[{"department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:49:34Z","status":"public","type":"journal_article","_id":"1277","issue":"39","volume":113,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 113","month":"09","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047203/","open_access":"1"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components.\r\n"}],"title":"Danger-associated peptide signaling in Arabidopsis requires clathrin","author":[{"first_name":"Fausto","full_name":"Ortiz Morea, Fausto","last_name":"Ortiz Morea"},{"last_name":"Savatin","full_name":"Savatin, Daniel","first_name":"Daniel"},{"full_name":"Dejonghe, Wim","last_name":"Dejonghe","first_name":"Wim"},{"full_name":"Kumar, Rahul","last_name":"Kumar","first_name":"Rahul"},{"full_name":"Luo, Yu","last_name":"Luo","first_name":"Yu"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"first_name":"Jos","full_name":"Van Begin, Jos","last_name":"Van Begin"},{"last_name":"Dressano","full_name":"Dressano, Keini","first_name":"Keini"},{"full_name":"De Oliveira, Guilherme","last_name":"De Oliveira","first_name":"Guilherme"},{"first_name":"Xiuyang","full_name":"Zhao, Xiuyang","last_name":"Zhao"},{"full_name":"Lu, Qing","last_name":"Lu","first_name":"Qing"},{"full_name":"Madder, Annemieke","last_name":"Madder","first_name":"Annemieke"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"De Moura","full_name":"De Moura, Daniel","first_name":"Daniel"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"}],"publist_id":"6039","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ortiz Morea F, Savatin D, Dejonghe W, Kumar R, Luo Y, Adamowski M, Van Begin J, Dressano K, De Oliveira G, Zhao X, Lu Q, Madder A, Friml J, De Moura D, Russinova E. 2016. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 113(39), 11028–11033.","chicago":"Ortiz Morea, Fausto, Daniel Savatin, Wim Dejonghe, Rahul Kumar, Yu Luo, Maciek Adamowski, Jos Van Begin, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1605588113.","apa":"Ortiz Morea, F., Savatin, D., Dejonghe, W., Kumar, R., Luo, Y., Adamowski, M., … Russinova, E. (2016). Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1605588113","ama":"Ortiz Morea F, Savatin D, Dejonghe W, et al. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 2016;113(39):11028-11033. doi:10.1073/pnas.1605588113","short":"F. Ortiz Morea, D. Savatin, W. Dejonghe, R. Kumar, Y. Luo, M. Adamowski, J. Van Begin, K. Dressano, G. De Oliveira, X. Zhao, Q. Lu, A. Madder, J. Friml, D. De Moura, E. Russinova, PNAS 113 (2016) 11028–11033.","ieee":"F. Ortiz Morea et al., “Danger-associated peptide signaling in Arabidopsis requires clathrin,” PNAS, vol. 113, no. 39. National Academy of Sciences, pp. 11028–11033, 2016.","mla":"Ortiz Morea, Fausto, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS, vol. 113, no. 39, National Academy of Sciences, 2016, pp. 11028–33, doi:10.1073/pnas.1605588113."},"date_created":"2018-12-11T11:51:06Z","doi":"10.1073/pnas.1605588113","date_published":"2016-09-27T00:00:00Z","page":"11028 - 11033","publication":"PNAS","day":"27","year":"2016","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","acknowledgement":"F.A.O.-M. was supported by special\r\nresearch funding from the Flemish Government for a joint doctorate fellowship\r\nat Ghent University, and funding from the Student Program\r\n–\r\nGraduate Studies\r\nPlan Program from the Coordination for the Improvement of Higher Educa-\r\ntion Personnel, Brazil, for a doctorate fellowship at the University of São Paulo.\r\nX.Z. and Q.L. are indebted to the China Science Council and G.P.d.O. to the\r\n“\r\nCiência sem Fronteiras\r\n”\r\nfor predoctoral fellowships. R.K. and Y.L. have re-\r\nceived postdoctoral fellowships from the Belgian Science Policy Office. This\r\nresearch was supported by Flanders Research Foundation Grant G008416N\r\n(to E.R.) and by the São Paulo Research Foundation and the National Council\r\nfor Scientific and Technological Development (CNPq) (D.S.d.M.). D.S.d.M. is a\r\nresearch fellow of CNPq.\r\nWe thank D. Van Damme, E. Mylle, M. Castro Silva-Filho,\r\nand J. Goeman for providing usefu\r\nl advice and technical assistance;\r\nI. Hara-Nishimura, J. Lin, G. Jürgens, M. A. Johnson, and P. Bozhkov for sharing\r\npublished materials; and M. Nowack and M. Fendrych for kindly donating the\r\npUBQ10::ATG8-YFP\r\n-expressing marker line."},{"pubrep_id":"654","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1344","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:45Z","ddc":["581"],"date_updated":"2021-01-12T06:50:01Z","intvolume":" 5","month":"09","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms.","lang":"eng"}],"ec_funded":1,"volume":5,"language":[{"iso":"eng"}],"file":[{"checksum":"9209541fbba00f24daad21a5d568540d","file_id":"4748","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:09:24Z","file_name":"IST-2016-693-v1+1_e19048-download.pdf","creator":"system","date_updated":"2020-07-14T12:44:45Z","file_size":5666343}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"e19048","title":"TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls","publist_id":"5908","author":[{"last_name":"Fendrych","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"last_name":"Leung","full_name":"Leung, Jeffrey","first_name":"Jeffrey"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fendrych, Matyas, et al. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife, vol. 5, e19048, eLife Sciences Publications, 2016, doi:10.7554/eLife.19048.","apa":"Fendrych, M., Leung, J., & Friml, J. (2016). TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.19048","ama":"Fendrych M, Leung J, Friml J. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 2016;5. doi:10.7554/eLife.19048","ieee":"M. Fendrych, J. Leung, and J. Friml, “TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls,” eLife, vol. 5. eLife Sciences Publications, 2016.","short":"M. Fendrych, J. Leung, J. Friml, ELife 5 (2016).","chicago":"Fendrych, Matyas, Jeffrey Leung, and Jiří Friml. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.19048.","ista":"Fendrych M, Leung J, Friml J. 2016. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 5, e19048."},"oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","acknowledgement":"The authors express their gratitude to Veronika Bierbaum, Robert Hauschild for help with MATLAB,\r\nDaniel von Wangenheim for the gravitropism assay. We are thankful to Bill Gray, Mark Estelle,\r\nMichael Prigge, Ottoline Leyser, Claudia Oecking for sharing the seeds with us. We thank Katelyn\r\nSageman-Furnas and the members of the Friml lab for critical reading of the manuscript. The\r\nresearch leading to these results has received funding from the People Programme (Marie Curie\r\nActions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant\r\nagreement n° 291734. This work was also supported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP).","date_created":"2018-12-11T11:51:29Z","date_published":"2016-09-14T00:00:00Z","doi":"10.7554/eLife.19048","publication":"eLife","day":"14","year":"2016","has_accepted_license":"1"},{"date_created":"2018-12-11T11:51:30Z","doi":"10.1038/nplants.2016.102","date_published":"2016-07-01T00:00:00Z","year":"2016","has_accepted_license":"1","publication":"Nature Plants","day":"01","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","publist_id":"5907","author":[{"full_name":"Molnar, Gergely","last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"title":"Plasma membrane: Negative attraction","citation":{"ieee":"G. Molnar, M. Fendrych, and J. Friml, “Plasma membrane: Negative attraction,” Nature Plants, vol. 2. Nature Publishing Group, 2016.","short":"G. Molnar, M. Fendrych, J. Friml, Nature Plants 2 (2016).","ama":"Molnar G, Fendrych M, Friml J. Plasma membrane: Negative attraction. Nature Plants. 2016;2. doi:10.1038/nplants.2016.102","apa":"Molnar, G., Fendrych, M., & Friml, J. (2016). Plasma membrane: Negative attraction. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2016.102","mla":"Molnar, Gergely, et al. “Plasma Membrane: Negative Attraction.” Nature Plants, vol. 2, 16102, Nature Publishing Group, 2016, doi:10.1038/nplants.2016.102.","ista":"Molnar G, Fendrych M, Friml J. 2016. Plasma membrane: Negative attraction. Nature Plants. 2, 16102.","chicago":"Molnar, Gergely, Matyas Fendrych, and Jiří Friml. “Plasma Membrane: Negative Attraction.” Nature Plants. Nature Publishing Group, 2016. https://doi.org/10.1038/nplants.2016.102."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"16102","volume":2,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"9ba65f558563b287f875f48fa9f30fb2","file_id":"4954","creator":"system","file_size":127781,"date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2018-1007-v1+1_Molnar_NatPlants_2016.pdf","date_created":"2018-12-12T10:12:36Z"},{"file_name":"IST-2018-1007-v1+2_Molnar_NatPlants_2016_editor_statement.pdf","date_created":"2018-12-12T10:12:37Z","file_size":430556,"date_updated":"2020-07-14T12:44:45Z","creator":"system","file_id":"4955","checksum":"550d252be808d8ca2b43e83dddb4212f","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"scopus_import":1,"intvolume":" 2","month":"07","abstract":[{"lang":"eng","text":"The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:44:45Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:50:02Z","ddc":["581"],"type":"journal_article","pubrep_id":"1007","status":"public","_id":"1345"},{"scopus_import":1,"intvolume":" 212","month":"10","abstract":[{"lang":"eng","text":"Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism."}],"oa_version":"Submitted Version","issue":"2","volume":212,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5108","checksum":"27fd841ceaf0403559d7048ef51500f9","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf","date_created":"2018-12-12T10:14:53Z","creator":"system","file_size":972763,"date_updated":"2020-07-14T12:44:47Z"}],"type":"journal_article","pubrep_id":"1006","status":"public","_id":"1372","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:47Z","date_updated":"2021-01-12T06:50:13Z","ddc":["581"],"oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","acknowledgement":"Funded by Ministry of Education, Youth and Sports Czech Republic. Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council. Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P","page":"497 - 509","date_created":"2018-12-11T11:51:38Z","doi":"10.1111/nph.14049","date_published":"2016-10-01T00:00:00Z","year":"2016","has_accepted_license":"1","publication":"New Phytologist","day":"01","author":[{"first_name":"Markéta","last_name":"Pernisová","full_name":"Pernisová, Markéta"},{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Prat","full_name":"Prat, Tomas"},{"first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","full_name":"Grones, Peter"},{"first_name":"Danka","full_name":"Haruštiaková, Danka","last_name":"Haruštiaková"},{"first_name":"Martina","full_name":"Matonohova, Martina","last_name":"Matonohova"},{"full_name":"Spíchal, Lukáš","last_name":"Spíchal","first_name":"Lukáš"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Jan","full_name":"Hejátko, Jan","last_name":"Hejátko"}],"publist_id":"5839","title":"Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis","citation":{"ista":"Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 212(2), 497–509.","chicago":"Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14049.","short":"M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal, T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509.","ieee":"M. Pernisová et al., “Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis,” New Phytologist, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016.","apa":"Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal, L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14049","ama":"Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 2016;212(2):497-509. doi:10.1111/nph.14049","mla":"Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:10.1111/nph.14049."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"JiFr"}],"ddc":["581"],"date_updated":"2021-01-12T06:50:33Z","status":"public","pubrep_id":"1005","type":"journal_article","_id":"1410","volume":250,"file":[{"date_updated":"2020-07-14T12:44:53Z","file_size":4338545,"creator":"dernst","date_created":"2019-04-17T07:41:57Z","file_name":"2016_PlantScience_Ugalde.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6331","checksum":"ca08de036e6ddc81e6f760e0ccdebd3f"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 250","scopus_import":1,"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis."}],"title":"Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development","publist_id":"5797","author":[{"first_name":"José","last_name":"Ugalde","full_name":"Ugalde, José"},{"first_name":"Cecilia","last_name":"Rodríguez Furlán","full_name":"Rodríguez Furlán, Cecilia"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"last_name":"Norambuena","full_name":"Norambuena, Lorena","first_name":"Lorena"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"León, Gabriel","last_name":"León","first_name":"Gabriel"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"}],"external_id":{"pmid":["27457979"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ugalde J, Rodríguez Furlán C, De Rycke R, Norambuena L, Friml J, León G, Tejos R. 2016. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 250, 10–19.","chicago":"Ugalde, José, Cecilia Rodríguez Furlán, Riet De Rycke, Lorena Norambuena, Jiří Friml, Gabriel León, and Ricardo Tejos. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science. Elsevier, 2016. https://doi.org/10.1016/j.plantsci.2016.05.014.","short":"J. Ugalde, C. Rodríguez Furlán, R. De Rycke, L. Norambuena, J. Friml, G. León, R. Tejos, Plant Science 250 (2016) 10–19.","ieee":"J. Ugalde et al., “Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development,” Plant Science, vol. 250. Elsevier, pp. 10–19, 2016.","apa":"Ugalde, J., Rodríguez Furlán, C., De Rycke, R., Norambuena, L., Friml, J., León, G., & Tejos, R. (2016). Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2016.05.014","ama":"Ugalde J, Rodríguez Furlán C, De Rycke R, et al. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 2016;250:10-19. doi:10.1016/j.plantsci.2016.05.014","mla":"Ugalde, José, et al. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science, vol. 250, Elsevier, 2016, pp. 10–19, doi:10.1016/j.plantsci.2016.05.014."},"doi":"10.1016/j.plantsci.2016.05.014","date_published":"2016-09-01T00:00:00Z","date_created":"2018-12-11T11:51:51Z","page":"10 - 19","day":"01","publication":"Plant Science","has_accepted_license":"1","year":"2016","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"the Odysseus Program of the Research Foundation-Flanders [G091608] to JF."},{"scopus_import":1,"month":"07","intvolume":" 211","abstract":[{"lang":"eng","text":"Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport."}],"oa_version":"Submitted Version","issue":"1","volume":211,"publication_status":"published","file":[{"file_size":3828383,"date_updated":"2020-07-14T12:44:53Z","creator":"system","file_name":"IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf","date_created":"2018-12-12T10:13:32Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"23522ced3508ffe7a4f247c4230e6493","file_id":"5016"}],"language":[{"iso":"eng"}],"type":"journal_article","status":"public","pubrep_id":"1004","_id":"1417","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:50:36Z","ddc":["581"],"quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, project CEITEC (CZ.1.05/1.1.00/02.0068) and the Czech Science Foundation GACR (project no. 13-4063 7S to J.F.)","page":"65 - 74","doi":"10.1111/nph.14019","date_published":"2016-07-01T00:00:00Z","date_created":"2018-12-11T11:51:54Z","has_accepted_license":"1","year":"2016","day":"01","publication":"New Phytologist","author":[{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon"},{"last_name":"Skůpa","full_name":"Skůpa, Petr","first_name":"Petr"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"first_name":"Ricardo","full_name":"Tejos, Ricardo","last_name":"Tejos"},{"first_name":"Petr","full_name":"Klíma, Petr","last_name":"Klíma"},{"first_name":"Mária","last_name":"Čarná","full_name":"Čarná, Mária"},{"last_name":"Rolčík","full_name":"Rolčík, Jakub","first_name":"Jakub"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"last_name":"Moreno","full_name":"Moreno, Ignacio","first_name":"Ignacio"},{"first_name":"Petre","full_name":"Dobrev, Petre","last_name":"Dobrev"},{"first_name":"Ariel","full_name":"Orellana, Ariel","last_name":"Orellana"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"publist_id":"5790","title":"PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis","citation":{"chicago":"Simon, Sibu, Petr Skůpa, Tom Viaene, Marta Zwiewka, Ricardo Tejos, Petr Klíma, Mária Čarná, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14019.","ista":"Simon S, Skůpa P, Viaene T, Zwiewka M, Tejos R, Klíma P, Čarná M, Rolčík J, De Rycke R, Moreno I, Dobrev P, Orellana A, Zažímalová E, Friml J. 2016. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 211(1), 65–74.","mla":"Simon, Sibu, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist, vol. 211, no. 1, Wiley-Blackwell, 2016, pp. 65–74, doi:10.1111/nph.14019.","apa":"Simon, S., Skůpa, P., Viaene, T., Zwiewka, M., Tejos, R., Klíma, P., … Friml, J. (2016). PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14019","ama":"Simon S, Skůpa P, Viaene T, et al. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 2016;211(1):65-74. doi:10.1111/nph.14019","short":"S. Simon, P. Skůpa, T. Viaene, M. Zwiewka, R. Tejos, P. Klíma, M. Čarná, J. Rolčík, R. De Rycke, I. Moreno, P. Dobrev, A. Orellana, E. Zažímalová, J. Friml, New Phytologist 211 (2016) 65–74.","ieee":"S. Simon et al., “PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis,” New Phytologist, vol. 211, no. 1. Wiley-Blackwell, pp. 65–74, 2016."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"text":"Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 11","month":"02","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":4297148,"date_updated":"2020-07-14T12:44:57Z","creator":"system","file_name":"IST-2016-521-v1+1_journal.pone.0147830.PDF","date_created":"2018-12-12T10:14:16Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5066","checksum":"6066146e527335030f83aa5924ab72a6"}],"issue":"2","volume":11,"_id":"1482","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"521","status":"public","date_updated":"2021-01-12T06:51:03Z","ddc":["570"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:57Z","acknowledgement":"We thank J. Traas, B. Müller and V. Reddy for providing seed materials and Y. Deb for advice regarding the laser ablation experiments. We specially thank Thomas Laux for stimulating discussions and support in the initial phase of this project.","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","year":"2016","has_accepted_license":"1","publication":"PLoS One","day":"01","date_created":"2018-12-11T11:52:17Z","date_published":"2016-02-01T00:00:00Z","doi":"10.1371/journal.pone.0147830","article_number":"e0147830","citation":{"mla":"Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:10.1371/journal.pone.0147830.","ieee":"M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization,” PLoS One, vol. 11, no. 2. Public Library of Science, 2016.","short":"M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016).","ama":"Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 2016;11(2). doi:10.1371/journal.pone.0147830","apa":"Adibi, M., Yoshida, S., Weijers, D., & Fleck, C. (2016). Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0147830","chicago":"Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0147830.","ista":"Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 11(2), e0147830."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Adibi","full_name":"Adibi, Milad","first_name":"Milad"},{"first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko","last_name":"Yoshida"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"last_name":"Fleck","full_name":"Fleck, Christian","first_name":"Christian"}],"publist_id":"5711","title":"Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization"},{"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"b229e5bb4676ec3e27b7b9ea603b3a63","file_id":"5155","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:15:34Z","file_name":"IST-2018-1002-v1+1_Chen_TICB_2016_proofs.pdf","creator":"system","date_updated":"2020-07-14T12:44:57Z","file_size":2329117}],"issue":"6","volume":26,"oa_version":"Submitted Version","scopus_import":1,"intvolume":" 26","month":"06","date_updated":"2021-01-12T06:51:04Z","ddc":["581"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:57Z","_id":"1484","article_type":"review","type":"journal_article","pubrep_id":"1002","status":"public","year":"2016","has_accepted_license":"1","publication":"Trends in Cell Biology","day":"01","page":"409 - 419","date_created":"2018-12-11T11:52:17Z","doi":"10.1016/j.tcb.2016.02.003","date_published":"2016-06-01T00:00:00Z","acknowledgement":"We thank Maciek Adamowski for helpful discussions and Qiang Zhu and Israel Ausin for critical reading of the manuscript. We sincerely apologize to colleagues whose work we could not include owing to space limitations.","oa":1,"publisher":"Cell Press","quality_controlled":"1","citation":{"chicago":"Chen, Xu, Shuang Wu, Zengyu Liu, and Jiří Friml. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology. Cell Press, 2016. https://doi.org/10.1016/j.tcb.2016.02.003.","ista":"Chen X, Wu S, Liu Z, Friml J. 2016. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 26(6), 409–419.","mla":"Chen, Xu, et al. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology, vol. 26, no. 6, Cell Press, 2016, pp. 409–19, doi:10.1016/j.tcb.2016.02.003.","ama":"Chen X, Wu S, Liu Z, Friml J. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 2016;26(6):409-419. doi:10.1016/j.tcb.2016.02.003","apa":"Chen, X., Wu, S., Liu, Z., & Friml, J. (2016). Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2016.02.003","short":"X. Chen, S. Wu, Z. Liu, J. Friml, Trends in Cell Biology 26 (2016) 409–419.","ieee":"X. Chen, S. Wu, Z. Liu, and J. Friml, “Environmental and endogenous control of cortical microtubule orientation,” Trends in Cell Biology, vol. 26, no. 6. Cell Press, pp. 409–419, 2016."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chen","full_name":"Chen, Xu","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wu, Shuang","last_name":"Wu","first_name":"Shuang"},{"first_name":"Zengyu","last_name":"Liu","full_name":"Liu, Zengyu"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ"}],"publist_id":"5704","title":"Environmental and endogenous control of cortical microtubule orientation"},{"oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to JF. ","page":"465 - 476","date_created":"2018-12-11T11:53:12Z","doi":"10.1007/s00344-015-9553-2","date_published":"2016-06-01T00:00:00Z","year":"2016","has_accepted_license":"1","publication":"Journal of Plant Growth Regulation","day":"01","publist_id":"5512","author":[{"last_name":"Zemová","full_name":"Zemová, Radka","first_name":"Radka"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"first_name":"Agnieszka","full_name":"Bielach, Agnieszka","last_name":"Bielach"},{"first_name":"Hélène","full_name":"Robert, Hélène","last_name":"Robert"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"title":"A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana","citation":{"ista":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. 2016. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 35(2), 465–476.","chicago":"Zemová, Radka, Marta Zwiewka, Agnieszka Bielach, Hélène Robert, and Jiří Friml. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation. Springer, 2016. https://doi.org/10.1007/s00344-015-9553-2.","ieee":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, and J. Friml, “A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana,” Journal of Plant Growth Regulation, vol. 35, no. 2. Springer, pp. 465–476, 2016.","short":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant Growth Regulation 35 (2016) 465–476.","apa":"Zemová, R., Zwiewka, M., Bielach, A., Robert, H., & Friml, J. (2016). A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. Springer. https://doi.org/10.1007/s00344-015-9553-2","ama":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 2016;35(2):465-476. doi:10.1007/s00344-015-9553-2","mla":"Zemová, Radka, et al. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation, vol. 35, no. 2, Springer, 2016, pp. 465–76, doi:10.1007/s00344-015-9553-2."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":" 35","month":"06","abstract":[{"text":"The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant growth and development including embryo and root patterning, lateral organ formation and growth responses to environmental stimuli. Auxin is directionally transported from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)] and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations are aligned with the direction of the auxin flow. Auxin itself regulates its own transport by modulation of the expression and subcellular localization of the auxin transporters. Increased auxin levels promote the transcription of PIN2 and AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged auxin exposure increases the turnover of PIN proteins and their degradation in the vacuole. In this study, we applied a forward genetic approach, to identify molecular components playing a role in the auxin-mediated degradation. We generated EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations and designed a screen for mutants with persistently strong fluorescent signals of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and established a role for auxin-mediated degradation in plant development.","lang":"eng"}],"oa_version":"Preprint","issue":"2","volume":35,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf","date_created":"2018-12-12T10:08:34Z","file_size":5637591,"date_updated":"2020-07-14T12:45:08Z","creator":"system","file_id":"4695","checksum":"0dc6a300cde6536ceedd2bcdd2060efb","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"type":"journal_article","pubrep_id":"1001","status":"public","_id":"1641","file_date_updated":"2020-07-14T12:45:08Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:52:11Z","ddc":["581"]},{"article_number":"11710","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Dejonghe, W., Kuenen, S., Mylle, E., Vasileva, M. K., Keech, O., Viotti, C., … Russinova, E. (2016). Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11710","ama":"Dejonghe W, Kuenen S, Mylle E, et al. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 2016;7. doi:10.1038/ncomms11710","ieee":"W. Dejonghe et al., “Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","short":"W. Dejonghe, S. Kuenen, E. Mylle, M.K. Vasileva, O. Keech, C. Viotti, J. Swerts, M. Fendrych, F. Ortiz Morea, K. Mishev, S. Delang, S. Scholl, X. Zarza, M. Heilmann, J. Kourelis, J. Kasprowicz, L. Nguyen, A. Drozdzecki, I. Van Houtte, A. Szatmári, M. Majda, G. Baisa, S. Bednarek, S. Robert, D. Audenaert, C. Testerink, T. Munnik, D. Van Damme, I. Heilmann, K. Schumacher, J. Winne, J. Friml, P. Verstreken, E. Russinova, Nature Communications 7 (2016).","mla":"Dejonghe, Wim, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” Nature Communications, vol. 7, 11710, Nature Publishing Group, 2016, doi:10.1038/ncomms11710.","ista":"Dejonghe W, Kuenen S, Mylle E, Vasileva MK, Keech O, Viotti C, Swerts J, Fendrych M, Ortiz Morea F, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis J, Kasprowicz J, Nguyen L, Drozdzecki A, Van Houtte I, Szatmári A, Majda M, Baisa G, Bednarek S, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. 2016. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 7, 11710.","chicago":"Dejonghe, Wim, Sabine Kuenen, Evelien Mylle, Mina K Vasileva, Olivier Keech, Corrado Viotti, Jef Swerts, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11710."},"title":"Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification","publist_id":"5906","author":[{"first_name":"Wim","last_name":"Dejonghe","full_name":"Dejonghe, Wim"},{"first_name":"Sabine","last_name":"Kuenen","full_name":"Kuenen, Sabine"},{"last_name":"Mylle","full_name":"Mylle, Evelien","first_name":"Evelien"},{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K","full_name":"Vasileva, Mina K","last_name":"Vasileva"},{"last_name":"Keech","full_name":"Keech, Olivier","first_name":"Olivier"},{"first_name":"Corrado","last_name":"Viotti","full_name":"Viotti, Corrado"},{"full_name":"Swerts, Jef","last_name":"Swerts","first_name":"Jef"},{"orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ortiz Morea, Fausto","last_name":"Ortiz Morea","first_name":"Fausto"},{"last_name":"Mishev","full_name":"Mishev, Kiril","first_name":"Kiril"},{"full_name":"Delang, Simon","last_name":"Delang","first_name":"Simon"},{"last_name":"Scholl","full_name":"Scholl, Stefan","first_name":"Stefan"},{"full_name":"Zarza, Xavier","last_name":"Zarza","first_name":"Xavier"},{"first_name":"Mareike","last_name":"Heilmann","full_name":"Heilmann, Mareike"},{"first_name":"Jiorgos","last_name":"Kourelis","full_name":"Kourelis, Jiorgos"},{"full_name":"Kasprowicz, Jaroslaw","last_name":"Kasprowicz","first_name":"Jaroslaw"},{"last_name":"Nguyen","full_name":"Nguyen, Le","first_name":"Le"},{"first_name":"Andrzej","full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki"},{"first_name":"Isabelle","full_name":"Van Houtte, Isabelle","last_name":"Van Houtte"},{"first_name":"Anna","last_name":"Szatmári","full_name":"Szatmári, Anna"},{"first_name":"Mateusz","last_name":"Majda","full_name":"Majda, Mateusz"},{"full_name":"Baisa, Gary","last_name":"Baisa","first_name":"Gary"},{"first_name":"Sebastian","full_name":"Bednarek, Sebastian","last_name":"Bednarek"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"first_name":"Dominique","last_name":"Audenaert","full_name":"Audenaert, Dominique"},{"first_name":"Christa","full_name":"Testerink, Christa","last_name":"Testerink"},{"first_name":"Teun","full_name":"Munnik, Teun","last_name":"Munnik"},{"first_name":"Daniël","last_name":"Van Damme","full_name":"Van Damme, Daniël"},{"full_name":"Heilmann, Ingo","last_name":"Heilmann","first_name":"Ingo"},{"first_name":"Karin","full_name":"Schumacher, Karin","last_name":"Schumacher"},{"first_name":"Johan","last_name":"Winne","full_name":"Winne, Johan"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Patrik","last_name":"Verstreken","full_name":"Verstreken, Patrik"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"}],"acknowledgement":"We thank Yvon Jaillais, Ikuko Hara-Nishimura, Akihiko Nakano, Takashi Ueda and Jinxing Lin for providing materials, Natasha Raikhel, Glenn Hicks, Steffen Vanneste, and Ricardo Tejos for useful suggestions, Patrick Callaerts for providing S2 Drosophila cell cultures, Michael Sixt for providing HeLa cells, Annick Bleys for literature searches, VIB Bio Imaging Core for help with imaging conditions and Martine De Cock for help in preparing the article. This work was supported by the Agency for Innovation by Science\r\nand Technology for a pre-doctoral fellowship to W.D.; the Research fund KU Leuven\r\n(GOA), a Methusalem grant of the Flemish government and VIB to S.K., J.K. and P.V.;\r\nby the Netherlands Organisation for Scientific Research (NWO) for ALW grants\r\n846.11.002 (C.T.) and 867.15.020 (T.M.); the European Research Council (project\r\nERC-2011-StG-20101109 PSDP) (to J.F.); a European Research Council (ERC) Starting\r\nGrant (grant 260678) (to P.V.), the Research Foundation-Flanders (grants G.0747.09,\r\nG094011 and G095511) (to P.V.), the Hercules Foundation, an Interuniversity Attraction\r\nPoles Poles Program, initiated by the Belgian State, Science Policy Office (to P.V.),\r\nthe Swedish VetenskapsRådet grant to O.K., the Ghent University ‘Bijzonder\r\nOnderzoek Fonds’ (BOF) for a predoctoral fellowship to F.A.O.-M., the Research\r\nFoundation-Flanders (FWO) to K.M. and E.R.","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"day":"08","publication":"Nature Communications","has_accepted_license":"1","year":"2016","date_published":"2016-06-08T00:00:00Z","doi":"10.1038/ncomms11710","date_created":"2018-12-11T11:51:30Z","_id":"1346","status":"public","pubrep_id":"653","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-09-07T12:54:35Z","file_date_updated":"2020-07-14T12:44:45Z","department":[{"_id":"JiFr"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane."}],"month":"06","intvolume":" 7","scopus_import":1,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e8dc81b3e44db5a7718d7f1501ce1aa7","file_id":"5369","date_updated":"2020-07-14T12:44:45Z","file_size":3532505,"creator":"system","date_created":"2018-12-12T10:18:47Z","file_name":"IST-2016-653-v1+1_ncomms11710_1_.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"id":"7172","status":"public","relation":"dissertation_contains"}]},"volume":7,"ec_funded":1},{"citation":{"mla":"Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling & Behavior, vol. 11, no. 6, e1191734, Taylor & Francis, 2016, doi:10.1080/15592324.2016.1191734.","short":"Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling & Behavior 11 (2016).","ieee":"Z. Liu et al., “The CLE gene family in Populus trichocarpa,” Plant Signaling & Behavior, vol. 11, no. 6. Taylor & Francis, 2016.","apa":"Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., & Wang, G. (2016). The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2016.1191734","ama":"Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. 2016;11(6). doi:10.1080/15592324.2016.1191734","chicago":"Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling & Behavior. Taylor & Francis, 2016. https://doi.org/10.1080/15592324.2016.1191734.","ista":"Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. 11(6), e1191734."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7308","author":[{"first_name":"Zhijun","last_name":"Liu","full_name":"Liu, Zhijun"},{"first_name":"Nan","last_name":"Yang","full_name":"Yang, Nan"},{"first_name":"Yanting","full_name":"Lv, Yanting","last_name":"Lv"},{"full_name":"Pan, Lixia","last_name":"Pan","first_name":"Lixia"},{"last_name":"Lv","full_name":"Lv, Shuo","first_name":"Shuo"},{"last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"full_name":"Wang, Guodong","last_name":"Wang","first_name":"Guodong"}],"article_processing_charge":"No","title":"The CLE gene family in Populus trichocarpa","article_number":"e1191734","year":"2016","day":"02","publication":"Plant Signaling & Behavior","doi":"10.1080/15592324.2016.1191734","date_published":"2016-06-02T00:00:00Z","date_created":"2018-12-11T11:46:53Z","acknowledgement":"We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading of the article. Work in our group is supported by the National Natural Science Foundation of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of Higher Education from the Ministry of Education of China (20120202120009), the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China (2014JM3064). ","publisher":"Taylor & Francis","quality_controlled":"1","oa":1,"date_updated":"2023-10-17T11:13:40Z","department":[{"_id":"JiFr"}],"_id":"510","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"issue":"6","volume":11,"abstract":[{"text":"The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. ","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/"}],"month":"06","intvolume":" 11"},{"has_accepted_license":"1","year":"2016","day":"21","publication":"Scientific Reports","date_published":"2016-09-21T00:00:00Z","doi":"10.1038/srep33754","date_created":"2018-12-11T11:51:05Z","acknowledgement":"We wish to thank Prof. Ewa U. Kurczyńska for initiation of this work and valuable advices. We thank Martine De Cock for help in preparing the manuscript. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), the European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637 S) to J.F., (GA 13-39982S) to E.B. and E.M. and in part by the European Regional Development Fund (project “CEITEC, Central European Institute of Technology”, CZ.1.05/1.1.00/02.0068).","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"citation":{"ista":"Mazur E, Benková E, Friml J. 2016. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 6, 33754.","chicago":"Mazur, Ewa, Eva Benková, and Jiří Friml. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33754.","ama":"Mazur E, Benková E, Friml J. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 2016;6. doi:10.1038/srep33754","apa":"Mazur, E., Benková, E., & Friml, J. (2016). Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep33754","short":"E. Mazur, E. Benková, J. Friml, Scientific Reports 6 (2016).","ieee":"E. Mazur, E. Benková, and J. Friml, “Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","mla":"Mazur, Ewa, et al. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific Reports, vol. 6, 33754, Nature Publishing Group, 2016, doi:10.1038/srep33754."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6042","author":[{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"external_id":{"pmid":["27649687"]},"article_processing_charge":"No","title":"Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis","article_number":"33754","publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:44:42Z","file_size":2895147,"date_created":"2018-12-12T10:13:25Z","file_name":"IST-2016-692-v1+1_srep33754.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"ee371fbc9124ad93157a95829264e4fe","file_id":"5008"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"545"}]},"volume":6,"abstract":[{"lang":"eng","text":"Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 6","date_updated":"2024-02-12T12:03:42Z","ddc":["581"],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:42Z","_id":"1274","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"692"},{"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants.","lang":"eng"}],"intvolume":" 1","month":"07","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","volume":1,"issue":"7","_id":"1383","status":"public","type":"journal_article","article_type":"original","date_updated":"2021-01-12T06:50:18Z","department":[{"_id":"JiFr"}],"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","publication":"Nature Plants","day":"06","year":"2015","date_created":"2018-12-11T11:51:42Z","doi":"10.1038/nplants.2015.94","date_published":"2015-07-06T00:00:00Z","article_number":"15094","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:10.1038/nplants.2015.94.","short":"L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015).","ieee":"L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing Group, 2015.","ama":"Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7). doi:10.1038/nplants.2015.94","apa":"Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94","chicago":"Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing Group, 2015. https://doi.org/10.1038/nplants.2015.94.","ista":"Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094."},"title":"V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis","article_processing_charge":"No","external_id":{"pmid":["27250258"]},"publist_id":"5827","author":[{"full_name":"Yu, Luo","last_name":"Yu","first_name":"Luo"},{"first_name":"Stefan","last_name":"Scholl","full_name":"Scholl, Stefan"},{"last_name":"Doering","full_name":"Doering, Anett","first_name":"Anett"},{"full_name":"Yi, Zhang","last_name":"Yi","first_name":"Zhang"},{"last_name":"Irani","full_name":"Irani, Niloufer","first_name":"Niloufer"},{"last_name":"Di Rubbo","full_name":"Di Rubbo, Simone","first_name":"Simone"},{"full_name":"Neumetzler, Lutz","last_name":"Neumetzler","first_name":"Lutz"},{"first_name":"Praveen","last_name":"Krishnamoorthy","full_name":"Krishnamoorthy, Praveen"},{"first_name":"Isabelle","last_name":"Van Houtte","full_name":"Van Houtte, Isabelle"},{"first_name":"Evelien","full_name":"Mylle, Evelien","last_name":"Mylle"},{"last_name":"Bischoff","full_name":"Bischoff, Volker","first_name":"Volker"},{"first_name":"Samantha","last_name":"Vernhettes","full_name":"Vernhettes, Samantha"},{"last_name":"Winne","full_name":"Winne, Johan","first_name":"Johan"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"full_name":"Stierhof, York","last_name":"Stierhof","first_name":"York"},{"first_name":"Karin","last_name":"Schumacher","full_name":"Schumacher, Karin"},{"full_name":"Persson, Staffan","last_name":"Persson","first_name":"Staffan"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"}]},{"title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","external_id":{"pmid":["32480670"]},"article_processing_charge":"No","publist_id":"5639","author":[{"last_name":"Yang","full_name":"Yang, Huaiyu","first_name":"Huaiyu"},{"first_name":"Jenny","full_name":"Von Der Fecht Bartenbach, Jenny","last_name":"Von Der Fecht Bartenbach"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Jan","last_name":"Lohmann","full_name":"Lohmann, Jan"},{"first_name":"Benjamin","last_name":"Neuhäuser","full_name":"Neuhäuser, Benjamin"},{"first_name":"Uwe","last_name":"Ludewig","full_name":"Ludewig, Uwe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.","chicago":"Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology. CSIRO, 2015. https://doi.org/10.1071/FP14171.","ieee":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” Functional Plant Biology, vol. 42, no. 3. CSIRO, pp. 239–251, 2015.","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","apa":"Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., & Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. CSIRO. https://doi.org/10.1071/FP14171","ama":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 2015;42(3):239-251. doi:10.1071/FP14171","mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” Functional Plant Biology, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:10.1071/FP14171."},"date_created":"2018-12-11T11:52:34Z","doi":"10.1071/FP14171","date_published":"2015-03-01T00:00:00Z","page":"239 - 251","publication":"Functional Plant Biology","day":"01","year":"2015","publisher":"CSIRO","quality_controlled":"1","department":[{"_id":"JiFr"}],"date_updated":"2022-05-24T09:02:24Z","status":"public","type":"journal_article","article_type":"original","_id":"1532","issue":"3","volume":42,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1445-4408"]},"intvolume":" 42","month":"03","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels.","lang":"eng"}]},{"abstract":[{"lang":"eng","text":"PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 6","month":"11","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5259","checksum":"3c06735fc7cd7e482ca830cbd26001bf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","date_created":"2018-12-12T10:17:07Z","file_size":1852268,"date_updated":"2020-07-14T12:45:01Z","creator":"system"}],"ec_funded":1,"volume":6,"_id":"1534","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"485","status":"public","date_updated":"2021-01-12T06:51:26Z","ddc":["570"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:01Z","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","year":"2015","has_accepted_license":"1","publication":"Nature Communications","day":"18","date_created":"2018-12-11T11:52:34Z","doi":"10.1038/ncomms9822","date_published":"2015-11-18T00:00:00Z","article_number":"8822","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications, vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822.","apa":"Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822","ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 2015;6. doi:10.1038/ncomms9822","ieee":"H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","short":"H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015).","chicago":"Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822.","ista":"Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Hongzhe","last_name":"Wang","full_name":"Wang, Hongzhe"},{"full_name":"Yang, Kezhen","last_name":"Yang","first_name":"Kezhen"},{"first_name":"Junjie","last_name":"Zou","full_name":"Zou, Junjie"},{"full_name":"Zhu, Lingling","last_name":"Zhu","first_name":"Lingling"},{"first_name":"Zidian","last_name":"Xie","full_name":"Xie, Zidian"},{"first_name":"Miyoterao","last_name":"Morita","full_name":"Morita, Miyoterao"},{"last_name":"Tasaka","full_name":"Tasaka, Masao","first_name":"Masao"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"first_name":"Erich","full_name":"Grotewold, Erich","last_name":"Grotewold"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Fred","last_name":"Sack","full_name":"Sack, Fred"},{"full_name":"Le, Jie","last_name":"Le","first_name":"Jie"}],"publist_id":"5637","title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism"},{"status":"public","type":"journal_article","_id":"1536","title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport","department":[{"_id":"JiFr"}],"author":[{"first_name":"Joëlle","last_name":"Sasse","full_name":"Sasse, Joëlle"},{"last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu"},{"last_name":"Gübeli","full_name":"Gübeli, Christian","first_name":"Christian"},{"first_name":"Guowei","last_name":"Liu","full_name":"Liu, Guowei"},{"last_name":"Cheng","full_name":"Cheng, Xi","first_name":"Xi"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"last_name":"Bouwmeester","full_name":"Bouwmeester, Harro","first_name":"Harro"},{"full_name":"Martinoia, Enrico","last_name":"Martinoia","first_name":"Enrico"},{"first_name":"Lorenzo","last_name":"Borghi","full_name":"Borghi, Lorenzo"}],"publist_id":"5635","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:27Z","citation":{"mla":"Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology, vol. 25, no. 5, Cell Press, 2015, pp. 647–55, doi:10.1016/j.cub.2015.01.015.","apa":"Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi, L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.01.015","ama":"Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 2015;25(5):647-655. doi:10.1016/j.cub.2015.01.015","short":"J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester, E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.","ieee":"J. Sasse et al., “Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport,” Current Biology, vol. 25, no. 5. Cell Press, pp. 647–655, 2015.","chicago":"Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” Current Biology. Cell Press, 2015. https://doi.org/10.1016/j.cub.2015.01.015.","ista":"Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 25(5), 647–655."},"intvolume":" 25","month":"02","quality_controlled":"1","scopus_import":1,"publisher":"Cell Press","acknowledgement":"This work was funded by a grant of the Swiss National Foundation to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands) for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel (University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel (University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for hints on protein quantification.","oa_version":"None","abstract":[{"text":"Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil.","lang":"eng"}],"date_created":"2018-12-11T11:52:35Z","doi":"10.1016/j.cub.2015.01.015","issue":"5","date_published":"2015-02-12T00:00:00Z","volume":25,"page":"647 - 655","language":[{"iso":"eng"}],"publication":"Current Biology","day":"12","publication_status":"published","year":"2015"},{"status":"public","type":"journal_article","_id":"1543","title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","department":[{"_id":"JiFr"}],"publist_id":"5628","author":[{"full_name":"Olvera Carrillo, Yadira","last_name":"Olvera Carrillo","first_name":"Yadira"},{"last_name":"Van Bel","full_name":"Van Bel, Michiel","first_name":"Michiel"},{"full_name":"Van Hautegem, Tom","last_name":"Van Hautegem","first_name":"Tom"},{"last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"last_name":"Huysmans","full_name":"Huysmans, Marlies","first_name":"Marlies"},{"first_name":"Mária","full_name":"Šimášková, Mária","last_name":"Šimášková"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"first_name":"Pierre","last_name":"Buscaill","full_name":"Buscaill, Pierre"},{"last_name":"Rivas","full_name":"Rivas, Susana","first_name":"Susana"},{"first_name":"Núria","full_name":"Coll, Núria","last_name":"Coll"},{"first_name":"Frederik","last_name":"Coppens","full_name":"Coppens, Frederik"},{"first_name":"Steven","last_name":"Maere","full_name":"Maere, Steven"},{"first_name":"Moritz","full_name":"Nowack, Moritz","last_name":"Nowack"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:30Z","citation":{"mla":"Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:10.1104/pp.15.00769.","ama":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 2015;169(4):2684-2699. doi:10.1104/pp.15.00769","apa":"Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.15.00769","ieee":"Y. Olvera Carrillo et al., “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” Plant Physiology, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015.","short":"Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699.","chicago":"Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” Plant Physiology. American Society of Plant Biologists, 2015. https://doi.org/10.1104/pp.15.00769.","ista":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699."},"intvolume":" 169","month":"12","scopus_import":1,"publisher":"American Society of Plant Biologists","oa_version":"None","abstract":[{"lang":"eng","text":"A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta."}],"date_created":"2018-12-11T11:52:38Z","volume":169,"doi":"10.1104/pp.15.00769","date_published":"2015-12-01T00:00:00Z","issue":"4","page":"2684 - 2699","publication":"Plant Physiology","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2015"},{"abstract":[{"text":"The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 66","month":"08","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:02Z","file_size":7753043,"date_created":"2018-12-12T10:14:02Z","file_name":"IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5051","checksum":"257919be0ce3d306185d3891ad7acf39"}],"issue":"15","volume":66,"_id":"1556","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"480","status":"public","date_updated":"2021-01-12T06:51:35Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"JiFr"}],"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","year":"2015","has_accepted_license":"1","publication":"Journal of Experimental Botany","day":"01","page":"4631 - 4642","date_created":"2018-12-11T11:52:42Z","doi":"10.1093/jxb/erv230","date_published":"2015-08-01T00:00:00Z","citation":{"chicago":"Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv230.","ista":"Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642.","mla":"Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230.","apa":"Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230","ama":"Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 2015;66(15):4631-4642. doi:10.1093/jxb/erv230","ieee":"Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” Journal of Experimental Botany, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015.","short":"Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5615","author":[{"first_name":"Yuebin","full_name":"Jia, Yuebin","last_name":"Jia"},{"last_name":"Tian","full_name":"Tian, Huiyu","first_name":"Huiyu"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang","orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang","last_name":"Li"},{"full_name":"Yu, Qianqian","last_name":"Yu","first_name":"Qianqian"},{"last_name":"Wang","full_name":"Wang, Lei","first_name":"Lei"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"}],"title":"The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development"},{"abstract":[{"lang":"eng","text":"CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation."}],"oa_version":"None","scopus_import":1,"quality_controlled":"1","publisher":"Company of Biologists","month":"02","intvolume":" 142","publication_status":"published","year":"2015","day":"15","publication":"Development","language":[{"iso":"eng"}],"page":"712 - 721","doi":"10.1242/dev.113225","date_published":"2015-02-15T00:00:00Z","issue":"4","volume":142,"date_created":"2018-12-11T11:52:42Z","_id":"1558","type":"journal_article","status":"public","date_updated":"2021-01-12T06:51:35Z","citation":{"ama":"Ivanchenko M, Zhu J, Wang B, et al. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 2015;142(4):712-721. doi:10.1242/dev.113225","apa":"Ivanchenko, M., Zhu, J., Wang, B., Medvecka, E., Du, Y., Azzarello, E., … Geisler, M. (2015). The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. Company of Biologists. https://doi.org/10.1242/dev.113225","ieee":"M. Ivanchenko et al., “The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation,” Development, vol. 142, no. 4. Company of Biologists, pp. 712–721, 2015.","short":"M. Ivanchenko, J. Zhu, B. Wang, E. Medvecka, Y. Du, E. Azzarello, S. Mancuso, M. Megraw, S. Filichkin, J. Dubrovsky, J. Friml, M. Geisler, Development 142 (2015) 712–721.","mla":"Ivanchenko, Maria, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 712–21, doi:10.1242/dev.113225.","ista":"Ivanchenko M, Zhu J, Wang B, Medvecka E, Du Y, Azzarello E, Mancuso S, Megraw M, Filichkin S, Dubrovsky J, Friml J, Geisler M. 2015. The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation. Development. 142(4), 712–721.","chicago":"Ivanchenko, Maria, Jinsheng Zhu, Bangjun Wang, Eva Medvecka, Yunlong Du, Elisa Azzarello, Stefano Mancuso, et al. “The Cyclophilin a DIAGEOTROPICA Gene Affects Auxin Transport in Both Root and Shoot to Control Lateral Root Formation.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.113225."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5613","author":[{"first_name":"Maria","full_name":"Ivanchenko, Maria","last_name":"Ivanchenko"},{"last_name":"Zhu","full_name":"Zhu, Jinsheng","first_name":"Jinsheng"},{"first_name":"Bangjun","last_name":"Wang","full_name":"Wang, Bangjun"},{"last_name":"Medvecka","full_name":"Medvecka, Eva","first_name":"Eva","id":"298814E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Du","full_name":"Du, Yunlong","first_name":"Yunlong"},{"last_name":"Azzarello","full_name":"Azzarello, Elisa","first_name":"Elisa"},{"last_name":"Mancuso","full_name":"Mancuso, Stefano","first_name":"Stefano"},{"last_name":"Megraw","full_name":"Megraw, Molly","first_name":"Molly"},{"full_name":"Filichkin, Sergei","last_name":"Filichkin","first_name":"Sergei"},{"first_name":"Joseph","full_name":"Dubrovsky, Joseph","last_name":"Dubrovsky"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"}],"title":"The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation","department":[{"_id":"JiFr"}]},{"publication_status":"published","language":[{"iso":"eng"}],"volume":12,"issue":"3","abstract":[{"lang":"eng","text":"The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species."}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/"}],"scopus_import":1,"intvolume":" 12","month":"02","date_updated":"2021-01-12T06:51:34Z","department":[{"_id":"JiFr"}],"_id":"1554","type":"journal_article","status":"public","year":"2015","publication":"Nature Methods","day":"26","page":"207 - 210","date_created":"2018-12-11T11:52:41Z","doi":"10.1038/nmeth.3279","date_published":"2015-02-26T00:00:00Z","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","citation":{"mla":"Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:10.1038/nmeth.3279.","ieee":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” Nature Methods, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015.","short":"C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210.","ama":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210. doi:10.1038/nmeth.3279","apa":"Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279","chicago":"Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279.","ista":"Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25643149"]},"author":[{"last_name":"Liao","full_name":"Liao, Cheyang","first_name":"Cheyang"},{"last_name":"Smet","full_name":"Smet, Wouter","first_name":"Wouter"},{"first_name":"Géraldine","full_name":"Brunoud, Géraldine","last_name":"Brunoud"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"}],"publist_id":"5617","title":"Reporters for sensitive and quantitative measurement of auxin response"}]