[{"type":"journal_article","fulldoi":"https://doi.org/10.1104/pp.113.217018","year":"2013","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"2","publisher":"American Society of Plant Biologists","day":"01","volume":162,"abstract":[{"lang":"eng","text":"The phytohormone auxin regulates virtually every aspect of plant development. To identify new genes involved in auxin activity, a genetic screen was performed for Arabidopsis (Arabidopsis thaliana) mutants with altered expression of the auxin-responsive reporter DR5rev:GFP. One of the mutants recovered in the screen, designated as weak auxin response3 (wxr3), exhibits much lower DR5rev:GFP expression when treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid and displays severe defects in root development. The wxr3 mutant decreases polar auxin transport and results in a disruption of the asymmetric auxin distribution. The levels of the auxin transporters AUXIN1 and PIN-FORMED are dramatically reduced in the wxr3 root tip. Molecular analyses demonstrate that WXR3 is ROOT ULTRAVIOLET B-SENSITIVE1 (RUS1), a member of the conserved Domain of Unknown Function647 protein family found in diverse eukaryotic organisms. Our data suggest that RUS1/WXR3 plays an essential role in the regulation of polar auxin transport by maintaining the proper level of auxin transporters on the plasma membrane."}],"scopus_import":"1","month":"06","publication":"Plant Physiology","external_id":{"pmid":["23580592"],"isi":["000319819900034"]},"oa":1,"article_processing_charge":"No","author":[{"last_name":"Yu","first_name":"Hong","full_name":"Yu, Hong"},{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"full_name":"Peer, Wendy","last_name":"Peer","first_name":"Wendy"},{"full_name":"Swarup, Ranjan","last_name":"Swarup","first_name":"Ranjan"},{"first_name":"Songqing","last_name":"Ye","full_name":"Ye, Songqing"},{"full_name":"Ge, Lei","last_name":"Ge","first_name":"Lei"},{"full_name":"Cohen, Jerry","first_name":"Jerry","last_name":"Cohen"},{"full_name":"Murphy, Angus","last_name":"Murphy","first_name":"Angus"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Estelle, Mark","last_name":"Estelle","first_name":"Mark"}],"pmid":1,"date_published":"2013-06-01T00:00:00Z","publication_status":"published","page":"965 - 976","isi":1,"title":"Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis","doi":"10.1104/pp.113.217018","quality_controlled":"1","_id":"2835","date_updated":"2025-09-29T13:48:15Z","intvolume":"       162","date_created":"2018-12-11T11:59:51Z","publist_id":"3964","language":[{"iso":"eng"}],"oa_version":"Submitted Version","status":"public","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668084/"}],"department":[{"_id":"JiFr"}],"citation":{"short":"H. Yu, M. Karampelias, S. Robert, W. Peer, R. Swarup, S. Ye, L. Ge, J. Cohen, A. Murphy, J. Friml, M. Estelle, Plant Physiology 162 (2013) 965–976.","chicago":"Yu, Hong, Michael Karampelias, Stéphanie Robert, Wendy Peer, Ranjan Swarup, Songqing Ye, Lei Ge, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3 Is Essential for Polar Auxin Transport in Arabidopsis.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1104/pp.113.217018\">https://doi.org/10.1104/pp.113.217018</a>.","apa":"Yu, H., Karampelias, M., Robert, S., Peer, W., Swarup, R., Ye, S., … Estelle, M. (2013). Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.113.217018\">https://doi.org/10.1104/pp.113.217018</a>","ieee":"H. Yu <i>et al.</i>, “Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis,” <i>Plant Physiology</i>, vol. 162, no. 2. American Society of Plant Biologists, pp. 965–976, 2013.","mla":"Yu, Hong, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3 Is Essential for Polar Auxin Transport in Arabidopsis.” <i>Plant Physiology</i>, vol. 162, no. 2, American Society of Plant Biologists, 2013, pp. 965–76, doi:<a href=\"https://doi.org/10.1104/pp.113.217018\">10.1104/pp.113.217018</a>.","ista":"Yu H, Karampelias M, Robert S, Peer W, Swarup R, Ye S, Ge L, Cohen J, Murphy A, Friml J, Estelle M. 2013. Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. Plant Physiology. 162(2), 965–976.","ama":"Yu H, Karampelias M, Robert S, et al. Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. <i>Plant Physiology</i>. 2013;162(2):965-976. doi:<a href=\"https://doi.org/10.1104/pp.113.217018\">10.1104/pp.113.217018</a>"}},{"issue":"9","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis"}],"fulldoi":"https://doi.org/10.1016/j.cub.2013.03.064","year":"2013","type":"journal_article","article_processing_charge":"No","publication":"Current Biology","external_id":{"isi":["000318750900035"]},"month":"05","scopus_import":"1","abstract":[{"text":"As soon as a seed germinates, plant growth relates to gravity to ensure that the root penetrates the soil and the shoot expands aerially. Whereas mechanisms of positive and negative orthogravitropism of primary roots and shoots are relatively well understood [1-3], lateral organs often show more complex growth behavior [4]. Lateral roots (LRs) seemingly suppress positive gravitropic growth and show a defined gravitropic set-point angle (GSA) that allows radial expansion of the root system (plagiotropism) [3, 4]. Despite its eminent importance for root architecture, it so far remains completely unknown how lateral organs partially suppress positive orthogravitropism. Here we show that the phytohormone auxin steers GSA formation and limits positive orthogravitropism in LR. Low and high auxin levels/signaling lead to radial or axial root systems, respectively. At a cellular level, it is the auxin transport-dependent regulation of asymmetric growth in the elongation zone that determines GSA. Our data suggest that strong repression of PIN4/PIN7 and transient PIN3 expression limit auxin redistribution in young LR columella cells. We conclude that PIN activity, by temporally limiting the asymmetric auxin fluxes in the tip of LRs, induces transient, differential growth responses in the elongation zone and, consequently, controls root architecture.","lang":"eng"}],"day":"06","volume":23,"publisher":"Cell Press","title":"An auxin transport mechanism restricts positive orthogravitropism in lateral roots","isi":1,"doi":"10.1016/j.cub.2013.03.064","author":[{"full_name":"Rosquete, Michel","last_name":"Rosquete","first_name":"Michel"},{"full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim","orcid":"0000-0002-6862-1247","first_name":"Daniel"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","last_name":"Marhavy","first_name":"Peter","full_name":"Marhavy, Peter"},{"first_name":"Elke","last_name":"Barbez","full_name":"Barbez, Elke"},{"full_name":"Stelzer, Ernst","first_name":"Ernst","last_name":"Stelzer"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"first_name":"Alexis","last_name":"Maizel","full_name":"Maizel, Alexis"},{"full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"}],"date_published":"2013-05-06T00:00:00Z","publication_status":"published","page":"817 - 822","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"citation":{"ieee":"M. Rosquete <i>et al.</i>, “An auxin transport mechanism restricts positive orthogravitropism in lateral roots,” <i>Current Biology</i>, vol. 23, no. 9. Cell Press, pp. 817–822, 2013.","ama":"Rosquete M, von Wangenheim D, Marhavý P, et al. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. <i>Current Biology</i>. 2013;23(9):817-822. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.03.064\">10.1016/j.cub.2013.03.064</a>","ista":"Rosquete M, von Wangenheim D, Marhavý P, Barbez E, Stelzer E, Benková E, Maizel A, Kleine Vehn J. 2013. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. 23(9), 817–822.","mla":"Rosquete, Michel, et al. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” <i>Current Biology</i>, vol. 23, no. 9, Cell Press, 2013, pp. 817–22, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.03.064\">10.1016/j.cub.2013.03.064</a>.","short":"M. Rosquete, D. von Wangenheim, P. Marhavý, E. Barbez, E. Stelzer, E. Benková, A. Maizel, J. Kleine Vehn, Current Biology 23 (2013) 817–822.","apa":"Rosquete, M., von Wangenheim, D., Marhavý, P., Barbez, E., Stelzer, E., Benková, E., … Kleine Vehn, J. (2013). An auxin transport mechanism restricts positive orthogravitropism in lateral roots. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.03.064\">https://doi.org/10.1016/j.cub.2013.03.064</a>","chicago":"Rosquete, Michel, Daniel von Wangenheim, Peter Marhavý, Elke Barbez, Ernst Stelzer, Eva Benková, Alexis Maizel, and Jürgen Kleine Vehn. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.03.064\">https://doi.org/10.1016/j.cub.2013.03.064</a>."},"status":"public","ec_funded":1,"oa_version":"None","publist_id":"3950","language":[{"iso":"eng"}],"intvolume":"        23","date_created":"2018-12-11T11:59:53Z","quality_controlled":"1","_id":"2844","date_updated":"2025-09-29T13:43:30Z"},{"type":"journal_article","year":"2013","fulldoi":"https://doi.org/10.1073/pnas.1300107110","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"9","publisher":"National Academy of Sciences","abstract":[{"lang":"eng","text":"Gravitropic bending of plant organs is mediated by an asymmetric signaling of the plant hormone auxin between the upper and lower side of the respective organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows asymmetric action during gravitropic responses. Immunodetection using an antibody against GA and monitoring GA signaling output by downstream degradation of DELLA proteins revealed an asymmetric GA distribution and response with the maximum at the lower side of gravistimulated roots. Genetic or pharmacological manipulation of GA levels or response affects gravity-mediated auxin redistribution and root bending response. The higher GA levels at the lower side of the root correlate with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane. The observed increase in PIN2 stability is caused by a specific GA effect on trafficking of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin A-sensitive endosomes. Our results suggest that asymmetric auxin distribution instructive for gravity-induced differential growth is consolidated by the asymmetric action of GA that stabilizes the PIN-dependent auxin stream along the lower side of gravistimulated roots."}],"scopus_import":"1","volume":110,"day":"26","month":"02","article_processing_charge":"No","oa":1,"external_id":{"isi":["000315841900083"],"pmid":["23391733"]},"publication":"PNAS","page":"3627 - 3632","date_published":"2013-02-26T00:00:00Z","author":[{"first_name":"Christian","last_name":"Löfke","full_name":"Löfke, Christian"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"last_name":"Heilmann","first_name":"Ingo","full_name":"Heilmann, Ingo"},{"first_name":"Marc","last_name":"Van Montagu","full_name":"Van Montagu, Marc"},{"last_name":"Teichmann","first_name":"Thomas","full_name":"Teichmann, Thomas"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí"}],"pmid":1,"publication_status":"published","doi":"10.1073/pnas.1300107110","isi":1,"title":"Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism","date_created":"2018-12-11T12:00:07Z","intvolume":"       110","_id":"2882","date_updated":"2025-09-29T13:34:38Z","quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"publist_id":"3879","citation":{"apa":"Löfke, C., Zwiewka, M., Heilmann, I., Van Montagu, M., Teichmann, T., &#38; Friml, J. (2013). Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1300107110\">https://doi.org/10.1073/pnas.1300107110</a>","chicago":"Löfke, Christian, Marta Zwiewka, Ingo Heilmann, Marc Van Montagu, Thomas Teichmann, and Jiří Friml. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1300107110\">https://doi.org/10.1073/pnas.1300107110</a>.","short":"C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml, PNAS 110 (2013) 3627–3632.","ista":"Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. 2013. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. PNAS. 110(9), 3627–3632.","ama":"Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism. <i>PNAS</i>. 2013;110(9):3627-3632. doi:<a href=\"https://doi.org/10.1073/pnas.1300107110\">10.1073/pnas.1300107110</a>","mla":"Löfke, Christian, et al. “Asymmetric Gibberellin Signaling Regulates Vacuolar Trafficking of PIN Auxin Transporters during Root Gravitropism.” <i>PNAS</i>, vol. 110, no. 9, National Academy of Sciences, 2013, pp. 3627–32, doi:<a href=\"https://doi.org/10.1073/pnas.1300107110\">10.1073/pnas.1300107110</a>.","ieee":"C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, and J. Friml, “Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism,” <i>PNAS</i>, vol. 110, no. 9. National Academy of Sciences, pp. 3627–3632, 2013."},"department":[{"_id":"JiFr"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/"}],"status":"public"},{"month":"01","article_processing_charge":"No","oa":1,"external_id":{"pmid":["23321285"],"isi":["000315572400017"]},"publication":"Plant Cell","acknowledgement":"We would thank Vincent Vincenzetti and Laurence Charrier for excellent technical assistance, A. von Arnim for the donation of BRET vectors, E. Spalding for TWD1-CFP, TWD1-CFP/29-1-GFP/ER-YFP, and ABCB4-GFP lines, M. Palmgren for discussion and support, and E. Martinoia for TT12 cDNA, support, and mentorship. Imaging data were partially collected at the Center for Advanced Bioimaging, University of Copenhagen, Denmark. This work was supported by grants from the Novartis Foundation (to M.G.), from the Danish Research School for Biotechnology (to M.G. and A.S.), from the Forschungskredit of the University of Zurich (to A.B.), from the Pool de Recherche of the University of Fribourg (to M.G.), and from the Swiss National Funds (to M.G.). M.G. dedicates this work to his father, who passed away during the resubmission process.","publisher":"American Society of Plant Biologists","abstract":[{"lang":"eng","text":"Plant architecture is influenced by the polar, cell-to-cell transport of auxin that is primarily provided and regulated by plasma membrane efflux catalysts of the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were shown to require the functionality of the FK506 binding protein42 TWISTED DWARF1 (TWD1), although underlying mechanisms are unclear. By genetic manipulation of TWD1 expression, we show here that TWD1 affects shootward root auxin reflux and, thus, downstream developmental traits, such as epidermal twisting and gravitropism of the root. Using immunological assays, we demonstrate a predominant lateral, mainly outward-facing, plasma membrane location for TWD1 in the root epidermis characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3. At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1. In planta bioluminescence resonance energy transfer analysis was used to verify specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein interaction at the plasma membrane, minimizing reflux from the root apoplast into the cytoplasm."}],"scopus_import":"1","volume":25,"day":"01","year":"2013","fulldoi":"https://doi.org/10.1105/tpc.112.105999","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"1","type":"journal_article","oa_version":"Submitted Version","language":[{"iso":"eng"}],"publist_id":"3878","citation":{"mla":"Wang, Bangjun, et al. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” <i>Plant Cell</i>, vol. 25, no. 1, American Society of Plant Biologists, 2013, pp. 202–14, doi:<a href=\"https://doi.org/10.1105/tpc.112.105999\">10.1105/tpc.112.105999</a>.","ama":"Wang B, Bailly A, Zwiewk M, et al. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. <i>Plant Cell</i>. 2013;25(1):202-214. doi:<a href=\"https://doi.org/10.1105/tpc.112.105999\">10.1105/tpc.112.105999</a>","ista":"Wang B, Bailly A, Zwiewk M, Henrichs S, Azzarello E, Mancuso S, Maeshima M, Friml J, Schulz A, Geisler M. 2013. Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 25(1), 202–214.","ieee":"B. Wang <i>et al.</i>, “Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane,” <i>Plant Cell</i>, vol. 25, no. 1. American Society of Plant Biologists, pp. 202–214, 2013.","apa":"Wang, B., Bailly, A., Zwiewk, M., Henrichs, S., Azzarello, E., Mancuso, S., … Geisler, M. (2013). Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.112.105999\">https://doi.org/10.1105/tpc.112.105999</a>","chicago":"Wang, Bangjun, Aurélien Bailly, Marta Zwiewk, Sina Henrichs, Elisa Azzarello, Stefano Mancuso, Masayoshi Maeshima, Jiří Friml, Alexander Schulz, and Markus Geisler. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter ABCB1 on the Root Plasma Membrane.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.112.105999\">https://doi.org/10.1105/tpc.112.105999</a>.","short":"B. Wang, A. Bailly, M. Zwiewk, S. Henrichs, E. Azzarello, S. Mancuso, M. Maeshima, J. Friml, A. Schulz, M. Geisler, Plant Cell 25 (2013) 202–214."},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/"}],"department":[{"_id":"JiFr"}],"status":"public","date_created":"2018-12-11T12:00:08Z","intvolume":"        25","_id":"2883","date_updated":"2025-09-29T13:34:07Z","quality_controlled":"1","page":"202 - 214","date_published":"2013-01-01T00:00:00Z","author":[{"last_name":"Wang","first_name":"Bangjun","full_name":"Wang, Bangjun"},{"full_name":"Bailly, Aurélien","first_name":"Aurélien","last_name":"Bailly"},{"full_name":"Zwiewk, Marta","first_name":"Marta","last_name":"Zwiewk"},{"full_name":"Henrichs, Sina","last_name":"Henrichs","first_name":"Sina"},{"first_name":"Elisa","last_name":"Azzarello","full_name":"Azzarello, Elisa"},{"full_name":"Mancuso, Stefano","last_name":"Mancuso","first_name":"Stefano"},{"full_name":"Maeshima, Masayoshi","last_name":"Maeshima","first_name":"Masayoshi"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"full_name":"Schulz, Alexander","last_name":"Schulz","first_name":"Alexander"},{"full_name":"Geisler, Markus","first_name":"Markus","last_name":"Geisler"}],"publication_status":"published","pmid":1,"doi":"10.1105/tpc.112.105999","isi":1,"title":"Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane"},{"day":"23","volume":32,"abstract":[{"lang":"eng","text":"The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth."}],"scopus_import":"1","publisher":"Wiley-Blackwell","corr_author":"1","external_id":{"pmid":["23211744"],"isi":["000316464500009"]},"publication":"EMBO Journal","oa":1,"article_processing_charge":"No","month":"01","type":"journal_article","issue":"2","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1038/emboj.2012.310","year":"2013","quality_controlled":"1","date_updated":"2025-09-29T13:28:19Z","_id":"2919","intvolume":"        32","date_created":"2018-12-11T12:00:20Z","status":"public","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/","open_access":"1"}],"department":[{"_id":"JiFr"}],"citation":{"ieee":"P. Baster <i>et al.</i>, “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism,” <i>EMBO Journal</i>, vol. 32, no. 2. Wiley-Blackwell, pp. 260–274, 2013.","ista":"Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274.","ama":"Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. 2013;32(2):260-274. doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>","mla":"Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>, vol. 32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>.","short":"P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald, B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274.","chicago":"Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste, Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>.","apa":"Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald, W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>"},"publist_id":"3818","language":[{"iso":"eng"}],"oa_version":"Submitted Version","isi":1,"title":"SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism","doi":"10.1038/emboj.2012.310","date_published":"2013-01-23T00:00:00Z","publication_status":"published","author":[{"full_name":"Baster, Pawel","first_name":"Pawel","last_name":"Baster","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","last_name":"Kania","first_name":"Urszula","full_name":"Kania, Urszula"},{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"full_name":"De Rybel, Bert","first_name":"Bert","last_name":"De Rybel"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"pmid":1,"page":"260 - 274"},{"quality_controlled":"1","_id":"507","date_updated":"2025-09-30T07:17:15Z","intvolume":"        25","date_created":"2018-12-11T11:46:52Z","status":"public","department":[{"_id":"JiFr"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/"}],"citation":{"short":"S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml, G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985.","apa":"Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013). Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114264\">https://doi.org/10.1105/tpc.113.114264</a>","chicago":"Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt, Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114264\">https://doi.org/10.1105/tpc.113.114264</a>.","ieee":"S. Kim <i>et al.</i>, “Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013.","mla":"Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.” <i>Plant Cell</i>, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:<a href=\"https://doi.org/10.1105/tpc.113.114264\">10.1105/tpc.113.114264</a>.","ama":"Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. <i>Plant Cell</i>. 2013;25(8):2970-2985. doi:<a href=\"https://doi.org/10.1105/tpc.113.114264\">10.1105/tpc.113.114264</a>","ista":"Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985."},"publist_id":"7312","language":[{"iso":"eng"}],"oa_version":"Submitted Version","isi":1,"title":"Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis","doi":"10.1105/tpc.113.114264","date_published":"2013-08-01T00:00:00Z","author":[{"last_name":"Kim","first_name":"Soo","full_name":"Kim, Soo"},{"first_name":"Zheng","last_name":"Xu","full_name":"Xu, Zheng"},{"first_name":"Kyungyoung","last_name":"Song","full_name":"Song, Kyungyoung"},{"first_name":"Dae","last_name":"Kim","full_name":"Kim, Dae"},{"last_name":"Kang","first_name":"Hyangju","full_name":"Kang, Hyangju"},{"full_name":"Reichardt, Ilka","last_name":"Reichardt","first_name":"Ilka"},{"full_name":"Sohn, Eun","last_name":"Sohn","first_name":"Eun"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"first_name":"Gerd","last_name":"Juergens","full_name":"Juergens, Gerd"},{"full_name":"Hwang, Inhwan","first_name":"Inhwan","last_name":"Hwang"}],"pmid":1,"publication_status":"published","page":"2970 - 2985","day":"01","volume":25,"abstract":[{"lang":"eng","text":"Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs."}],"scopus_import":"1","publisher":"American Society of Plant Biologists","external_id":{"pmid":["23975898"],"isi":["000324920500019"]},"publication":"Plant Cell","oa":1,"article_processing_charge":"No","month":"08","type":"journal_article","issue":"8","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1105/tpc.113.114264","year":"2013"},{"type":"journal_article","fulldoi":"https://doi.org/10.1105/tpc.113.114058","year":"2013","issue":"8","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Society of Plant Biologists","day":"01","volume":25,"scopus_import":"1","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. "}],"month":"08","external_id":{"isi":["000324920500020"],"pmid":["23975899"]},"publication":"Plant Cell","oa":1,"article_processing_charge":"No","author":[{"full_name":"Di Rubbo, Simone","first_name":"Simone","last_name":"Di Rubbo"},{"full_name":"Irani, Niloufer","last_name":"Irani","first_name":"Niloufer"},{"full_name":"Kim, Soo","first_name":"Soo","last_name":"Kim"},{"last_name":"Xu","first_name":"Zheng","full_name":"Xu, Zheng"},{"first_name":"Astrid","last_name":"Gadeyne","full_name":"Gadeyne, Astrid"},{"last_name":"Dejonghe","first_name":"Wim","full_name":"Dejonghe, Wim"},{"last_name":"Vanhoutte","first_name":"Isabelle","full_name":"Vanhoutte, Isabelle"},{"last_name":"Persiau","first_name":"Geert","full_name":"Persiau, Geert"},{"full_name":"Eeckhout, Dominique","last_name":"Eeckhout","first_name":"Dominique"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","orcid":"0000-0002-1998-6741","first_name":"Sibu","full_name":"Simon, Sibu"},{"full_name":"Song, Kyungyoung","last_name":"Song","first_name":"Kyungyoung"},{"full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"De Jaeger, Geert","first_name":"Geert","last_name":"De Jaeger"},{"full_name":"Van Damme, Daniël","first_name":"Daniël","last_name":"Van Damme"},{"full_name":"Hwang, Inhwan","last_name":"Hwang","first_name":"Inhwan"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"}],"date_published":"2013-08-01T00:00:00Z","publication_status":"published","pmid":1,"page":"2986 - 2997","isi":1,"title":"The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis","doi":"10.1105/tpc.113.114058","quality_controlled":"1","date_updated":"2025-09-30T07:15:45Z","_id":"509","intvolume":"        25","date_created":"2018-12-11T11:46:52Z","publist_id":"7311","language":[{"iso":"eng"}],"oa_version":"Submitted Version","status":"public","department":[{"_id":"JiFr"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/"}],"citation":{"apa":"Di Rubbo, S., Irani, N., Kim, S., Xu, Z., Gadeyne, A., Dejonghe, W., … Russinova, E. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114058\">https://doi.org/10.1105/tpc.113.114058</a>","chicago":"Di Rubbo, Simone, Niloufer Irani, Soo Kim, Zheng Xu, Astrid Gadeyne, Wim Dejonghe, Isabelle Vanhoutte, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114058\">https://doi.org/10.1105/tpc.113.114058</a>.","short":"S. Di Rubbo, N. Irani, S. Kim, Z. Xu, A. Gadeyne, W. Dejonghe, I. Vanhoutte, G. Persiau, D. Eeckhout, S. Simon, K. Song, J. Kleine Vehn, J. Friml, G. De Jaeger, D. Van Damme, I. Hwang, E. Russinova, Plant Cell 25 (2013) 2986–2997.","ista":"Di Rubbo S, Irani N, Kim S, Xu Z, Gadeyne A, Dejonghe W, Vanhoutte I, Persiau G, Eeckhout D, Simon S, Song K, Kleine Vehn J, Friml J, De Jaeger G, Van Damme D, Hwang I, Russinova E. 2013. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 25(8), 2986–2997.","ama":"Di Rubbo S, Irani N, Kim S, et al. The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. <i>Plant Cell</i>. 2013;25(8):2986-2997. doi:<a href=\"https://doi.org/10.1105/tpc.113.114058\">10.1105/tpc.113.114058</a>","mla":"Di Rubbo, Simone, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” <i>Plant Cell</i>, vol. 25, no. 8, American Society of Plant Biologists, 2013, pp. 2986–97, doi:<a href=\"https://doi.org/10.1105/tpc.113.114058\">10.1105/tpc.113.114058</a>.","ieee":"S. Di Rubbo <i>et al.</i>, “The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis,” <i>Plant Cell</i>, vol. 25, no. 8. American Society of Plant Biologists, pp. 2986–2997, 2013."}},{"month":"10","publication":"Plant Cell","external_id":{"isi":["000327723100019"],"pmid":["24163311"]},"article_processing_charge":"No","oa":1,"publisher":"American Society of Plant Biologists","ddc":["580"],"volume":25,"day":"01","abstract":[{"text":"The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms.","lang":"eng"}],"scopus_import":"1","year":"2013","fulldoi":"https://doi.org/10.1105/tpc.113.114421","issue":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","language":[{"iso":"eng"}],"publist_id":"7309","oa_version":"Published Version","status":"public","citation":{"short":"A. Pěnčík, B. Simonovik, S. Petersson, E. Henyková, S. Simon, K. Greenham, Y. Zhang, M. Kowalczyk, M. Estelle, E. Zažímalová, O. Novák, G. Sandberg, K. Ljung, Plant Cell 25 (2013) 3858–3870.","apa":"Pěnčík, A., Simonovik, B., Petersson, S., Henyková, E., Simon, S., Greenham, K., … Ljung, K. (2013). Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.113.114421\">https://doi.org/10.1105/tpc.113.114421</a>","chicago":"Pěnčík, Aleš, Biljana Simonovik, Sara Petersson, Eva Henyková, Sibu Simon, Kathleen Greenham, Yi Zhang, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” <i>Plant Cell</i>. American Society of Plant Biologists, 2013. <a href=\"https://doi.org/10.1105/tpc.113.114421\">https://doi.org/10.1105/tpc.113.114421</a>.","ieee":"A. Pěnčík <i>et al.</i>, “Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid,” <i>Plant Cell</i>, vol. 25, no. 10. American Society of Plant Biologists, pp. 3858–3870, 2013.","ama":"Pěnčík A, Simonovik B, Petersson S, et al. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. <i>Plant Cell</i>. 2013;25(10):3858-3870. doi:<a href=\"https://doi.org/10.1105/tpc.113.114421\">10.1105/tpc.113.114421</a>","ista":"Pěnčík A, Simonovik B, Petersson S, Henyková E, Simon S, Greenham K, Zhang Y, Kowalczyk M, Estelle M, Zažímalová E, Novák O, Sandberg G, Ljung K. 2013. Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid. Plant Cell. 25(10), 3858–3870.","mla":"Pěnčík, Aleš, et al. “Regulation of Auxin Homeostasis and Gradients in Arabidopsis Roots through the Formation of the Indole-3-Acetic Acid Catabolite 2-Oxindole-3-Acetic Acid.” <i>Plant Cell</i>, vol. 25, no. 10, American Society of Plant Biologists, 2013, pp. 3858–70, doi:<a href=\"https://doi.org/10.1105/tpc.113.114421\">10.1105/tpc.113.114421</a>."},"main_file_link":[{"open_access":"1","url":"www.doi.org/10.1105/tpc.113.114421"}],"department":[{"_id":"JiFr"}],"date_updated":"2026-06-18T18:52:18Z","_id":"511","quality_controlled":"1","date_created":"2018-12-11T11:46:53Z","intvolume":"        25","page":"3858 - 3870","author":[{"full_name":"Pěnčík, Aleš","first_name":"Aleš","last_name":"Pěnčík"},{"first_name":"Biljana","last_name":"Simonovik","full_name":"Simonovik, Biljana"},{"first_name":"Sara","last_name":"Petersson","full_name":"Petersson, Sara"},{"first_name":"Eva","last_name":"Henyková","full_name":"Henyková, Eva"},{"full_name":"Simon, Sibu","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","orcid":"0000-0002-1998-6741"},{"full_name":"Greenham, Kathleen","first_name":"Kathleen","last_name":"Greenham"},{"first_name":"Yi","last_name":"Zhang","full_name":"Zhang, Yi"},{"full_name":"Kowalczyk, Mariusz","last_name":"Kowalczyk","first_name":"Mariusz"},{"full_name":"Estelle, Mark","first_name":"Mark","last_name":"Estelle"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"last_name":"Sandberg","first_name":"Göran","full_name":"Sandberg, Göran"},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"}],"publication_status":"published","pmid":1,"date_published":"2013-10-01T00:00:00Z","doi":"10.1105/tpc.113.114421","isi":1,"title":"Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid"},{"type":"journal_article","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"1","year":"2013","fulldoi":"https://doi.org/10.1038/msb.2013.40","abstract":[{"text":"In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin‐responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue‐specific transcriptional regulation of cell‐identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin‐response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome‐level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.","lang":"eng"}],"scopus_import":"1","volume":9,"day":"10","has_accepted_license":"1","ddc":["581"],"publisher":"Nature Publishing Group","article_processing_charge":"No","oa":1,"external_id":{"isi":["000325297700001"]},"publication":"Molecular Systems Biology","month":"09","doi":"10.1038/msb.2013.40","isi":1,"file_date_updated":"2020-07-14T12:46:36Z","title":"A map of cell type‐specific auxin responses","publication_status":"published","author":[{"full_name":"Bargmann, Bastiaan","last_name":"Bargmann","first_name":"Bastiaan"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"first_name":"Gabriel","last_name":"Krouk","full_name":"Krouk, Gabriel"},{"first_name":"Tal","last_name":"Nawy","full_name":"Nawy, Tal"},{"first_name":"Idan","last_name":"Efroni","full_name":"Efroni, Idan"},{"first_name":"Eilon","last_name":"Shani","full_name":"Shani, Eilon"},{"last_name":"Choe","first_name":"Goh","full_name":"Choe, Goh"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"full_name":"Bergmann, Dominique","last_name":"Bergmann","first_name":"Dominique"},{"full_name":"Estelle, Mark","first_name":"Mark","last_name":"Estelle"},{"first_name":"Kenneth","last_name":"Birnbaum","full_name":"Birnbaum, Kenneth"}],"file":[{"file_name":"IST-2018-936-v1+1_2008_Barton_A_map.pdf","file_id":"4644","access_level":"open_access","content_type":"application/pdf","file_size":3257692,"creator":"system","date_created":"2018-12-12T10:07:46Z","relation":"main_file","date_updated":"2020-07-14T12:46:36Z","checksum":"9c4fbe793af4bb22b3fe50cc677a39bf"}],"date_published":"2013-09-10T00:00:00Z","pubrep_id":"936","date_created":"2018-12-11T11:46:55Z","intvolume":"         9","_id":"516","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"date_updated":"2025-09-30T07:11:42Z","quality_controlled":"1","article_number":"688","citation":{"chicago":"Bargmann, Bastiaan, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni, Eilon Shani, Goh Choe, et al. “A Map of Cell Type‐specific Auxin Responses.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/msb.2013.40\">https://doi.org/10.1038/msb.2013.40</a>.","apa":"Bargmann, B., Vanneste, S., Krouk, G., Nawy, T., Efroni, I., Shani, E., … Birnbaum, K. (2013). A map of cell type‐specific auxin responses. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/msb.2013.40\">https://doi.org/10.1038/msb.2013.40</a>","short":"B. Bargmann, S. Vanneste, G. Krouk, T. Nawy, I. Efroni, E. Shani, G. Choe, J. Friml, D. Bergmann, M. Estelle, K. Birnbaum, Molecular Systems Biology 9 (2013).","mla":"Bargmann, Bastiaan, et al. “A Map of Cell Type‐specific Auxin Responses.” <i>Molecular Systems Biology</i>, vol. 9, no. 1, 688, Nature Publishing Group, 2013, doi:<a href=\"https://doi.org/10.1038/msb.2013.40\">10.1038/msb.2013.40</a>.","ista":"Bargmann B, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann D, Estelle M, Birnbaum K. 2013. A map of cell type‐specific auxin responses. Molecular Systems Biology. 9(1), 688.","ama":"Bargmann B, Vanneste S, Krouk G, et al. A map of cell type‐specific auxin responses. <i>Molecular Systems Biology</i>. 2013;9(1). doi:<a href=\"https://doi.org/10.1038/msb.2013.40\">10.1038/msb.2013.40</a>","ieee":"B. Bargmann <i>et al.</i>, “A map of cell type‐specific auxin responses,” <i>Molecular Systems Biology</i>, vol. 9, no. 1. Nature Publishing Group, 2013."},"department":[{"_id":"JiFr"}],"status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"publist_id":"7303"},{"page":"2513 - 2518","date_published":"2013-12-16T00:00:00Z","publication_status":"published","author":[{"full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T"},{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"last_name":"Smith","first_name":"Richard","full_name":"Smith, Richard"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"doi":"10.1016/j.cub.2013.10.038","title":"Modeling framework for the establishment of the apical-basal embryonic axis in plants","isi":1,"language":[{"iso":"eng"}],"publist_id":"7292","oa_version":"None","ec_funded":1,"status":"public","citation":{"short":"K.T. Wabnik, H. Robert, R. Smith, J. Friml, Current Biology 23 (2013) 2513–2518.","apa":"Wabnik, K. T., Robert, H., Smith, R., &#38; Friml, J. (2013). Modeling framework for the establishment of the apical-basal embryonic axis in plants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">https://doi.org/10.1016/j.cub.2013.10.038</a>","chicago":"Wabnik, Krzysztof T, Hélène Robert, Richard Smith, and Jiří Friml. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">https://doi.org/10.1016/j.cub.2013.10.038</a>.","ieee":"K. T. Wabnik, H. Robert, R. Smith, and J. Friml, “Modeling framework for the establishment of the apical-basal embryonic axis in plants,” <i>Current Biology</i>, vol. 23, no. 24. Cell Press, pp. 2513–2518, 2013.","ista":"Wabnik KT, Robert H, Smith R, Friml J. 2013. Modeling framework for the establishment of the apical-basal embryonic axis in plants. Current Biology. 23(24), 2513–2518.","ama":"Wabnik KT, Robert H, Smith R, Friml J. Modeling framework for the establishment of the apical-basal embryonic axis in plants. <i>Current Biology</i>. 2013;23(24):2513-2518. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">10.1016/j.cub.2013.10.038</a>","mla":"Wabnik, Krzysztof T., et al. “Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.” <i>Current Biology</i>, vol. 23, no. 24, Cell Press, 2013, pp. 2513–18, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.10.038\">10.1016/j.cub.2013.10.038</a>."},"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"_id":"527","date_updated":"2025-09-30T07:10:38Z","quality_controlled":"1","date_created":"2018-12-11T11:46:58Z","intvolume":"        23","year":"2013","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"fulldoi":"https://doi.org/10.1016/j.cub.2013.10.038","issue":"24","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","month":"12","publication":"Current Biology","external_id":{"isi":["000328918900032"]},"article_processing_charge":"No","publisher":"Cell Press","corr_author":"1","volume":23,"day":"16","abstract":[{"text":"The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters [1], whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery [2-7] that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles [8]. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis [9]. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development.","lang":"eng"}],"scopus_import":"1"},{"doi":"10.1016/j.cub.2013.09.039","title":"Local auxin sources orient the apical basal axis in arabidopsis embryos","isi":1,"page":"2506 - 2512","date_published":"2013-12-16T00:00:00Z","author":[{"full_name":"Robert, Hélène","first_name":"Hélène","last_name":"Robert"},{"full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","first_name":"Peter"},{"full_name":"Stepanova, Anna","first_name":"Anna","last_name":"Stepanova"},{"last_name":"Robles","first_name":"Linda","full_name":"Robles, Linda"},{"first_name":"Annemarie","last_name":"Lokerse","full_name":"Lokerse, Annemarie"},{"full_name":"Alonso, Jose","last_name":"Alonso","first_name":"Jose"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"publication_status":"published","_id":"528","date_updated":"2025-09-30T07:10:06Z","quality_controlled":"1","date_created":"2018-12-11T11:46:59Z","intvolume":"        23","status":"public","citation":{"ieee":"H. Robert <i>et al.</i>, “Local auxin sources orient the apical basal axis in arabidopsis embryos,” <i>Current Biology</i>, vol. 23, no. 24. Cell Press, pp. 2506–2512, 2013.","mla":"Robert, Hélène, et al. “Local Auxin Sources Orient the Apical Basal Axis in Arabidopsis Embryos.” <i>Current Biology</i>, vol. 23, no. 24, Cell Press, 2013, pp. 2506–12, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">10.1016/j.cub.2013.09.039</a>.","ama":"Robert H, Grones P, Stepanova A, et al. Local auxin sources orient the apical basal axis in arabidopsis embryos. <i>Current Biology</i>. 2013;23(24):2506-2512. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">10.1016/j.cub.2013.09.039</a>","ista":"Robert H, Grones P, Stepanova A, Robles L, Lokerse A, Alonso J, Weijers D, Friml J. 2013. Local auxin sources orient the apical basal axis in arabidopsis embryos. Current Biology. 23(24), 2506–2512.","short":"H. Robert, P. Grones, A. Stepanova, L. Robles, A. Lokerse, J. Alonso, D. Weijers, J. Friml, Current Biology 23 (2013) 2506–2512.","chicago":"Robert, Hélène, Peter Grones, Anna Stepanova, Linda Robles, Annemarie Lokerse, Jose Alonso, Dolf Weijers, and Jiří Friml. “Local Auxin Sources Orient the Apical Basal Axis in Arabidopsis Embryos.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">https://doi.org/10.1016/j.cub.2013.09.039</a>.","apa":"Robert, H., Grones, P., Stepanova, A., Robles, L., Lokerse, A., Alonso, J., … Friml, J. (2013). Local auxin sources orient the apical basal axis in arabidopsis embryos. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.09.039\">https://doi.org/10.1016/j.cub.2013.09.039</a>"},"department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"publist_id":"7291","oa_version":"None","ec_funded":1,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"24","year":"2013","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1016/j.cub.2013.09.039","volume":23,"day":"16","scopus_import":"1","abstract":[{"text":"Establishment of the embryonic axis foreshadows the main body axis of adults both in plants and in animals, but underlying mechanisms are considered distinct. Plants utilize directional, cell-to-cell transport of the growth hormone auxin [1, 2] to generate an asymmetric auxin response that specifies the embryonic apical-basal axis [3-6]. The auxin flow directionality depends on the polarized subcellular localization of PIN-FORMED (PIN) auxin transporters [7, 8]. It remains unknown which mechanisms and spatial cues guide cell polarization and axis orientation in early embryos. Herein, we provide conceptually novel insights into the formation of embryonic axis in Arabidopsis by identifying a crucial role of localized tryptophan-dependent auxin biosynthesis [9-12]. Local auxin production at the base of young embryos and the accompanying PIN7-mediated auxin flow toward the proembryo are required for the apical auxin response maximum and the specification of apical embryonic structures. Later in embryogenesis, the precisely timed onset of localized apical auxin biosynthesis mediates PIN1 polarization, basal auxin response maximum, and specification of the root pole. Thus, the tight spatiotemporal control of distinct local auxin sources provides a necessary, non-cell-autonomous trigger for the coordinated cell polarization and subsequent apical-basal axis orientation during embryogenesis and, presumably, also for other polarization events during postembryonic plant life [13, 14].","lang":"eng"}],"publisher":"Cell Press","corr_author":"1","external_id":{"isi":["000328918900031"]},"publication":"Current Biology","article_processing_charge":"No","month":"12"},{"language":[{"iso":"eng"}],"publist_id":"4460","oa_version":"Published Version","ec_funded":1,"status":"public","citation":{"ieee":"S. Simon <i>et al.</i>, “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” <i>New Phytologist</i>, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>.","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. 2013;200(4):1034-1048. doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>.","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>"},"department":[{"_id":"JiFr"}],"main_file_link":[{"url":"https://doi.org/10.1111/nph.12437","open_access":"1"}],"_id":"2443","date_updated":"2026-07-28T09:29:45Z","quality_controlled":"1","date_created":"2018-12-11T11:57:41Z","intvolume":"       200","OA_type":"free access","page":"1034 - 1048","author":[{"full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","last_name":"Simon","first_name":"Sibu"},{"first_name":"Martin","last_name":"Kubeš","full_name":"Kubeš, Martin"},{"first_name":"Pawel","last_name":"Baster","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","full_name":"Baster, Pawel"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"last_name":"Dobrev","first_name":"Petre","full_name":"Dobrev, Petre"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"}],"date_published":"2013-12-01T00:00:00Z","publication_status":"published","doi":"10.1111/nph.12437","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","isi":1,"das_tickbox":"1","month":"12","external_id":{"isi":["000330955300012"]},"publication":"New Phytologist","article_processing_charge":"No","oa":1,"publisher":"Wiley","ddc":["580"],"acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","volume":200,"day":"01","scopus_import":"1","abstract":[{"text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.","lang":"eng"}],"year":"2013","fulldoi":"https://doi.org/10.1111/nph.12437","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","article_type":"original","type":"journal_article"}]