jierui, Mai Thu Bui, Juncai Ma, Fabian Künzl, Lorenzo Picchianti, Juan Carlos De La Concepcion, Yixuan Chen, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” Journal of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202203139.","apa":"Zhao, J., Bui, M. T., Ma, J., Künzl, F., Picchianti, L., De La Concepcion, J. C., … Dagdas, Y. (2022). Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202203139","mla":"Zhao, Jierui, et al. “Plant Autophagosomes Mature into Amphisomes Prior to Their Delivery to the Central Vacuole.” Journal of Cell Biology, vol. 221, no. 12, e202203139, Rockefeller University Press, 2022, doi:10.1083/jcb.202203139.","short":"J. Zhao, M.T. Bui, J. Ma, F. Künzl, L. Picchianti, J.C. De La Concepcion, Y. Chen, S. Petsangouraki, A. Mohseni, M. García-Leon, M.S. Gomez, C. Giannini, D. Gwennogan, R. Kobylinska, M. Clavel, S. Schellmann, Y. Jaillais, J. Friml, B.-H. Kang, Y. Dagdas, Journal of Cell Biology 221 (2022).","ieee":"J. Zhao et al., “Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole,” Journal of Cell Biology, vol. 221, no. 12. Rockefeller University Press, 2022.","ista":"Zhao J, Bui MT, Ma J, Künzl F, Picchianti L, De La Concepcion JC, Chen Y, Petsangouraki S, Mohseni A, García-Leon M, Gomez MS, Giannini C, Gwennogan D, Kobylinska R, Clavel M, Schellmann S, Jaillais Y, Friml J, Kang B-H, Dagdas Y. 2022. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 221(12), e202203139.","ama":"Zhao J, Bui MT, Ma J, et al. Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole. Journal of Cell Biology. 2022;221(12). doi:10.1083/jcb.202203139"}},{"pmid":1,"author":[{"first_name":"Jian","last_name":"Huang","full_name":"Huang, Jian"},{"first_name":"Lei","last_name":"Zhao","full_name":"Zhao, Lei"},{"last_name":"Malik","first_name":"Shikha","full_name":"Malik, Shikha"},{"full_name":"Gentile, Benjamin R.","first_name":"Benjamin R.","last_name":"Gentile"},{"full_name":"Xiong, Va","last_name":"Xiong","first_name":"Va"},{"last_name":"Arazi","first_name":"Tzahi","full_name":"Arazi, Tzahi"},{"first_name":"Heather A.","last_name":"Owen","full_name":"Owen, Heather A."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"full_name":"Zhao, Dazhong","last_name":"Zhao","first_name":"Dazhong"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":13,"keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"title":"Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis","article_processing_charge":"No","publication_status":"published","external_id":{"pmid":["36379956"],"isi":["000884426700001"]},"abstract":[{"text":"Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants.","lang":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-022-34723-6","publication":"Nature Communications","date_created":"2023-01-12T12:02:41Z","year":"2022","article_number":"6960","has_accepted_license":"1","ddc":["580"],"file":[{"creator":"dernst","success":1,"file_name":"2022_NatureCommunications_Huang.pdf","content_type":"application/pdf","date_created":"2023-01-23T11:17:33Z","date_updated":"2023-01-23T11:17:33Z","file_size":3375249,"checksum":"233922a7b9507d9d48591e6799e4526e","relation":"main_file","access_level":"open_access","file_id":"12346"}],"quality_controlled":"1","scopus_import":"1","_id":"12130","intvolume":" 13","oa_version":"Published Version","article_type":"original","type":"journal_article","acknowledgement":"We thank A. Cheung,W. Lukowitz, V.Walbot, D.Weijers, and R. Yadegari for critically reading the manuscript; E. Xiong and G. Zhang for preparing some experiments, T. Schuck, J. Gonnering, and P. Engevold for plant care, the Arabidopsis Biological Resource Center (ABRC) for ARF10,ARF16, ARF17, EMS1,MIR160a BAC clones and cDNAs, the SALK_090804 seed, T. Nakagawa for pGBW vectors, Y. Zhao for the YUC1 cDNA, Q. Chen for the pHEE401E vector, R. Yadegari for pAT5G01860::n1GFP, pAT5G45980:n1GFP, pAT5G50490::n1GFP, pAT5G56200:n1GFP vectors, and D.Weijers for the pGreenII KAN SV40-3×GFP and R2D2 vectors, W. Yang for the splmutant, Y. Qin for the pKNU::KNU-VENUS vector and seed, G. Tang for the STTM160/160-48 vector, and L. Colombo for pPIN1::PIN1-GFP spl and pin1-5 seeds. This work was supported by the US National Science Foundation (NSF)-Israel Binational Science Foundation (BSF) research grant to D.Z. (IOS-1322796) and T.A. (2012756). D.Z. also\r\ngratefully acknowledges supports of the Shaw Scientist Award from the Greater Milwaukee Foundation, USDA National Institute of Food and Agriculture (NIFA, 2022-67013-36294), the UWM Discovery and Innovation Grant, the Bradley Catalyst Award from the UWM Research\r\nFoundation, and WiSys and UW System Applied Research Funding Programs.","date_published":"2022-11-15T00:00:00Z","language":[{"iso":"eng"}],"month":"11","date_updated":"2025-07-08T09:01:02Z","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","isi":1,"file_date_updated":"2023-01-23T11:17:33Z","oa":1,"day":"15","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"citation":{"ista":"Huang J, Zhao L, Malik S, Gentile BR, Xiong V, Arazi T, Owen HA, Friml J, Zhao D. 2022. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 13, 6960.","ama":"Huang J, Zhao L, Malik S, et al. Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. 2022;13. doi:10.1038/s41467-022-34723-6","short":"J. Huang, L. Zhao, S. Malik, B.R. Gentile, V. Xiong, T. Arazi, H.A. Owen, J. Friml, D. Zhao, Nature Communications 13 (2022).","ieee":"J. Huang et al., “Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis,” Nature Communications, vol. 13. Springer Nature, 2022.","mla":"Huang, Jian, et al. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” Nature Communications, vol. 13, 6960, Springer Nature, 2022, doi:10.1038/s41467-022-34723-6.","apa":"Huang, J., Zhao, L., Malik, S., Gentile, B. R., Xiong, V., Arazi, T., … Zhao, D. (2022). Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-34723-6","chicago":"Huang, Jian, Lei Zhao, Shikha Malik, Benjamin R. Gentile, Va Xiong, Tzahi Arazi, Heather A. Owen, Jiří Friml, and Dazhong Zhao. “Specification of Female Germline by MicroRNA Orchestrated Auxin Signaling in Arabidopsis.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-34723-6."}},{"isi":1,"oa":1,"language":[{"iso":"eng"}],"month":"11","date_published":"2022-11-03T00:00:00Z","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","date_updated":"2025-04-14T07:45:02Z","article_type":"original","oa_version":"Submitted Version","intvolume":" 611","acknowledgement":"This research was supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria. We thank C. Gehring for suggestions and advice; and K. U. Torii and G. Stacey for seeds and plasmids. This project was funded by a European Research Council Advanced Grant (ETAP-742985). M.F.K. and R.N. acknowledge the support of the EU MSCA-IF project CrysPINs (792329). M.K. was supported by the project POWR.03.05.00-00-Z302/17 Universitas Copernicana Thoruniensis in Futuro–IDS “Academia Copernicana”. CIDG acknowledges support from UKRI under Future Leaders Fellowship grant number MR/T020652/1.","type":"journal_article","_id":"12144","scopus_import":"1","citation":{"mla":"Qi, Linlin, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” Nature, vol. 611, no. 7934, Springer Nature, 2022, pp. 133–38, doi:10.1038/s41586-022-05369-7.","apa":"Qi, L., Kwiatkowski, M., Chen, H., Hörmayer, L., Sinclair, S. A., Zou, M., … Friml, J. (2022). Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05369-7","chicago":"Qi, Linlin, Mateusz Kwiatkowski, Huihuang Chen, Lukas Hörmayer, Scott A Sinclair, Minxia Zou, Charo I. del Genio, et al. “Adenylate Cyclase Activity of TIR1/AFB Auxin Receptors in Plants.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-05369-7.","ama":"Qi L, Kwiatkowski M, Chen H, et al. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 2022;611(7934):133-138. doi:10.1038/s41586-022-05369-7","ista":"Qi L, Kwiatkowski M, Chen H, Hörmayer L, Sinclair SA, Zou M, del Genio CI, Kubeš MF, Napier R, Jaworski K, Friml J. 2022. Adenylate cyclase activity of TIR1/AFB auxin receptors in plants. Nature. 611(7934), 133–138.","short":"L. Qi, M. Kwiatkowski, H. Chen, L. Hörmayer, S.A. Sinclair, M. Zou, C.I. del Genio, M.F. Kubeš, R. Napier, K. Jaworski, J. Friml, Nature 611 (2022) 133–138.","ieee":"L. Qi et al., “Adenylate cyclase activity of TIR1/AFB auxin receptors in plants,” Nature, vol. 611, no. 7934. Springer Nature, pp. 133–138, 2022."},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"day":"03","status":"public","page":"133-138","article_processing_charge":"No","abstract":[{"text":"The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants.","lang":"eng"}],"external_id":{"isi":["000875061600013"],"pmid":["36289340"]},"publication_status":"published","title":"Adenylate cyclase activity of TIR1/AFB auxin receptors in plants","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Qi","first_name":"Linlin","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin"},{"last_name":"Kwiatkowski","first_name":"Mateusz","full_name":"Kwiatkowski, Mateusz"},{"last_name":"Chen","first_name":"Huihuang","id":"83c96512-15b2-11ec-abd3-b7eede36184f","full_name":"Chen, Huihuang"},{"first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926"},{"last_name":"Sinclair","first_name":"Scott A","full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zou","first_name":"Minxia","full_name":"Zou, Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"full_name":"del Genio, Charo I.","last_name":"del Genio","first_name":"Charo I."},{"full_name":"Kubeš, Martin F.","first_name":"Martin F.","last_name":"Kubeš"},{"last_name":"Napier","first_name":"Richard","full_name":"Napier, Richard"},{"first_name":"Krzysztof","last_name":"Jaworski","full_name":"Jaworski, Krzysztof"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"volume":611,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"pmid":1,"corr_author":"1","quality_controlled":"1","main_file_link":[{"url":"http://wrap.warwick.ac.uk/168325/1/WRAP-denylate-cyclase-activity-TIR1-AFB-auxin-receptors-root-growth-22.pdf","open_access":"1"}],"year":"2022","date_created":"2023-01-12T12:06:05Z","issue":"7934","doi":"10.1038/s41586-022-05369-7","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publication":"Nature"}]