[{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Nodzyński, Tomasz, Steffen Vanneste, Marta Zwiewka, Markéta Pernisová, Jan Hejátko, and Jiří Friml. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” Molecular Plant. Cell Press, 2016. https://doi.org/10.1016/j.molp.2016.08.010.","ista":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. 2016. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 9(11), 1504–1519.","mla":"Nodzyński, Tomasz, et al. “Enquiry into the Topology of Plasma Membrane Localized PIN Auxin Transport Components.” Molecular Plant, vol. 9, no. 11, Cell Press, 2016, pp. 1504–19, doi:10.1016/j.molp.2016.08.010.","ieee":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, and J. Friml, “Enquiry into the topology of plasma membrane localized PIN auxin transport components,” Molecular Plant, vol. 9, no. 11. Cell Press, pp. 1504–1519, 2016.","short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 1504–1519.","ama":"Nodzyński T, Vanneste S, Zwiewka M, Pernisová M, Hejátko J, Friml J. Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. 2016;9(11):1504-1519. doi:10.1016/j.molp.2016.08.010","apa":"Nodzyński, T., Vanneste, S., Zwiewka, M., Pernisová, M., Hejátko, J., & Friml, J. (2016). Enquiry into the topology of plasma membrane localized PIN auxin transport components. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2016.08.010"},"title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","author":[{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"last_name":"Hejátko","full_name":"Hejátko, Jan","first_name":"Jan"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"6213","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"publication":"Molecular Plant","day":"07","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:50:23Z","doi":"10.1016/j.molp.2016.08.010","date_published":"2016-11-07T00:00:00Z","page":"1504 - 1519","acknowledgement":"This research has been financially supported by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) (T.N., M.Z., M.P., J.H.), Czech Science Foundation (13-40637S [J.F., M.Z.], 13-39982S [J.H.]); Research Foundation Flanders (Grant number FWO09/PDO/196) (S.V.) and the European Research Council (project ERC-2011-StG-20101109-PSDP) (J.F.). We thank David G. Robinson and Ranjan Swarup for sharing published material; Maria Šimášková, Mamoona Khan, Eva Benková for technical assistance; and R. Tejos, J. Kleine-Vehn, and E. Feraru for helpful discussions.","oa":1,"publisher":"Cell Press","quality_controlled":"1","ddc":["581"],"date_updated":"2021-01-12T06:48:37Z","file_date_updated":"2018-12-12T10:13:22Z","department":[{"_id":"JiFr"}],"_id":"1145","pubrep_id":"746","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"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5004","file_size":5005876,"date_updated":"2018-12-12T10:13:22Z","creator":"system","file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf","date_created":"2018-12-12T10:13:22Z"}],"publication_status":"published","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":9,"issue":"11","oa_version":"Published Version","abstract":[{"text":"Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors","lang":"eng"}],"intvolume":" 9","month":"11","scopus_import":1},{"scopus_import":1,"intvolume":" 6","month":"11","abstract":[{"text":"Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016.","lang":"eng"}],"oa_version":"Published Version","volume":6,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2018-12-12T10:09:28Z","file_size":1587544,"date_created":"2018-12-12T10:09:28Z","file_name":"IST-2017-745-v1+1_srep35955.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4752"}],"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)"},"type":"journal_article","pubrep_id":"745","status":"public","_id":"1147","file_date_updated":"2018-12-12T10:09:28Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:48:38Z","ddc":["581"],"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II., supported by the project “CEITEC–Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) and the Agronomy faculty grant from Mendel University “IGA AF MENDELU” (IP 14/2013).","date_created":"2018-12-11T11:50:24Z","doi":"10.1038/srep35955","date_published":"2016-11-08T00:00:00Z","year":"2016","has_accepted_license":"1","publication":"Scientific Reports","day":"08","article_number":"35955","author":[{"first_name":"Jozef","full_name":"Balla, Jozef","last_name":"Balla"},{"first_name":"Zuzana","last_name":"Medved'Ová","full_name":"Medved'Ová, Zuzana"},{"first_name":"Petr","full_name":"Kalousek, Petr","last_name":"Kalousek"},{"first_name":"Natálie","full_name":"Matiješčuková, Natálie","last_name":"Matiješčuková"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Reinöhl","full_name":"Reinöhl, Vilém","first_name":"Vilém"},{"first_name":"Stanislav","full_name":"Procházka, Stanislav","last_name":"Procházka"}],"publist_id":"6211","title":"Auxin flow mediated competition between axillary buds to restore apical dominance","citation":{"mla":"Balla, Jozef, et al. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” Scientific Reports, vol. 6, 35955, Nature Publishing Group, 2016, doi:10.1038/srep35955.","ama":"Balla J, Medved’Ová Z, Kalousek P, et al. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 2016;6. doi:10.1038/srep35955","apa":"Balla, J., Medved’Ová, Z., Kalousek, P., Matiješčuková, N., Friml, J., Reinöhl, V., & Procházka, S. (2016). Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep35955","ieee":"J. Balla et al., “Auxin flow mediated competition between axillary buds to restore apical dominance,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016).","chicago":"Balla, Jozef, Zuzana Medved’Ová, Petr Kalousek, Natálie Matiješčuková, Jiří Friml, Vilém Reinöhl, and Stanislav Procházka. “Auxin Flow Mediated Competition between Axillary Buds to Restore Apical Dominance.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep35955.","ista":"Balla J, Medved’Ová Z, Kalousek P, Matiješčuková N, Friml J, Reinöhl V, Procházka S. 2016. Auxin flow mediated competition between axillary buds to restore apical dominance. Scientific Reports. 6, 35955."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"citation":{"chicago":"Simonini, Sara, Joyita Deb, Laila Moubayidin, Pauline Stephenson, Manoj Valluru, Alejandra Freire Rios, Karim Sorefan, Dolf Weijers, Jiří Friml, and Lars Östergaard. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” Genes and Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.285361.116.","ista":"Simonini S, Deb J, Moubayidin L, Stephenson P, Valluru M, Freire Rios A, Sorefan K, Weijers D, Friml J, Östergaard L. 2016. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 30(20), 2286–2296.","mla":"Simonini, Sara, et al. “A Noncanonical Auxin Sensing Mechanism Is Required for Organ Morphogenesis in Arabidopsis.” Genes and Development, vol. 30, no. 20, Cold Spring Harbor Laboratory Press, 2016, pp. 2286–96, doi:10.1101/gad.285361.116.","apa":"Simonini, S., Deb, J., Moubayidin, L., Stephenson, P., Valluru, M., Freire Rios, A., … Östergaard, L. (2016). A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.285361.116","ama":"Simonini S, Deb J, Moubayidin L, et al. A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis. Genes and Development. 2016;30(20):2286-2296. doi:10.1101/gad.285361.116","ieee":"S. Simonini et al., “A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis,” Genes and Development, vol. 30, no. 20. Cold Spring Harbor Laboratory Press, pp. 2286–2296, 2016.","short":"S. Simonini, J. Deb, L. Moubayidin, P. Stephenson, M. Valluru, A. Freire Rios, K. Sorefan, D. Weijers, J. Friml, L. Östergaard, Genes and Development 30 (2016) 2286–2296."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Sara","last_name":"Simonini","full_name":"Simonini, Sara"},{"last_name":"Deb","full_name":"Deb, Joyita","first_name":"Joyita"},{"first_name":"Laila","full_name":"Moubayidin, Laila","last_name":"Moubayidin"},{"full_name":"Stephenson, Pauline","last_name":"Stephenson","first_name":"Pauline"},{"full_name":"Valluru, Manoj","last_name":"Valluru","first_name":"Manoj"},{"first_name":"Alejandra","last_name":"Freire Rios","full_name":"Freire Rios, Alejandra"},{"last_name":"Sorefan","full_name":"Sorefan, Karim","first_name":"Karim"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Lars","last_name":"Östergaard","full_name":"Östergaard, Lars"}],"publist_id":"6207","external_id":{"pmid":["27898393"]},"title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","has_accepted_license":"1","year":"2016","day":"15","publication":"Genes and Development","page":"2286 - 2296","date_published":"2016-10-15T00:00:00Z","doi":"10.1101/gad.285361.116","date_created":"2018-12-11T11:50:25Z","acknowledgement":"We thank Norwich Research Park Bioimaging, Grant Calder, Roy\r\nDunford, Caroline Smith, Paul Thomas, and Mark Youles for\r\ntechnical support; Charlie Scutt, Alejandro Ferrando, and George\r\nLomonossoff for plasmids; Toshiro Ito for seeds; Brendan Davies\r\nand Barry Causier for the REGIA library; and Mark Buttner,\r\nSimona Masiero, Fabio Rossi, Doris Wagner, and Jun Xiao for\r\nhelp and material. We are also grateful to Stefano Bencivenga,\r\nMarie Brüser, Friederike Jantzen, Lukasz Langowski, Xinran Li,\r\nand Nicola Stacey for discussions and helpful comments on the\r\nmanuscript. This work was supported by grants BB/M004112/1\r\nand BB/I017232/1 (Crop Improvement Research Club) to L.Ø.\r\nfrom the Biotechnological and Biological Sciences Research\r\nCouncil, and Institute Strategic Programme grant (BB/J004553/\r\n1) to the John Innes Centre. S.S., J.D., and L.Ø conceived the ex-\r\nperiments. ","quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory Press","oa":1,"date_updated":"2021-01-12T06:48:39Z","ddc":["570"],"department":[{"_id":"JiFr"}],"file_date_updated":"2019-01-25T09:32:55Z","_id":"1151","type":"journal_article","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","publication_status":"published","file":[{"file_id":"5882","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-01-25T09:32:55Z","file_name":"2016_GeneDev_Simonini.pdf","date_updated":"2019-01-25T09:32:55Z","file_size":1419263,"creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"20","volume":30,"abstract":[{"lang":"eng","text":"Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al."}],"pmid":1,"oa_version":"Published Version","scopus_import":1,"month":"10","intvolume":" 30"},{"publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1,"acknowledgement":"We thank Martine De Cock and Annick Bleys for help in preparing the manuscript, Daniel Van Damme for sharing material and stimulating discussion, and Rudiger Simon for support during revision of the manuscript.\r\nThis work was supported by grants from the European Research Council (StartingIndependentResearchGrantERC-2007-Stg-207362-HCPO)and the Czech Science Foundation (GACR CZ.1.07/2.3.00/20.0043) to E.B.\r\nand Natural Sciences and Engineering Research Council of Canada Discovery Grant 2014-05325 to P.P. K.W. acknowledges funding from a Human Frontier Science Program Long-Term Fellowship (LT-000209-2014).","doi":"10.1105/tpc.15.00569","date_published":"2016-10-01T00:00:00Z","date_created":"2018-12-11T11:50:26Z","page":"2464 - 2477","day":"01","publication":"Plant Cell","year":"2016","project":[{"grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"A model of differential growth guided apical hook formation in plants","publist_id":"6205","author":[{"first_name":"Petra","full_name":"Žádníková, Petra","last_name":"Žádníková"},{"first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik"},{"first_name":"Anas","last_name":"Abuzeineh","full_name":"Abuzeineh, Anas"},{"last_name":"Gallemí","full_name":"Gallemí, Marçal","first_name":"Marçal"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"last_name":"Smith","full_name":"Smith, Richard","first_name":"Richard"},{"first_name":"Dirk","last_name":"Inze","full_name":"Inze, Dirk"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Prusinkiewicz, Przemysław","last_name":"Prusinkiewicz","first_name":"Przemysław"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Žádníková, Petra, et al. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell, vol. 28, no. 10, American Society of Plant Biologists, 2016, pp. 2464–77, doi:10.1105/tpc.15.00569.","apa":"Žádníková, P., Wabnik, K. T., Abuzeineh, A., Gallemí, M., Van Der Straeten, D., Smith, R., … Benková, E. (2016). A model of differential growth guided apical hook formation in plants. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.15.00569","ama":"Žádníková P, Wabnik KT, Abuzeineh A, et al. A model of differential growth guided apical hook formation in plants. Plant Cell. 2016;28(10):2464-2477. doi:10.1105/tpc.15.00569","short":"P. Žádníková, K.T. Wabnik, A. Abuzeineh, M. Gallemí, D. Van Der Straeten, R. Smith, D. Inze, J. Friml, P. Prusinkiewicz, E. Benková, Plant Cell 28 (2016) 2464–2477.","ieee":"P. Žádníková et al., “A model of differential growth guided apical hook formation in plants,” Plant Cell, vol. 28, no. 10. American Society of Plant Biologists, pp. 2464–2477, 2016.","chicago":"Žádníková, Petra, Krzysztof T Wabnik, Anas Abuzeineh, Marçal Gallemí, Dominique Van Der Straeten, Richard Smith, Dirk Inze, Jiří Friml, Przemysław Prusinkiewicz, and Eva Benková. “A Model of Differential Growth Guided Apical Hook Formation in Plants.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00569.","ista":"Žádníková P, Wabnik KT, Abuzeineh A, Gallemí M, Van Der Straeten D, Smith R, Inze D, Friml J, Prusinkiewicz P, Benková E. 2016. A model of differential growth guided apical hook formation in plants. Plant Cell. 28(10), 2464–2477."},"month":"10","intvolume":" 28","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved."}],"volume":28,"issue":"10","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"1153","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"date_updated":"2021-01-12T06:48:40Z"},{"day":"21","publication":"Current Biology","has_accepted_license":"1","year":"2016","doi":"10.1016/j.cub.2016.08.067","date_published":"2016-11-21T00:00:00Z","date_created":"2018-12-11T11:50:44Z","page":"3026 - 3032","acknowledgement":"We thank Dr. Jie Li (Key Laboratory of Plant Molecular Physiology, Chinese Academy of Science, China) for the pPIN3::PIN3-GFP/DII::VENUS line and Martine De Cock for help in preparing the manuscript. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), by the Czech Science Foundation GAČR (GA13-40637S) to J.F., and by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to H.S.R. H.R. is indebted to the Agency for Innovation by Science and Technology (IWT) for a predoctoral fellowship.\r\n","publisher":"Cell Press","quality_controlled":"1","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Rakusová H, Abbas M, Han H, Song S, Robert H, Friml J. 2016. Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. Current Biology. 26(22), 3026–3032.","chicago":"Rakusová, Hana, Mohamad Abbas, Huibin Han, Siyuan Song, Hélène Robert, and Jiří Friml. “Termination of Shoot Gravitropic Responses by Auxin Feedback on PIN3 Polarity.” Current Biology. Cell Press, 2016. https://doi.org/10.1016/j.cub.2016.08.067.","short":"H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, J. Friml, Current Biology 26 (2016) 3026–3032.","ieee":"H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, and J. Friml, “Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity,” Current Biology, vol. 26, no. 22. Cell Press, pp. 3026–3032, 2016.","apa":"Rakusová, H., Abbas, M., Han, H., Song, S., Robert, H., & Friml, J. (2016). Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2016.08.067","ama":"Rakusová H, Abbas M, Han H, Song S, Robert H, Friml J. Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. Current Biology. 2016;26(22):3026-3032. doi:10.1016/j.cub.2016.08.067","mla":"Rakusová, Hana, et al. “Termination of Shoot Gravitropic Responses by Auxin Feedback on PIN3 Polarity.” Current Biology, vol. 26, no. 22, Cell Press, 2016, pp. 3026–32, doi:10.1016/j.cub.2016.08.067."},"title":"Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity","publist_id":"6138","author":[{"first_name":"Hana","full_name":"Rakusová, Hana","last_name":"Rakusová"},{"full_name":"Abbas, Mohamad","last_name":"Abbas","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","first_name":"Mohamad"},{"full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Siyuan","last_name":"Song","full_name":"Song, Siyuan"},{"first_name":"Hélène","full_name":"Robert, Hélène","last_name":"Robert"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"file":[{"file_name":"IST-2018-1008-v1+1_Rakusova_CurrBiol_2016_proof.pdf","date_created":"2018-12-12T10:09:33Z","file_size":5391923,"date_updated":"2020-07-14T12:44:39Z","creator":"system","checksum":"79ed2498185a027cf51a8f88100379e6","file_id":"4757","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":26,"issue":"22","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"Plants adjust their growth according to gravity. Gravitropism involves gravity perception, signal transduction, and asymmetric growth response, with organ bending as a consequence [1]. Asymmetric growth results from the asymmetric distribution of the plant-specific signaling molecule auxin [2] that is generated by lateral transport, mediated in the hypocotyl predominantly by the auxin transporter PIN-FORMED3 (PIN3) [3–5]. Gravity stimulation polarizes PIN3 to the bottom sides of endodermal cells, correlating with increased auxin accumulation in adjacent tissues at the lower side of the stimulated organ, where auxin induces cell elongation and, hence, organ bending. A curvature response allows the hypocotyl to resume straight growth at a defined angle [6], implying that at some point auxin symmetry is restored to prevent overbending. Here, we present initial insights into cellular and molecular mechanisms that lead to the termination of the tropic response. We identified an auxin feedback on PIN3 polarization as underlying mechanism that restores symmetry of the PIN3-dependent auxin flow. Thus, two mechanistically distinct PIN3 polarization events redirect auxin fluxes at different time points of the gravity response: first, gravity-mediated redirection of PIN3-mediated auxin flow toward the lower hypocotyl side, where auxin gradually accumulates and promotes growth, and later PIN3 polarization to the opposite cell side, depleting this auxin maximum to end the bending. Accordingly, genetic or pharmacological interference with the late PIN3 polarization prevents termination of the response and leads to hypocotyl overbending. This observation reveals a role of auxin feedback on PIN polarity in the termination of the tropic response. © 2016 Elsevier Ltd","lang":"eng"}],"month":"11","intvolume":" 26","scopus_import":1,"ddc":["581"],"date_updated":"2021-01-12T06:49:08Z","file_date_updated":"2020-07-14T12:44:39Z","department":[{"_id":"JiFr"}],"_id":"1212","status":"public","pubrep_id":"1008","type":"journal_article"},{"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":2990459,"date_updated":"2020-07-14T12:44:39Z","file_name":"IST-2016-711-v1+1_770cf1e0-612f-4e85-a500-54b6349fbbab_7654_-_jaroslav_michalko.pdf","date_created":"2018-12-12T10:15:33Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"c9e50bb6096a7ba4a832969935820f19","file_id":"5154"}],"publication_status":"published","ec_funded":1,"volume":5,"oa_version":"Published Version","abstract":[{"text":"The Auxin Binding Protein 1 (ABP1) is one of the most studied proteins in plants. Since decades ago, it has been the prime receptor candidate for the plant hormone auxin with a plethora of described functions in auxin signaling and development. The developmental importance of ABP1 has recently been questioned by identification of Arabidopsis thaliana abp1 knock-out alleles that show no obvious phenotypes under normal growth conditions. In this study, we examined the contradiction between the normal growth and development of the abp1 knock-outs and the strong morphological defects observed in three different ethanol-inducible abp1 knock-down mutants ( abp1-AS, SS12K, SS12S). By analyzing segregating populations of abp1 knock-out vs. abp1 knock-down crosses we show that the strong morphological defects that were believed to be the result of conditional down-regulation of ABP1 can be reproduced also in the absence of the functional ABP1 protein. This data suggests that the phenotypes in abp1 knock-down lines are due to the off-target effects and asks for further reflections on the biological function of ABP1 or alternative explanations for the missing phenotypic defects in the abp1 loss-of-function alleles.","lang":"eng"}],"intvolume":" 5","month":"01","scopus_import":"1","ddc":["581"],"date_updated":"2022-03-24T09:12:49Z","file_date_updated":"2020-07-14T12:44:39Z","department":[{"_id":"JiFr"}],"_id":"1221","pubrep_id":"711","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)"},"article_type":"original","type":"journal_article","publication":"F1000 Research ","day":"20","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:50:47Z","date_published":"2016-01-20T00:00:00Z","doi":"10.12688/f1000research.7654.1","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”. MG was supported by the scholarship \"Stipendien der Stipendienstiftung der Republik Österreich\". Work by EH and CPR were supported by ANR blanc ANR-14-CE11-0018. We would like to thank Mark Estelle and Yunde Zhao for provid\r\n-\r\ning \r\nabp1-c1\r\n, \r\nabp1-TD1 \r\nand \r\nabp1-WTc1 \r\nseeds. We thank Emeline \r\nHuault for technical assistance.","oa":1,"quality_controlled":"1","publisher":"F1000 Research","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Michalko, Jaroslav, et al. “Strong Morphological Defects in Conditional Arabidopsis Abp1 Knock-down Mutants Generated in Absence of Functional ABP1 Protein.” F1000 Research , vol. 5, 86, F1000 Research, 2016, doi:10.12688/f1000research.7654.1.","short":"J. Michalko, M. Glanc, C. Perrot Rechenmann, J. Friml, F1000 Research 5 (2016).","ieee":"J. Michalko, M. Glanc, C. Perrot Rechenmann, and J. Friml, “Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein,” F1000 Research , vol. 5. F1000 Research, 2016.","ama":"Michalko J, Glanc M, Perrot Rechenmann C, Friml J. Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein. F1000 Research . 2016;5. doi:10.12688/f1000research.7654.1","apa":"Michalko, J., Glanc, M., Perrot Rechenmann, C., & Friml, J. (2016). Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein. F1000 Research . F1000 Research. https://doi.org/10.12688/f1000research.7654.1","chicago":"Michalko, Jaroslav, Matous Glanc, Catherine Perrot Rechenmann, and Jiří Friml. “Strong Morphological Defects in Conditional Arabidopsis Abp1 Knock-down Mutants Generated in Absence of Functional ABP1 Protein.” F1000 Research . F1000 Research, 2016. https://doi.org/10.12688/f1000research.7654.1.","ista":"Michalko J, Glanc M, Perrot Rechenmann C, Friml J. 2016. Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein. F1000 Research . 5, 86."},"title":"Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein","article_processing_charge":"No","author":[{"id":"483727CA-F248-11E8-B48F-1D18A9856A87","first_name":"Jaroslav","last_name":"Michalko","full_name":"Michalko, Jaroslav"},{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","last_name":"Glanc"},{"last_name":"Perrot Rechenmann","full_name":"Perrot Rechenmann, Catherine","first_name":"Catherine"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"6113","article_number":"86","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Wangenheim, Daniel von, Amparo Rosero, George Komis, Olga Šamajová, Miroslav Ovečka, Boris Voigt, and Jozef Šamaj. “Endosomal Interactions during Root Hair Growth.” Frontiers in Plant Science. Frontiers Research Foundation, 2016. https://doi.org/10.3389/fpls.2015.01262.","ista":"von Wangenheim D, Rosero A, Komis G, Šamajová O, Ovečka M, Voigt B, Šamaj J. 2016. Endosomal interactions during root hair growth. Frontiers in Plant Science. 6(JAN2016), 1262.","mla":"von Wangenheim, Daniel, et al. “Endosomal Interactions during Root Hair Growth.” Frontiers in Plant Science, vol. 6, no. JAN2016, 1262, Frontiers Research Foundation, 2016, doi:10.3389/fpls.2015.01262.","apa":"von Wangenheim, D., Rosero, A., Komis, G., Šamajová, O., Ovečka, M., Voigt, B., & Šamaj, J. (2016). Endosomal interactions during root hair growth. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.01262","ama":"von Wangenheim D, Rosero A, Komis G, et al. Endosomal interactions during root hair growth. Frontiers in Plant Science. 2016;6(JAN2016). doi:10.3389/fpls.2015.01262","short":"D. von Wangenheim, A. Rosero, G. Komis, O. Šamajová, M. Ovečka, B. Voigt, J. Šamaj, Frontiers in Plant Science 6 (2016).","ieee":"D. von Wangenheim et al., “Endosomal interactions during root hair growth,” Frontiers in Plant Science, vol. 6, no. JAN2016. Frontiers Research Foundation, 2016."},"title":"Endosomal interactions during root hair growth","author":[{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel","last_name":"Von Wangenheim"},{"full_name":"Rosero, Amparo","last_name":"Rosero","first_name":"Amparo"},{"full_name":"Komis, George","last_name":"Komis","first_name":"George"},{"last_name":"Šamajová","full_name":"Šamajová, Olga","first_name":"Olga"},{"first_name":"Miroslav","last_name":"Ovečka","full_name":"Ovečka, Miroslav"},{"last_name":"Voigt","full_name":"Voigt, Boris","first_name":"Boris"},{"full_name":"Šamaj, Jozef","last_name":"Šamaj","first_name":"Jozef"}],"publist_id":"6094","article_number":"1262","day":"29","publication":"Frontiers in Plant Science","has_accepted_license":"1","year":"2016","date_published":"2016-01-29T00:00:00Z","doi":"10.3389/fpls.2015.01262","date_created":"2018-12-11T11:50:53Z","acknowledgement":"This work was supported by National Program for Sustainability I (grant no. LO1204) provided by the Czech Ministry of Education and by Institutional Fund of Palacký University Olomouc (GK and OŠ).\r\nWe thank Sabine Fischer for help with the statistics.","publisher":"Frontiers Research Foundation","quality_controlled":"1","oa":1,"ddc":["581"],"date_updated":"2021-01-12T06:49:18Z","file_date_updated":"2020-07-14T12:44:41Z","department":[{"_id":"JiFr"}],"_id":"1238","status":"public","pubrep_id":"710","type":"journal_article","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)"},"file":[{"creator":"system","file_size":1640550,"date_updated":"2020-07-14T12:44:41Z","file_name":"IST-2016-710-v1+1_fpls-06-01262.pdf","date_created":"2018-12-12T10:09:36Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4760","checksum":"3127eab844d53564bf47e2b6b42f1ca0"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6,"issue":"JAN2016","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The dynamic localization of endosomal compartments labeled with targeted fluorescent protein tags is routinely followed by time lapse fluorescence microscopy approaches and single particle tracking algorithms. In this way trajectories of individual endosomes can be mapped and linked to physiological processes as cell growth. However, other aspects of dynamic behavior including endosomal interactions are difficult to follow in this manner. Therefore, we characterized the localization and dynamic properties of early and late endosomes throughout the entire course of root hair formation by means of spinning disc time lapse imaging and post-acquisition automated multitracking and quantitative analysis. Our results show differential motile behavior of early and late endosomes and interactions of late endosomes that may be specified to particular root hair domains. Detailed data analysis revealed a particular transient interaction between late endosomes—termed herein as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially located in the root hair tip interacted as dancing-endosomes and traveled short distances during this interaction. Finally, sizes of early and late endosomes were addressed by means of super-resolution structured illumination microscopy (SIM) to corroborate measurements on the spinning disc. This is a first study providing quantitative microscopic data on dynamic spatio-temporal interactions of endosomes during root hair tip growth."}],"month":"01","intvolume":" 6","scopus_import":1},{"title":"ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling","author":[{"last_name":"Karampelias","full_name":"Karampelias, Michael","first_name":"Michael"},{"full_name":"Neyt, Pia","last_name":"Neyt","first_name":"Pia"},{"full_name":"De Groeve, Steven","last_name":"De Groeve","first_name":"Steven"},{"first_name":"Stijn","full_name":"Aesaert, Stijn","last_name":"Aesaert"},{"first_name":"Griet","last_name":"Coussens","full_name":"Coussens, Griet"},{"full_name":"Rolčík, Jakub","last_name":"Rolčík","first_name":"Jakub"},{"full_name":"Bruno, Leonardo","last_name":"Bruno","first_name":"Leonardo"},{"first_name":"Nancy","last_name":"De Winne","full_name":"De Winne, Nancy"},{"full_name":"Van Minnebruggen, Annemie","last_name":"Van Minnebruggen","first_name":"Annemie"},{"first_name":"Marc","last_name":"Van Montagu","full_name":"Van Montagu, Marc"},{"first_name":"Maria","full_name":"Ponce, Maria","last_name":"Ponce"},{"last_name":"Micol","full_name":"Micol, José","first_name":"José"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Jaeger, Geert","last_name":"De Jaeger","first_name":"Geert"},{"first_name":"Mieke","last_name":"Van Lijsebettens","full_name":"Van Lijsebettens, Mieke"}],"publist_id":"6081","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce M, Micol J, Friml J, De Jaeger G, Van Lijsebettens M. 2016. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 113(10), 2768–2773.","chicago":"Karampelias, Michael, Pia Neyt, Steven De Groeve, Stijn Aesaert, Griet Coussens, Jakub Rolčík, Leonardo Bruno, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1501343112.","apa":"Karampelias, M., Neyt, P., De Groeve, S., Aesaert, S., Coussens, G., Rolčík, J., … Van Lijsebettens, M. (2016). ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1501343112","ama":"Karampelias M, Neyt P, De Groeve S, et al. ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. PNAS. 2016;113(10):2768-2773. doi:10.1073/pnas.1501343112","short":"M. Karampelias, P. Neyt, S. De Groeve, S. Aesaert, G. Coussens, J. Rolčík, L. Bruno, N. De Winne, A. Van Minnebruggen, M. Van Montagu, M. Ponce, J. Micol, J. Friml, G. De Jaeger, M. Van Lijsebettens, PNAS 113 (2016) 2768–2773.","ieee":"M. Karampelias et al., “ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling,” PNAS, vol. 113, no. 10. National Academy of Sciences, pp. 2768–2773, 2016.","mla":"Karampelias, Michael, et al. “ROTUNDA3 Function in Plant Development by Phosphatase 2A-Mediated Regulation of Auxin Transporter Recycling.” PNAS, vol. 113, no. 10, National Academy of Sciences, 2016, pp. 2768–73, doi:10.1073/pnas.1501343112."},"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"date_created":"2018-12-11T11:50:56Z","doi":"10.1073/pnas.1501343112","date_published":"2016-03-08T00:00:00Z","page":"2768 - 2773","publication":"PNAS","day":"08","year":"2016","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","acknowledgement":"This work was supported by the Ghent University Special Research Fund (M.K.), the European Research Council (Project ERC-2011-StG-20101109-PSDP) (to J.F.), and the Körber European Science Foun-\r\ndation (J.F.). S.D.G. is indebted to the Agency for Science and Technology for\r\na predoctoral fellowship.","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:49:22Z","status":"public","type":"journal_article","_id":"1247","ec_funded":1,"volume":113,"issue":"10","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 113","month":"03","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"The shaping of organs in plants depends on the intercellular flow of the phytohormone auxin, of which the directional signaling is determined by the polar subcellular localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID kinase, which act antagonistically to mediate their apical-basal polar delivery. Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant phenotypes [i.e., reduced apical dominance, primary root length, lateral root emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia; decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems; hypergravitropic root growth and response; increased IAA levels in shoot apices; and reduced auxin accumulation in root meristems] support a role for RON3 in auxin biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3 might act in PIN transporter trafficking. Indeed, pharmacological interference with vesicle trafficking processes revealed that single ron3-2 and double ron3-2 rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our data indicate that RON3 contributes to auxin-mediated development by playing a role in PIN recycling and polarity establishment through regulation of the PP2A complex activity.","lang":"eng"}]},{"date_updated":"2021-01-12T06:49:24Z","department":[{"_id":"JiFr"}],"_id":"1251","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":28,"oa_version":"Submitted Version","abstract":[{"text":"Plant growth and architecture is regulated by the polar distribution of the hormone auxin. Polarity and flexibility of this process is provided by constant cycling of auxin transporter vesicles along actin filaments, coordinated by a positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic acid (NPA), counteracting the effect of auxin; however, underlying targets and mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant, although likely indirect, TWD1 interactor, and show TWD1-dependent regulation of actin filament organization and dynamics and that TWD1 is required for NPA-mediated actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence of efflux transporters, and as a consequence act7 and twd1 share developmental and physiological phenotypes indicative of defects in auxin transport. These can be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide evidence that TWD1 determines downstreamlocations of auxin efflux transporters by adjusting actin filament debundling and dynamizing processes and mediating NPA action on the latter. This function appears to be evolutionary conserved since TWD1 expression in budding yeast alters actin polarization and cell polarity and provides NPA sensitivity.","lang":"eng"}],"month":"04","intvolume":" 28","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Zhu J, Bailly A, Zwiewka M, et al. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 2016;28(4):930-948. doi:10.1105/tpc.15.00726","apa":"Zhu, J., Bailly, A., Zwiewka, M., Sovero, V., Di Donato, M., Ge, P., … Geisler, M. (2016). TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.15.00726","ieee":"J. Zhu et al., “TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics,” Plant Cell, vol. 28, no. 4. American Society of Plant Biologists, pp. 930–948, 2016.","short":"J. Zhu, A. Bailly, M. Zwiewka, V. Sovero, M. Di Donato, P. Ge, J. Oehri, B. Aryal, P. Hao, M. Linnert, N. Burgardt, C. Lücke, M. Weiwad, M. Michel, O. Weiergräber, S. Pollmann, E. Azzarello, S. Mancuso, N. Ferro, Y. Fukao, C. Hoffmann, R. Wedlich Söldner, J. Friml, C. Thomas, M. Geisler, Plant Cell 28 (2016) 930–948.","mla":"Zhu, Jinsheng, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell, vol. 28, no. 4, American Society of Plant Biologists, 2016, pp. 930–48, doi:10.1105/tpc.15.00726.","ista":"Zhu J, Bailly A, Zwiewka M, Sovero V, Di Donato M, Ge P, Oehri J, Aryal B, Hao P, Linnert M, Burgardt N, Lücke C, Weiwad M, Michel M, Weiergräber O, Pollmann S, Azzarello E, Mancuso S, Ferro N, Fukao Y, Hoffmann C, Wedlich Söldner R, Friml J, Thomas C, Geisler M. 2016. TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics. Plant Cell. 28(4), 930–948.","chicago":"Zhu, Jinsheng, Aurélien Bailly, Marta Zwiewka, Valpuri Sovero, Martin Di Donato, Pei Ge, Jacqueline Oehri, et al. “TWISTED DWARF1 Mediates the Action of Auxin Transport Inhibitors on Actin Cytoskeleton Dynamics.” Plant Cell. American Society of Plant Biologists, 2016. https://doi.org/10.1105/tpc.15.00726."},"title":"TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics","author":[{"full_name":"Zhu, Jinsheng","last_name":"Zhu","first_name":"Jinsheng"},{"full_name":"Bailly, Aurélien","last_name":"Bailly","first_name":"Aurélien"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"first_name":"Valpuri","last_name":"Sovero","full_name":"Sovero, Valpuri"},{"first_name":"Martin","last_name":"Di Donato","full_name":"Di Donato, Martin"},{"full_name":"Ge, Pei","last_name":"Ge","first_name":"Pei"},{"last_name":"Oehri","full_name":"Oehri, Jacqueline","first_name":"Jacqueline"},{"full_name":"Aryal, Bibek","last_name":"Aryal","first_name":"Bibek"},{"first_name":"Pengchao","full_name":"Hao, Pengchao","last_name":"Hao"},{"last_name":"Linnert","full_name":"Linnert, Miriam","first_name":"Miriam"},{"first_name":"Noelia","full_name":"Burgardt, Noelia","last_name":"Burgardt"},{"first_name":"Christian","full_name":"Lücke, Christian","last_name":"Lücke"},{"first_name":"Matthias","full_name":"Weiwad, Matthias","last_name":"Weiwad"},{"last_name":"Michel","full_name":"Michel, Max","first_name":"Max"},{"last_name":"Weiergräber","full_name":"Weiergräber, Oliver","first_name":"Oliver"},{"first_name":"Stephan","full_name":"Pollmann, Stephan","last_name":"Pollmann"},{"first_name":"Elisa","last_name":"Azzarello","full_name":"Azzarello, Elisa"},{"first_name":"Stefano","full_name":"Mancuso, Stefano","last_name":"Mancuso"},{"first_name":"Noel","full_name":"Ferro, Noel","last_name":"Ferro"},{"last_name":"Fukao","full_name":"Fukao, Yoichiro","first_name":"Yoichiro"},{"first_name":"Céline","last_name":"Hoffmann","full_name":"Hoffmann, Céline"},{"first_name":"Roland","last_name":"Wedlich Söldner","full_name":"Wedlich Söldner, Roland"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Clément","last_name":"Thomas","full_name":"Thomas, Clément"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"}],"publist_id":"6078","day":"01","publication":"Plant Cell","year":"2016","date_published":"2016-04-01T00:00:00Z","doi":"10.1105/tpc.15.00726","date_created":"2018-12-11T11:50:57Z","page":"930 - 948","acknowledgement":" This work was supported by grants from the European Social Fund (CZ.1.07/2.3.00/20.0043), the Czech Science Foundation GAČR (GA13-40637S) to J.F. and M.Z., the Ministry of Education, Youth, and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to M.Z., the Ministry for Higher Education and Research of Luxembourg (REC-LOCM-20140703) to C.T., the Partial Funding Program for Short Stays Abroad of CONICET Argentina (to N.I.B.), Swiss National Funds, the Pool de Recherche of the University of Fribourg, and the Novartis Foundation (all to M.G.). ","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1},{"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_updated":"2021-01-12T06:49:29Z","status":"public","type":"journal_article","_id":"1264","volume":171,"issue":"3","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 171","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936568/"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"n contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively."}],"title":"Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier","publist_id":"6059","author":[{"first_name":"Gloria","last_name":"Sancho Andrés","full_name":"Sancho Andrés, Gloria"},{"first_name":"Esther","last_name":"Soriano Ortega","full_name":"Soriano Ortega, Esther"},{"first_name":"Caiji","last_name":"Gao","full_name":"Gao, Caiji"},{"first_name":"Joan","full_name":"Bernabé Orts, Joan","last_name":"Bernabé Orts"},{"orcid":"0000-0002-8600-0671","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha"},{"id":"420AB15A-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Müller, Anna","last_name":"Müller"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"last_name":"Jiang","full_name":"Jiang, Liwen","first_name":"Liwen"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aniento, Fernando","last_name":"Aniento","first_name":"Fernando"},{"first_name":"Maria","full_name":"Marcote, Maria","last_name":"Marcote"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Sancho Andrés, G., Soriano Ortega, E., Gao, C., Bernabé Orts, J., Narasimhan, M., Müller, A., … Marcote, M. (2016). Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00373","ama":"Sancho Andrés G, Soriano Ortega E, Gao C, et al. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 2016;171(3):1965-1982. doi:10.1104/pp.16.00373","ieee":"G. Sancho Andrés et al., “Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier,” Plant Physiology, vol. 171, no. 3. American Society of Plant Biologists, pp. 1965–1982, 2016.","short":"G. Sancho Andrés, E. Soriano Ortega, C. Gao, J. Bernabé Orts, M. Narasimhan, A. Müller, R. Tejos, L. Jiang, J. Friml, F. Aniento, M. Marcote, Plant Physiology 171 (2016) 1965–1982.","mla":"Sancho Andrés, Gloria, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology, vol. 171, no. 3, American Society of Plant Biologists, 2016, pp. 1965–82, doi:10.1104/pp.16.00373.","ista":"Sancho Andrés G, Soriano Ortega E, Gao C, Bernabé Orts J, Narasimhan M, Müller A, Tejos R, Jiang L, Friml J, Aniento F, Marcote M. 2016. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 171(3), 1965–1982.","chicago":"Sancho Andrés, Gloria, Esther Soriano Ortega, Caiji Gao, Joan Bernabé Orts, Madhumitha Narasimhan, Anna Müller, Ricardo Tejos, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00373."},"project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_published":"2016-07-01T00:00:00Z","doi":"10.1104/pp.16.00373","date_created":"2018-12-11T11:51:01Z","page":"1965 - 1982","day":"01","publication":"Plant Physiology","year":"2016","publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1,"acknowledgement":"We thank Dr. R. Offringa (Leiden University) for providing the GST-\r\nPIN-CL construct; Sandra Richter and Gerd Jurgens (University of Tübin-\r\ngen) for providing the estradiol-inducible PIN1-RFP construct and the\r\ngnl1 mutant expressing BFA-sensitive GNL1; F.J. Santonja (University of Valencia)\r\nfor help with the statistical analysis; Jurgen Kleine-Vehn, Elke Barbez, and\r\nEva Benkova for helpful discussions; the Salk Institute Genomic Analysis\r\nLaboratory for providing the sequence-indexed Arabidopsis T-DNA in-\r\nsertion mutants; and the greenhouse section and the microscopy section\r\nof SCSIE (University of Valencia) and Pilar Selvi for excellent technical\r\nassistance."},{"page":"11028 - 11033","date_published":"2016-09-27T00:00:00Z","doi":"10.1073/pnas.1605588113","date_created":"2018-12-11T11:51:06Z","year":"2016","day":"27","publication":"PNAS","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"acknowledgement":"F.A.O.-M. was supported by special\r\nresearch funding from the Flemish Government for a joint doctorate fellowship\r\nat Ghent University, and funding from the Student Program\r\n–\r\nGraduate Studies\r\nPlan Program from the Coordination for the Improvement of Higher Educa-\r\ntion Personnel, Brazil, for a doctorate fellowship at the University of São Paulo.\r\nX.Z. and Q.L. are indebted to the China Science Council and G.P.d.O. to the\r\n“\r\nCiência sem Fronteiras\r\n”\r\nfor predoctoral fellowships. R.K. and Y.L. have re-\r\nceived postdoctoral fellowships from the Belgian Science Policy Office. This\r\nresearch was supported by Flanders Research Foundation Grant G008416N\r\n(to E.R.) and by the São Paulo Research Foundation and the National Council\r\nfor Scientific and Technological Development (CNPq) (D.S.d.M.). D.S.d.M. is a\r\nresearch fellow of CNPq.\r\nWe thank D. Van Damme, E. Mylle, M. Castro Silva-Filho,\r\nand J. Goeman for providing usefu\r\nl advice and technical assistance;\r\nI. Hara-Nishimura, J. Lin, G. Jürgens, M. A. Johnson, and P. Bozhkov for sharing\r\npublished materials; and M. Nowack and M. Fendrych for kindly donating the\r\npUBQ10::ATG8-YFP\r\n-expressing marker line.","publist_id":"6039","author":[{"first_name":"Fausto","last_name":"Ortiz Morea","full_name":"Ortiz Morea, Fausto"},{"first_name":"Daniel","full_name":"Savatin, Daniel","last_name":"Savatin"},{"first_name":"Wim","last_name":"Dejonghe","full_name":"Dejonghe, Wim"},{"full_name":"Kumar, Rahul","last_name":"Kumar","first_name":"Rahul"},{"full_name":"Luo, Yu","last_name":"Luo","first_name":"Yu"},{"last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jos","last_name":"Van Begin","full_name":"Van Begin, Jos"},{"last_name":"Dressano","full_name":"Dressano, Keini","first_name":"Keini"},{"first_name":"Guilherme","last_name":"De Oliveira","full_name":"De Oliveira, Guilherme"},{"last_name":"Zhao","full_name":"Zhao, Xiuyang","first_name":"Xiuyang"},{"last_name":"Lu","full_name":"Lu, Qing","first_name":"Qing"},{"full_name":"Madder, Annemieke","last_name":"Madder","first_name":"Annemieke"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Moura, Daniel","last_name":"De Moura","first_name":"Daniel"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"}],"title":"Danger-associated peptide signaling in Arabidopsis requires clathrin","citation":{"mla":"Ortiz Morea, Fausto, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS, vol. 113, no. 39, National Academy of Sciences, 2016, pp. 11028–33, doi:10.1073/pnas.1605588113.","short":"F. Ortiz Morea, D. Savatin, W. Dejonghe, R. Kumar, Y. Luo, M. Adamowski, J. Van Begin, K. Dressano, G. De Oliveira, X. Zhao, Q. Lu, A. Madder, J. Friml, D. De Moura, E. Russinova, PNAS 113 (2016) 11028–11033.","ieee":"F. Ortiz Morea et al., “Danger-associated peptide signaling in Arabidopsis requires clathrin,” PNAS, vol. 113, no. 39. National Academy of Sciences, pp. 11028–11033, 2016.","apa":"Ortiz Morea, F., Savatin, D., Dejonghe, W., Kumar, R., Luo, Y., Adamowski, M., … Russinova, E. (2016). Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1605588113","ama":"Ortiz Morea F, Savatin D, Dejonghe W, et al. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 2016;113(39):11028-11033. doi:10.1073/pnas.1605588113","chicago":"Ortiz Morea, Fausto, Daniel Savatin, Wim Dejonghe, Rahul Kumar, Yu Luo, Maciek Adamowski, Jos Van Begin, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1605588113.","ista":"Ortiz Morea F, Savatin D, Dejonghe W, Kumar R, Luo Y, Adamowski M, Van Begin J, Dressano K, De Oliveira G, Zhao X, Lu Q, Madder A, Friml J, De Moura D, Russinova E. 2016. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 113(39), 11028–11033."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"39","volume":113,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047203/","open_access":"1"}],"month":"09","intvolume":" 113","abstract":[{"lang":"eng","text":"The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components.\r\n"}],"oa_version":"Preprint","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:49:34Z","type":"journal_article","status":"public","_id":"1277"},{"_id":"1344","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)"},"type":"journal_article","pubrep_id":"654","status":"public","date_updated":"2021-01-12T06:50:01Z","ddc":["581"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:45Z","abstract":[{"text":"Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 5","month":"09","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":5666343,"date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2016-693-v1+1_e19048-download.pdf","date_created":"2018-12-12T10:09:24Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"9209541fbba00f24daad21a5d568540d","file_id":"4748"}],"ec_funded":1,"volume":5,"article_number":"e19048","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"apa":"Fendrych, M., Leung, J., & Friml, J. (2016). TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.19048","ama":"Fendrych M, Leung J, Friml J. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 2016;5. doi:10.7554/eLife.19048","short":"M. Fendrych, J. Leung, J. Friml, ELife 5 (2016).","ieee":"M. Fendrych, J. Leung, and J. Friml, “TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls,” eLife, vol. 5. eLife Sciences Publications, 2016.","mla":"Fendrych, Matyas, et al. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife, vol. 5, e19048, eLife Sciences Publications, 2016, doi:10.7554/eLife.19048.","ista":"Fendrych M, Leung J, Friml J. 2016. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 5, e19048.","chicago":"Fendrych, Matyas, Jeffrey Leung, and Jiří Friml. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.19048."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych"},{"first_name":"Jeffrey","last_name":"Leung","full_name":"Leung, Jeffrey"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"publist_id":"5908","title":"TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls","acknowledgement":"The authors express their gratitude to Veronika Bierbaum, Robert Hauschild for help with MATLAB,\r\nDaniel von Wangenheim for the gravitropism assay. We are thankful to Bill Gray, Mark Estelle,\r\nMichael Prigge, Ottoline Leyser, Claudia Oecking for sharing the seeds with us. We thank Katelyn\r\nSageman-Furnas and the members of the Friml lab for critical reading of the manuscript. The\r\nresearch leading to these results has received funding from the People Programme (Marie Curie\r\nActions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant\r\nagreement n° 291734. This work was also supported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP).","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","year":"2016","has_accepted_license":"1","publication":"eLife","day":"14","date_created":"2018-12-11T11:51:29Z","date_published":"2016-09-14T00:00:00Z","doi":"10.7554/eLife.19048"},{"citation":{"mla":"Molnar, Gergely, et al. “Plasma Membrane: Negative Attraction.” Nature Plants, vol. 2, 16102, Nature Publishing Group, 2016, doi:10.1038/nplants.2016.102.","short":"G. Molnar, M. Fendrych, J. Friml, Nature Plants 2 (2016).","ieee":"G. Molnar, M. Fendrych, and J. Friml, “Plasma membrane: Negative attraction,” Nature Plants, vol. 2. Nature Publishing Group, 2016.","apa":"Molnar, G., Fendrych, M., & Friml, J. (2016). Plasma membrane: Negative attraction. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2016.102","ama":"Molnar G, Fendrych M, Friml J. Plasma membrane: Negative attraction. Nature Plants. 2016;2. doi:10.1038/nplants.2016.102","chicago":"Molnar, Gergely, Matyas Fendrych, and Jiří Friml. “Plasma Membrane: Negative Attraction.” Nature Plants. Nature Publishing Group, 2016. https://doi.org/10.1038/nplants.2016.102.","ista":"Molnar G, Fendrych M, Friml J. 2016. Plasma membrane: Negative attraction. Nature Plants. 2, 16102."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5907","author":[{"full_name":"Molnar, Gergely","last_name":"Molnar","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fendrych","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"title":"Plasma membrane: Negative attraction","article_number":"16102","has_accepted_license":"1","year":"2016","day":"01","publication":"Nature Plants","doi":"10.1038/nplants.2016.102","date_published":"2016-07-01T00:00:00Z","date_created":"2018-12-11T11:51:30Z","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"date_updated":"2021-01-12T06:50:02Z","ddc":["581"],"file_date_updated":"2020-07-14T12:44:45Z","department":[{"_id":"JiFr"}],"_id":"1345","type":"journal_article","status":"public","pubrep_id":"1007","publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"9ba65f558563b287f875f48fa9f30fb2","file_id":"4954","creator":"system","date_updated":"2020-07-14T12:44:45Z","file_size":127781,"date_created":"2018-12-12T10:12:36Z","file_name":"IST-2018-1007-v1+1_Molnar_NatPlants_2016.pdf"},{"checksum":"550d252be808d8ca2b43e83dddb4212f","file_id":"4955","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:12:37Z","file_name":"IST-2018-1007-v1+2_Molnar_NatPlants_2016_editor_statement.pdf","creator":"system","date_updated":"2020-07-14T12:44:45Z","file_size":430556}],"language":[{"iso":"eng"}],"volume":2,"abstract":[{"lang":"eng","text":"The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components."}],"oa_version":"Published Version","scopus_import":1,"month":"07","intvolume":" 2"},{"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:47Z","date_updated":"2021-01-12T06:50:13Z","ddc":["581"],"type":"journal_article","status":"public","pubrep_id":"1006","_id":"1372","volume":212,"issue":"2","publication_status":"published","file":[{"checksum":"27fd841ceaf0403559d7048ef51500f9","file_id":"5108","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf","date_created":"2018-12-12T10:14:53Z","creator":"system","file_size":972763,"date_updated":"2020-07-14T12:44:47Z"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"10","intvolume":" 212","abstract":[{"lang":"eng","text":"Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism."}],"oa_version":"Submitted Version","publist_id":"5839","author":[{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"full_name":"Prat, Tomas","last_name":"Prat","first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"last_name":"Haruštiaková","full_name":"Haruštiaková, Danka","first_name":"Danka"},{"first_name":"Martina","last_name":"Matonohova","full_name":"Matonohova, Martina"},{"first_name":"Lukáš","full_name":"Spíchal, Lukáš","last_name":"Spíchal"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"first_name":"Jan","full_name":"Hejátko, Jan","last_name":"Hejátko"}],"title":"Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis","citation":{"ista":"Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 212(2), 497–509.","chicago":"Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14049.","apa":"Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal, L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14049","ama":"Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 2016;212(2):497-509. doi:10.1111/nph.14049","ieee":"M. Pernisová et al., “Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis,” New Phytologist, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016.","short":"M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal, T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509.","mla":"Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:10.1111/nph.14049."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"497 - 509","doi":"10.1111/nph.14049","date_published":"2016-10-01T00:00:00Z","date_created":"2018-12-11T11:51:38Z","has_accepted_license":"1","year":"2016","day":"01","publication":"New Phytologist","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"acknowledgement":"Funded by Ministry of Education, Youth and Sports Czech Republic. Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council. Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P"},{"acknowledgement":"the Odysseus Program of the Research Foundation-Flanders [G091608] to JF.","quality_controlled":"1","publisher":"Elsevier","oa":1,"has_accepted_license":"1","year":"2016","day":"01","publication":"Plant Science","page":"10 - 19","doi":"10.1016/j.plantsci.2016.05.014","date_published":"2016-09-01T00:00:00Z","date_created":"2018-12-11T11:51:51Z","citation":{"mla":"Ugalde, José, et al. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science, vol. 250, Elsevier, 2016, pp. 10–19, doi:10.1016/j.plantsci.2016.05.014.","apa":"Ugalde, J., Rodríguez Furlán, C., De Rycke, R., Norambuena, L., Friml, J., León, G., & Tejos, R. (2016). Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2016.05.014","ama":"Ugalde J, Rodríguez Furlán C, De Rycke R, et al. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 2016;250:10-19. doi:10.1016/j.plantsci.2016.05.014","ieee":"J. Ugalde et al., “Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development,” Plant Science, vol. 250. Elsevier, pp. 10–19, 2016.","short":"J. Ugalde, C. Rodríguez Furlán, R. De Rycke, L. Norambuena, J. Friml, G. León, R. Tejos, Plant Science 250 (2016) 10–19.","chicago":"Ugalde, José, Cecilia Rodríguez Furlán, Riet De Rycke, Lorena Norambuena, Jiří Friml, Gabriel León, and Ricardo Tejos. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science. Elsevier, 2016. https://doi.org/10.1016/j.plantsci.2016.05.014.","ista":"Ugalde J, Rodríguez Furlán C, De Rycke R, Norambuena L, Friml J, León G, Tejos R. 2016. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 250, 10–19."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"José","full_name":"Ugalde, José","last_name":"Ugalde"},{"full_name":"Rodríguez Furlán, Cecilia","last_name":"Rodríguez Furlán","first_name":"Cecilia"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"first_name":"Lorena","last_name":"Norambuena","full_name":"Norambuena, Lorena"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Gabriel","last_name":"León","full_name":"León, Gabriel"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"}],"publist_id":"5797","external_id":{"pmid":["27457979"]},"title":"Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development","abstract":[{"text":"The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","scopus_import":1,"month":"09","intvolume":" 250","publication_status":"published","file":[{"file_id":"6331","checksum":"ca08de036e6ddc81e6f760e0ccdebd3f","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2016_PlantScience_Ugalde.pdf","date_created":"2019-04-17T07:41:57Z","creator":"dernst","file_size":4338545,"date_updated":"2020-07-14T12:44:53Z"}],"language":[{"iso":"eng"}],"volume":250,"_id":"1410","type":"journal_article","status":"public","pubrep_id":"1005","date_updated":"2021-01-12T06:50:33Z","ddc":["581"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:53Z"},{"citation":{"ista":"Simon S, Skůpa P, Viaene T, Zwiewka M, Tejos R, Klíma P, Čarná M, Rolčík J, De Rycke R, Moreno I, Dobrev P, Orellana A, Zažímalová E, Friml J. 2016. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 211(1), 65–74.","chicago":"Simon, Sibu, Petr Skůpa, Tom Viaene, Marta Zwiewka, Ricardo Tejos, Petr Klíma, Mária Čarná, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14019.","ieee":"S. Simon et al., “PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis,” New Phytologist, vol. 211, no. 1. Wiley-Blackwell, pp. 65–74, 2016.","short":"S. Simon, P. Skůpa, T. Viaene, M. Zwiewka, R. Tejos, P. Klíma, M. Čarná, J. Rolčík, R. De Rycke, I. Moreno, P. Dobrev, A. Orellana, E. Zažímalová, J. Friml, New Phytologist 211 (2016) 65–74.","apa":"Simon, S., Skůpa, P., Viaene, T., Zwiewka, M., Tejos, R., Klíma, P., … Friml, J. (2016). PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14019","ama":"Simon S, Skůpa P, Viaene T, et al. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 2016;211(1):65-74. doi:10.1111/nph.14019","mla":"Simon, Sibu, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist, vol. 211, no. 1, Wiley-Blackwell, 2016, pp. 65–74, doi:10.1111/nph.14019."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5790","author":[{"orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","last_name":"Simon","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Petr","full_name":"Skůpa, Petr","last_name":"Skůpa"},{"first_name":"Tom","full_name":"Viaene, Tom","last_name":"Viaene"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"first_name":"Ricardo","full_name":"Tejos, Ricardo","last_name":"Tejos"},{"first_name":"Petr","full_name":"Klíma, Petr","last_name":"Klíma"},{"full_name":"Čarná, Mária","last_name":"Čarná","first_name":"Mária"},{"first_name":"Jakub","full_name":"Rolčík, Jakub","last_name":"Rolčík"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"full_name":"Moreno, Ignacio","last_name":"Moreno","first_name":"Ignacio"},{"full_name":"Dobrev, Petre","last_name":"Dobrev","first_name":"Petre"},{"full_name":"Orellana, Ariel","last_name":"Orellana","first_name":"Ariel"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis","year":"2016","has_accepted_license":"1","publication":"New Phytologist","day":"01","page":"65 - 74","date_created":"2018-12-11T11:51:54Z","date_published":"2016-07-01T00:00:00Z","doi":"10.1111/nph.14019","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, project CEITEC (CZ.1.05/1.1.00/02.0068) and the Czech Science Foundation GACR (project no. 13-4063 7S to J.F.)","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","date_updated":"2021-01-12T06:50:36Z","ddc":["581"],"file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"JiFr"}],"_id":"1417","type":"journal_article","pubrep_id":"1004","status":"public","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5016","checksum":"23522ced3508ffe7a4f247c4230e6493","date_updated":"2020-07-14T12:44:53Z","file_size":3828383,"creator":"system","date_created":"2018-12-12T10:13:32Z","file_name":"IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf"}],"volume":211,"issue":"1","abstract":[{"lang":"eng","text":"Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport."}],"oa_version":"Submitted Version","scopus_import":1,"intvolume":" 211","month":"07"},{"has_accepted_license":"1","year":"2016","day":"01","publication":"PLoS One","date_published":"2016-02-01T00:00:00Z","doi":"10.1371/journal.pone.0147830","date_created":"2018-12-11T11:52:17Z","acknowledgement":"We thank J. Traas, B. Müller and V. Reddy for providing seed materials and Y. Deb for advice regarding the laser ablation experiments. We specially thank Thomas Laux for stimulating discussions and support in the initial phase of this project.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"citation":{"chicago":"Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0147830.","ista":"Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 11(2), e0147830.","mla":"Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:10.1371/journal.pone.0147830.","ieee":"M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization,” PLoS One, vol. 11, no. 2. Public Library of Science, 2016.","short":"M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016).","ama":"Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 2016;11(2). doi:10.1371/journal.pone.0147830","apa":"Adibi, M., Yoshida, S., Weijers, D., & Fleck, C. (2016). Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0147830"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5711","author":[{"last_name":"Adibi","full_name":"Adibi, Milad","first_name":"Milad"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida","full_name":"Yoshida, Saiko"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"first_name":"Christian","last_name":"Fleck","full_name":"Fleck, Christian"}],"title":"Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization","article_number":"e0147830","publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5066","checksum":"6066146e527335030f83aa5924ab72a6","creator":"system","date_updated":"2020-07-14T12:44:57Z","file_size":4297148,"date_created":"2018-12-12T10:14:16Z","file_name":"IST-2016-521-v1+1_journal.pone.0147830.PDF"}],"language":[{"iso":"eng"}],"issue":"2","volume":11,"abstract":[{"lang":"eng","text":"Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation."}],"oa_version":"Published Version","scopus_import":1,"month":"02","intvolume":" 11","date_updated":"2021-01-12T06:51:03Z","ddc":["570"],"file_date_updated":"2020-07-14T12:44:57Z","department":[{"_id":"JiFr"}],"_id":"1482","type":"journal_article","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","pubrep_id":"521"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chen X, Wu S, Liu Z, Friml J. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 2016;26(6):409-419. doi:10.1016/j.tcb.2016.02.003","apa":"Chen, X., Wu, S., Liu, Z., & Friml, J. (2016). Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2016.02.003","ieee":"X. Chen, S. Wu, Z. Liu, and J. Friml, “Environmental and endogenous control of cortical microtubule orientation,” Trends in Cell Biology, vol. 26, no. 6. Cell Press, pp. 409–419, 2016.","short":"X. Chen, S. Wu, Z. Liu, J. Friml, Trends in Cell Biology 26 (2016) 409–419.","mla":"Chen, Xu, et al. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology, vol. 26, no. 6, Cell Press, 2016, pp. 409–19, doi:10.1016/j.tcb.2016.02.003.","ista":"Chen X, Wu S, Liu Z, Friml J. 2016. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 26(6), 409–419.","chicago":"Chen, Xu, Shuang Wu, Zengyu Liu, and Jiří Friml. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology. Cell Press, 2016. https://doi.org/10.1016/j.tcb.2016.02.003."},"title":"Environmental and endogenous control of cortical microtubule orientation","author":[{"last_name":"Chen","full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"first_name":"Shuang","last_name":"Wu","full_name":"Wu, Shuang"},{"last_name":"Liu","full_name":"Liu, Zengyu","first_name":"Zengyu"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ","full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"publist_id":"5704","day":"01","publication":"Trends in Cell Biology","has_accepted_license":"1","year":"2016","date_published":"2016-06-01T00:00:00Z","doi":"10.1016/j.tcb.2016.02.003","date_created":"2018-12-11T11:52:17Z","page":"409 - 419","acknowledgement":"We thank Maciek Adamowski for helpful discussions and Qiang Zhu and Israel Ausin for critical reading of the manuscript. We sincerely apologize to colleagues whose work we could not include owing to space limitations.","publisher":"Cell Press","quality_controlled":"1","oa":1,"ddc":["581"],"date_updated":"2021-01-12T06:51:04Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:57Z","_id":"1484","status":"public","pubrep_id":"1002","article_type":"review","type":"journal_article","file":[{"file_name":"IST-2018-1002-v1+1_Chen_TICB_2016_proofs.pdf","date_created":"2018-12-12T10:15:34Z","creator":"system","file_size":2329117,"date_updated":"2020-07-14T12:44:57Z","checksum":"b229e5bb4676ec3e27b7b9ea603b3a63","file_id":"5155","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":26,"issue":"6","oa_version":"Submitted Version","month":"06","intvolume":" 26","scopus_import":1},{"_id":"1641","pubrep_id":"1001","status":"public","type":"journal_article","ddc":["581"],"date_updated":"2021-01-12T06:52:11Z","file_date_updated":"2020-07-14T12:45:08Z","department":[{"_id":"JiFr"}],"oa_version":"Preprint","abstract":[{"text":"The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant growth and development including embryo and root patterning, lateral organ formation and growth responses to environmental stimuli. Auxin is directionally transported from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)] and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations are aligned with the direction of the auxin flow. Auxin itself regulates its own transport by modulation of the expression and subcellular localization of the auxin transporters. Increased auxin levels promote the transcription of PIN2 and AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged auxin exposure increases the turnover of PIN proteins and their degradation in the vacuole. In this study, we applied a forward genetic approach, to identify molecular components playing a role in the auxin-mediated degradation. We generated EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations and designed a screen for mutants with persistently strong fluorescent signals of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and established a role for auxin-mediated degradation in plant development.","lang":"eng"}],"intvolume":" 35","month":"06","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf","date_created":"2018-12-12T10:08:34Z","creator":"system","file_size":5637591,"date_updated":"2020-07-14T12:45:08Z","checksum":"0dc6a300cde6536ceedd2bcdd2060efb","file_id":"4695","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","issue":"2","volume":35,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 2016;35(2):465-476. doi:10.1007/s00344-015-9553-2","apa":"Zemová, R., Zwiewka, M., Bielach, A., Robert, H., & Friml, J. (2016). A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. Springer. https://doi.org/10.1007/s00344-015-9553-2","ieee":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, and J. Friml, “A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana,” Journal of Plant Growth Regulation, vol. 35, no. 2. Springer, pp. 465–476, 2016.","short":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant Growth Regulation 35 (2016) 465–476.","mla":"Zemová, Radka, et al. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation, vol. 35, no. 2, Springer, 2016, pp. 465–76, doi:10.1007/s00344-015-9553-2.","ista":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. 2016. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 35(2), 465–476.","chicago":"Zemová, Radka, Marta Zwiewka, Agnieszka Bielach, Hélène Robert, and Jiří Friml. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation. Springer, 2016. https://doi.org/10.1007/s00344-015-9553-2."},"title":"A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana","author":[{"full_name":"Zemová, Radka","last_name":"Zemová","first_name":"Radka"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"last_name":"Bielach","full_name":"Bielach, Agnieszka","first_name":"Agnieszka"},{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5512","acknowledgement":"European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to JF. ","oa":1,"publisher":"Springer","quality_controlled":"1","publication":"Journal of Plant Growth Regulation","day":"01","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:53:12Z","doi":"10.1007/s00344-015-9553-2","date_published":"2016-06-01T00:00:00Z","page":"465 - 476"},{"oa_version":"Published Version","abstract":[{"text":"ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane.","lang":"eng"}],"intvolume":" 7","month":"06","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:18:47Z","file_name":"IST-2016-653-v1+1_ncomms11710_1_.pdf","creator":"system","date_updated":"2020-07-14T12:44:45Z","file_size":3532505,"file_id":"5369","checksum":"e8dc81b3e44db5a7718d7f1501ce1aa7","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","ec_funded":1,"volume":7,"related_material":{"record":[{"id":"7172","status":"public","relation":"dissertation_contains"}]},"_id":"1346","pubrep_id":"653","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)"},"type":"journal_article","ddc":["570"],"date_updated":"2023-09-07T12:54:35Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:45Z","acknowledgement":"We thank Yvon Jaillais, Ikuko Hara-Nishimura, Akihiko Nakano, Takashi Ueda and Jinxing Lin for providing materials, Natasha Raikhel, Glenn Hicks, Steffen Vanneste, and Ricardo Tejos for useful suggestions, Patrick Callaerts for providing S2 Drosophila cell cultures, Michael Sixt for providing HeLa cells, Annick Bleys for literature searches, VIB Bio Imaging Core for help with imaging conditions and Martine De Cock for help in preparing the article. This work was supported by the Agency for Innovation by Science\r\nand Technology for a pre-doctoral fellowship to W.D.; the Research fund KU Leuven\r\n(GOA), a Methusalem grant of the Flemish government and VIB to S.K., J.K. and P.V.;\r\nby the Netherlands Organisation for Scientific Research (NWO) for ALW grants\r\n846.11.002 (C.T.) and 867.15.020 (T.M.); the European Research Council (project\r\nERC-2011-StG-20101109 PSDP) (to J.F.); a European Research Council (ERC) Starting\r\nGrant (grant 260678) (to P.V.), the Research Foundation-Flanders (grants G.0747.09,\r\nG094011 and G095511) (to P.V.), the Hercules Foundation, an Interuniversity Attraction\r\nPoles Poles Program, initiated by the Belgian State, Science Policy Office (to P.V.),\r\nthe Swedish VetenskapsRådet grant to O.K., the Ghent University ‘Bijzonder\r\nOnderzoek Fonds’ (BOF) for a predoctoral fellowship to F.A.O.-M., the Research\r\nFoundation-Flanders (FWO) to K.M. and E.R.","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature Communications","day":"08","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:51:30Z","date_published":"2016-06-08T00:00:00Z","doi":"10.1038/ncomms11710","article_number":"11710","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"W. Dejonghe et al., “Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","short":"W. Dejonghe, S. Kuenen, E. Mylle, M.K. Vasileva, O. Keech, C. Viotti, J. Swerts, M. Fendrych, F. Ortiz Morea, K. Mishev, S. Delang, S. Scholl, X. Zarza, M. Heilmann, J. Kourelis, J. Kasprowicz, L. Nguyen, A. Drozdzecki, I. Van Houtte, A. Szatmári, M. Majda, G. Baisa, S. Bednarek, S. Robert, D. Audenaert, C. Testerink, T. Munnik, D. Van Damme, I. Heilmann, K. Schumacher, J. Winne, J. Friml, P. Verstreken, E. Russinova, Nature Communications 7 (2016).","ama":"Dejonghe W, Kuenen S, Mylle E, et al. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 2016;7. doi:10.1038/ncomms11710","apa":"Dejonghe, W., Kuenen, S., Mylle, E., Vasileva, M. K., Keech, O., Viotti, C., … Russinova, E. (2016). Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11710","mla":"Dejonghe, Wim, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” Nature Communications, vol. 7, 11710, Nature Publishing Group, 2016, doi:10.1038/ncomms11710.","ista":"Dejonghe W, Kuenen S, Mylle E, Vasileva MK, Keech O, Viotti C, Swerts J, Fendrych M, Ortiz Morea F, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis J, Kasprowicz J, Nguyen L, Drozdzecki A, Van Houtte I, Szatmári A, Majda M, Baisa G, Bednarek S, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. 2016. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 7, 11710.","chicago":"Dejonghe, Wim, Sabine Kuenen, Evelien Mylle, Mina K Vasileva, Olivier Keech, Corrado Viotti, Jef Swerts, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11710."},"title":"Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification","author":[{"first_name":"Wim","last_name":"Dejonghe","full_name":"Dejonghe, Wim"},{"first_name":"Sabine","full_name":"Kuenen, Sabine","last_name":"Kuenen"},{"first_name":"Evelien","last_name":"Mylle","full_name":"Mylle, Evelien"},{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K","full_name":"Vasileva, Mina K","last_name":"Vasileva"},{"full_name":"Keech, Olivier","last_name":"Keech","first_name":"Olivier"},{"first_name":"Corrado","full_name":"Viotti, Corrado","last_name":"Viotti"},{"last_name":"Swerts","full_name":"Swerts, Jef","first_name":"Jef"},{"orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fausto","full_name":"Ortiz Morea, Fausto","last_name":"Ortiz Morea"},{"full_name":"Mishev, Kiril","last_name":"Mishev","first_name":"Kiril"},{"first_name":"Simon","full_name":"Delang, Simon","last_name":"Delang"},{"last_name":"Scholl","full_name":"Scholl, Stefan","first_name":"Stefan"},{"first_name":"Xavier","last_name":"Zarza","full_name":"Zarza, Xavier"},{"full_name":"Heilmann, Mareike","last_name":"Heilmann","first_name":"Mareike"},{"last_name":"Kourelis","full_name":"Kourelis, Jiorgos","first_name":"Jiorgos"},{"first_name":"Jaroslaw","last_name":"Kasprowicz","full_name":"Kasprowicz, Jaroslaw"},{"first_name":"Le","full_name":"Nguyen, Le","last_name":"Nguyen"},{"full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki","first_name":"Andrzej"},{"first_name":"Isabelle","full_name":"Van Houtte, Isabelle","last_name":"Van Houtte"},{"full_name":"Szatmári, Anna","last_name":"Szatmári","first_name":"Anna"},{"first_name":"Mateusz","full_name":"Majda, Mateusz","last_name":"Majda"},{"full_name":"Baisa, Gary","last_name":"Baisa","first_name":"Gary"},{"first_name":"Sebastian","last_name":"Bednarek","full_name":"Bednarek, Sebastian"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"first_name":"Dominique","last_name":"Audenaert","full_name":"Audenaert, Dominique"},{"first_name":"Christa","last_name":"Testerink","full_name":"Testerink, Christa"},{"full_name":"Munnik, Teun","last_name":"Munnik","first_name":"Teun"},{"last_name":"Van Damme","full_name":"Van Damme, Daniël","first_name":"Daniël"},{"first_name":"Ingo","last_name":"Heilmann","full_name":"Heilmann, Ingo"},{"first_name":"Karin","full_name":"Schumacher, Karin","last_name":"Schumacher"},{"last_name":"Winne","full_name":"Winne, Johan","first_name":"Johan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"full_name":"Verstreken, Patrik","last_name":"Verstreken","first_name":"Patrik"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"}],"publist_id":"5906"},{"status":"public","type":"journal_article","_id":"510","department":[{"_id":"JiFr"}],"date_updated":"2023-10-17T11:13:40Z","intvolume":" 11","month":"06","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. "}],"issue":"6","volume":11,"language":[{"iso":"eng"}],"publication_status":"published","article_number":"e1191734","title":"The CLE gene family in Populus trichocarpa","article_processing_charge":"No","publist_id":"7308","author":[{"last_name":"Liu","full_name":"Liu, Zhijun","first_name":"Zhijun"},{"last_name":"Yang","full_name":"Yang, Nan","first_name":"Nan"},{"first_name":"Yanting","last_name":"Lv","full_name":"Lv, Yanting"},{"full_name":"Pan, Lixia","last_name":"Pan","first_name":"Lixia"},{"first_name":"Shuo","full_name":"Lv, Shuo","last_name":"Lv"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin","full_name":"Han, Huibin","last_name":"Han"},{"full_name":"Wang, Guodong","last_name":"Wang","first_name":"Guodong"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling & Behavior, vol. 11, no. 6, e1191734, Taylor & Francis, 2016, doi:10.1080/15592324.2016.1191734.","short":"Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling & Behavior 11 (2016).","ieee":"Z. Liu et al., “The CLE gene family in Populus trichocarpa,” Plant Signaling & Behavior, vol. 11, no. 6. Taylor & Francis, 2016.","apa":"Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., & Wang, G. (2016). The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2016.1191734","ama":"Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. 2016;11(6). doi:10.1080/15592324.2016.1191734","chicago":"Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling & Behavior. Taylor & Francis, 2016. https://doi.org/10.1080/15592324.2016.1191734.","ista":"Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. 11(6), e1191734."},"oa":1,"publisher":"Taylor & Francis","quality_controlled":"1","acknowledgement":"We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading of the article. Work in our group is supported by the National Natural Science Foundation of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of Higher Education from the Ministry of Education of China (20120202120009), the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China (2014JM3064). ","date_created":"2018-12-11T11:46:53Z","date_published":"2016-06-02T00:00:00Z","doi":"10.1080/15592324.2016.1191734","publication":"Plant Signaling & Behavior","day":"02","year":"2016"},{"status":"public","pubrep_id":"692","type":"journal_article","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)"},"_id":"1274","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:42Z","ddc":["581"],"date_updated":"2024-02-12T12:03:42Z","month":"09","intvolume":" 6","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis.","lang":"eng"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"545"}]},"volume":6,"file":[{"date_created":"2018-12-12T10:13:25Z","file_name":"IST-2016-692-v1+1_srep33754.pdf","creator":"system","date_updated":"2020-07-14T12:44:42Z","file_size":2895147,"file_id":"5008","checksum":"ee371fbc9124ad93157a95829264e4fe","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","article_number":"33754","title":"Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis","author":[{"full_name":"Mazur, Ewa","last_name":"Mazur","first_name":"Ewa"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"6042","article_processing_charge":"No","external_id":{"pmid":["27649687"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Mazur, Ewa, Eva Benková, and Jiří Friml. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33754.","ista":"Mazur E, Benková E, Friml J. 2016. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 6, 33754.","mla":"Mazur, Ewa, et al. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific Reports, vol. 6, 33754, Nature Publishing Group, 2016, doi:10.1038/srep33754.","apa":"Mazur, E., Benková, E., & Friml, J. (2016). Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep33754","ama":"Mazur E, Benková E, Friml J. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 2016;6. doi:10.1038/srep33754","ieee":"E. Mazur, E. Benková, and J. Friml, “Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"E. Mazur, E. Benková, J. Friml, Scientific Reports 6 (2016)."},"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"acknowledgement":"We wish to thank Prof. Ewa U. Kurczyńska for initiation of this work and valuable advices. We thank Martine De Cock for help in preparing the manuscript. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), the European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637 S) to J.F., (GA 13-39982S) to E.B. and E.M. and in part by the European Regional Development Fund (project “CEITEC, Central European Institute of Technology”, CZ.1.05/1.1.00/02.0068).","doi":"10.1038/srep33754","date_published":"2016-09-21T00:00:00Z","date_created":"2018-12-11T11:51:05Z","day":"21","publication":"Scientific Reports","has_accepted_license":"1","year":"2016"},{"type":"journal_article","article_type":"original","status":"public","_id":"1383","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:50:18Z","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/","open_access":"1"}],"month":"07","intvolume":" 1","abstract":[{"text":"In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"volume":1,"issue":"7","publication_status":"published","language":[{"iso":"eng"}],"article_number":"15094","publist_id":"5827","author":[{"first_name":"Luo","full_name":"Yu, Luo","last_name":"Yu"},{"first_name":"Stefan","last_name":"Scholl","full_name":"Scholl, Stefan"},{"full_name":"Doering, Anett","last_name":"Doering","first_name":"Anett"},{"first_name":"Zhang","last_name":"Yi","full_name":"Yi, Zhang"},{"last_name":"Irani","full_name":"Irani, Niloufer","first_name":"Niloufer"},{"first_name":"Simone","last_name":"Di Rubbo","full_name":"Di Rubbo, Simone"},{"full_name":"Neumetzler, Lutz","last_name":"Neumetzler","first_name":"Lutz"},{"full_name":"Krishnamoorthy, Praveen","last_name":"Krishnamoorthy","first_name":"Praveen"},{"full_name":"Van Houtte, Isabelle","last_name":"Van Houtte","first_name":"Isabelle"},{"last_name":"Mylle","full_name":"Mylle, Evelien","first_name":"Evelien"},{"first_name":"Volker","last_name":"Bischoff","full_name":"Bischoff, Volker"},{"last_name":"Vernhettes","full_name":"Vernhettes, Samantha","first_name":"Samantha"},{"first_name":"Johan","last_name":"Winne","full_name":"Winne, Johan"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Stierhof","full_name":"Stierhof, York","first_name":"York"},{"first_name":"Karin","last_name":"Schumacher","full_name":"Schumacher, Karin"},{"first_name":"Staffan","last_name":"Persson","full_name":"Persson, Staffan"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"}],"article_processing_charge":"No","external_id":{"pmid":["27250258"]},"title":"V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis","citation":{"chicago":"Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing Group, 2015. https://doi.org/10.1038/nplants.2015.94.","ista":"Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094.","mla":"Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:10.1038/nplants.2015.94.","ama":"Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7). doi:10.1038/nplants.2015.94","apa":"Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94","short":"L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015).","ieee":"L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing Group, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"date_published":"2015-07-06T00:00:00Z","doi":"10.1038/nplants.2015.94","date_created":"2018-12-11T11:51:42Z","year":"2015","day":"06","publication":"Nature Plants"},{"type":"journal_article","article_type":"original","status":"public","_id":"1532","department":[{"_id":"JiFr"}],"date_updated":"2022-05-24T09:02:24Z","scopus_import":"1","intvolume":" 42","month":"03","abstract":[{"text":"Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels.","lang":"eng"}],"pmid":1,"oa_version":"None","volume":42,"issue":"3","publication_status":"published","publication_identifier":{"issn":["1445-4408"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"pmid":["32480670"]},"author":[{"first_name":"Huaiyu","last_name":"Yang","full_name":"Yang, Huaiyu"},{"last_name":"Von Der Fecht Bartenbach","full_name":"Von Der Fecht Bartenbach, Jenny","first_name":"Jenny"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Jan","last_name":"Lohmann","full_name":"Lohmann, Jan"},{"last_name":"Neuhäuser","full_name":"Neuhäuser, Benjamin","first_name":"Benjamin"},{"first_name":"Uwe","last_name":"Ludewig","full_name":"Ludewig, Uwe"}],"publist_id":"5639","title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","citation":{"chicago":"Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology. CSIRO, 2015. https://doi.org/10.1071/FP14171.","ista":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.","mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:10.1071/FP14171.","ama":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 2015;42(3):239-251. doi:10.1071/FP14171","apa":"Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., & Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. CSIRO. https://doi.org/10.1071/FP14171","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","ieee":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” Functional Plant Biology, vol. 42, no. 3. CSIRO, pp. 239–251, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"CSIRO","quality_controlled":"1","page":"239 - 251","date_created":"2018-12-11T11:52:34Z","doi":"10.1071/FP14171","date_published":"2015-03-01T00:00:00Z","year":"2015","publication":"Functional Plant Biology","day":"01"},{"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"has_accepted_license":"1","year":"2015","day":"18","publication":"Nature Communications","doi":"10.1038/ncomms9822","date_published":"2015-11-18T00:00:00Z","date_created":"2018-12-11T11:52:34Z","article_number":"8822","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"citation":{"ista":"Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822.","chicago":"Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822.","ieee":"H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","short":"H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015).","apa":"Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822","ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 2015;6. doi:10.1038/ncomms9822","mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications, vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Hongzhe","full_name":"Wang, Hongzhe","last_name":"Wang"},{"first_name":"Kezhen","full_name":"Yang, Kezhen","last_name":"Yang"},{"full_name":"Zou, Junjie","last_name":"Zou","first_name":"Junjie"},{"first_name":"Lingling","full_name":"Zhu, Lingling","last_name":"Zhu"},{"first_name":"Zidian","last_name":"Xie","full_name":"Xie, Zidian"},{"last_name":"Morita","full_name":"Morita, Miyoterao","first_name":"Miyoterao"},{"first_name":"Masao","last_name":"Tasaka","full_name":"Tasaka, Masao"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Erich","full_name":"Grotewold, Erich","last_name":"Grotewold"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Sack","full_name":"Sack, Fred","first_name":"Fred"},{"full_name":"Le, Jie","last_name":"Le","first_name":"Jie"}],"publist_id":"5637","title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","abstract":[{"text":"PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"11","intvolume":" 6","publication_status":"published","file":[{"file_id":"5259","checksum":"3c06735fc7cd7e482ca830cbd26001bf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","date_created":"2018-12-12T10:17:07Z","creator":"system","file_size":1852268,"date_updated":"2020-07-14T12:45:01Z"}],"language":[{"iso":"eng"}],"volume":6,"ec_funded":1,"_id":"1534","type":"journal_article","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","pubrep_id":"485","date_updated":"2021-01-12T06:51:26Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:01Z","department":[{"_id":"JiFr"}]},{"abstract":[{"lang":"eng","text":"Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil."}],"acknowledgement":"This work was funded by a grant of the Swiss National Foundation to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands) for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel (University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel (University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for hints on protein quantification.","oa_version":"None","quality_controlled":"1","scopus_import":1,"publisher":"Cell Press","intvolume":" 25","month":"02","publication_status":"published","year":"2015","publication":"Current Biology","language":[{"iso":"eng"}],"day":"12","page":"647 - 655","date_created":"2018-12-11T11:52:35Z","doi":"10.1016/j.cub.2015.01.015","volume":25,"date_published":"2015-02-12T00:00:00Z","issue":"5","_id":"1536","type":"journal_article","status":"public","citation":{"mla":"Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology, vol. 25, no. 5, Cell Press, 2015, pp. 647–55, doi:10.1016/j.cub.2015.01.015.","short":"J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester, E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.","ieee":"J. Sasse et al., “Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport,” Current Biology, vol. 25, no. 5. Cell Press, pp. 647–655, 2015.","apa":"Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi, L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.01.015","ama":"Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 2015;25(5):647-655. doi:10.1016/j.cub.2015.01.015","chicago":"Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology. Cell Press, 2015. https://doi.org/10.1016/j.cub.2015.01.015.","ista":"Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 25(5), 647–655."},"date_updated":"2021-01-12T06:51:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Sasse","full_name":"Sasse, Joëlle","first_name":"Joëlle"},{"full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","full_name":"Gübeli, Christian","last_name":"Gübeli"},{"first_name":"Guowei","full_name":"Liu, Guowei","last_name":"Liu"},{"first_name":"Xi","full_name":"Cheng, Xi","last_name":"Cheng"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bouwmeester, Harro","last_name":"Bouwmeester","first_name":"Harro"},{"full_name":"Martinoia, Enrico","last_name":"Martinoia","first_name":"Enrico"},{"full_name":"Borghi, Lorenzo","last_name":"Borghi","first_name":"Lorenzo"}],"publist_id":"5635","title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport","department":[{"_id":"JiFr"}]},{"date_created":"2018-12-11T11:52:38Z","volume":169,"doi":"10.1104/pp.15.00769","date_published":"2015-12-01T00:00:00Z","issue":"4","page":"2684 - 2699","publication":"Plant Physiology","language":[{"iso":"eng"}],"day":"01","year":"2015","publication_status":"published","intvolume":" 169","month":"12","publisher":"American Society of Plant Biologists","scopus_import":1,"oa_version":"None","abstract":[{"lang":"eng","text":"A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta."}],"title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","department":[{"_id":"JiFr"}],"publist_id":"5628","author":[{"first_name":"Yadira","full_name":"Olvera Carrillo, Yadira","last_name":"Olvera Carrillo"},{"first_name":"Michiel","full_name":"Van Bel, Michiel","last_name":"Van Bel"},{"first_name":"Tom","last_name":"Van Hautegem","full_name":"Van Hautegem, Tom"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"first_name":"Marlies","full_name":"Huysmans, Marlies","last_name":"Huysmans"},{"first_name":"Mária","full_name":"Šimášková, Mária","last_name":"Šimášková"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"full_name":"Buscaill, Pierre","last_name":"Buscaill","first_name":"Pierre"},{"last_name":"Rivas","full_name":"Rivas, Susana","first_name":"Susana"},{"last_name":"Coll","full_name":"Coll, Núria","first_name":"Núria"},{"last_name":"Coppens","full_name":"Coppens, Frederik","first_name":"Frederik"},{"full_name":"Maere, Steven","last_name":"Maere","first_name":"Steven"},{"last_name":"Nowack","full_name":"Nowack, Moritz","first_name":"Moritz"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699.","chicago":"Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology. American Society of Plant Biologists, 2015. https://doi.org/10.1104/pp.15.00769.","ieee":"Y. Olvera Carrillo et al., “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” Plant Physiology, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015.","short":"Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699.","apa":"Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.15.00769","ama":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 2015;169(4):2684-2699. doi:10.1104/pp.15.00769","mla":"Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:10.1104/pp.15.00769."},"date_updated":"2021-01-12T06:51:30Z","status":"public","type":"journal_article","_id":"1543"},{"ddc":["570"],"date_updated":"2021-01-12T06:51:35Z","file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"JiFr"}],"_id":"1556","pubrep_id":"480","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)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5051","checksum":"257919be0ce3d306185d3891ad7acf39","date_updated":"2020-07-14T12:45:02Z","file_size":7753043,"creator":"system","date_created":"2018-12-12T10:14:02Z","file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf"}],"publication_status":"published","issue":"15","volume":66,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators."}],"intvolume":" 66","month":"08","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230.","ieee":"Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” Journal of Experimental Botany, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015.","short":"Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642.","ama":"Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 2015;66(15):4631-4642. doi:10.1093/jxb/erv230","apa":"Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230","chicago":"Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv230.","ista":"Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642."},"title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development","publist_id":"5615","author":[{"first_name":"Yuebin","last_name":"Jia","full_name":"Jia, Yuebin"},{"first_name":"Huiyu","full_name":"Tian, Huiyu","last_name":"Tian"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang","last_name":"Li","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang"},{"first_name":"Qianqian","full_name":"Yu, Qianqian","last_name":"Yu"},{"first_name":"Lei","last_name":"Wang","full_name":"Wang, Lei"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"last_name":"Ding","full_name":"Ding, Zhaojun","first_name":"Zhaojun"}],"publication":"Journal of Experimental Botany","day":"01","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:52:42Z","doi":"10.1093/jxb/erv230","date_published":"2015-08-01T00:00:00Z","page":"4631 - 4642","oa":1,"quality_controlled":"1","publisher":"Oxford University Press"},{"scopus_import":1,"publisher":"Company of Biologists","quality_controlled":"1","month":"02","intvolume":" 142","abstract":[{"lang":"eng","text":"CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation."}],"oa_version":"None","page":"712 - 721","issue":"4","doi":"10.1242/dev.113225","date_published":"2015-02-15T00:00:00Z","volume":142,"date_created":"2018-12-11T11:52:42Z","publication_status":"published","year":"2015","day":"15","language":[{"iso":"eng"}],"publication":"Development","type":"journal_article","status":"public","_id":"1558","author":[{"full_name":"Ivanchenko, Maria","last_name":"Ivanchenko","first_name":"Maria"},{"first_name":"Jinsheng","last_name":"Zhu","full_name":"Zhu, Jinsheng"},{"first_name":"Bangjun","last_name":"Wang","full_name":"Wang, Bangjun"},{"full_name":"Medvecka, Eva","last_name":"Medvecka","id":"298814E2-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"first_name":"Yunlong","last_name":"Du","full_name":"Du, Yunlong"},{"last_name":"Azzarello","full_name":"Azzarello, Elisa","first_name":"Elisa"},{"first_name":"Stefano","last_name":"Mancuso","full_name":"Mancuso, Stefano"},{"full_name":"Megraw, Molly","last_name":"Megraw","first_name":"Molly"},{"first_name":"Sergei","last_name":"Filichkin","full_name":"Filichkin, Sergei"},{"first_name":"Joseph","full_name":"Dubrovsky, Joseph","last_name":"Dubrovsky"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"}],"publist_id":"5613","department":[{"_id":"JiFr"}],"title":"The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation","date_updated":"2021-01-12T06:51:35Z","citation":{"chicago":"Ivanchenko, Maria, Jinsheng Zhu, Bangjun Wang, Eva Medvecka, Yunlong Du, Elisa Azzarello, Stefano Mancuso, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.113225.","ista":"Ivanchenko M, Zhu J, Wang B, Medvecka E, Du Y, Azzarello E, Mancuso S, Megraw M, Filichkin S, Dubrovsky J, Friml J, Geisler M. 2015. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 142(4), 712–721.","mla":"Ivanchenko, Maria, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 712–21, doi:10.1242/dev.113225.","apa":"Ivanchenko, M., Zhu, J., Wang, B., Medvecka, E., Du, Y., Azzarello, E., … Geisler, M. (2015). The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. Company of Biologists. https://doi.org/10.1242/dev.113225","ama":"Ivanchenko M, Zhu J, Wang B, et al. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 2015;142(4):712-721. doi:10.1242/dev.113225","ieee":"M. Ivanchenko et al., “The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation,” Development, vol. 142, no. 4. Company of Biologists, pp. 712–721, 2015.","short":"M. Ivanchenko, J. Zhu, B. Wang, E. Medvecka, Y. Du, E. Azzarello, S. Mancuso, M. Megraw, S. Filichkin, J. Dubrovsky, J. Friml, M. Geisler, Development 142 (2015) 712–721."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"page":"207 - 210","doi":"10.1038/nmeth.3279","date_published":"2015-02-26T00:00:00Z","date_created":"2018-12-11T11:52:41Z","year":"2015","day":"26","publication":"Nature Methods","publist_id":"5617","author":[{"first_name":"Cheyang","full_name":"Liao, Cheyang","last_name":"Liao"},{"first_name":"Wouter","last_name":"Smet","full_name":"Smet, Wouter"},{"last_name":"Brunoud","full_name":"Brunoud, Géraldine","first_name":"Géraldine"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"first_name":"Teva","full_name":"Vernoux, Teva","last_name":"Vernoux"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"}],"external_id":{"pmid":["25643149"]},"title":"Reporters for sensitive and quantitative measurement of auxin response","citation":{"chicago":"Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279.","ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210.","mla":"Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:10.1038/nmeth.3279.","ieee":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” Nature Methods, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","ama":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210. doi:10.1038/nmeth.3279","apa":"Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/"}],"month":"02","intvolume":" 12","abstract":[{"text":"The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","issue":"3","volume":12,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1554","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:51:34Z"},{"author":[{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu","last_name":"Chen"},{"full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"publist_id":"5609","title":"Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles","citation":{"short":"P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E. Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065.","ieee":"P. Grones et al., “Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles,” Journal of Experimental Botany, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015.","ama":"Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 2015;66(16):5055-5065. doi:10.1093/jxb/erv177","apa":"Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T., … Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv177","mla":"Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany, vol. 66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:10.1093/jxb/erv177.","ista":"Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065.","chicago":"Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv177."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"page":"5055 - 5065","date_created":"2018-12-11T11:52:44Z","doi":"10.1093/jxb/erv177","date_published":"2015-08-01T00:00:00Z","year":"2015","publication":"Journal of Experimental Botany","day":"01","quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG- 20101109-PSDP to JF); the European Social Fund and the state budget of the Czech Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR) [project 13-40637S to JF].","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"date_updated":"2023-02-23T10:04:26Z","article_type":"original","type":"journal_article","status":"public","_id":"1562","ec_funded":1,"volume":66,"issue":"16","publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"intvolume":" 66","month":"08","abstract":[{"text":"The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor.","lang":"eng"}],"oa_version":"None"},{"article_number":"8821","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821.","short":"Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015).","ieee":"Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","apa":"Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821","ama":"Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821","chicago":"Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821.","ista":"Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821."},"title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development","author":[{"full_name":"Chen, Qian","last_name":"Chen","first_name":"Qian"},{"first_name":"Yang","full_name":"Liu, Yang","last_name":"Liu"},{"last_name":"Maere","full_name":"Maere, Steven","first_name":"Steven"},{"first_name":"Eunkyoung","full_name":"Lee, Eunkyoung","last_name":"Lee"},{"last_name":"Van Isterdael","full_name":"Van Isterdael, Gert","first_name":"Gert"},{"full_name":"Xie, Zidian","last_name":"Xie","first_name":"Zidian"},{"first_name":"Wei","full_name":"Xuan, Wei","last_name":"Xuan"},{"full_name":"Lucas, Jessica","last_name":"Lucas","first_name":"Jessica"},{"full_name":"Vassileva, Valya","last_name":"Vassileva","first_name":"Valya"},{"full_name":"Kitakura, Saeko","last_name":"Kitakura","first_name":"Saeko"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Marhavy","orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik"},{"first_name":"Niko","full_name":"Geldner, Niko","last_name":"Geldner"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"last_name":"Le","full_name":"Le, Jie","first_name":"Jie"},{"first_name":"Hidehiro","last_name":"Fukaki","full_name":"Fukaki, Hidehiro"},{"full_name":"Grotewold, Erich","last_name":"Grotewold","first_name":"Erich"},{"last_name":"Li","full_name":"Li, Chuanyou","first_name":"Chuanyou"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Fred","full_name":"Sack, Fred","last_name":"Sack"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"}],"publist_id":"5597","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","publication":"Nature Communications","day":"18","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:52:48Z","doi":"10.1038/ncomms9821","date_published":"2015-11-18T00:00:00Z","_id":"1574","pubrep_id":"477","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)"},"type":"journal_article","ddc":["580"],"date_updated":"2021-01-12T06:51:42Z","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:02Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level."}],"intvolume":" 6","month":"11","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:14:32Z","file_name":"IST-2016-477-v1+1_ncomms9821.pdf","creator":"system","date_updated":"2020-07-14T12:45:02Z","file_size":1701815,"file_id":"5085","checksum":"8ff5c108899b548806e1cb7a302fe76d","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","volume":6},{"title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","publist_id":"5602","author":[{"first_name":"Siamsa","last_name":"Doyle","full_name":"Doyle, Siamsa"},{"last_name":"Haegera","full_name":"Haegera, Ash","first_name":"Ash"},{"last_name":"Vain","full_name":"Vain, Thomas","first_name":"Thomas"},{"full_name":"Rigala, Adeline","last_name":"Rigala","first_name":"Adeline"},{"first_name":"Corrado","full_name":"Viotti, Corrado","last_name":"Viotti"},{"first_name":"Małgorzata","last_name":"Łangowskaa","full_name":"Łangowskaa, Małgorzata"},{"last_name":"Maa","full_name":"Maa, Qian","first_name":"Qian"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Raikhel, Natasha","last_name":"Raikhel","first_name":"Natasha"},{"last_name":"Hickse","full_name":"Hickse, Glenn","first_name":"Glenn"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815.","chicago":"Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112.","ama":"Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112","apa":"Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112","short":"S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.","ieee":"S. Doyle et al., “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015.","mla":"Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112."},"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"doi":"10.1073/pnas.1424856112","date_published":"2015-02-17T00:00:00Z","date_created":"2018-12-11T11:52:46Z","page":"E806 - E815","day":"17","publication":"PNAS","year":"2015","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). ","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:51:39Z","status":"public","type":"journal_article","_id":"1569","issue":"7","volume":112,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 112","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.","lang":"eng"}]},{"article_number":"8717","project":[{"call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362"},{"name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Šimášková, J. O’Brien, M. Khan-Djamei, G. Van Noorden, K. Ötvös, A. Vieten, I. De Clercq, J. Van Haperen, C. Cuesta, K. Hoyerová, S. Vanneste, P. Marhavý, K.T. Wabnik, F. Van Breusegem, M. Nowack, A. Murphy, J. Friml, D. Weijers, T. Beeckman, E. Benková, Nature Communications 6 (2015).","ieee":"M. Šimášková et al., “Cytokinin response factors regulate PIN-FORMED auxin transporters,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","ama":"Šimášková M, O’Brien J, Khan-Djamei M, et al. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. 2015;6. doi:10.1038/ncomms9717","apa":"Šimášková, M., O’Brien, J., Khan-Djamei, M., Van Noorden, G., Ötvös, K., Vieten, A., … Benková, E. (2015). Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9717","mla":"Šimášková, Mária, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin Transporters.” Nature Communications, vol. 6, 8717, Nature Publishing Group, 2015, doi:10.1038/ncomms9717.","ista":"Šimášková M, O’Brien J, Khan-Djamei M, Van Noorden G, Ötvös K, Vieten A, De Clercq I, Van Haperen J, Cuesta C, Hoyerová K, Vanneste S, Marhavý P, Wabnik KT, Van Breusegem F, Nowack M, Murphy A, Friml J, Weijers D, Beeckman T, Benková E. 2015. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. 6, 8717.","chicago":"Šimášková, Mária, José O’Brien, Mamoona Khan-Djamei, Giel Van Noorden, Krisztina Ötvös, Anne Vieten, Inge De Clercq, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin Transporters.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9717."},"title":"Cytokinin response factors regulate PIN-FORMED auxin transporters","publist_id":"5513","author":[{"first_name":"Mária","full_name":"Šimášková, Mária","last_name":"Šimášková"},{"last_name":"O'Brien","full_name":"O'Brien, José","first_name":"José"},{"full_name":"Khan-Djamei, Mamoona","last_name":"Khan-Djamei","id":"391B5BBC-F248-11E8-B48F-1D18A9856A87","first_name":"Mamoona"},{"last_name":"Van Noorden","full_name":"Van Noorden, Giel","first_name":"Giel"},{"orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina"},{"full_name":"Vieten, Anne","last_name":"Vieten","first_name":"Anne"},{"full_name":"De Clercq, Inge","last_name":"De Clercq","first_name":"Inge"},{"last_name":"Van Haperen","full_name":"Van Haperen, Johanna","first_name":"Johanna"},{"last_name":"Cuesta","orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela"},{"first_name":"Klára","last_name":"Hoyerová","full_name":"Hoyerová, Klára"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter","last_name":"Marhavy"},{"first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","last_name":"Wabnik"},{"full_name":"Van Breusegem, Frank","last_name":"Van Breusegem","first_name":"Frank"},{"last_name":"Nowack","full_name":"Nowack, Moritz","first_name":"Moritz"},{"last_name":"Murphy","full_name":"Murphy, Angus","first_name":"Angus"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ","first_name":"Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"acknowledgement":"This work was supported by the European Research Council Starting Independent Research grant (ERC-2007-Stg-207362-HCPO to E.B., M.S., C.C.), by the Ghent University Multidisciplinary Research Partnership ‘Biotechnology for a Sustainable Economy’ no.01MRB510W, by the Research Foundation—Flanders (grant 3G033711 to J.-A.O.), by the Austrian Science Fund (FWF01_I1774S) to K.Ö.,E.B., and by the Interuniversity Attraction Poles Programme (IUAP P7/29 ‘MARS’) initiated by the Belgian Science Policy Office. I.D.C. and S.V. are post-doctoral fellows of the Research Foundation—Flanders (FWO). This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF).","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"day":"01","publication":"Nature Communications","has_accepted_license":"1","year":"2015","date_published":"2015-01-01T00:00:00Z","doi":"10.1038/ncomms9717","date_created":"2018-12-11T11:53:12Z","_id":"1640","status":"public","pubrep_id":"1020","type":"journal_article","ddc":["580"],"date_updated":"2021-01-12T06:52:11Z","file_date_updated":"2020-07-14T12:45:08Z","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"oa_version":"Submitted Version","abstract":[{"text":"Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"month":"01","intvolume":" 6","scopus_import":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5358","checksum":"c2c84bca37401435fedf76bad0ba0579","file_size":1471217,"date_updated":"2020-07-14T12:45:08Z","creator":"system","file_name":"IST-2018-1020-v1+1_Simaskova_et_al_NatCom_2015.pdf","date_created":"2018-12-12T10:18:36Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6,"ec_funded":1},{"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","page":"1175 - 1187","doi":"10.1016/j.molp.2015.03.007","date_published":"2015-08-03T00:00:00Z","date_created":"2018-12-11T11:54:11Z","year":"2015","day":"03","publication":"Molecular Plant","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"author":[{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"last_name":"Friml","full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ"}],"publist_id":"5287","title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","citation":{"chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2015.03.007.","ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:10.1016/j.molp.2015.03.007.","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” Molecular Plant, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015.","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187.","ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 2015;8(8):1175-1187. doi:10.1016/j.molp.2015.03.007","apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., & Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2015.03.007"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"08","intvolume":" 8","abstract":[{"text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.","lang":"eng"}],"oa_version":"None","volume":8,"issue":"8","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1819","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:24Z"},{"day":"01","language":[{"iso":"eng"}],"publication":"Biochimica et Biophysica Acta - Molecular Cell Research","year":"2015","publication_status":"published","issue":"9","volume":1853,"doi":"10.1016/j.bbamcr.2015.02.017","date_published":"2015-09-01T00:00:00Z","date_created":"2018-12-11T11:54:21Z","page":"2168 - 2172","oa_version":"None","acknowledgement":"The contributing authors were supported by the Ghent University Special Research Fund (to E.H.), the Interuniversity Attraction Poles Programme (IAP VI/33 and IUAP P7/29 ‘MARS’), the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), and the Research Foundation Flanders (to S.V.).","abstract":[{"text":"Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.","lang":"eng"}],"month":"09","intvolume":" 1853","scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Himschoot E, Beeckman T, Friml J, Vanneste S. 2015. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(9), 2168–2172.","chicago":"Himschoot, Ellie, Tom Beeckman, Jiří Friml, and Steffen Vanneste. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2015.02.017.","apa":"Himschoot, E., Beeckman, T., Friml, J., & Vanneste, S. (2015). Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2015.02.017","ama":"Himschoot E, Beeckman T, Friml J, Vanneste S. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(9):2168-2172. doi:10.1016/j.bbamcr.2015.02.017","short":"E. Himschoot, T. Beeckman, J. Friml, S. Vanneste, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 2168–2172.","ieee":"E. Himschoot, T. Beeckman, J. Friml, and S. Vanneste, “Calcium is an organizer of cell polarity in plants,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9. Elsevier, pp. 2168–2172, 2015.","mla":"Himschoot, Ellie, et al. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9, Elsevier, 2015, pp. 2168–72, doi:10.1016/j.bbamcr.2015.02.017."},"date_updated":"2021-01-12T06:53:36Z","department":[{"_id":"JiFr"}],"title":"Calcium is an organizer of cell polarity in plants","publist_id":"5252","author":[{"full_name":"Himschoot, Ellie","last_name":"Himschoot","first_name":"Ellie"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"last_name":"Friml","full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596","first_name":"Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"}],"_id":"1849","status":"public","type":"journal_article"},{"citation":{"mla":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant, vol. 8, no. 3, Elsevier, 2015, pp. 356–58, doi:10.1016/j.molp.2014.12.013.","ama":"Grones P, Friml J. ABP1: Finally docking. Molecular Plant. 2015;8(3):356-358. doi:10.1016/j.molp.2014.12.013","apa":"Grones, P., & Friml, J. (2015). ABP1: Finally docking. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2014.12.013","ieee":"P. Grones and J. Friml, “ABP1: Finally docking,” Molecular Plant, vol. 8, no. 3. Elsevier, pp. 356–358, 2015.","short":"P. Grones, J. Friml, Molecular Plant 8 (2015) 356–358.","chicago":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2014.12.013.","ista":"Grones P, Friml J. 2015. ABP1: Finally docking. Molecular Plant. 8(3), 356–358."},"date_updated":"2021-01-12T06:53:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Grones","full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5254","department":[{"_id":"JiFr"}],"title":"ABP1: Finally docking","_id":"1847","type":"journal_article","status":"public","year":"2015","publication_status":"published","publication":"Molecular Plant","language":[{"iso":"eng"}],"day":"02","page":"356 - 358","date_created":"2018-12-11T11:54:20Z","date_published":"2015-03-02T00:00:00Z","doi":"10.1016/j.molp.2014.12.013","issue":"3","volume":8,"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637S).","oa_version":"None","scopus_import":1,"quality_controlled":"1","publisher":"Elsevier","intvolume":" 8","month":"03"},{"date_updated":"2021-01-12T06:53:43Z","department":[{"_id":"JiFr"}],"_id":"1865","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":142,"ec_funded":1,"oa_version":"None","abstract":[{"text":"The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop betweenMONOPTEROS(ARF5)-dependent auxin signalling and auxin transport. ThisMONOPTEROSdependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling.","lang":"eng"}],"month":"02","intvolume":" 142","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Robert H, Grunewald W, Sauer M, Cannoot B, Soriano M, Swarup R, Weijers D, Bennett M, Boutilier K, Friml J. 2015. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 142(4), 702–711.","chicago":"Robert, Hélène, Wim Grunewald, Michael Sauer, Bernard Cannoot, Mercedes Soriano, Ranjan Swarup, Dolf Weijers, Malcolm Bennett, Kim Boutilier, and Jiří Friml. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.115832.","apa":"Robert, H., Grunewald, W., Sauer, M., Cannoot, B., Soriano, M., Swarup, R., … Friml, J. (2015). Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. Company of Biologists. https://doi.org/10.1242/dev.115832","ama":"Robert H, Grunewald W, Sauer M, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 2015;142(4):702-711. doi:10.1242/dev.115832","ieee":"H. Robert et al., “Plant embryogenesis requires AUX/LAX-mediated auxin influx,” Development, vol. 142, no. 4. Company of Biologists, pp. 702–711, 2015.","short":"H. Robert, W. Grunewald, M. Sauer, B. Cannoot, M. Soriano, R. Swarup, D. Weijers, M. Bennett, K. Boutilier, J. Friml, Development 142 (2015) 702–711.","mla":"Robert, Hélène, et al. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 702–11, doi:10.1242/dev.115832."},"title":"Plant embryogenesis requires AUX/LAX-mediated auxin influx","publist_id":"5231","author":[{"last_name":"Robert","full_name":"Robert, Hélène","first_name":"Hélène"},{"last_name":"Grunewald","full_name":"Grunewald, Wim","first_name":"Wim"},{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"last_name":"Cannoot","full_name":"Cannoot, Bernard","first_name":"Bernard"},{"first_name":"Mercedes","last_name":"Soriano","full_name":"Soriano, Mercedes"},{"first_name":"Ranjan","last_name":"Swarup","full_name":"Swarup, Ranjan"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"first_name":"Malcolm","last_name":"Bennett","full_name":"Bennett, Malcolm"},{"full_name":"Boutilier, Kim","last_name":"Boutilier","first_name":"Kim"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"15","publication":"Development","year":"2015","doi":"10.1242/dev.115832","date_published":"2015-02-15T00:00:00Z","date_created":"2018-12-11T11:54:26Z","page":"702 - 711","acknowledgement":"W.G. is a post-doctoral fellow of the Research Foundation Flanders. H.S.R. is supported by Employment of Best Young Scientists for International Cooperation Empowerment [CZ.1.07/2.3.00/30.0037], co-financed by the European Social Fund and the state budget of the Czech Republic. Mi.S. was funded by the Ramón y Cajal program. This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], project ‘CEITEC – Central European Institute of Technology’ [CZ.1.05/1.1.00/02.0068], the European Social Fund [CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GACR [GA13-40637S] to J.F. We acknowledge funding from the Biological and Biotechnological Science Research Council (BBSRC) and Engineering Physics Science Research Council (EPSRC) to R.S. and M.B","quality_controlled":"1","publisher":"Company of Biologists"},{"type":"journal_article","status":"public","pubrep_id":"563","_id":"1871","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:19Z","date_updated":"2021-01-12T06:53:45Z","ddc":["570"],"scopus_import":1,"month":"01","intvolume":" 128","abstract":[{"text":"The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction.","lang":"eng"}],"oa_version":"Submitted Version","issue":"1","volume":128,"publication_status":"published","file":[{"file_name":"IST-2016-563-v1+1_1.full.pdf","date_created":"2018-12-12T10:11:00Z","file_size":1688844,"date_updated":"2020-07-14T12:45:19Z","creator":"system","file_id":"4852","checksum":"24c779f4cd9d549ca6833e26f486be27","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publist_id":"5225","author":[{"first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter","last_name":"Grones"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"title":"Auxin transporters and binding proteins at a glance","citation":{"mla":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science, vol. 128, no. 1, Company of Biologists, 2015, pp. 1–7, doi:10.1242/jcs.159418.","ieee":"P. Grones and J. Friml, “Auxin transporters and binding proteins at a glance,” Journal of Cell Science, vol. 128, no. 1. Company of Biologists, pp. 1–7, 2015.","short":"P. Grones, J. Friml, Journal of Cell Science 128 (2015) 1–7.","apa":"Grones, P., & Friml, J. (2015). Auxin transporters and binding proteins at a glance. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.159418","ama":"Grones P, Friml J. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 2015;128(1):1-7. doi:10.1242/jcs.159418","chicago":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science. Company of Biologists, 2015. https://doi.org/10.1242/jcs.159418.","ista":"Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 128(1), 1–7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Company of Biologists","oa":1,"acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP]; European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GAČR [grant number GA13-40637S]","page":"1 - 7","date_published":"2015-01-01T00:00:00Z","doi":"10.1242/jcs.159418","date_created":"2018-12-11T11:54:28Z","has_accepted_license":"1","year":"2015","day":"01","publication":"Journal of Cell Science"},{"acknowledgement":"The Zeiss Merlin with Gatan 3View2XP and Zeiss Auriga were acquired through a CLEM grant from Minister Ingrid Lieten to the VIB Bio-Imaging-Core. Michiel Krols and Saskia Lippens are the recipients of a fellowship from the FWO (Fonds Wetenschappelijk Onderzoek) of Flanders.","oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","publication":"Journal of Microscopy","day":"01","year":"2015","has_accepted_license":"1","date_created":"2018-12-11T11:54:30Z","date_published":"2015-08-01T00:00:00Z","doi":"10.1111/jmi.12211","page":"80 - 96","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kremer, A., et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy, vol. 259, no. 2, Wiley-Blackwell, 2015, pp. 80–96, doi:10.1111/jmi.12211.","short":"A. Kremer, S. Lippens, S. Bartunkova, B. Asselbergh, C. Blanpain, M. Fendrych, A. Goossens, M. Holt, S. Janssens, M. Krols, J. Larsimont, C. Mc Guire, M. Nowack, X. Saelens, A. Schertel, B. Schepens, M. Slezak, V. Timmerman, C. Theunis, R. Van Brempt, Y. Visser, C. Guérin, Journal of Microscopy 259 (2015) 80–96.","ieee":"A. Kremer et al., “Developing 3D SEM in a broad biological context,” Journal of Microscopy, vol. 259, no. 2. Wiley-Blackwell, pp. 80–96, 2015.","ama":"Kremer A, Lippens S, Bartunkova S, et al. Developing 3D SEM in a broad biological context. Journal of Microscopy. 2015;259(2):80-96. doi:10.1111/jmi.12211","apa":"Kremer, A., Lippens, S., Bartunkova, S., Asselbergh, B., Blanpain, C., Fendrych, M., … Guérin, C. (2015). Developing 3D SEM in a broad biological context. Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/jmi.12211","chicago":"Kremer, A, Stefaan Lippens, Sonia Bartunkova, Bob Asselbergh, Cendric Blanpain, Matyas Fendrych, A Goossens, et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy. Wiley-Blackwell, 2015. https://doi.org/10.1111/jmi.12211.","ista":"Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont J, Mc Guire C, Nowack M, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, Van Brempt R, Visser Y, Guérin C. 2015. Developing 3D SEM in a broad biological context. Journal of Microscopy. 259(2), 80–96."},"title":"Developing 3D SEM in a broad biological context","publist_id":"5218","author":[{"full_name":"Kremer, A","last_name":"Kremer","first_name":"A"},{"first_name":"Stefaan","last_name":"Lippens","full_name":"Lippens, Stefaan"},{"full_name":"Bartunkova, Sonia","last_name":"Bartunkova","first_name":"Sonia"},{"last_name":"Asselbergh","full_name":"Asselbergh, Bob","first_name":"Bob"},{"full_name":"Blanpain, Cendric","last_name":"Blanpain","first_name":"Cendric"},{"last_name":"Fendrych","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"first_name":"A","full_name":"Goossens, A","last_name":"Goossens"},{"last_name":"Holt","full_name":"Holt, Matthew","first_name":"Matthew"},{"last_name":"Janssens","full_name":"Janssens, Sophie","first_name":"Sophie"},{"first_name":"Michiel","full_name":"Krols, Michiel","last_name":"Krols"},{"first_name":"Jean","last_name":"Larsimont","full_name":"Larsimont, Jean"},{"first_name":"Conor","full_name":"Mc Guire, Conor","last_name":"Mc Guire"},{"first_name":"Moritz","full_name":"Nowack, Moritz","last_name":"Nowack"},{"first_name":"Xavier","last_name":"Saelens","full_name":"Saelens, Xavier"},{"last_name":"Schertel","full_name":"Schertel, Andreas","first_name":"Andreas"},{"last_name":"Schepens","full_name":"Schepens, B","first_name":"B"},{"first_name":"M","last_name":"Slezak","full_name":"Slezak, M"},{"first_name":"Vincent","last_name":"Timmerman","full_name":"Timmerman, Vincent"},{"first_name":"Clara","last_name":"Theunis","full_name":"Theunis, Clara"},{"first_name":"Ronald","last_name":"Van Brempt","full_name":"Van Brempt, Ronald"},{"last_name":"Visser","full_name":"Visser, Y","first_name":"Y"},{"first_name":"Christophe","last_name":"Guérin","full_name":"Guérin, Christophe"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions."}],"intvolume":" 259","month":"08","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf","date_created":"2018-12-12T10:11:19Z","file_size":2899898,"date_updated":"2020-07-14T12:45:19Z","creator":"system","file_id":"4872","checksum":"3649c5372d1644062d728ea9287e367f","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","issue":"2","volume":259,"_id":"1879","pubrep_id":"459","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)"},"type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:53:48Z","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:19Z"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:47Z","citation":{"apa":"Cires Rodriguez, E., & Prieto, J. (2015). Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. Springer. https://doi.org/10.1007/s10265-014-0691-6","ama":"Cires Rodriguez E, Prieto J. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 2015;128(2):223-238. doi:10.1007/s10265-014-0691-6","short":"E. Cires Rodriguez, J. Prieto, Journal of Plant Research 128 (2015) 223–238.","ieee":"E. Cires Rodriguez and J. Prieto, “Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula,” Journal of Plant Research, vol. 128, no. 2. Springer, pp. 223–238, 2015.","mla":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” Journal of Plant Research, vol. 128, no. 2, Springer, 2015, pp. 223–38, doi:10.1007/s10265-014-0691-6.","ista":"Cires Rodriguez E, Prieto J. 2015. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 128(2), 223–238.","chicago":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” Journal of Plant Research. Springer, 2015. https://doi.org/10.1007/s10265-014-0691-6."},"title":"Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula","department":[{"_id":"JiFr"}],"author":[{"first_name":"Eduardo","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Cires Rodriguez, Eduardo","last_name":"Cires Rodriguez"},{"first_name":"José","full_name":"Prieto, José","last_name":"Prieto"}],"publist_id":"5217","_id":"1878","status":"public","type":"journal_article","day":"24","language":[{"iso":"eng"}],"publication":"Journal of Plant Research","year":"2015","publication_status":"published","doi":"10.1007/s10265-014-0691-6","issue":"2","date_published":"2015-01-24T00:00:00Z","volume":128,"date_created":"2018-12-11T11:54:30Z","page":"223 - 238","oa_version":"None","abstract":[{"lang":"eng","text":"Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian Peninsula, with some localized populations in the French Pyrenees. Within the genus, a dozen species have been recognized based on morphological diversity, most of them with limited distribution area, in small populations and frequently with potential threats to their survival. To date, however, a molecular evaluation of the current systematic treatments has not been carried out. The aim of the present study is to infer phylogenetic relationships among its subordinate taxa by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS) DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by both ITS and rps16 intron sequence analyses. Furthermore, time estimates using BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44–15.26 Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61–21.00 Myr HPD, for rps16 intron)."}],"month":"01","intvolume":" 128","quality_controlled":"1","publisher":"Springer","scopus_import":1},{"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology (IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions) of the European Union","oa_version":"None","scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","intvolume":" 23","month":"02","publication_status":"published","year":"2015","language":[{"iso":"eng"}],"publication":"Current Opinion in Plant Biology","day":"01","page":"116 - 123","ec_funded":1,"date_created":"2018-12-11T11:54:51Z","volume":23,"issue":"2","doi":"10.1016/j.pbi.2014.12.002","date_published":"2015-02-01T00:00:00Z","_id":"1944","type":"journal_article","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"status":"public","citation":{"ieee":"H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants,” Current Opinion in Plant Biology, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.","short":"H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015) 116–123.","apa":"Rakusová, H., Fendrych, M., & Friml, J. (2015). Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2014.12.002","ama":"Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 2015;23(2):116-123. doi:10.1016/j.pbi.2014.12.002","mla":"Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current Opinion in Plant Biology, vol. 23, no. 2, Elsevier, 2015, pp. 116–23, doi:10.1016/j.pbi.2014.12.002.","ista":"Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 23(2), 116–123.","chicago":"Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current Opinion in Plant Biology. Elsevier, 2015. https://doi.org/10.1016/j.pbi.2014.12.002."},"date_updated":"2021-01-12T06:54:15Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5140","author":[{"last_name":"Rakusová","full_name":"Rakusová, Hana","first_name":"Hana"},{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"department":[{"_id":"JiFr"}],"title":"Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants"},{"publist_id":"7285","author":[{"first_name":"Wenyang","last_name":"Li","full_name":"Li, Wenyang"},{"last_name":"Ma","full_name":"Ma, Mengdi","first_name":"Mengdi"},{"full_name":"Feng, Ying","last_name":"Feng","first_name":"Ying"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang","full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","last_name":"Li"},{"full_name":"Wang, Yichuan","last_name":"Wang","first_name":"Yichuan"},{"full_name":"Ma, Yutong","last_name":"Ma","first_name":"Yutong"},{"last_name":"Li","full_name":"Li, Mingzhe","first_name":"Mingzhe"},{"first_name":"Fengying","full_name":"An, Fengying","last_name":"An"},{"first_name":"Hongwei","full_name":"Guo, Hongwei","last_name":"Guo"}],"title":"EIN2-directed translational regulation of ethylene signaling in arabidopsis","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T08:01:27Z","citation":{"ista":"Li W, Ma M, Feng Y, Li H, Wang Y, Ma Y, Li M, An F, Guo H. 2015. EIN2-directed translational regulation of ethylene signaling in arabidopsis. Cell. 163(3), 670–683.","chicago":"Li, Wenyang, Mengdi Ma, Ying Feng, Hongjiang Li, Yichuan Wang, Yutong Ma, Mingzhe Li, Fengying An, and Hongwei Guo. “EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.09.037.","ama":"Li W, Ma M, Feng Y, et al. EIN2-directed translational regulation of ethylene signaling in arabidopsis. Cell. 2015;163(3):670-683. doi:10.1016/j.cell.2015.09.037","apa":"Li, W., Ma, M., Feng, Y., Li, H., Wang, Y., Ma, Y., … Guo, H. (2015). EIN2-directed translational regulation of ethylene signaling in arabidopsis. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.09.037","ieee":"W. Li et al., “EIN2-directed translational regulation of ethylene signaling in arabidopsis,” Cell, vol. 163, no. 3. Cell Press, pp. 670–683, 2015.","short":"W. Li, M. Ma, Y. Feng, H. Li, Y. Wang, Y. Ma, M. Li, F. An, H. Guo, Cell 163 (2015) 670–683.","mla":"Li, Wenyang, et al. “EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis.” Cell, vol. 163, no. 3, Cell Press, 2015, pp. 670–83, doi:10.1016/j.cell.2015.09.037."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"532","page":"670 - 683","date_created":"2018-12-11T11:47:00Z","doi":"10.1016/j.cell.2015.09.037","date_published":"2015-10-22T00:00:00Z","volume":163,"issue":"3","year":"2015","publication_status":"published","language":[{"iso":"eng"}],"publication":"Cell","day":"22","publisher":"Cell Press","scopus_import":1,"quality_controlled":"1","intvolume":" 163","month":"10","abstract":[{"lang":"eng","text":"Ethylene is a gaseous phytohormone that plays vital roles in plant growth and development. Previous studies uncovered EIN2 as an essential signal transducer linking ethylene perception on ER to transcriptional regulation in the nucleus through a “cleave and shuttle” model. In this study, we report another mechanism of EIN2-mediated ethylene signaling, whereby EIN2 imposes the translational repression of EBF1 and EBF2 mRNA. We find that the EBF1/2 3′ UTRs mediate EIN2-directed translational repression and identify multiple poly-uridylates (PolyU) motifs as functional cis elements of 3′ UTRs. Furthermore, we demonstrate that ethylene induces EIN2 to associate with 3′ UTRs and target EBF1/2 mRNA to cytoplasmic processing-body (P-body) through interacting with multiple P-body factors, including EIN5 and PABs. Our study illustrates translational regulation as a key step in ethylene signaling and presents mRNA 3′ UTR functioning as a “signal transducer” to sense and relay cellular signaling in plants."}],"oa_version":"None"},{"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/"}],"month":"01","intvolume":" 27","abstract":[{"lang":"eng","text":"Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well."}],"oa_version":"Submitted Version","pmid":1,"issue":"1","volume":27,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"938"}]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1591","department":[{"_id":"JiFr"}],"date_updated":"2023-09-07T12:06:09Z","quality_controlled":"1","publisher":"American Society of Plant Biologists","oa":1,"page":"20 - 32","date_published":"2015-01-20T00:00:00Z","doi":"10.1105/tpc.114.134874","date_created":"2018-12-11T11:52:54Z","year":"2015","day":"20","publication":"Plant Cell","author":[{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5580","external_id":{"pmid":["25604445"]},"title":"PIN-dependent auxin transport: Action, regulation, and evolution","citation":{"mla":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 20–32, doi:10.1105/tpc.114.134874.","short":"M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32.","ieee":"M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation, and evolution,” Plant Cell, vol. 27, no. 1. American Society of Plant Biologists, pp. 20–32, 2015.","apa":"Adamowski, M., & Friml, J. (2015). PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.134874","ama":"Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 2015;27(1):20-32. doi:10.1105/tpc.114.134874","chicago":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” Plant Cell. American Society of Plant Biologists, 2015. https://doi.org/10.1105/tpc.114.134874.","ista":"Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 27(1), 20–32."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"JiFr"},{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:44:59Z","ddc":["570"],"date_updated":"2023-10-10T14:10:24Z","pubrep_id":"497","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)"},"type":"journal_article","_id":"1509","ec_funded":1,"volume":4,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","date_created":"2018-12-12T10:16:12Z","creator":"system","file_size":4414248,"date_updated":"2020-07-14T12:44:59Z","file_id":"5198","checksum":"8beae5cbe988e1060265ae7de2ee8306","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","intvolume":" 4","month":"10","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1.","lang":"eng"}],"title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","article_processing_charge":"No","publist_id":"5668","author":[{"last_name":"Michalko","full_name":"Michalko, Jaroslav","first_name":"Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87"},{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta","last_name":"Dravecka","orcid":"0000-0002-2519-8004","full_name":"Dravecka, Marta"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","last_name":"Bollenbach"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research , vol. 4, F1000 Research, 2015, doi:10.12688/f1000research.7143.1.","apa":"Michalko, J., Lukacisinova, M., Bollenbach, M. T., & Friml, J. (2015). Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . F1000 Research. https://doi.org/10.12688/f1000research.7143.1","ama":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 2015;4. doi:10.12688/f1000research.7143.1","ieee":"J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” F1000 Research , vol. 4. F1000 Research, 2015.","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research 4 (2015).","chicago":"Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research . F1000 Research, 2015. https://doi.org/10.12688/f1000research.7143.1.","ista":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 4."},"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"date_created":"2018-12-11T11:52:26Z","date_published":"2015-10-01T00:00:00Z","doi":"10.12688/f1000research.7143.1","publication":"F1000 Research ","day":"01","year":"2015","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"F1000 Research","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research: Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset 3. Dataset 3, 10.5256/f1000research.7143.d104554"},{"month":"04","quality_controlled":"1","scopus_import":1,"publisher":"Springer","oa_version":"None","abstract":[{"text":"The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants.","lang":"eng"}],"date_created":"2018-12-11T11:54:07Z","date_published":"2014-04-01T00:00:00Z","doi":"10.1007/978-3-7091-1526-8_8","page":"143 - 170","publication":"Auxin and Its Role in Plant Development","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2014","status":"public","type":"book_chapter","_id":"1806","editor":[{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"title":"Auxin on the road navigated by cellular PIN polarity","department":[{"_id":"JiFr"}],"publist_id":"5304","author":[{"last_name":"Baster","full_name":"Baster, Pawel","first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:19Z","citation":{"mla":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8.","ama":"Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8","apa":"Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8","short":"P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.","ieee":"P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170.","chicago":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8.","ista":"Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170."}},{"intvolume":" 24","month":"10","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01074821"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner."}],"issue":"19","volume":24,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"1852","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:37Z","oa":1,"quality_controlled":"1","publisher":"Cell Press","acknowledgement":"This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ","date_created":"2018-12-11T11:54:22Z","date_published":"2014-10-06T00:00:00Z","doi":"10.1016/j.cub.2014.08.036","page":"2335 - 2342","publication":"Current Biology","day":"06","year":"2014","title":"An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis","author":[{"first_name":"Massimiliano","last_name":"Sassi","full_name":"Sassi, Massimiliano"},{"last_name":"Ali","full_name":"Ali, Olivier","first_name":"Olivier"},{"first_name":"Frédéric","last_name":"Boudon","full_name":"Boudon, Frédéric"},{"last_name":"Cloarec","full_name":"Cloarec, Gladys","first_name":"Gladys"},{"first_name":"Ursula","last_name":"Abad","full_name":"Abad, Ursula"},{"last_name":"Cellier","full_name":"Cellier, Coralie","first_name":"Coralie"},{"last_name":"Chen","full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"full_name":"Gilles, Benjamin","last_name":"Gilles","first_name":"Benjamin"},{"last_name":"Milani","full_name":"Milani, Pascale","first_name":"Pascale"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Teva","full_name":"Vernoux, Teva","last_name":"Vernoux"},{"last_name":"Godin","full_name":"Godin, Christophe","first_name":"Christophe"},{"last_name":"Hamant","full_name":"Hamant, Olivier","first_name":"Olivier"},{"first_name":"Jan","full_name":"Traas, Jan","last_name":"Traas"}],"publist_id":"5248","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas, J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.08.036","ama":"Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 2014;24(19):2335-2342. doi:10.1016/j.cub.2014.08.036","short":"M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B. Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current Biology 24 (2014) 2335–2342.","ieee":"M. Sassi et al., “An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis,” Current Biology, vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.","mla":"Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology, vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:10.1016/j.cub.2014.08.036.","ista":"Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 24(19), 2335–2342.","chicago":"Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.08.036."}},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/","open_access":"1"}],"scopus_import":"1","intvolume":" 516","month":"12","abstract":[{"lang":"eng","text":"The prominent and evolutionarily ancient role of the plant hormone auxin is the regulation of cell expansion. Cell expansion requires ordered arrangement of the cytoskeleton but molecular mechanisms underlying its regulation by signalling molecules including auxin are unknown. Here we show in the model plant Arabidopsis thaliana that in elongating cells exogenous application of auxin or redistribution of endogenous auxin induces very rapid microtubule re-orientation from transverse to longitudinal, coherent with the inhibition of cell expansion. This fast auxin effect requires auxin binding protein 1 (ABP1) and involves a contribution of downstream signalling components such as ROP6 GTPase, ROP-interactive protein RIC1 and the microtubule-severing protein katanin. These components are required for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell elongation in roots and dark-grown hypocotyls as well as asymmetric growth during gravitropic responses."}],"oa_version":"Submitted Version","pmid":1,"ec_funded":1,"issue":"729","volume":516,"publication_status":"published","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"1862","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"EvBe"}],"date_updated":"2022-05-23T08:26:44Z","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","acknowledgement":"We thank R. Dixit for performing complementary experiments, D. W. Ehrhardt and T. Hashimoto for providing the seeds of TUB6–RFP and EB1b–GFP respectively, E. Zazimalova, J. Petrasek and M. Fendrych for discussing the manuscript and J. Leung for text optimization. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), ANR blanc AuxiWall project (ANR-11-BSV5-0007, to C.P.-R. and L.G.) and the Agency for Innovation by Science and Technology (IWT) (to H.R.). This work benefited from the facilities and expertise of the Imagif Cell Biology platform (http://www.imagif.cnrs.fr), which is supported by the Conseil Général de l’Essonne.","page":"90 - 93","date_created":"2018-12-11T11:54:25Z","date_published":"2014-12-04T00:00:00Z","doi":"10.1038/nature13889","year":"2014","publication":"Nature","day":"04","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"article_processing_charge":"No","external_id":{"pmid":["25409144"]},"publist_id":"5237","author":[{"last_name":"Chen","full_name":"Chen, Xu","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurie","full_name":"Grandont, Laurie","last_name":"Grandont"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang","full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","last_name":"Li"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"full_name":"Paque, Sébastien","last_name":"Paque","first_name":"Sébastien"},{"last_name":"Abuzeineh","full_name":"Abuzeineh, Anas","first_name":"Anas"},{"full_name":"Rakusova, Hana","last_name":"Rakusova","first_name":"Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"first_name":"Catherine","full_name":"Perrot Rechenmann, Catherine","last_name":"Perrot Rechenmann"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"title":"Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules","citation":{"chicago":"Chen, Xu, Laurie Grandont, Hongjiang Li, Robert Hauschild, Sébastien Paque, Anas Abuzeineh, Hana Rakusova, Eva Benková, Catherine Perrot Rechenmann, and Jiří Friml. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13889.","ista":"Chen X, Grandont L, Li H, Hauschild R, Paque S, Abuzeineh A, Rakusova H, Benková E, Perrot Rechenmann C, Friml J. 2014. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 516(729), 90–93.","mla":"Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature, vol. 516, no. 729, Nature Publishing Group, 2014, pp. 90–93, doi:10.1038/nature13889.","ama":"Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 2014;516(729):90-93. doi:10.1038/nature13889","apa":"Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., … Friml, J. (2014). Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13889","short":"X. Chen, L. Grandont, H. Li, R. Hauschild, S. Paque, A. Abuzeineh, H. Rakusova, E. Benková, C. Perrot Rechenmann, J. Friml, Nature 516 (2014) 90–93.","ieee":"X. Chen et al., “Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules,” Nature, vol. 516, no. 729. Nature Publishing Group, pp. 90–93, 2014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:53:53Z","status":"public","type":"journal_article","_id":"1893","volume":111,"issue":"7","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 111","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/"}],"oa_version":"Submitted Version","abstract":[{"text":"Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.","lang":"eng"}],"title":"SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis","author":[{"full_name":"Nováková, Petra","last_name":"Nováková","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra"},{"full_name":"Hirsch, Sibylle","last_name":"Hirsch","first_name":"Sibylle"},{"last_name":"Feraru","full_name":"Feraru, Elena","first_name":"Elena"},{"last_name":"Tejos","full_name":"Tejos, Ricardo","first_name":"Ricardo"},{"first_name":"Ringo","last_name":"Van Wijk","full_name":"Van Wijk, Ringo"},{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"full_name":"Heilmann, Mareike","last_name":"Heilmann","first_name":"Mareike"},{"first_name":"Jennifer","last_name":"Lerche","full_name":"Lerche, Jennifer"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"first_name":"Mugurel","last_name":"Feraru","full_name":"Feraru, Mugurel"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"last_name":"Van Montagu","full_name":"Van Montagu, Marc","first_name":"Marc"},{"last_name":"Heilmann","full_name":"Heilmann, Ingo","first_name":"Ingo"},{"full_name":"Munnik, Teun","last_name":"Munnik","first_name":"Teun"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"publist_id":"5202","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS, vol. 111, no. 7, National Academy of Sciences, 2014, pp. 2818–23, doi:10.1073/pnas.1324264111.","apa":"Marhavá, P., Hirsch, S., Feraru, E., Tejos, R., Van Wijk, R., Viaene, T., … Friml, J. (2014). SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1324264111","ama":"Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 2014;111(7):2818-2823. doi:10.1073/pnas.1324264111","short":"P. Marhavá, S. Hirsch, E. Feraru, R. Tejos, R. Van Wijk, T. Viaene, M. Heilmann, J. Lerche, R. De Rycke, M. Feraru, P. Grones, M. Van Montagu, I. Heilmann, T. Munnik, J. Friml, PNAS 111 (2014) 2818–2823.","ieee":"P. Marhavá et al., “SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis,” PNAS, vol. 111, no. 7. National Academy of Sciences, pp. 2818–2823, 2014.","chicago":"Marhavá, Petra, Sibylle Hirsch, Elena Feraru, Ricardo Tejos, Ringo Van Wijk, Tom Viaene, Mareike Heilmann, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1324264111.","ista":"Marhavá P, Hirsch S, Feraru E, Tejos R, Van Wijk R, Viaene T, Heilmann M, Lerche J, De Rycke R, Feraru M, Grones P, Van Montagu M, Heilmann I, Munnik T, Friml J. 2014. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 111(7), 2818–2823."},"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"date_published":"2014-02-18T00:00:00Z","doi":"10.1073/pnas.1324264111","date_created":"2018-12-11T11:54:34Z","page":"2818 - 2823","day":"18","publication":"PNAS","year":"2014","publisher":"National Academy of Sciences","oa":1,"acknowledgement":"This work was supported by grants from the Research Foundation-Flanders (Odysseus)."},{"abstract":[{"lang":"eng","text":"GNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants."}],"acknowledgement":"This work was supported by the Odysseus Program of the Research Foundation-Flanders (J.F.).","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/"}],"oa":1,"scopus_import":1,"publisher":"American Society of Plant Biologists","intvolume":" 26","month":"07","publication_status":"published","year":"2014","language":[{"iso":"eng"}],"publication":"Plant Cell","day":"01","page":"3062 - 3076","date_created":"2018-12-11T11:54:36Z","issue":"7","volume":26,"doi":"10.1105/tpc.114.125880","date_published":"2014-07-01T00:00:00Z","_id":"1897","type":"journal_article","status":"public","citation":{"short":"S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias, M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26 (2014) 3062–3076.","ieee":"S. Naramoto et al., “Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,” Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076, 2014.","ama":"Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880","apa":"Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias, M., … Friml, J. (2014). Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880","mla":"Naramoto, Satoshi, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014, pp. 3062–76, doi:10.1105/tpc.114.125880.","ista":"Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 26(7), 3062–3076.","chicago":"Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.125880."},"date_updated":"2021-01-12T06:53:55Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5199","author":[{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"first_name":"Marisa","full_name":"Otegui, Marisa","last_name":"Otegui"},{"first_name":"Natsumaro","last_name":"Kutsuna","full_name":"Kutsuna, Natsumaro"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"first_name":"Tomoko","last_name":"Dainobu","full_name":"Dainobu, Tomoko"},{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"last_name":"Fujimoto","full_name":"Fujimoto, Masaru","first_name":"Masaru"},{"first_name":"Elena","full_name":"Feraru, Elena","last_name":"Feraru"},{"full_name":"Miki, Daisuke","last_name":"Miki","first_name":"Daisuke"},{"last_name":"Fukuda","full_name":"Fukuda, Hiroo","first_name":"Hiroo"},{"last_name":"Nakano","full_name":"Nakano, Akihiko","first_name":"Akihiko"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"department":[{"_id":"JiFr"}],"title":"Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis"}]