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Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. "}],"page":"138","citation":{"chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th1075.","mla":"Narasimhan, Madhumitha. Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants . Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th1075.","short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019.","ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","apa":"Narasimhan, M. (2019). Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th1075","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075"},"date_published":"2019-02-04T00:00:00Z","day":"04","article_processing_charge":"No","has_accepted_license":"1"},{"doi":"10.1016/j.cell.2019.04.015","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"external_id":{"isi":["000466843000015"],"pmid":["31051107"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"month":"05","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"9992"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/"}]},"author":[{"full_name":"Marhavá, Petra","last_name":"Marhavá","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida","full_name":"Yoshida, Saiko"},{"full_name":"Marhavy, Peter","first_name":"Peter","last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"volume":177,"date_updated":"2024-03-28T23:30:10Z","date_created":"2019-04-28T21:59:14Z","pmid":1,"year":"2019","publisher":"Elsevier","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:28Z","date_published":"2019-05-02T00:00:00Z","citation":{"ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” Cell, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., & Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.015","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13.","ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015","chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.015.","short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:10.1016/j.cell.2019.04.015."},"publication":"Cell","page":"957-969.e13","article_processing_charge":"No","has_accepted_license":"1","day":"02","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"6411","relation":"main_file","date_updated":"2020-07-14T12:47:28Z","date_created":"2019-05-13T06:12:45Z","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","file_name":"2019_Cell_Marhava.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":10272032}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6351","intvolume":" 177","ddc":["570"],"status":"public","title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","issue":"4","abstract":[{"text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.","lang":"eng"}],"type":"journal_article"},{"file_date_updated":"2020-07-14T12:47:45Z","ec_funded":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JiFr"}],"year":"2019","pmid":1,"date_created":"2019-10-14T07:00:24Z","date_updated":"2024-03-28T23:30:10Z","volume":52,"author":[{"full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"related_material":{"record":[{"id":"9992","relation":"dissertation_contains","status":"public"}]},"month":"12","publication_identifier":{"issn":["1369-5266"]},"quality_controlled":"1","isi":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000502890600017"],"pmid":["31585333"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.pbi.2019.08.006","type":"journal_article","abstract":[{"text":"Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration.","lang":"eng"}],"title":"Targeted cell ablation-based insights into wound healing and restorative patterning","ddc":["580"],"status":"public","intvolume":" 52","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6943","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1659288,"file_name":"2019_CurrentOpinionPlant_Hoermayer.pdf","access_level":"open_access","date_created":"2019-10-14T14:48:21Z","date_updated":"2020-07-14T12:47:45Z","checksum":"d6fd68a6e965f1efe3f0bf2d2070a616","file_id":"6946","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"124-130","publication":"Current Opinion in Plant Biology","citation":{"chicago":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology. Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.08.006.","short":"L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130.","mla":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology, vol. 52, Elsevier, 2019, pp. 124–30, doi:10.1016/j.pbi.2019.08.006.","apa":"Hörmayer, L., & Friml, J. (2019). Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.08.006","ieee":"L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound healing and restorative patterning,” Current Opinion in Plant Biology, vol. 52. Elsevier, pp. 124–130, 2019.","ista":"Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130.","ama":"Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 2019;52:124-130. doi:10.1016/j.pbi.2019.08.006"},"date_published":"2019-12-01T00:00:00Z"},{"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"month":"06","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.19.00201"}],"oa":1,"external_id":{"isi":["000470086100045"],"pmid":["30936248"]},"language":[{"iso":"eng"}],"doi":"10.1104/pp.19.00201","ec_funded":1,"publisher":"ASPB","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2019","acknowledgement":"We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.), and the European Union’s Horizon2020 program (European Research Council grant agreement no. 742985 to J.F.).","volume":180,"date_created":"2019-04-09T08:38:20Z","date_updated":"2024-03-28T23:30:38Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"},{"relation":"dissertation_contains","status":"public","id":"8822"}]},"author":[{"first_name":"A","last_name":"Oochi","full_name":"Oochi, A"},{"first_name":"Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195","full_name":"Hajny, Jakub"},{"last_name":"Fukui","first_name":"K","full_name":"Fukui, K"},{"last_name":"Nakao","first_name":"Y","full_name":"Nakao, Y"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C"},{"full_name":"Quareshy, M","last_name":"Quareshy","first_name":"M"},{"last_name":"Takahashi","first_name":"K","full_name":"Takahashi, K"},{"full_name":"Kinoshita, T","first_name":"T","last_name":"Kinoshita"},{"full_name":"Harborough, SR","last_name":"Harborough","first_name":"SR"},{"full_name":"Kepinski, S","last_name":"Kepinski","first_name":"S"},{"last_name":"Kasahara","first_name":"H","full_name":"Kasahara, H"},{"first_name":"RM","last_name":"Napier","full_name":"Napier, RM"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"full_name":"Hayashi, KI","last_name":"Hayashi","first_name":"KI"}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"1152-1165","article_type":"original","citation":{"ieee":"A. Oochi et al., “Pinstatic acid promotes auxin transport by inhibiting PIN internalization,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 1152–1165, 2019.","apa":"Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., … Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. ASPB. https://doi.org/10.1104/pp.19.00201","ista":"Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 180(2), 1152–1165.","ama":"Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 2019;180(2):1152-1165. doi:10.1104/pp.19.00201","chicago":"Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy, K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.19.00201.","short":"A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi, T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K. Hayashi, Plant Physiology 180 (2019) 1152–1165.","mla":"Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 1152–65, doi:10.1104/pp.19.00201."},"publication":"Plant Physiology","date_published":"2019-06-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport."}],"intvolume":" 180","status":"public","title":"Pinstatic acid promotes auxin transport by inhibiting PIN internalization","_id":"6260","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version"},{"file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"article_number":"3337","date_updated":"2024-03-28T23:30:44Z","date_created":"2019-07-11T12:00:32Z","volume":20,"author":[{"full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publisher":"MDPI","department":[{"_id":"JiFr"}],"year":"2019","pmid":1,"month":"07","publication_identifier":{"eissn":["1422-0067"]},"language":[{"iso":"eng"}],"doi":"10.3390/ijms20133337","isi":1,"quality_controlled":"1","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000477041100221"],"pmid":["31284661"]},"oa":1,"abstract":[{"text":"Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation.","lang":"eng"}],"issue":"13","type":"journal_article","file":[{"file_size":3330291,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_JournalMolecularScience_Adamowski.pdf","checksum":"dd9d1cbb933a72ceb666c9667890ac51","date_created":"2019-07-17T06:17:15Z","date_updated":"2020-07-14T12:47:34Z","relation":"main_file","file_id":"6645"}],"oa_version":"Published Version","title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling","status":"public","ddc":["580"],"intvolume":" 20","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6627","day":"07","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2019-07-07T00:00:00Z","article_type":"original","publication":"International Journal of Molecular Sciences","citation":{"ama":"Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337","apa":"Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337","ieee":"M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019.","ista":"Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337.","short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019).","mla":"Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.","chicago":"Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337."}},{"date_published":"2018-03-01T00:00:00Z","page":"95 - 102","citation":{"mla":"Trinh, Hoang, et al. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102, doi:10.1007/978-1-4939-7747-5_7.","short":"H. Trinh, I. Verstraeten, D. Geelen, in:, Root Development , Springer Nature, 2018, pp. 95–102.","chicago":"Trinh, Hoang, Inge Verstraeten, and Danny Geelen. “In Vitro Assay for Induction of Adventitious Rooting on Intact Arabidopsis Hypocotyls.” In Root Development , 1761:95–102. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-7747-5_7.","ama":"Trinh H, Verstraeten I, Geelen D. In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . Vol 1761. Springer Nature; 2018:95-102. doi:10.1007/978-1-4939-7747-5_7","ista":"Trinh H, Verstraeten I, Geelen D. 2018.In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In: Root Development . MIMB, vol. 1761, 95–102.","ieee":"H. Trinh, I. Verstraeten, and D. Geelen, “In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls,” in Root Development , vol. 1761, Springer Nature, 2018, pp. 95–102.","apa":"Trinh, H., Verstraeten, I., & Geelen, D. (2018). In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls. In Root Development (Vol. 1761, pp. 95–102). Springer Nature. https://doi.org/10.1007/978-1-4939-7747-5_7"},"publication":"Root Development ","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"None","intvolume":" 1761","title":"In vitro assay for induction of adventitious rooting on intact arabidopsis hypocotyls","status":"public","_id":"408","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Adventitious roots (AR) are de novo formed roots that emerge from any part of the plant or from callus in tissue culture, except root tissue. The plant tissue origin and the method by which they are induced determine the physiological properties of emerged ARs. Hence, a standard method encompassing all types of AR does not exist. Here we describe a method for the induction and analysis of AR that emerge from the etiolated hypocotyl of dicot plants. The hypocotyl is formed during embryogenesis and shows a determined developmental pattern which usually does not involve AR formation. However, the hypocotyl shows propensity to form de novo roots under specific circumstances such as removal of the root system, high humidity or flooding, or during de-etiolation. The hypocotyl AR emerge from a pericycle-like cell layer surrounding the vascular tissue of the central cylinder, which is reminiscent to the developmental program of lateral roots. Here we propose an easy protocol for in vitro hypocotyl AR induction from etiolated Arabidopsis seedlings.","lang":"eng"}],"alternative_title":["MIMB"],"type":"book_chapter","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-7747-5_7","quality_controlled":"1","external_id":{"pmid":["29525951"]},"publication_identifier":{"issn":["1064-3745"]},"month":"03","volume":1761,"date_created":"2018-12-11T11:46:18Z","date_updated":"2021-01-12T07:54:21Z","author":[{"full_name":"Trinh, Hoang","last_name":"Trinh","first_name":"Hoang"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","first_name":"Inge","last_name":"Verstraeten","full_name":"Verstraeten, Inge"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"}],"department":[{"_id":"JiFr"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2018","publist_id":"7421"},{"quality_controlled":"1","page":"131 - 143","publication":"Root Development. Methods and Protocols","citation":{"chicago":"Karampelias, Michael, Ricardo Tejos, Jiří Friml, and Steffen Vanneste. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” In Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, 1761:131–43. MIMB. Springer, 2018. https://doi.org/10.1007/978-1-4939-7747-5_10.","short":"M. Karampelias, R. Tejos, J. Friml, S. Vanneste, in:, D. Ristova, E. Barbez (Eds.), Root Development. Methods and Protocols, Springer, 2018, pp. 131–143.","mla":"Karampelias, Michael, et al. “Optimized Whole Mount in Situ Immunolocalization for Arabidopsis Thaliana Root Meristems and Lateral Root Primordia.” Root Development. Methods and Protocols, edited by Daniela Ristova and Elke Barbez, vol. 1761, Springer, 2018, pp. 131–43, doi:10.1007/978-1-4939-7747-5_10.","ieee":"M. Karampelias, R. Tejos, J. Friml, and S. Vanneste, “Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia,” in Root Development. Methods and Protocols, vol. 1761, D. Ristova and E. Barbez, Eds. Springer, 2018, pp. 131–143.","apa":"Karampelias, M., Tejos, R., Friml, J., & Vanneste, S. (2018). Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In D. Ristova & E. Barbez (Eds.), Root Development. Methods and Protocols (Vol. 1761, pp. 131–143). Springer. https://doi.org/10.1007/978-1-4939-7747-5_10","ista":"Karampelias M, Tejos R, Friml J, Vanneste S. 2018.Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Root Development. Methods and Protocols. Methods in Molecular Biology, vol. 1761, 131–143.","ama":"Karampelias M, Tejos R, Friml J, Vanneste S. Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia. In: Ristova D, Barbez E, eds. Root Development. Methods and Protocols. Vol 1761. MIMB. Springer; 2018:131-143. doi:10.1007/978-1-4939-7747-5_10"},"language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-7747-5_10","date_published":"2018-03-11T00:00:00Z","series_title":"MIMB","scopus_import":1,"month":"03","day":"11","title":"Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia","publication_status":"published","status":"public","department":[{"_id":"JiFr"}],"publisher":"Springer","intvolume":" 1761","editor":[{"full_name":"Ristova, Daniela","last_name":"Ristova","first_name":"Daniela"},{"full_name":"Barbez, Elke","first_name":"Elke","last_name":"Barbez"}],"year":"2018","_id":"411","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:46:20Z","date_updated":"2021-01-12T07:54:34Z","volume":1761,"oa_version":"None","author":[{"last_name":"Karampelias","first_name":"Michael","full_name":"Karampelias, Michael"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","abstract":[{"lang":"eng","text":"Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins."}],"publist_id":"7418"},{"publist_id":"7710","ec_funded":1,"year":"2018","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"last_name":"Abbas","first_name":"Mohamad","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abbas, Mohamad"},{"full_name":"Hernández, García J","last_name":"Hernández","first_name":"García J"},{"last_name":"Pollmann","first_name":"Stephan","full_name":"Pollmann, Stephan"},{"last_name":"Samodelov","first_name":"Sophia L","full_name":"Samodelov, Sophia L"},{"full_name":"Kolb, Martina","first_name":"Martina","last_name":"Kolb"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Ulrich Z","last_name":"Hammes","full_name":"Hammes, Ulrich Z"},{"last_name":"Zurbriggen","first_name":"Matias D","full_name":"Zurbriggen, Matias D"},{"full_name":"Blázquez, Miguel","first_name":"Miguel","last_name":"Blázquez"},{"first_name":"David","last_name":"Alabadí","full_name":"Alabadí, David"}],"volume":115,"date_updated":"2023-09-08T13:24:40Z","date_created":"2018-12-11T11:45:11Z","month":"06","oa":1,"external_id":{"isi":["000436245000096"]},"main_file_link":[{"url":"http://eprints.nottingham.ac.uk/52388/","open_access":"1"}],"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1806565115","language":[{"iso":"eng"}],"type":"journal_article","issue":"26","abstract":[{"text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.","lang":"eng"}],"_id":"203","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 115","status":"public","title":"Auxin methylation is required for differential growth in Arabidopsis","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"26","citation":{"short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115.","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115","ieee":"M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869."},"publication":"PNAS","page":"6864-6869","date_published":"2018-06-26T00:00:00Z"},{"quality_controlled":"1","isi":1,"citation":{"short":"L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018).","mla":"Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475.","chicago":"Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475.","ama":"Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 2018. doi:10.1111/pce.13475","ieee":"L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” Plant Cell and Environment. Wiley, 2018.","apa":"Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.13475","ista":"Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment."},"external_id":{"pmid":["30378140"],"isi":["000459014800021"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30378140","open_access":"1"}],"oa":1,"publication":"Plant Cell and Environment","language":[{"iso":"eng"}],"doi":"10.1111/pce.13475","date_published":"2018-10-31T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["01407791"]},"article_processing_charge":"No","month":"10","day":"31","publisher":"Wiley","department":[{"_id":"JiFr"}],"title":"CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana","publication_status":"epub_ahead","status":"public","pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5830","year":"2018","oa_version":"Published Version","date_updated":"2023-09-11T12:43:31Z","date_created":"2019-01-13T22:59:11Z","author":[{"first_name":"Luosha","last_name":"Zhang","full_name":"Zhang, Luosha"},{"last_name":"Shi","first_name":"Xiong","full_name":"Shi, Xiong"},{"first_name":"Yutao","last_name":"Zhang","full_name":"Zhang, Yutao"},{"full_name":"Wang, Jiajing","last_name":"Wang","first_name":"Jiajing"},{"first_name":"Jingwei","last_name":"Yang","full_name":"Yang, Jingwei"},{"full_name":"Ishida, Takashi","first_name":"Takashi","last_name":"Ishida"},{"first_name":"Wenqian","last_name":"Jiang","full_name":"Jiang, Wenqian"},{"full_name":"Han, Xiangyu","last_name":"Han","first_name":"Xiangyu"},{"first_name":"Jingke","last_name":"Kang","full_name":"Kang, Jingke"},{"last_name":"Wang","first_name":"Xuening","full_name":"Wang, Xuening"},{"full_name":"Pan, Lixia","last_name":"Pan","first_name":"Lixia"},{"full_name":"Lv, Shuo","first_name":"Shuo","last_name":"Lv"},{"first_name":"Bing","last_name":"Cao","full_name":"Cao, Bing"},{"first_name":"Yonghong","last_name":"Zhang","full_name":"Zhang, Yonghong"},{"full_name":"Wu, Jinbin","last_name":"Wu","first_name":"Jinbin"},{"full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin"},{"first_name":"Zhubing","last_name":"Hu","full_name":"Hu, Zhubing"},{"full_name":"Cui, Langjun","last_name":"Cui","first_name":"Langjun"},{"full_name":"Sawa, Shinichiro","last_name":"Sawa","first_name":"Shinichiro"},{"last_name":"He","first_name":"Junmin","full_name":"He, Junmin"},{"full_name":"Wang, Guodong","first_name":"Guodong","last_name":"Wang"}],"type":"journal_article","abstract":[{"text":"CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.","lang":"eng"}]},{"acknowledgement":"We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology, Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for Science), and Y. Gu (Penn State University) for making available the materials used in this study;\r\n...funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 282300.\r\nCC BY NC ND","year":"2018","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Salanenka, Yuliya","last_name":"Salanenka","first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"full_name":"Löfke, Christian","last_name":"Löfke","first_name":"Christian"},{"full_name":"Tabata, Kaori","id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0","last_name":"Tabata","first_name":"Kaori"},{"last_name":"Naramoto","first_name":"Satoshi","full_name":"Naramoto, Satoshi"},{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"volume":115,"date_updated":"2023-09-11T14:06:34Z","date_created":"2018-12-11T11:46:25Z","publist_id":"7395","ec_funded":1,"file_date_updated":"2020-07-14T12:46:26Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"isi":["000429012500073"]},"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1721760115","language":[{"iso":"eng"}],"month":"04","_id":"428","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 115","ddc":["580"],"status":"public","title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","file":[{"checksum":"1fcf7223fb8f99559cfa80bd6f24ce44","date_updated":"2020-07-14T12:46:26Z","date_created":"2018-12-17T12:30:14Z","file_id":"5700","relation":"main_file","creator":"dernst","file_size":1924101,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_PNAS_Salanenka.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"14","abstract":[{"text":"The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses.","lang":"eng"}],"citation":{"ama":"Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 2018;115(14):3716-3721. doi:10.1073/pnas.1721760115","ista":"Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721.","apa":"Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc, M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721760115","ieee":"Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane,” PNAS, vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.","mla":"Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS, vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.","short":"Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc, J. Friml, PNAS 115 (2018) 3716–3721.","chicago":"Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115."},"publication":"PNAS","page":" 3716 - 3721","date_published":"2018-04-03T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"03"},{"date_updated":"2023-09-13T08:24:17Z","date_created":"2018-12-11T11:45:35Z","volume":4,"author":[{"full_name":"Gao, Zhen","first_name":"Zhen","last_name":"Gao"},{"last_name":"Daneva","first_name":"Anna","full_name":"Daneva, Anna"},{"first_name":"Yuliya","last_name":"Salanenka","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","full_name":"Salanenka, Yuliya"},{"full_name":"Van Durme, Matthias","first_name":"Matthias","last_name":"Van Durme"},{"full_name":"Huysmans, Marlies","first_name":"Marlies","last_name":"Huysmans"},{"last_name":"Lin","first_name":"Zongcheng","full_name":"Lin, Zongcheng"},{"full_name":"De Winter, Freya","last_name":"De Winter","first_name":"Freya"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"first_name":"Mansour","last_name":"Karimi","full_name":"Karimi, Mansour"},{"full_name":"Van De Velde, Jan","last_name":"Van De Velde","first_name":"Jan"},{"full_name":"Vandepoele, Klaas","first_name":"Klaas","last_name":"Vandepoele"},{"full_name":"Van De Walle, Davy","first_name":"Davy","last_name":"Van De Walle"},{"full_name":"Dewettinck, Koen","last_name":"Dewettinck","first_name":"Koen"},{"first_name":"Bart","last_name":"Lambrecht","full_name":"Lambrecht, Bart"},{"full_name":"Nowack, Moritz","first_name":"Moritz","last_name":"Nowack"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","year":"2018","acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","publist_id":"7619","language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0160-7","quality_controlled":"1","isi":1,"external_id":{"isi":["000435571000017"]},"month":"05","oa_version":"None","title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","status":"public","intvolume":" 4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"280","abstract":[{"text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.","lang":"eng"}],"issue":"6","type":"journal_article","date_published":"2018-05-28T00:00:00Z","page":"365 - 375","publication":"Nature Plants","citation":{"short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7.","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7.","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375. doi:10.1038/s41477-018-0160-7","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0160-7","ieee":"Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375."},"day":"28","article_processing_charge":"No","scopus_import":"1"},{"day":"16","article_processing_charge":"No","scopus_import":"1","date_published":"2018-07-16T00:00:00Z","publication":"Nature Plants","citation":{"chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0204-z.","mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:10.1038/s41477-018-0204-z.","short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0204-z","ieee":"H. Robert et al., “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 2018;4(8):548-553. doi:10.1038/s41477-018-0204-z"},"page":"548 - 553","abstract":[{"lang":"eng","text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development."}],"issue":"8","type":"journal_article","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"158","status":"public","title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","intvolume":" 4","month":"07","doi":"10.1038/s41477-018-0204-z","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["30013211"],"isi":["000443861300011"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211"}],"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"ec_funded":1,"publist_id":"7763","author":[{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"full_name":"Park, Chulmin","last_name":"Park","first_name":"Chulmin"},{"full_name":"Gutièrrez, Carla","first_name":"Carla","last_name":"Gutièrrez"},{"full_name":"Wójcikowska, Barbara","first_name":"Barbara","last_name":"Wójcikowska"},{"first_name":"Aleš","last_name":"Pěnčík","full_name":"Pěnčík, Aleš"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"last_name":"Chen","first_name":"Junyi","full_name":"Chen, Junyi"},{"first_name":"Wim","last_name":"Grunewald","full_name":"Grunewald, Wim"},{"first_name":"Thomas","last_name":"Dresselhaus","full_name":"Dresselhaus, Thomas"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"last_name":"Laux","first_name":"Thomas","full_name":"Laux, Thomas"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/","description":"News on IST Homepage","relation":"press_release"}]},"date_updated":"2023-09-13T08:53:28Z","date_created":"2018-12-11T11:44:56Z","volume":4,"year":"2018","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","pmid":1,"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}]},{"month":"05","isi":1,"quality_controlled":"1","external_id":{"isi":["000426870500012"],"pmid":["29360148"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/pce.13153","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:46:32Z","publist_id":"7359","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley-Blackwell","year":"2018","acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","pmid":1,"date_created":"2018-12-11T11:46:36Z","date_updated":"2023-09-13T09:03:18Z","volume":41,"author":[{"full_name":"Fan, Ligang","first_name":"Ligang","last_name":"Fan"},{"full_name":"Zhao, Lei","last_name":"Zhao","first_name":"Lei"},{"full_name":"Hu, Wei","first_name":"Wei","last_name":"Hu"},{"first_name":"Weina","last_name":"Li","full_name":"Li, Weina"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"last_name":"Strnad","first_name":"Miroslav","full_name":"Strnad, Miroslav"},{"orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","first_name":"Sibu","full_name":"Simon, Sibu"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"first_name":"Jinbo","last_name":"Shen","full_name":"Shen, Jinbo"},{"full_name":"Jiang, Liwen","first_name":"Liwen","last_name":"Jiang"},{"last_name":"Qiu","first_name":"Quan","full_name":"Qiu, Quan"}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"850 - 864","publication":"Plant, Cell and Environment","citation":{"ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153","ieee":"L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153","ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864.","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153.","chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153."},"date_published":"2018-05-01T00:00:00Z","type":"journal_article","abstract":[{"text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. ","lang":"eng"}],"ddc":["580"],"title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","status":"public","intvolume":" 41","_id":"462","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"6a20f843565f962cb20281cdf5e40914","date_created":"2019-11-18T16:22:22Z","date_updated":"2020-07-14T12:46:32Z","relation":"main_file","file_id":"7042","content_type":"application/pdf","file_size":1937976,"creator":"dernst","access_level":"open_access","file_name":"2018_PlantCellEnv_Fan.pdf"}],"oa_version":"Submitted Version"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"192","intvolume":" 4","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway."}],"citation":{"chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1.","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:10.1038/s41477-018-0190-1.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459.","ieee":"M. Fendrych et al., “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459. doi:10.1038/s41477-018-0190-1"},"publication":"Nature Plants","page":"453 - 459","article_type":"original","date_published":"2018-06-25T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"25","pmid":1,"year":"2018","department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/"}]},"author":[{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Akhmanova, Maria","last_name":"Akhmanova","first_name":"Maria","orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"full_name":"Hagihara, Shinya","last_name":"Hagihara","first_name":"Shinya"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"first_name":"Naoyuki","last_name":"Uchida","full_name":"Uchida, Naoyuki"},{"full_name":"Torii, Keiko U","last_name":"Torii","first_name":"Keiko U"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"volume":4,"date_created":"2018-12-11T11:45:07Z","date_updated":"2023-09-15T12:11:03Z","publist_id":"7728","external_id":{"isi":["000443221200017"],"pmid":["29942048"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41477-018-0190-1","language":[{"iso":"eng"}],"month":"06"},{"intvolume":" 19","status":"public","title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","ddc":["580"],"_id":"14","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_size":2200593,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_IJMS_Hille.pdf","checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","date_created":"2018-12-17T16:04:11Z","date_updated":"2020-07-14T12:44:50Z","relation":"main_file","file_id":"5719"}],"type":"journal_article","issue":"11","abstract":[{"text":"The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta.","lang":"eng"}],"article_type":"original","citation":{"ama":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 2018;19(11). doi:10.3390/ijms19113566","ista":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11).","ieee":"S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” International Journal of Molecular Sciences, vol. 19, no. 11. MDPI, 2018.","apa":"Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566","mla":"Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018, doi:10.3390/ijms19113566.","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","chicago":"Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566."},"publication":"International Journal of Molecular Sciences","date_published":"2018-11-12T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"12","publisher":"MDPI","department":[{"_id":"DaSi"},{"_id":"JiFr"}],"publication_status":"published","acknowledgement":"European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml.","year":"2018","volume":19,"date_created":"2018-12-11T11:44:09Z","date_updated":"2023-09-18T08:09:32Z","author":[{"last_name":"Hille","first_name":"Sander","full_name":"Hille, Sander"},{"full_name":"Akhmanova, Maria","last_name":"Akhmanova","first_name":"Maria","orcid":"0000-0003-1522-3162","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Glanc, Matous","first_name":"Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"ec_funded":1,"publist_id":"8042","file_date_updated":"2020-07-14T12:44:50Z","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000451528500282"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/ijms19113566","publication_identifier":{"eissn":["1422-0067"]},"month":"11"},{"publication":"Journal of Experimental Botany","citation":{"ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624."},"page":"4609 - 4624","date_published":"2018-08-31T00:00:00Z","scopus_import":"1","day":"31","article_processing_charge":"No","has_accepted_license":"1","_id":"36","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","status":"public","ddc":["581"],"intvolume":" 69","oa_version":"Published Version","file":[{"file_id":"5741","relation":"main_file","date_created":"2018-12-18T09:47:51Z","date_updated":"2020-07-14T12:46:13Z","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","file_name":"2018_JournalExperimBotany_Vu.pdf","access_level":"open_access","creator":"dernst","file_size":3359316,"content_type":"application/pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity."}],"issue":"19","external_id":{"isi":["000443568700010"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1093/jxb/ery204","language":[{"iso":"eng"}],"month":"08","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","year":"2018","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","author":[{"last_name":"Vu","first_name":"Lam","full_name":"Vu, Lam"},{"full_name":"Zhu, Tingting","first_name":"Tingting","last_name":"Zhu"},{"full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte","first_name":"Brigitte"},{"last_name":"Gevaert","first_name":"Kris","full_name":"Gevaert, Kris"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"}],"date_updated":"2023-09-19T10:00:46Z","date_created":"2018-12-11T11:44:17Z","volume":69,"file_date_updated":"2020-07-14T12:46:13Z","publist_id":"8019"},{"type":"journal_article","abstract":[{"text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.","lang":"eng"}],"issue":"2","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","status":"public","intvolume":" 174","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"148","oa_version":"Published Version","scopus_import":"1","day":"12","article_processing_charge":"No","page":"448 - 464.e24","publication":"Cell","citation":{"ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033","ieee":"T. Nishiyama et al., “The Chara genome: Secondary complexity and implications for plant terrestrialization,” Cell, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 2018;174(2):448-464.e24. doi:10.1016/j.cell.2018.06.033","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell. Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033.","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24."},"date_published":"2018-07-12T00:00:00Z","ec_funded":1,"publist_id":"7774","publication_status":"published","publisher":"Cell Press","department":[{"_id":"JiFr"}],"year":"2018","acknowledgement":"In-Data-Review","pmid":1,"date_updated":"2023-09-19T10:02:47Z","date_created":"2018-12-11T11:44:53Z","volume":174,"author":[{"full_name":"Nishiyama, Tomoaki","first_name":"Tomoaki","last_name":"Nishiyama"},{"full_name":"Sakayama, Hidetoshi","first_name":"Hidetoshi","last_name":"Sakayama"},{"full_name":"De Vries, Jan","last_name":"De Vries","first_name":"Jan"},{"full_name":"Buschmann, Henrik","last_name":"Buschmann","first_name":"Henrik"},{"full_name":"Saint Marcoux, Denis","last_name":"Saint Marcoux","first_name":"Denis"},{"full_name":"Ullrich, Kristian","last_name":"Ullrich","first_name":"Kristian"},{"last_name":"Haas","first_name":"Fabian","full_name":"Haas, Fabian"},{"first_name":"Lisa","last_name":"Vanderstraeten","full_name":"Vanderstraeten, Lisa"},{"full_name":"Becker, Dirk","first_name":"Dirk","last_name":"Becker"},{"full_name":"Lang, Daniel","last_name":"Lang","first_name":"Daniel"},{"full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě","first_name":"Stanislav"},{"full_name":"Rombauts, Stephane","first_name":"Stephane","last_name":"Rombauts"},{"full_name":"Wilhelmsson, Per","first_name":"Per","last_name":"Wilhelmsson"},{"first_name":"Philipp","last_name":"Janitza","full_name":"Janitza, Philipp"},{"first_name":"Ramona","last_name":"Kern","full_name":"Kern, Ramona"},{"last_name":"Heyl","first_name":"Alexander","full_name":"Heyl, Alexander"},{"first_name":"Florian","last_name":"Rümpler","full_name":"Rümpler, Florian"},{"first_name":"Luz","last_name":"Calderón Villalobos","full_name":"Calderón Villalobos, Luz"},{"full_name":"Clay, John","first_name":"John","last_name":"Clay"},{"full_name":"Skokan, Roman","first_name":"Roman","last_name":"Skokan"},{"first_name":"Atsushi","last_name":"Toyoda","full_name":"Toyoda, Atsushi"},{"full_name":"Suzuki, Yutaka","last_name":"Suzuki","first_name":"Yutaka"},{"full_name":"Kagoshima, Hiroshi","last_name":"Kagoshima","first_name":"Hiroshi"},{"first_name":"Elio","last_name":"Schijlen","full_name":"Schijlen, Elio"},{"first_name":"Navindra","last_name":"Tajeshwar","full_name":"Tajeshwar, Navindra"},{"full_name":"Catarino, Bruno","first_name":"Bruno","last_name":"Catarino"},{"full_name":"Hetherington, Alexander","last_name":"Hetherington","first_name":"Alexander"},{"first_name":"Assia","last_name":"Saltykova","full_name":"Saltykova, Assia"},{"first_name":"Clemence","last_name":"Bonnot","full_name":"Bonnot, Clemence"},{"full_name":"Breuninger, Holger","first_name":"Holger","last_name":"Breuninger"},{"full_name":"Symeonidi, Aikaterini","first_name":"Aikaterini","last_name":"Symeonidi"},{"first_name":"Guru","last_name":"Radhakrishnan","full_name":"Radhakrishnan, Guru"},{"full_name":"Van Nieuwerburgh, Filip","last_name":"Van Nieuwerburgh","first_name":"Filip"},{"full_name":"Deforce, Dieter","last_name":"Deforce","first_name":"Dieter"},{"first_name":"Caren","last_name":"Chang","full_name":"Chang, Caren"},{"first_name":"Kenneth","last_name":"Karol","full_name":"Karol, Kenneth"},{"full_name":"Hedrich, Rainer","last_name":"Hedrich","first_name":"Rainer"},{"first_name":"Peter","last_name":"Ulvskov","full_name":"Ulvskov, Peter"},{"first_name":"Gernot","last_name":"Glöckner","full_name":"Glöckner, Gernot"},{"first_name":"Charles","last_name":"Delwiche","full_name":"Delwiche, Charles"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"last_name":"Van De Peer","first_name":"Yves","full_name":"Van De Peer, Yves"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"full_name":"Beilby, Mary","last_name":"Beilby","first_name":"Mary"},{"full_name":"Dolan, Liam","first_name":"Liam","last_name":"Dolan"},{"first_name":"Yuji","last_name":"Kohara","full_name":"Kohara, Yuji"},{"full_name":"Sugano, Sumio","last_name":"Sugano","first_name":"Sumio"},{"full_name":"Fujiyama, Asao","first_name":"Asao","last_name":"Fujiyama"},{"full_name":"Delaux, Pierre Marc","first_name":"Pierre Marc","last_name":"Delaux"},{"full_name":"Quint, Marcel","first_name":"Marcel","last_name":"Quint"},{"full_name":"Theissen, Gunter","first_name":"Gunter","last_name":"Theissen"},{"last_name":"Hagemann","first_name":"Martin","full_name":"Hagemann, Martin"},{"last_name":"Harholt","first_name":"Jesper","full_name":"Harholt, Jesper"},{"last_name":"Dunand","first_name":"Christophe","full_name":"Dunand, Christophe"},{"full_name":"Zachgo, Sabine","first_name":"Sabine","last_name":"Zachgo"},{"first_name":"Jane","last_name":"Langdale","full_name":"Langdale, Jane"},{"full_name":"Maumus, Florian","first_name":"Florian","last_name":"Maumus"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"last_name":"Gould","first_name":"Sven B","full_name":"Gould, Sven B"},{"full_name":"Rensing, Stefan","last_name":"Rensing","first_name":"Stefan"}],"month":"07","isi":1,"quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"external_id":{"isi":["000438482800019"],"pmid":["30007417"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2018.06.033"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development."}],"issue":"10","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","status":"public","intvolume":" 30","_id":"147","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","scopus_import":"1","day":"12","article_processing_charge":"No","article_type":"original","page":"2553 - 2572","publication":"The Plant Cell","citation":{"ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 2018;30(10):2553-2572. doi:10.1105/tpc.18.00127","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.","ieee":"U. Kania et al., “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” The Plant Cell, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. Oxford University Press. https://doi.org/10.1105/tpc.18.00127","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:10.1105/tpc.18.00127.","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell. Oxford University Press, 2018. https://doi.org/10.1105/tpc.18.00127."},"date_published":"2018-11-12T00:00:00Z","ec_funded":1,"publist_id":"7776","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"year":"2018","acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","pmid":1,"date_updated":"2023-09-19T10:09:12Z","date_created":"2018-12-11T11:44:52Z","volume":30,"author":[{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","last_name":"Kania","full_name":"Kania, Urszula"},{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"full_name":"Lu, Qing","last_name":"Lu","first_name":"Qing"},{"full_name":"Hicks, Glenn R","last_name":"Hicks","first_name":"Glenn R"},{"full_name":"Nerinckx, Wim","last_name":"Nerinckx","first_name":"Wim"},{"first_name":"Kiril","last_name":"Mishev","full_name":"Mishev, Kiril"},{"full_name":"Peurois, Francois","last_name":"Peurois","first_name":"Francois"},{"full_name":"Cherfils, Jacqueline","last_name":"Cherfils","first_name":"Jacqueline"},{"last_name":"De","first_name":"Rycke Riet Maria","full_name":"De, Rycke Riet Maria"},{"full_name":"Grones, Peter","last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"first_name":"Eugenia","last_name":"Russinova","full_name":"Russinova, Eugenia"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"}],"month":"11","publication_identifier":{"issn":["1040-4651"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"},{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"main_file_link":[{"url":"https://doi.org/10.1105/tpc.18.00127","open_access":"1"}],"oa":1,"external_id":{"pmid":["30018156"],"isi":["000450000500023"]},"language":[{"iso":"eng"}],"doi":"10.1105/tpc.18.00127"},{"scopus_import":"1","day":"30","has_accepted_license":"1","article_processing_charge":"No","publication":"Nature Plants","citation":{"chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0212-z.","mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:10.1038/s41477-018-0212-z.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604.","ieee":"C. L. Shi et al., “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0212-z","ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 2018;4(8):596-604. doi:10.1038/s41477-018-0212-z"},"article_type":"original","page":"596 - 604","date_published":"2018-07-30T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity."}],"issue":"8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"146","title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","status":"public","ddc":["580"],"intvolume":" 4","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2018_NaturePlants_Shi.pdf","creator":"dernst","file_size":226829,"content_type":"application/pdf","file_id":"7043","relation":"main_file","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","date_updated":"2020-07-14T12:44:56Z","date_created":"2019-11-18T16:24:07Z"}],"month":"07","external_id":{"pmid":["30061750"],"isi":["000443861300016"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41477-018-0212-z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:56Z","publist_id":"7777","year":"2018","pmid":1,"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}],"author":[{"first_name":"Chun Lin","last_name":"Shi","full_name":"Shi, Chun Lin"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel"},{"last_name":"Herrmann","first_name":"Ullrich","full_name":"Herrmann, Ullrich"},{"last_name":"Wildhagen","first_name":"Mari","full_name":"Wildhagen, Mari"},{"full_name":"Kulik, Ivan","first_name":"Ivan","last_name":"Kulik","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB"},{"full_name":"Kopf, Andreas","last_name":"Kopf","first_name":"Andreas"},{"full_name":"Ishida, Takashi","first_name":"Takashi","last_name":"Ishida"},{"full_name":"Olsson, Vilde","first_name":"Vilde","last_name":"Olsson"},{"full_name":"Anker, Mari Kristine","first_name":"Mari Kristine","last_name":"Anker"},{"first_name":"Markus","last_name":"Albert","full_name":"Albert, Markus"},{"full_name":"Butenko, Melinka A","first_name":"Melinka A","last_name":"Butenko"},{"full_name":"Felix, Georg","first_name":"Georg","last_name":"Felix"},{"last_name":"Sawa","first_name":"Shinichiro","full_name":"Sawa, Shinichiro"},{"last_name":"Claassen","first_name":"Manfred","full_name":"Claassen, Manfred"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"last_name":"Aalen","first_name":"Reidunn B","full_name":"Aalen, Reidunn B"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/"}]},"date_created":"2018-12-11T11:44:52Z","date_updated":"2023-09-19T10:08:45Z","volume":4},{"publication":"Journal of Experimental Botany","citation":{"ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378.","apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., & Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery097","ieee":"T. R. Moturu et al., “Molecular evolution and diversification of the SMXL gene family,” Journal of Experimental Botany, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018.","ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 2018;69(9):2367-2378. doi:10.1093/jxb/ery097","chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery097.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” Journal of Experimental Botany, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:10.1093/jxb/ery097.","short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378."},"article_type":"original","page":"2367-2378","date_published":"2018-04-13T00:00:00Z","scopus_import":"1","keyword":["Plant Science","Physiology"],"day":"13","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10881","title":"Molecular evolution and diversification of the SMXL gene family","status":"public","intvolume":" 69","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants."}],"issue":"9","external_id":{"pmid":["29538714"],"isi":["000430727000016"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"doi":"10.1093/jxb/ery097","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"year":"2018","acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. ","pmid":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"author":[{"full_name":"Moturu, Taraka Ramji","first_name":"Taraka Ramji","last_name":"Moturu"},{"last_name":"Thula","first_name":"Sravankumar","full_name":"Thula, Sravankumar"},{"full_name":"Singh, Ravi Kumar","first_name":"Ravi Kumar","last_name":"Singh"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"last_name":"Vařeková","first_name":"Radka Svobodová","full_name":"Vařeková, Radka Svobodová"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Simon, Sibu","last_name":"Simon","first_name":"Sibu"}],"date_updated":"2023-09-19T15:10:43Z","date_created":"2022-03-18T12:43:22Z","volume":69,"ec_funded":1},{"abstract":[{"text":"Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis.","lang":"eng"}],"issue":"2","type":"journal_article","pubrep_id":"988","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2017_adamowski_PATELLINS_are.pdf","content_type":"application/pdf","file_size":14925985,"creator":"dernst","relation":"main_file","file_id":"6299","checksum":"bf156c20a4f117b4b932370d54cbac8c","date_created":"2019-04-12T08:46:32Z","date_updated":"2020-07-14T12:48:15Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"913","title":"PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana","status":"public","ddc":["581"],"intvolume":" 131","day":"29","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-01-29T00:00:00Z","publication":"Journal of Cell Science","citation":{"chicago":"Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer, Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.204198.","short":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J. Friml, Journal of Cell Science 131 (2018).","mla":"Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science, vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:10.1242/jcs.204198.","apa":"Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L., & Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.204198","ieee":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana,” Journal of Cell Science, vol. 131, no. 2. Company of Biologists, 2018.","ista":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. 2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.","ama":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 2018;131(2). doi:10.1242/jcs.204198"},"file_date_updated":"2020-07-14T12:48:15Z","publist_id":"6530","ec_funded":1,"article_number":"jcs.204198","author":[{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"},{"first_name":"Cecilia","last_name":"Rodríguez Furlán","full_name":"Rodríguez Furlán, Cecilia"},{"first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"full_name":"Sauer, Michael","first_name":"Michael","last_name":"Sauer"},{"first_name":"Lorena","last_name":"Norambuena","full_name":"Norambuena, Lorena"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"date_updated":"2023-09-26T15:47:50Z","date_created":"2018-12-11T11:49:10Z","volume":131,"year":"2018","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Company of Biologists","month":"01","publication_identifier":{"issn":["00219533"]},"doi":"10.1242/jcs.204198","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000424842400019"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}]},{"type":"journal_article","issue":"12","abstract":[{"text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment.","lang":"eng"}],"intvolume":" 4","status":"public","title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5673","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"03","page":"1082-1088","citation":{"chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants. Nature Research, 2018. https://doi.org/10.1038/s41477-018-0318-3.","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” Nature Plants, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:10.1038/s41477-018-0318-3.","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” Nature Plants, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.","apa":"Glanc, M., Fendrych, M., & Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. Nature Research. https://doi.org/10.1038/s41477-018-0318-3","ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.","ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 2018;4(12):1082-1088. doi:10.1038/s41477-018-0318-3"},"publication":"Nature Plants","date_published":"2018-12-03T00:00:00Z","ec_funded":1,"publisher":"Nature Research","department":[{"_id":"JiFr"}],"publication_status":"published","pmid":1,"year":"2018","volume":4,"date_created":"2018-12-16T22:59:18Z","date_updated":"2023-10-17T12:19:28Z","author":[{"orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"}],"publication_identifier":{"issn":["2055-0278"]},"month":"12","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833","open_access":"1"}],"external_id":{"isi":["000454576600017"],"pmid":["30518833"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0318-3"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"412","title":"A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis","ddc":["580"],"status":"public","intvolume":" 30","file":[{"file_name":"2018_PlantCell_Adamowski.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":4407538,"file_id":"11406","relation":"main_file","date_created":"2022-05-23T09:12:38Z","date_updated":"2022-05-23T09:12:38Z","success":1,"checksum":"4e165e653b67d3f0684697f21aace5a1"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a cellular trafficking process in which cargoes and lipids are internalized from the plasma membrane into vesicles coated with clathrin and adaptor proteins. CME is essential for many developmental and physiological processes in plants, but its underlying mechanism is not well characterised compared to that in yeast and animal systems. Here, we searched for new factors involved in CME in Arabidopsis thaliana by performing Tandem Affinity Purification of proteins that interact with clathrin light chain, a principal component of the clathrin coat. Among the confirmed interactors, we found two putative homologues of the clathrin-coat uncoating factor auxilin previously described in non-plant systems. Overexpression of AUXILIN-LIKE1 and AUXILIN-LIKE2 in A. thaliana caused an arrest of seedling growth and development. This was concomitant with inhibited endocytosis due to blocking of clathrin recruitment after the initial step of adaptor protein binding to the plasma membrane. By contrast, auxilin-like(1/2) loss-of-function lines did not present endocytosis-related developmental or cellular phenotypes under normal growth conditions. This work contributes to the on-going characterization of the endocytotic machinery in plants and provides a robust tool for conditionally and specifically interfering with CME in A. thaliana.","lang":"eng"}],"issue":"3","publication":"The Plant Cell","citation":{"ama":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 2018;30(3):700-716. doi:10.1105/tpc.17.00785","apa":"Adamowski, M., Narasimhan, M., Kania, U., Glanc, M., De Jaeger, G., & Friml, J. (2018). A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.17.00785","ieee":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, and J. Friml, “A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis,” The Plant Cell, vol. 30, no. 3. American Society of Plant Biologists, pp. 700–716, 2018.","ista":"Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J. 2018. A functional study of AUXILIN LIKE1 and 2 two putative clathrin uncoating factors in Arabidopsis. The Plant Cell. 30(3), 700–716.","short":"M. Adamowski, M. Narasimhan, U. Kania, M. Glanc, G. De Jaeger, J. Friml, The Plant Cell 30 (2018) 700–716.","mla":"Adamowski, Maciek, et al. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell, vol. 30, no. 3, American Society of Plant Biologists, 2018, pp. 700–16, doi:10.1105/tpc.17.00785.","chicago":"Adamowski, Maciek, Madhumitha Narasimhan, Urszula Kania, Matous Glanc, Geert De Jaeger, and Jiří Friml. “A Functional Study of AUXILIN LIKE1 and 2 Two Putative Clathrin Uncoating Factors in Arabidopsis.” The Plant Cell. American Society of Plant Biologists, 2018. https://doi.org/10.1105/tpc.17.00785."},"article_type":"original","page":"700 - 716","date_published":"2018-04-09T00:00:00Z","scopus_import":"1","day":"09","has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"We thank James Matthew Watson, Monika Borowska, and Peggy Stolt-Bergner at ProTech Facility of the Vienna Biocenter Core Facilities for the CRISPR/CAS9 construct; Anna Müller for assistance with molecular cloning; Sebastian Bednarek, Liwen Jiang, and Daniël Van Damme for sharing published material; Matyáš Fendrych, Daniël Van Damme, and Lindy Abas for valuable discussions; and Martine De Cock for help with correcting the manuscript. This work was supported by the European Research Council under the European Union Seventh Framework Programme (FP7/2007-2013)/ERC Grant 282300 and by the Ministry of Education of the Czech Republic/MŠMT project NPUI-LO1417.","year":"2018","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","author":[{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski","full_name":"Adamowski, Maciek"},{"full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Urszula","last_name":"Kania","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Kania, Urszula"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"related_material":{"record":[{"id":"6269","relation":"dissertation_contains","status":"public"}]},"date_updated":"2024-03-28T23:30:06Z","date_created":"2018-12-11T11:46:20Z","volume":30,"file_date_updated":"2022-05-23T09:12:38Z","ec_funded":1,"publist_id":"7417","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000429441400018"],"pmid":["29511054"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"doi":"10.1105/tpc.17.00785","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]}},{"publication":"PLoS Genetics","citation":{"ama":"Prat T, Hajny J, Grunewald W, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 2018;14(1). doi:10.1371/journal.pgen.1007177","apa":"Prat, T., Hajny, J., Grunewald, W., Vasileva, M. K., Molnar, G., Tejos, R., … Friml, J. (2018). WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007177","ieee":"T. Prat et al., “WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity,” PLoS Genetics, vol. 14, no. 1. Public Library of Science, 2018.","ista":"Prat T, Hajny J, Grunewald W, Vasileva MK, Molnar G, Tejos R, Schmid M, Sauer M, Friml J. 2018. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genetics. 14(1).","short":"T. Prat, J. Hajny, W. Grunewald, M.K. Vasileva, G. Molnar, R. Tejos, M. Schmid, M. Sauer, J. Friml, PLoS Genetics 14 (2018).","mla":"Prat, Tomas, et al. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics, vol. 14, no. 1, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007177.","chicago":"Prat, Tomas, Jakub Hajny, Wim Grunewald, Mina K Vasileva, Gergely Molnar, Ricardo Tejos, Markus Schmid, Michael Sauer, and Jiří Friml. “WRKY23 Is a Component of the Transcriptional Network Mediating Auxin Feedback on PIN Polarity.” PLoS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007177."},"date_published":"2018-01-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"Yes","has_accepted_license":"1","ddc":["581"],"title":"WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity","status":"public","intvolume":" 14","_id":"449","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_size":24709062,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-967-v1+1_journal.pgen.1007177.pdf","access_level":"open_access","date_created":"2018-12-12T10:10:52Z","date_updated":"2020-07-14T12:46:30Z","checksum":"0276d66788ec076f4924164a39e6a712","relation":"main_file","file_id":"4843"}],"pubrep_id":"967","type":"journal_article","abstract":[{"lang":"eng","text":"Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development."}],"issue":"1","isi":1,"quality_controlled":"1","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000423718600034"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1007177","month":"01","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"JiFr"}],"year":"2018","date_created":"2018-12-11T11:46:32Z","date_updated":"2024-03-28T23:30:38Z","volume":14,"author":[{"full_name":"Prat, Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","last_name":"Prat","first_name":"Tomas"},{"full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"full_name":"Vasileva, Mina K","last_name":"Vasileva","first_name":"Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Molnar, Gergely","last_name":"Molnar","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"first_name":"Markus","last_name":"Schmid","full_name":"Schmid, Markus"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"related_material":{"record":[{"id":"1127","status":"public","relation":"dissertation_contains"},{"id":"7172","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"8822"}]},"file_date_updated":"2020-07-14T12:46:30Z","publist_id":"7373","ec_funded":1},{"article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1","date_published":"2018-07-06T00:00:00Z","citation":{"ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-28188-1","ieee":"P. Grones et al., “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” Scientific Reports, vol. 8, no. 1. Springer, 2018.","apa":"Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., & Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. Springer. https://doi.org/10.1038/s41598-018-28188-1","ista":"Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279.","short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018).","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports, vol. 8, no. 1, 10279, Springer, 2018, doi:10.1038/s41598-018-28188-1.","chicago":"Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” Scientific Reports. Springer, 2018. https://doi.org/10.1038/s41598-018-28188-1."},"publication":"Scientific Reports","issue":"1","abstract":[{"lang":"eng","text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals."}],"type":"journal_article","file":[{"file_id":"5714","relation":"main_file","date_created":"2018-12-17T15:38:56Z","date_updated":"2020-07-14T12:45:20Z","checksum":"266b03f4fb8198e83141617aaa99dcab","file_name":"2018_ScientificReports_Grones.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2413876}],"oa_version":"Published Version","intvolume":" 8","title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","status":"public","ddc":["581"],"_id":"191","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"07","language":[{"iso":"eng"}],"doi":"10.1038/s41598-018-28188-1","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"},{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000437673200053"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publist_id":"7729","ec_funded":1,"file_date_updated":"2020-07-14T12:45:20Z","article_number":"10279","volume":8,"date_updated":"2024-03-28T23:30:38Z","date_created":"2018-12-11T11:45:06Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8822"}]},"author":[{"full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","first_name":"Peter"},{"id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda F","last_name":"Abas","full_name":"Abas, Melinda F"},{"full_name":"Hajny, Jakub","last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jones","first_name":"Angharad","full_name":"Jones, Angharad"},{"last_name":"Waidmann","first_name":"Sascha","full_name":"Waidmann, Sascha"},{"full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"}],"department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Springer","publication_status":"published","year":"2018"},{"has_accepted_license":"1","article_processing_charge":"No","day":"05","article_type":"original","citation":{"chicago":"Li, Lanxin, Gabriel Krens, Matyas Fendrych, and Jiří Friml. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol. Bio-protocol, 2018. https://doi.org/10.21769/BioProtoc.2685.","mla":"Li, Lanxin, et al. “Real-Time Analysis of Auxin Response, Cell Wall PH and Elongation in Arabidopsis Thaliana Hypocotyls.” Bio-Protocol, vol. 8, no. 1, Bio-protocol, 2018, doi:10.21769/BioProtoc.2685.","short":"L. Li, G. Krens, M. Fendrych, J. Friml, Bio-Protocol 8 (2018).","ista":"Li L, Krens G, Fendrych M, Friml J. 2018. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 8(1).","apa":"Li, L., Krens, G., Fendrych, M., & Friml, J. (2018). Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-Protocol. Bio-protocol. https://doi.org/10.21769/BioProtoc.2685","ieee":"L. Li, G. Krens, M. Fendrych, and J. Friml, “Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls,” Bio-protocol, vol. 8, no. 1. Bio-protocol, 2018.","ama":"Li L, Krens G, Fendrych M, Friml J. Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls. Bio-protocol. 2018;8(1). doi:10.21769/BioProtoc.2685"},"publication":"Bio-protocol","date_published":"2018-01-05T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH.","lang":"eng"}],"intvolume":" 8","status":"public","ddc":["576","581"],"title":"Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"442","oa_version":"Published Version","file":[{"creator":"system","file_size":11352389,"content_type":"application/pdf","file_name":"IST-2018-970-v1+1_2018_Lanxin_Real-time_analysis.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:29Z","date_created":"2018-12-12T10:17:43Z","checksum":"6644ba698206eda32b0abf09128e63e3","file_id":"5299","relation":"main_file"}],"pubrep_id":"970","publication_identifier":{"eissn":["2331-8325"]},"month":"01","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.21769/BioProtoc.2685","publist_id":"7381","ec_funded":1,"file_date_updated":"2020-07-14T12:46:29Z","department":[{"_id":"JiFr"},{"_id":"Bio"}],"publisher":"Bio-protocol","publication_status":"published","year":"2018","acknowledgement":"This protocol was adapted from Fendrych et al., 2016. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, and Austrian Science Fund (FWF) [M 2128-B21]. ","volume":8,"date_created":"2018-12-11T11:46:30Z","date_updated":"2024-03-28T23:30:43Z","related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","last_name":"Krens"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}]},{"month":"12","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.3390/ijms18122587","language":[{"iso":"eng"}],"article_number":"2587","file_date_updated":"2020-07-14T12:47:10Z","publist_id":"7242","year":"2017","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"MDPI","author":[{"full_name":"Olatunji, Damilola","first_name":"Damilola","last_name":"Olatunji"},{"full_name":"Geelen, Danny","first_name":"Danny","last_name":"Geelen"},{"last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"}],"date_updated":"2021-01-12T08:03:16Z","date_created":"2018-12-11T11:47:15Z","volume":18,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"International Journal of Molecular Sciences","citation":{"ama":"Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 2017;18(12). doi:10.3390/ijms18122587","ista":"Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 18(12), 2587.","apa":"Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms18122587","ieee":"D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels in plant root development,” International Journal of Molecular Sciences, vol. 18, no. 12. MDPI, 2017.","mla":"Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences, vol. 18, no. 12, 2587, MDPI, 2017, doi:10.3390/ijms18122587.","short":"D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017).","chicago":"Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587."},"date_published":"2017-12-01T00:00:00Z","type":"journal_article","abstract":[{"text":"In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.","lang":"eng"}],"issue":"12","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"572","ddc":["580"],"title":"Control of endogenous auxin levels in plant root development","status":"public","intvolume":" 18","pubrep_id":"917","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-917-v1+1_ijms-18-02587.pdf","file_size":920962,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4718","checksum":"82d51f11e493f7eec02976d9a9a9805e","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:08:55Z"}]},{"publist_id":"7076","pmid":1,"year":"2017","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"first_name":"Barbara","last_name":"Möller","full_name":"Möller, Barbara"},{"last_name":"Ten Hove","first_name":"Colette","full_name":"Ten Hove, Colette"},{"full_name":"Xiang, Daoquan","last_name":"Xiang","first_name":"Daoquan"},{"full_name":"Williams, Nerys","last_name":"Williams","first_name":"Nerys"},{"full_name":"López, Lorena","first_name":"Lorena","last_name":"López"},{"first_name":"Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko"},{"full_name":"Smit, Margot","last_name":"Smit","first_name":"Margot"},{"last_name":"Datla","first_name":"Raju","full_name":"Datla, Raju"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"}],"volume":114,"date_updated":"2021-01-12T08:08:02Z","date_created":"2018-12-11T11:47:45Z","publication_identifier":{"issn":["00278424"]},"month":"03","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/","open_access":"1"}],"oa":1,"external_id":{"pmid":["28265057"]},"quality_controlled":"1","doi":"10.1073/pnas.1616493114","language":[{"iso":"eng"}],"type":"journal_article","issue":"12","abstract":[{"text":"Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator.","lang":"eng"}],"_id":"657","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 114","title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","status":"public","oa_version":"Submitted Version","scopus_import":1,"day":"21","citation":{"chicago":"Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1616493114.","mla":"Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS, vol. 114, no. 12, National Academy of Sciences, 2017, pp. E2533–39, doi:10.1073/pnas.1616493114.","short":"B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit, R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539.","ista":"Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539.","ieee":"B. Möller et al., “Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo,” PNAS, vol. 114, no. 12. National Academy of Sciences, pp. E2533–E2539, 2017.","apa":"Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S., … Weijers, D. (2017). Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1616493114","ama":"Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 2017;114(12):E2533-E2539. doi:10.1073/pnas.1616493114"},"publication":"PNAS","page":"E2533 - E2539","date_published":"2017-03-21T00:00:00Z"},{"type":"journal_article","abstract":[{"text":"The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background, resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed under the control of their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. ","lang":"eng"}],"issue":"1","status":"public","title":"EXO70C2 is a key regulatory factor for optimal tip growth of pollen","ddc":["580"],"intvolume":" 174","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"669","file":[{"file_name":"2017_PlantPhysio_Synek.pdf","access_level":"open_access","file_size":2176903,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7041","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-11-18T16:16:18Z","checksum":"97155acc6aa5f0d0a78e0589a932fe02"}],"oa_version":"Submitted Version","scopus_import":1,"day":"01","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"223 - 240","publication":"Plant Physiology","citation":{"short":"L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 223–240.","mla":"Synek, Lukáš, et al. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 223–40, doi:10.1104/pp.16.01282.","chicago":"Synek, Lukáš, Nemanja Vukašinović, Ivan Kulich, Michal Hála, Klára Aldorfová, Matyas Fendrych, and Viktor Žárský. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.01282.","ama":"Synek L, Vukašinović N, Kulich I, et al. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 2017;174(1):223-240. doi:10.1104/pp.16.01282","ieee":"L. Synek et al., “EXO70C2 is a key regulatory factor for optimal tip growth of pollen,” Plant Physiology, vol. 174, no. 1. American Society of Plant Biologists, pp. 223–240, 2017.","apa":"Synek, L., Vukašinović, N., Kulich, I., Hála, M., Aldorfová, K., Fendrych, M., & Žárský, V. (2017). EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01282","ista":"Synek L, Vukašinović N, Kulich I, Hála M, Aldorfová K, Fendrych M, Žárský V. 2017. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 174(1), 223–240."},"date_published":"2017-05-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:37Z","publist_id":"7058","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","year":"2017","pmid":1,"date_created":"2018-12-11T11:47:49Z","date_updated":"2021-01-12T08:08:35Z","volume":174,"author":[{"first_name":"Lukáš","last_name":"Synek","full_name":"Synek, Lukáš"},{"last_name":"Vukašinović","first_name":"Nemanja","full_name":"Vukašinović, Nemanja"},{"last_name":"Kulich","first_name":"Ivan","full_name":"Kulich, Ivan"},{"full_name":"Hála, Michal","last_name":"Hála","first_name":"Michal"},{"last_name":"Aldorfová","first_name":"Klára","full_name":"Aldorfová, Klára"},{"full_name":"Fendrych, Matyas","first_name":"Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"last_name":"Žárský","first_name":"Viktor","full_name":"Žárský, Viktor"}],"month":"05","publication_identifier":{"issn":["00320889"]},"quality_controlled":"1","oa":1,"external_id":{"pmid":["28356503"]},"language":[{"iso":"eng"}],"doi":"10.1104/pp.16.01282"},{"_id":"722","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["581"],"status":"public","title":"Shaping 3D root system architecture","intvolume":" 27","pubrep_id":"982","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"6332","date_created":"2019-04-17T07:46:40Z","date_updated":"2020-07-14T12:47:54Z","checksum":"e45588b21097b408da6276a3e5eedb2e","file_name":"2017_CurrentBiology_Morris.pdf","access_level":"open_access","file_size":1576593,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","abstract":[{"text":"Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises.","lang":"eng"}],"issue":"17","publication":"Current Biology","citation":{"ama":"Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. Current Biology. 2017;27(17):R919-R930. doi:10.1016/j.cub.2017.06.043","ista":"Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D, Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology. 27(17), R919–R930.","ieee":"E. Morris et al., “Shaping 3D root system architecture,” Current Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","apa":"Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.06.043","mla":"Morris, Emily, et al. “Shaping 3D Root System Architecture.” Current Biology, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:10.1016/j.cub.2017.06.043.","short":"E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T. Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K. Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930.","chicago":"Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.06.043."},"page":"R919 - R930","date_published":"2017-09-11T00:00:00Z","scopus_import":1,"day":"11","has_accepted_license":"1","year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Cell Press","author":[{"last_name":"Morris","first_name":"Emily","full_name":"Morris, Emily"},{"full_name":"Griffiths, Marcus","last_name":"Griffiths","first_name":"Marcus"},{"full_name":"Golebiowska, Agata","first_name":"Agata","last_name":"Golebiowska"},{"full_name":"Mairhofer, Stefan","last_name":"Mairhofer","first_name":"Stefan"},{"full_name":"Burr Hersey, Jasmine","first_name":"Jasmine","last_name":"Burr Hersey"},{"first_name":"Tatsuaki","last_name":"Goh","full_name":"Goh, Tatsuaki"},{"full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim","first_name":"Daniel"},{"full_name":"Atkinson, Brian","first_name":"Brian","last_name":"Atkinson"},{"full_name":"Sturrock, Craig","last_name":"Sturrock","first_name":"Craig"},{"first_name":"Jonathan","last_name":"Lynch","full_name":"Lynch, Jonathan"},{"first_name":"Kris","last_name":"Vissenberg","full_name":"Vissenberg, Kris"},{"full_name":"Ritz, Karl","last_name":"Ritz","first_name":"Karl"},{"full_name":"Wells, Darren","last_name":"Wells","first_name":"Darren"},{"last_name":"Mooney","first_name":"Sacha","full_name":"Mooney, Sacha"},{"full_name":"Bennett, Malcolm","first_name":"Malcolm","last_name":"Bennett"}],"date_updated":"2021-01-12T08:12:29Z","date_created":"2018-12-11T11:48:08Z","volume":27,"file_date_updated":"2020-07-14T12:47:54Z","publist_id":"6956","ec_funded":1,"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["28898665"]},"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"doi":"10.1016/j.cub.2017.06.043","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["09609822"]}},{"publication_identifier":{"issn":["2663-337X"]},"month":"06","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_842","oa":1,"publist_id":"6483","file_date_updated":"2020-07-14T12:48:15Z","date_created":"2018-12-11T11:49:18Z","date_updated":"2023-09-07T12:06:09Z","related_material":{"record":[{"id":"1591","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","year":"2017","has_accepted_license":"1","article_processing_charge":"No","day":"02","date_published":"2017-06-02T00:00:00Z","page":"117","citation":{"short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","mla":"Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842.","chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","apa":"Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria."},"abstract":[{"lang":"eng","text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"file_name":"2017_Adamowski-Thesis_Source.docx","access_level":"closed","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":46903863,"file_id":"6215","relation":"source_file","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:20Z","checksum":"193425764d9aaaed3ac57062a867b315"},{"checksum":"df5ab01be81f821e1b958596a1ec8d21","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:19Z","relation":"main_file","file_id":"6216","file_size":8698888,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_Adamowski-Thesis.pdf"}],"oa_version":"Published Version","pubrep_id":"842","title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","status":"public","ddc":["581","583","580"],"_id":"938","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"file_date_updated":"2021-02-22T11:52:56Z","publist_id":"6233","date_created":"2018-12-11T11:50:17Z","date_updated":"2023-09-19T10:39:33Z","author":[{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Prat","full_name":"Prat, Tomas"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"449"}]},"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","year":"2017","acknowledgement":"I would like to first acknowledge my supervisor Jiří Friml for support, kind advice and patience. It was a pleasure to be a part of your lab, Jiří. I will remember the atmosphere present in auxin lab at VIB in Ghent and at IST in Klosterneuburg forever. I would like to thank all past and present lab members for the friendship and friendly and scientific environment in the groups. It was so nice to cooperate with you, guys. There was always someone who helped me with experiments, troubleshoot issues coming from our work etc. At this place, I would like to thank especially to Gergo Molnár. I’m happy (and lucky) that I have met him; he naturally became my tutor and guide through my PhD. From no one else during my entire professional career, I’ve learned that much.","month":"01","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"language":[{"iso":"eng"}],"oa":1,"abstract":[{"text":"Plant hormone auxin and its transport between cells belong to the most important\r\nmechanisms controlling plant development. Auxin itself could change localization of PINs and\r\nthereby control direction of its own flow. We performed an expression profiling experiment\r\nin Arabidopsis roots to identify potential regulators of PIN polarity which are transcriptionally\r\nregulated by auxin signalling. We identified several novel regulators and performed a detailed\r\ncharacterization of the transcription factor WRKY23 (At2g47260) and its role in auxin\r\nfeedback on PIN polarity. Gain-of-function and dominant-negative mutants revealed that\r\nWRKY23 plays a crucial role in mediating the auxin effect on PIN polarity. In concordance,\r\ntypical polar auxin transport processes such as gravitropism and leaf vascular pattern\r\nformation were disturbed by interfering with WRKY23 function.\r\nIn order to identify direct targets of WRKY23, we performed consequential expression\r\nprofiling experiments using a WRKY23 inducible gain-of-function line and dominant-negative\r\nWRKY23 line that is defunct in PIN re-arrangement. Among several genes mostly related to\r\nthe groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE\r\nTRANSPORTER 1 (LHT1; At5g40780), a small amino acid permease gene from the amino\r\nacid/auxin permease family (AAAP), we present its detailed characterisation in auxin feedback\r\non PIN repolarization, identified its transcriptional regulation, we propose a potential\r\nmechanism of its action. Moreover, we identified also a member of receptor-like protein\r\nkinase LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1;\r\nLRRK1; At1g05700), which also affects auxin-dependent PIN re-arrangement. We described\r\nits transcriptional behaviour, subcellular localization. Based on global expression data, we\r\ntried to identify ligand responsible for mechanism of signalling and suggest signalling partner\r\nand interactors. Additionally, we described role of novel phytohormone group, strigolactone,\r\nin auxin-dependent PIN re-arrangement, that could be a fundament for future studies in this\r\nfield.\r\nOur results provide first insights into an auxin transcriptional network targeting PIN\r\nlocalization and thus regulating plant development. We highlighted WRKY23 transcriptional\r\nnetwork and characterised its mediatory role in plant development. We identified direct\r\neffectors of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement and\r\nPIN-dependent auxin transport processes.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"access_level":"closed","file_name":"IST_Austria_Thesis_Tomáš_Prát.pdf","file_size":10285946,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6209","checksum":"d192c7c6c5ea32c8432437286dc4909e","date_created":"2019-04-05T08:45:14Z","date_updated":"2019-04-05T08:45:14Z"},{"access_level":"open_access","file_name":"2017_Thesis_Prat.pdf","file_size":9802991,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"9185","checksum":"bab18b52cf98145926042d8ed99fdb3b","success":1,"date_created":"2021-02-22T11:52:56Z","date_updated":"2021-02-22T11:52:56Z"}],"oa_version":"Published Version","status":"public","title":"Identification of novel regulators of PIN polarity and development of novel auxin sensor","ddc":["580"],"_id":"1127","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"12","article_processing_charge":"No","has_accepted_license":"1","date_published":"2017-01-12T00:00:00Z","page":"131","citation":{"ista":"Prat T. 2017. Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria.","ieee":"T. Prat, “Identification of novel regulators of PIN polarity and development of novel auxin sensor,” Institute of Science and Technology Austria, 2017.","apa":"Prat, T. (2017). Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria.","ama":"Prat T. Identification of novel regulators of PIN polarity and development of novel auxin sensor. 2017.","chicago":"Prat, Tomas. “Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor.” Institute of Science and Technology Austria, 2017.","mla":"Prat, Tomas. Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor. Institute of Science and Technology Austria, 2017.","short":"T. Prat, Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor, Institute of Science and Technology Austria, 2017."}},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2017-01-01T00:00:00Z","publication":"Plant Physiology","citation":{"mla":"Steenackers, Ward, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology, vol. 173, no. 1, American Society of Plant Biologists, 2017, pp. 552–65, doi:10.1104/pp.16.00943.","short":"W. Steenackers, P. Klíma, M. Quareshy, I. Cesarino, R. Kumpf, S. Corneillie, P. Araújo, T. Viaene, G. Goeminne, M. Nowack, K. Ljung, J. Friml, J. Blakeslee, O. Novák, E. Zažímalová, R. Napier, W. Boerjan, B. Vanholme, Plant Physiology 173 (2017) 552–565.","chicago":"Steenackers, Ward, Petr Klíma, Mussa Quareshy, Igor Cesarino, Robert Kumpf, Sander Corneillie, Pedro Araújo, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.00943.","ama":"Steenackers W, Klíma P, Quareshy M, et al. Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. 2017;173(1):552-565. doi:10.1104/pp.16.00943","ista":"Steenackers W, Klíma P, Quareshy M, Cesarino I, Kumpf R, Corneillie S, Araújo P, Viaene T, Goeminne G, Nowack M, Ljung K, Friml J, Blakeslee J, Novák O, Zažímalová E, Napier R, Boerjan W, Vanholme B. 2017. Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. 173(1), 552–565.","ieee":"W. Steenackers et al., “Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation,” Plant Physiology, vol. 173, no. 1. American Society of Plant Biologists, pp. 552–565, 2017.","apa":"Steenackers, W., Klíma, P., Quareshy, M., Cesarino, I., Kumpf, R., Corneillie, S., … Vanholme, B. (2017). Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00943"},"article_type":"original","page":"552 - 565","abstract":[{"text":"Auxin steers numerous physiological processes in plants, making the tight control of its endogenous levels and spatiotemporal distribution a necessity. This regulation is achieved by different mechanisms, including auxin biosynthesis, metabolic conversions, degradation, and transport. Here, we introduce cis-cinnamic acid (c-CA) as a novel and unique addition to a small group of endogenous molecules affecting in planta auxin concentrations. c-CA is the photo-isomerization product of the phenylpropanoid pathway intermediate trans-CA (t-CA). When grown on c-CA-containing medium, an evolutionary diverse set of plant species were shown to exhibit phenotypes characteristic for high auxin levels, including inhibition of primary root growth, induction of root hairs, and promotion of adventitious and lateral rooting. By molecular docking and receptor binding assays, we showed that c-CA itself is neither an auxin nor an anti-auxin, and auxin profiling data revealed that c-CA does not significantly interfere with auxin biosynthesis. Single cell-based auxin accumulation assays showed that c-CA, and not t-CA, is a potent inhibitor of auxin efflux. Auxin signaling reporters detected changes in spatiotemporal distribution of the auxin response along the root of c-CA-treated plants, and long-distance auxin transport assays showed no inhibition of rootward auxin transport. Overall, these results suggest that the phenotypes of c-CA-treated plants are the consequence of a local change in auxin accumulation, induced by the inhibition of auxin efflux. This work reveals a novel mechanism how plants may regulate auxin levels and adds a novel, naturally occurring molecule to the chemical toolbox for the studies of auxin homeostasis.","lang":"eng"}],"issue":"1","type":"journal_article","file":[{"access_level":"open_access","file_name":"2016_PlantPhysi_Steenackers.pdf","creator":"dernst","content_type":"application/pdf","file_size":4109142,"file_id":"7040","relation":"main_file","checksum":"fd4d1cfe7ed70e54bb12ae3881f3fb91","date_updated":"2020-07-14T12:44:36Z","date_created":"2019-11-18T16:12:25Z"}],"oa_version":"Submitted Version","_id":"1159","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation","status":"public","ddc":["580"],"intvolume":" 173","month":"01","publication_identifier":{"issn":["0032-0889"]},"doi":"10.1104/pp.16.00943","language":[{"iso":"eng"}],"external_id":{"isi":["000394135800041"],"pmid":["27837086"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"file_date_updated":"2020-07-14T12:44:36Z","publist_id":"6199","ec_funded":1,"author":[{"full_name":"Steenackers, Ward","last_name":"Steenackers","first_name":"Ward"},{"full_name":"Klíma, Petr","first_name":"Petr","last_name":"Klíma"},{"first_name":"Mussa","last_name":"Quareshy","full_name":"Quareshy, Mussa"},{"last_name":"Cesarino","first_name":"Igor","full_name":"Cesarino, Igor"},{"full_name":"Kumpf, Robert","first_name":"Robert","last_name":"Kumpf"},{"last_name":"Corneillie","first_name":"Sander","full_name":"Corneillie, Sander"},{"full_name":"Araújo, Pedro","first_name":"Pedro","last_name":"Araújo"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"full_name":"Goeminne, Geert","first_name":"Geert","last_name":"Goeminne"},{"full_name":"Nowack, Moritz","first_name":"Moritz","last_name":"Nowack"},{"last_name":"Ljung","first_name":"Karin","full_name":"Ljung, Karin"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"Blakeslee, Joshua","first_name":"Joshua","last_name":"Blakeslee"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"full_name":"Napier, Richard","first_name":"Richard","last_name":"Napier"},{"full_name":"Boerjan, Wout","last_name":"Boerjan","first_name":"Wout"},{"full_name":"Vanholme, Bartel","last_name":"Vanholme","first_name":"Bartel"}],"date_created":"2018-12-11T11:50:28Z","date_updated":"2023-09-20T11:29:17Z","volume":173,"year":"2017","pmid":1,"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}]},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"06","citation":{"mla":"Kuhn, Benjamin, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” Scientific Reports, vol. 7, 41906, Nature Publishing Group, 2017, doi:10.1038/srep41906.","short":"B. Kuhn, T. Nodzyński, S. Errafi, R. Bucher, S. Gupta, B. Aryal, P. Dobrev, L. Bigler, M. Geisler, E. Zažímalová, J. Friml, C. Ringli, Scientific Reports 7 (2017).","chicago":"Kuhn, Benjamin, Tomasz Nodzyński, Sanae Errafi, Rahel Bucher, Shibu Gupta, Bibek Aryal, Petre Dobrev, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41906.","ama":"Kuhn B, Nodzyński T, Errafi S, et al. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 2017;7. doi:10.1038/srep41906","ista":"Kuhn B, Nodzyński T, Errafi S, Bucher R, Gupta S, Aryal B, Dobrev P, Bigler L, Geisler M, Zažímalová E, Friml J, Ringli C. 2017. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 7, 41906.","ieee":"B. Kuhn et al., “Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity,” Scientific Reports, vol. 7. Nature Publishing Group, 2017.","apa":"Kuhn, B., Nodzyński, T., Errafi, S., Bucher, R., Gupta, S., Aryal, B., … Ringli, C. (2017). Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep41906"},"publication":"Scientific Reports","date_published":"2017-02-06T00:00:00Z","type":"journal_article","abstract":[{"text":"The phytohormone auxin is a major determinant and regulatory component important for plant development. Auxin transport between cells is mediated by a complex system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization and activity is thought to be influenced by phosphatases and kinases. Flavonols have been shown to alter auxin transport activity and changes in flavonol accumulation in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants show wild type-like auxin transport activity while levels of free auxin are not affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization. In vivo analysis of PINOID action, a kinase known to influence PIN protein localization in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID activity. Together, these data suggest that flavonols affect auxin transport by modifying the antagonistic kinase/phosphatase equilibrium.","lang":"eng"}],"_id":"1110","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 7","title":"Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity","status":"public","ddc":["581"],"pubrep_id":"803","file":[{"access_level":"open_access","file_name":"IST-2017-803-v1+1_srep41906.pdf","creator":"system","content_type":"application/pdf","file_size":1654496,"file_id":"5328","relation":"main_file","date_created":"2018-12-12T10:18:09Z","date_updated":"2018-12-12T10:18:09Z"}],"oa_version":"Published Version","publication_identifier":{"issn":["20452322"]},"month":"02","external_id":{"isi":["000393367600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1038/srep41906","language":[{"iso":"eng"}],"article_number":"41906","ec_funded":1,"publist_id":"6258","file_date_updated":"2018-12-12T10:18:09Z","year":"2017","acknowledgement":"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 (GA13-40637S) [JF].","publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Kuhn, Benjamin","last_name":"Kuhn","first_name":"Benjamin"},{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"last_name":"Errafi","first_name":"Sanae","full_name":"Errafi, Sanae"},{"first_name":"Rahel","last_name":"Bucher","full_name":"Bucher, Rahel"},{"last_name":"Gupta","first_name":"Shibu","full_name":"Gupta, Shibu"},{"last_name":"Aryal","first_name":"Bibek","full_name":"Aryal, Bibek"},{"full_name":"Dobrev, Petre","first_name":"Petre","last_name":"Dobrev"},{"full_name":"Bigler, Laurent","first_name":"Laurent","last_name":"Bigler"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"last_name":"Ringli","first_name":"Christoph","full_name":"Ringli, Christoph"}],"volume":7,"date_updated":"2023-09-20T11:35:35Z","date_created":"2018-12-11T11:50:12Z"},{"month":"08","publication_identifier":{"issn":["00320781"]},"doi":"10.1093/pcp/pcx118","language":[{"iso":"eng"}],"external_id":{"pmid":["29016942"],"isi":["000413220400019"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:48:06Z","publist_id":"6854","article_number":"1801-1811","author":[{"full_name":"Kitakura, Saeko","first_name":"Saeko","last_name":"Kitakura"},{"full_name":"Adamowski, Maciek","last_name":"Adamowski","first_name":"Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Matsuura, Yuki","last_name":"Matsuura","first_name":"Yuki"},{"first_name":"Luca","last_name":"Santuari","full_name":"Santuari, Luca"},{"full_name":"Kouno, Hirotaka","last_name":"Kouno","first_name":"Hirotaka"},{"last_name":"Arima","first_name":"Kohei","full_name":"Arima, Kohei"},{"first_name":"Christian","last_name":"Hardtke","full_name":"Hardtke, Christian"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"first_name":"Tatsuo","last_name":"Kakimoto","full_name":"Kakimoto, Tatsuo"},{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"}],"date_created":"2018-12-11T11:48:34Z","date_updated":"2023-09-27T11:00:19Z","volume":58,"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","day":"21","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2017-08-21T00:00:00Z","publication":"Plant and Cell Physiology","citation":{"short":"S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima, C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).","mla":"Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology, vol. 58, no. 10, 1801–1811, Oxford University Press, 2017, doi:10.1093/pcp/pcx118.","chicago":"Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and Cell Physiology. Oxford University Press, 2017. https://doi.org/10.1093/pcp/pcx118.","ama":"Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 2017;58(10). doi:10.1093/pcp/pcx118","ieee":"S. Kitakura et al., “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,” Plant and Cell Physiology, vol. 58, no. 10. Oxford University Press, 2017.","apa":"Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima, K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcx118","ista":"Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 58(10), 1801–1811."},"abstract":[{"text":"Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA), which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been revealed fully. In a previous study, we have identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2 as a crucial component of this BFA action at the level of TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.","lang":"eng"}],"issue":"10","type":"journal_article","pubrep_id":"1009","oa_version":"Submitted Version","file":[{"file_id":"6333","relation":"main_file","date_created":"2019-04-17T07:52:34Z","date_updated":"2020-07-14T12:48:06Z","checksum":"bd3e3a94d55416739cbb19624bb977f8","file_name":"2017_PlantCellPhysio_Kitakura.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1352913}],"_id":"799","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["581"],"status":"public","title":"BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana","intvolume":" 58"},{"abstract":[{"lang":"eng","text":"Development of vascular tissue is a remarkable example of intercellular communication and coordinated development involving hormonal signaling and tissue polarity. Thus far, studies on vascular patterning and regeneration have been conducted mainly in trees—woody plants—with a well-developed layer of vascular cambium and secondary tissues. Trees are difficult to use as genetic models, i.e., due to long generation time, unstable environmental conditions, and lack of available mutants and transgenic lines. Therefore, the use of the main genetic model plant Arabidopsis thaliana (L.) Heynh., with a wealth of available marker and transgenic lines, provides a unique opportunity to address molecular mechanism of vascular tissue formation and regeneration. With specific treatments, the tiny weed Arabidopsis can serve as a model to understand the growth of mighty trees and interconnect a tree physiology with molecular genetics and cell biology of Arabidopsis."}],"alternative_title":["Agricultural and Biological Sciences"],"type":"book_chapter","file":[{"relation":"main_file","file_id":"4969","checksum":"e1f05e5850dfd9f9434d2d373ca61941","date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T10:12:49Z","access_level":"open_access","file_name":"IST-2018-929-v1+1_56106.pdf","content_type":"application/pdf","file_size":7443683,"creator":"system"}],"oa_version":"Published Version","pubrep_id":"929","ddc":["581"],"status":"public","title":"Vascular tissue development and regeneration in the model plant arabidopsis","_id":"545","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"17","has_accepted_license":"1","series_title":"Plant Engineering","date_published":"2017-11-17T00:00:00Z","page":"113 - 140","publication":"Plant Engineering","citation":{"ista":"Mazur E, Friml J. 2017.Vascular tissue development and regeneration in the model plant arabidopsis. In: Plant Engineering. Agricultural and Biological Sciences, , 113–140.","apa":"Mazur, E., & Friml, J. (2017). Vascular tissue development and regeneration in the model plant arabidopsis. In S. Jurić (Ed.), Plant Engineering (pp. 113–140). InTech. https://doi.org/10.5772/intechopen.69712","ieee":"E. Mazur and J. Friml, “Vascular tissue development and regeneration in the model plant arabidopsis,” in Plant Engineering, S. Jurić, Ed. InTech, 2017, pp. 113–140.","ama":"Mazur E, Friml J. Vascular tissue development and regeneration in the model plant arabidopsis. In: Jurić S, ed. Plant Engineering. Plant Engineering. InTech; 2017:113-140. doi:10.5772/intechopen.69712","chicago":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” In Plant Engineering, edited by Snježana Jurić, 113–40. Plant Engineering. InTech, 2017. https://doi.org/10.5772/intechopen.69712.","mla":"Mazur, Ewa, and Jiří Friml. “Vascular Tissue Development and Regeneration in the Model Plant Arabidopsis.” Plant Engineering, edited by Snježana Jurić, InTech, 2017, pp. 113–40, doi:10.5772/intechopen.69712.","short":"E. Mazur, J. Friml, in:, S. Jurić (Ed.), Plant Engineering, InTech, 2017, pp. 113–140."},"file_date_updated":"2020-07-14T12:46:58Z","ec_funded":1,"publist_id":"7269","date_created":"2018-12-11T11:47:05Z","date_updated":"2024-02-12T12:03:42Z","author":[{"full_name":"Mazur, Ewa","first_name":"Ewa","last_name":"Mazur"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"related_material":{"record":[{"id":"1274","relation":"earlier_version","status":"public"}]},"publication_status":"published","publisher":"InTech","department":[{"_id":"JiFr"}],"editor":[{"last_name":"Jurić","first_name":"Snježana","full_name":"Jurić, Snježana"}],"year":"2017","month":"11","language":[{"iso":"eng"}],"doi":"10.5772/intechopen.69712","quality_controlled":"1","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"date_published":"2017-06-19T00:00:00Z","citation":{"mla":"von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife, vol. 6, e26792, eLife Sciences Publications, 2017, doi:10.7554/eLife.26792.","short":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml, ELife 6 (2017).","chicago":"Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone, Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy for Vertically Grown Roots.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.26792.","ama":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 2017;6. doi:10.7554/eLife.26792","ista":"von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017. Live tracking of moving samples in confocal microscopy for vertically grown roots. eLife. 6, e26792.","apa":"von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., & Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically grown roots. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.26792","ieee":"D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J. Friml, “Live tracking of moving samples in confocal microscopy for vertically grown roots,” eLife, vol. 6. eLife Sciences Publications, 2017."},"publication":"eLife","has_accepted_license":"1","article_processing_charge":"Yes","day":"19","scopus_import":"1","pubrep_id":"847","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5315","checksum":"9af3398cb0d81f99d79016a616df22e9","date_created":"2018-12-12T10:17:57Z","date_updated":"2020-07-14T12:48:15Z","access_level":"open_access","file_name":"IST-2017-847-v1+1_elife-26792-v2.pdf","file_size":19581847,"content_type":"application/pdf","creator":"system"}],"_id":"946","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 6","ddc":["570"],"title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","status":"public","abstract":[{"text":"Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.","lang":"eng"}],"type":"journal_article","doi":"10.7554/eLife.26792","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000404728300001"]},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"2572ED28-B435-11E9-9278-68D0E5697425","grant_number":"M02128","call_identifier":"FWF","name":"Molecular basis of root growth inhibition by auxin"},{"grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425","name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF"},{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"month":"06","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5566"}]},"author":[{"first_name":"Daniel","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel"},{"full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas"},{"full_name":"Barone, Vanessa","first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"volume":6,"date_created":"2018-12-11T11:49:21Z","date_updated":"2024-02-21T13:49:34Z","year":"2017","acknowledgement":"Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013 no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop at IST Austria for their contribution to the microscope setup and to Yvonne Kemper for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility","publisher":"eLife Sciences Publications","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"CaHe"},{"_id":"EvBe"}],"publication_status":"published","publist_id":"6471","ec_funded":1,"file_date_updated":"2020-07-14T12:48:15Z","article_number":"e26792"},{"month":"01","external_id":{"isi":["000397847200041"]},"oa":1,"isi":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"doi":"10.3791/55044","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"article_number":"e55044","file_date_updated":"2018-12-12T10:16:32Z","publist_id":"6302","ec_funded":1,"year":"2017","publication_status":"published","publisher":"Journal of Visualized Experiments","department":[{"_id":"JiFr"},{"_id":"Bio"}],"author":[{"full_name":"Von Wangenheim, Daniel","last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"5565","status":"public","relation":"popular_science"}]},"date_updated":"2024-02-21T13:49:12Z","date_created":"2018-12-11T11:50:01Z","volume":2017,"scopus_import":"1","day":"18","article_processing_charge":"No","has_accepted_license":"1","publication":"Journal of visualized experiments JoVE","citation":{"mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:10.3791/55044.","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017).","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE. Journal of Visualized Experiments, 2017. https://doi.org/10.3791/55044.","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017;2017(119). doi:10.3791/55044","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of Visualized Experiments JoVE. Journal of Visualized Experiments. https://doi.org/10.3791/55044","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” Journal of visualized experiments JoVE, vol. 2017, no. 119. Journal of Visualized Experiments, 2017."},"date_published":"2017-01-18T00:00:00Z","type":"journal_article","abstract":[{"text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. ","lang":"eng"}],"issue":"119","_id":"1078","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["580"],"title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","status":"public","intvolume":" 2017","pubrep_id":"808","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":57678,"creator":"system","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:31Z","date_updated":"2018-12-12T10:16:31Z","relation":"main_file","file_id":"5219"},{"access_level":"open_access","file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","content_type":"application/pdf","file_size":1317820,"creator":"system","relation":"main_file","file_id":"5220","date_updated":"2018-12-12T10:16:32Z","date_created":"2018-12-12T10:16:32Z"}]},{"month":"04","day":"10","article_processing_charge":"No","has_accepted_license":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"oa":1,"citation":{"ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel, Institute of Science and Technology Austria, 10.15479/AT:ISTA:66.","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel.” Institute of Science and Technology Austria, 2017.","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:66","ama":"von Wangenheim D, Hauschild R, Friml J. Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel. 2017. doi:10.15479/AT:ISTA:66","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:66.","mla":"von Wangenheim, Daniel, et al. Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:66.","short":"D. von Wangenheim, R. Hauschild, J. Friml, (2017)."},"date_published":"2017-04-10T00:00:00Z","doi":"10.15479/AT:ISTA:66","datarep_id":"66","type":"research_data","abstract":[{"lang":"eng","text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. \r\nThe Video is licensed under a CC BY NC ND license. "}],"file_date_updated":"2020-07-14T12:47:03Z","ec_funded":1,"publist_id":"6302","ddc":["580"],"status":"public","title":"Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"},{"_id":"Bio"}],"_id":"5565","acknowledgement":"fund: FP7-ERC 0101109","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","date_updated":"2024-02-21T13:49:13Z","date_created":"2018-12-12T12:31:34Z","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-66-v1+1_WangenheimHighResolution55044-NEW_1.mp4","file_size":101497758,"content_type":"video/mp4","creator":"system","relation":"main_file","file_id":"5599","checksum":"b7552fc23540a85dc5a22fd4484eae71","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:02:33Z"}],"author":[{"full_name":"Von Wangenheim, Daniel","last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"related_material":{"record":[{"id":"1078","status":"public","relation":"research_paper"}]}},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/celldisc.2016.18","language":[{"iso":"eng"}],"month":"07","acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","year":"2016","publication_status":"published","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"Nature Publishing Group","author":[{"full_name":"Łangowski, Łukasz","last_name":"Łangowski","first_name":"Łukasz"},{"orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T"},{"full_name":"Li, Hongjiang","first_name":"Hongjiang","last_name":"Li","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Naramoto","first_name":"Satoshi","full_name":"Naramoto, Satoshi"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:50:02Z","date_updated":"2021-01-12T06:48:08Z","volume":2,"article_number":"16018","file_date_updated":"2018-12-12T10:13:33Z","ec_funded":1,"publist_id":"6299","publication":"Cell Discovery","citation":{"ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018.","apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., & Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. Nature Publishing Group. https://doi.org/10.1038/celldisc.2016.18","ieee":"Ł. Łangowski et al., “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” Cell Discovery, vol. 2. Nature Publishing Group, 2016.","ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2016;2. doi:10.1038/celldisc.2016.18","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” Cell Discovery. Nature Publishing Group, 2016. https://doi.org/10.1038/celldisc.2016.18.","mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” Cell Discovery, vol. 2, 16018, Nature Publishing Group, 2016, doi:10.1038/celldisc.2016.18.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016)."},"date_published":"2016-07-19T00:00:00Z","scopus_import":1,"day":"19","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1081","title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","ddc":["580"],"status":"public","intvolume":" 2","pubrep_id":"757","file":[{"access_level":"open_access","file_name":"IST-2017-757-v1+1_celldisc201618.pdf","file_size":5261671,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5017","date_updated":"2018-12-12T10:13:33Z","date_created":"2018-12-12T10:13:33Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.","lang":"eng"}]},{"scopus_import":1,"day":"07","has_accepted_license":"1","publication":"Molecular Plant","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.","short":"T. Nodzyński, S. Vanneste, M. Zwiewka, M. Pernisová, J. Hejátko, J. Friml, Molecular Plant 9 (2016) 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.","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","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.","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"},"page":"1504 - 1519","date_published":"2016-11-07T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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"}],"issue":"11","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1145","status":"public","ddc":["581"],"title":"Enquiry into the topology of plasma membrane localized PIN auxin transport components","intvolume":" 9","pubrep_id":"746","file":[{"date_updated":"2018-12-12T10:13:22Z","date_created":"2018-12-12T10:13:22Z","relation":"main_file","file_id":"5004","content_type":"application/pdf","file_size":5005876,"creator":"system","access_level":"open_access","file_name":"IST-2017-746-v1+1_1-s2.0-S1674205216301915-main.pdf"}],"oa_version":"Published Version","month":"11","oa":1,"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.molp.2016.08.010","language":[{"iso":"eng"}],"file_date_updated":"2018-12-12T10:13:22Z","publist_id":"6213","ec_funded":1,"year":"2016","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.","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Cell Press","author":[{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"last_name":"Pernisová","first_name":"Markéta","full_name":"Pernisová, Markéta"},{"last_name":"Hejátko","first_name":"Jan","full_name":"Hejátko, Jan"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"date_updated":"2021-01-12T06:48:37Z","date_created":"2018-12-11T11:50:23Z","volume":9},{"scopus_import":1,"has_accepted_license":"1","day":"08","citation":{"ieee":"J. Balla et al., “Auxin flow mediated competition between axillary buds to restore apical dominance,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","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","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.","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","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.","short":"J. Balla, Z. Medved’Ová, P. Kalousek, N. Matiješčuková, J. Friml, V. Reinöhl, S. Procházka, Scientific Reports 6 (2016).","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."},"publication":"Scientific Reports","date_published":"2016-11-08T00:00:00Z","type":"journal_article","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"}],"_id":"1147","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","ddc":["581"],"title":"Auxin flow mediated competition between axillary buds to restore apical dominance","status":"public","pubrep_id":"745","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:09:28Z","date_updated":"2018-12-12T10:09:28Z","relation":"main_file","file_id":"4752","content_type":"application/pdf","file_size":1587544,"creator":"system","access_level":"open_access","file_name":"IST-2017-745-v1+1_srep35955.pdf"}],"month":"11","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1038/srep35955","language":[{"iso":"eng"}],"article_number":"35955","publist_id":"6211","file_date_updated":"2018-12-12T10:09:28Z","year":"2016","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).","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"full_name":"Balla, Jozef","last_name":"Balla","first_name":"Jozef"},{"full_name":"Medved'Ová, Zuzana","first_name":"Zuzana","last_name":"Medved'Ová"},{"full_name":"Kalousek, Petr","last_name":"Kalousek","first_name":"Petr"},{"first_name":"Natálie","last_name":"Matiješčuková","full_name":"Matiješčuková, Natálie"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reinöhl, Vilém","last_name":"Reinöhl","first_name":"Vilém"},{"full_name":"Procházka, Stanislav","last_name":"Procházka","first_name":"Stanislav"}],"volume":6,"date_updated":"2021-01-12T06:48:38Z","date_created":"2018-12-11T11:50:24Z"},{"date_updated":"2021-01-12T06:48:39Z","date_created":"2018-12-11T11:50:25Z","volume":30,"author":[{"first_name":"Sara","last_name":"Simonini","full_name":"Simonini, Sara"},{"full_name":"Deb, Joyita","first_name":"Joyita","last_name":"Deb"},{"full_name":"Moubayidin, Laila","first_name":"Laila","last_name":"Moubayidin"},{"first_name":"Pauline","last_name":"Stephenson","full_name":"Stephenson, Pauline"},{"first_name":"Manoj","last_name":"Valluru","full_name":"Valluru, Manoj"},{"full_name":"Freire Rios, Alejandra","first_name":"Alejandra","last_name":"Freire Rios"},{"full_name":"Sorefan, Karim","first_name":"Karim","last_name":"Sorefan"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"first_name":"Lars","last_name":"Östergaard","full_name":"Östergaard, Lars"}],"publication_status":"published","publisher":"Cold Spring Harbor Laboratory Press","department":[{"_id":"JiFr"}],"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. ","year":"2016","pmid":1,"file_date_updated":"2019-01-25T09:32:55Z","publist_id":"6207","language":[{"iso":"eng"}],"doi":"10.1101/gad.285361.116","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["27898393"]},"month":"10","file":[{"content_type":"application/pdf","file_size":1419263,"creator":"dernst","access_level":"open_access","file_name":"2016_GeneDev_Simonini.pdf","success":1,"date_created":"2019-01-25T09:32:55Z","date_updated":"2019-01-25T09:32:55Z","relation":"main_file","file_id":"5882"}],"oa_version":"Published Version","ddc":["570"],"title":"A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis","status":"public","intvolume":" 30","_id":"1151","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"issue":"20","type":"journal_article","date_published":"2016-10-15T00:00:00Z","page":"2286 - 2296","publication":"Genes and Development","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.","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.","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.","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.","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.","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"},"day":"15","has_accepted_license":"1","scopus_import":1},{"quality_controlled":"1","project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5134968/"}],"language":[{"iso":"eng"}],"doi":"10.1105/tpc.15.00569","month":"10","publication_status":"published","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","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).","year":"2016","date_created":"2018-12-11T11:50:26Z","date_updated":"2021-01-12T06:48:40Z","volume":28,"author":[{"full_name":"Žádníková, Petra","last_name":"Žádníková","first_name":"Petra"},{"first_name":"Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T"},{"full_name":"Abuzeineh, Anas","first_name":"Anas","last_name":"Abuzeineh"},{"first_name":"Marçal","last_name":"Gallemí","full_name":"Gallemí, Marçal"},{"last_name":"Van Der Straeten","first_name":"Dominique","full_name":"Van Der Straeten, Dominique"},{"full_name":"Smith, Richard","first_name":"Richard","last_name":"Smith"},{"last_name":"Inze","first_name":"Dirk","full_name":"Inze, Dirk"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"last_name":"Prusinkiewicz","first_name":"Przemysław","full_name":"Prusinkiewicz, Przemysław"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"publist_id":"6205","ec_funded":1,"page":"2464 - 2477","publication":"Plant Cell","citation":{"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","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.","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.","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","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.","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.","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."},"date_published":"2016-10-01T00:00:00Z","scopus_import":1,"day":"01","status":"public","title":"A model of differential growth guided apical hook formation in plants","intvolume":" 28","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1153","oa_version":"Submitted Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"10"},{"year":"2016","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","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Cell Press","author":[{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"},{"first_name":"Mohamad","last_name":"Abbas","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abbas, Mohamad"},{"full_name":"Han, Huibin","first_name":"Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Siyuan","last_name":"Song","full_name":"Song, Siyuan"},{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"}],"date_updated":"2021-01-12T06:49:08Z","date_created":"2018-12-11T11:50:44Z","volume":26,"file_date_updated":"2020-07-14T12:44:39Z","publist_id":"6138","ec_funded":1,"oa":1,"quality_controlled":"1","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"doi":"10.1016/j.cub.2016.08.067","language":[{"iso":"eng"}],"month":"11","_id":"1212","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity","ddc":["581"],"status":"public","intvolume":" 26","pubrep_id":"1008","file":[{"file_id":"4757","relation":"main_file","date_created":"2018-12-12T10:09:33Z","date_updated":"2020-07-14T12:44:39Z","checksum":"79ed2498185a027cf51a8f88100379e6","file_name":"IST-2018-1008-v1+1_Rakusova_CurrBiol_2016_proof.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":5391923}],"oa_version":"Submitted Version","type":"journal_article","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"}],"issue":"22","publication":"Current Biology","citation":{"short":"H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, J. Friml, Current Biology 26 (2016) 3026–3032.","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.","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.","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","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","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.","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."},"page":"3026 - 3032","date_published":"2016-11-21T00:00:00Z","scopus_import":1,"day":"21","has_accepted_license":"1"},{"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"}],"type":"journal_article","file":[{"checksum":"c9e50bb6096a7ba4a832969935820f19","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:15:33Z","relation":"main_file","file_id":"5154","content_type":"application/pdf","file_size":2990459,"creator":"system","access_level":"open_access","file_name":"IST-2016-711-v1+1_770cf1e0-612f-4e85-a500-54b6349fbbab_7654_-_jaroslav_michalko.pdf"}],"oa_version":"Published Version","pubrep_id":"711","intvolume":" 5","status":"public","title":"Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein","ddc":["581"],"_id":"1221","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"No","day":"20","scopus_import":"1","date_published":"2016-01-20T00:00:00Z","article_type":"original","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).","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.","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","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.","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","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."},"publication":"F1000 Research ","publist_id":"6113","ec_funded":1,"file_date_updated":"2020-07-14T12:44:39Z","article_number":"86","volume":5,"date_created":"2018-12-11T11:50:47Z","date_updated":"2022-03-24T09:12:49Z","author":[{"full_name":"Michalko, Jaroslav","id":"483727CA-F248-11E8-B48F-1D18A9856A87","last_name":"Michalko","first_name":"Jaroslav"},{"full_name":"Glanc, Matous","first_name":"Matous","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783"},{"last_name":"Perrot Rechenmann","first_name":"Catherine","full_name":"Perrot Rechenmann, Catherine"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"department":[{"_id":"JiFr"}],"publisher":"F1000 Research","publication_status":"published","year":"2016","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.","month":"01","language":[{"iso":"eng"}],"doi":"10.12688/f1000research.7654.1","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"date_updated":"2021-01-12T06:49:18Z","date_created":"2018-12-11T11:50:53Z","volume":6,"author":[{"last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","full_name":"Von Wangenheim, Daniel"},{"full_name":"Rosero, Amparo","last_name":"Rosero","first_name":"Amparo"},{"first_name":"George","last_name":"Komis","full_name":"Komis, George"},{"first_name":"Olga","last_name":"Šamajová","full_name":"Šamajová, Olga"},{"first_name":"Miroslav","last_name":"Ovečka","full_name":"Ovečka, Miroslav"},{"full_name":"Voigt, Boris","first_name":"Boris","last_name":"Voigt"},{"last_name":"Šamaj","first_name":"Jozef","full_name":"Šamaj, Jozef"}],"publication_status":"published","publisher":"Frontiers Research Foundation","department":[{"_id":"JiFr"}],"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.","year":"2016","file_date_updated":"2020-07-14T12:44:41Z","publist_id":"6094","article_number":"1262","language":[{"iso":"eng"}],"doi":"10.3389/fpls.2015.01262","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"01","file":[{"checksum":"3127eab844d53564bf47e2b6b42f1ca0","date_created":"2018-12-12T10:09:36Z","date_updated":"2020-07-14T12:44:41Z","file_id":"4760","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1640550,"access_level":"open_access","file_name":"IST-2016-710-v1+1_fpls-06-01262.pdf"}],"oa_version":"Published Version","pubrep_id":"710","title":"Endosomal interactions during root hair growth","status":"public","ddc":["581"],"intvolume":" 6","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1238","abstract":[{"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.","lang":"eng"}],"issue":"JAN2016","type":"journal_article","date_published":"2016-01-29T00:00:00Z","publication":"Frontiers in Plant Science","citation":{"ieee":"D. von Wangenheim et al., “Endosomal interactions during root hair growth,” Frontiers in Plant Science, vol. 6, no. JAN2016. Frontiers Research Foundation, 2016.","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","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.","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","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.","short":"D. von Wangenheim, A. Rosero, G. Komis, O. Šamajová, M. Ovečka, B. Voigt, J. Šamaj, Frontiers in Plant Science 6 (2016).","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."},"day":"29","has_accepted_license":"1","scopus_import":1},{"status":"public","title":"ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling","intvolume":" 113","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1247","oa_version":"Submitted Version","type":"journal_article","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"}],"issue":"10","page":"2768 - 2773","publication":"PNAS","citation":{"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.","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.","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.","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.","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","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.","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"},"date_published":"2016-03-08T00:00:00Z","scopus_import":1,"day":"08","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"year":"2016","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.","date_created":"2018-12-11T11:50:56Z","date_updated":"2021-01-12T06:49:22Z","volume":113,"author":[{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"last_name":"Neyt","first_name":"Pia","full_name":"Neyt, Pia"},{"full_name":"De Groeve, Steven","first_name":"Steven","last_name":"De Groeve"},{"last_name":"Aesaert","first_name":"Stijn","full_name":"Aesaert, Stijn"},{"full_name":"Coussens, Griet","last_name":"Coussens","first_name":"Griet"},{"last_name":"Rolčík","first_name":"Jakub","full_name":"Rolčík, Jakub"},{"first_name":"Leonardo","last_name":"Bruno","full_name":"Bruno, Leonardo"},{"full_name":"De Winne, Nancy","last_name":"De Winne","first_name":"Nancy"},{"first_name":"Annemie","last_name":"Van Minnebruggen","full_name":"Van Minnebruggen, Annemie"},{"full_name":"Van Montagu, Marc","first_name":"Marc","last_name":"Van Montagu"},{"last_name":"Ponce","first_name":"Maria","full_name":"Ponce, Maria"},{"full_name":"Micol, José","last_name":"Micol","first_name":"José"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"first_name":"Geert","last_name":"De Jaeger","full_name":"De Jaeger, Geert"},{"full_name":"Van Lijsebettens, Mieke","first_name":"Mieke","last_name":"Van Lijsebettens"}],"ec_funded":1,"publist_id":"6081","quality_controlled":"1","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791031/"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1501343112","month":"03"},{"day":"01","scopus_import":1,"date_published":"2016-04-01T00:00:00Z","page":"930 - 948","publication":"Plant Cell","citation":{"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.","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.","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","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.","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."},"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"}],"issue":"4","type":"journal_article","oa_version":"Submitted Version","title":"TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics","status":"public","intvolume":" 28","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1251","month":"04","language":[{"iso":"eng"}],"doi":"10.1105/tpc.15.00726","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863381/","open_access":"1"}],"publist_id":"6078","date_updated":"2021-01-12T06:49:24Z","date_created":"2018-12-11T11:50:57Z","volume":28,"author":[{"last_name":"Zhu","first_name":"Jinsheng","full_name":"Zhu, Jinsheng"},{"full_name":"Bailly, Aurélien","last_name":"Bailly","first_name":"Aurélien"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"full_name":"Sovero, Valpuri","last_name":"Sovero","first_name":"Valpuri"},{"first_name":"Martin","last_name":"Di Donato","full_name":"Di Donato, Martin"},{"last_name":"Ge","first_name":"Pei","full_name":"Ge, Pei"},{"full_name":"Oehri, Jacqueline","first_name":"Jacqueline","last_name":"Oehri"},{"last_name":"Aryal","first_name":"Bibek","full_name":"Aryal, Bibek"},{"last_name":"Hao","first_name":"Pengchao","full_name":"Hao, Pengchao"},{"full_name":"Linnert, Miriam","last_name":"Linnert","first_name":"Miriam"},{"full_name":"Burgardt, Noelia","first_name":"Noelia","last_name":"Burgardt"},{"full_name":"Lücke, Christian","last_name":"Lücke","first_name":"Christian"},{"full_name":"Weiwad, Matthias","last_name":"Weiwad","first_name":"Matthias"},{"last_name":"Michel","first_name":"Max","full_name":"Michel, Max"},{"first_name":"Oliver","last_name":"Weiergräber","full_name":"Weiergräber, Oliver"},{"first_name":"Stephan","last_name":"Pollmann","full_name":"Pollmann, Stephan"},{"last_name":"Azzarello","first_name":"Elisa","full_name":"Azzarello, Elisa"},{"full_name":"Mancuso, Stefano","first_name":"Stefano","last_name":"Mancuso"},{"full_name":"Ferro, Noel","first_name":"Noel","last_name":"Ferro"},{"full_name":"Fukao, Yoichiro","first_name":"Yoichiro","last_name":"Fukao"},{"first_name":"Céline","last_name":"Hoffmann","full_name":"Hoffmann, Céline"},{"first_name":"Roland","last_name":"Wedlich Söldner","full_name":"Wedlich Söldner, Roland"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Thomas, Clément","first_name":"Clément","last_name":"Thomas"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","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.). ","year":"2016"},{"issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1264","intvolume":" 171","title":"Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier","status":"public","day":"01","scopus_import":1,"date_published":"2016-07-01T00:00:00Z","citation":{"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.","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.","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.","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","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.","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","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."},"publication":"Plant Physiology","page":"1965 - 1982","publist_id":"6059","ec_funded":1,"author":[{"first_name":"Gloria","last_name":"Sancho Andrés","full_name":"Sancho Andrés, Gloria"},{"full_name":"Soriano Ortega, Esther","last_name":"Soriano Ortega","first_name":"Esther"},{"full_name":"Gao, Caiji","last_name":"Gao","first_name":"Caiji"},{"first_name":"Joan","last_name":"Bernabé Orts","full_name":"Bernabé Orts, Joan"},{"full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","last_name":"Narasimhan"},{"first_name":"Anna","last_name":"Müller","id":"420AB15A-F248-11E8-B48F-1D18A9856A87","full_name":"Müller, Anna"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"full_name":"Jiang, Liwen","first_name":"Liwen","last_name":"Jiang"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"first_name":"Fernando","last_name":"Aniento","full_name":"Aniento, Fernando"},{"last_name":"Marcote","first_name":"Maria","full_name":"Marcote, Maria"}],"volume":171,"date_created":"2018-12-11T11:51:01Z","date_updated":"2021-01-12T06:49:29Z","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.","year":"2016","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"American Society of Plant Biologists","publication_status":"published","month":"07","doi":"10.1104/pp.16.00373","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936568/","open_access":"1"}],"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1"}]