[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"url":"https://doi.org/10.1093/plcell/koad324","open_access":"1"}],"date_published":"2023-12-23T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"language":[{"iso":"eng"}],"keyword":["Cell Biology","Plant Science"],"publication":"The Plant Cell","has_accepted_license":"1","month":"12","article_number":"koad324","oa_version":"Published Version","extern":"1","ddc":["580"],"date_updated":"2024-01-03T12:43:41Z","citation":{"ista":"Zhou L-Z, Wang L, Chen X, Ge Z, Mergner J, Li X, Küster B, Längst G, Qu L-J, Dresselhaus T. 2023. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell., koad324.","short":"L.-Z. Zhou, L. Wang, X. Chen, Z. Ge, J. Mergner, X. Li, B. Küster, G. Längst, L.-J. Qu, T. Dresselhaus, The Plant Cell (2023).","mla":"Zhou, Liang-Zi, et al. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” <i>The Plant Cell</i>, koad324, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/plcell/koad324\">10.1093/plcell/koad324</a>.","chicago":"Zhou, Liang-Zi, Lele Wang, Xia Chen, Zengxiang Ge, Julia Mergner, Xingli Li, Bernhard Küster, Gernot Längst, Li-Jia Qu, and Thomas Dresselhaus. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” <i>The Plant Cell</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/plcell/koad324\">https://doi.org/10.1093/plcell/koad324</a>.","ieee":"L.-Z. Zhou <i>et al.</i>, “The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize,” <i>The Plant Cell</i>. Oxford University Press, 2023.","apa":"Zhou, L.-Z., Wang, L., Chen, X., Ge, Z., Mergner, J., Li, X., … Dresselhaus, T. (2023). The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koad324\">https://doi.org/10.1093/plcell/koad324</a>","ama":"Zhou L-Z, Wang L, Chen X, et al. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. <i>The Plant Cell</i>. 2023. doi:<a href=\"https://doi.org/10.1093/plcell/koad324\">10.1093/plcell/koad324</a>"},"year":"2023","abstract":[{"lang":"eng","text":"Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants."}],"doi":"10.1093/plcell/koad324","day":"23","quality_controlled":"1","article_type":"original","publisher":"Oxford University Press","author":[{"full_name":"Zhou, Liang-Zi","first_name":"Liang-Zi","last_name":"Zhou"},{"full_name":"Wang, Lele","first_name":"Lele","last_name":"Wang"},{"full_name":"Chen, Xia","last_name":"Chen","first_name":"Xia"},{"first_name":"Zengxiang","last_name":"Ge","orcid":"0000-0001-9381-3577","full_name":"Ge, Zengxiang","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8"},{"first_name":"Julia","last_name":"Mergner","full_name":"Mergner, Julia"},{"full_name":"Li, Xingli","first_name":"Xingli","last_name":"Li"},{"full_name":"Küster, Bernhard","last_name":"Küster","first_name":"Bernhard"},{"full_name":"Längst, Gernot","first_name":"Gernot","last_name":"Längst"},{"full_name":"Qu, Li-Jia","first_name":"Li-Jia","last_name":"Qu"},{"first_name":"Thomas","last_name":"Dresselhaus","full_name":"Dresselhaus, Thomas"}],"_id":"14726","title":"The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize","publication_status":"epub_ahead","article_processing_charge":"No","date_created":"2024-01-02T11:19:37Z"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/plcell/koac346"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-06-01T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"oa":1,"language":[{"iso":"eng"}],"keyword":["Cell Biology","Plant Science"],"publication":"The Plant Cell","oa_version":"Published Version","month":"06","article_number":"koac346","volume":35,"extern":"1","date_updated":"2023-10-04T09:48:43Z","citation":{"mla":"Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” <i>The Plant Cell</i>, vol. 35, no. 6, koac346, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/plcell/koac346\">10.1093/plcell/koac346</a>.","short":"P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth, K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J. Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).","ista":"Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 35(6), koac346.","ama":"Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling open questions in plant RNA biology. <i>The Plant Cell</i>. 2023;35(6). doi:<a href=\"https://doi.org/10.1093/plcell/koac346\">10.1093/plcell/koac346</a>","apa":"Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth, L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling open questions in plant RNA biology. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac346\">https://doi.org/10.1093/plcell/koac346</a>","ieee":"P. A. Manavella <i>et al.</i>, “Beyond transcription: compelling open questions in plant RNA biology,” <i>The Plant Cell</i>, vol. 35, no. 6. Oxford University Press, 2023.","chicago":"Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson, Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” <i>The Plant Cell</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/plcell/koac346\">https://doi.org/10.1093/plcell/koac346</a>."},"year":"2023","external_id":{"pmid":["36477566"]},"doi":"10.1093/plcell/koac346","day":"01","abstract":[{"lang":"eng","text":"The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader."}],"quality_controlled":"1","publisher":"Oxford University Press","article_type":"original","pmid":1,"_id":"12669","scopus_import":"1","author":[{"full_name":"Manavella, Pablo A","first_name":"Pablo A","last_name":"Manavella"},{"first_name":"Micaela A","last_name":"Godoy Herz","full_name":"Godoy Herz, Micaela A"},{"first_name":"Alberto R","last_name":"Kornblihtt","full_name":"Kornblihtt, Alberto R"},{"last_name":"Sorenson","first_name":"Reed","full_name":"Sorenson, Reed"},{"first_name":"Leslie E","last_name":"Sieburth","full_name":"Sieburth, Leslie E"},{"full_name":"Nakaminami, Kentaro","last_name":"Nakaminami","first_name":"Kentaro"},{"full_name":"Seki, Motoaki","first_name":"Motoaki","last_name":"Seki"},{"full_name":"Ding, Yiliang","last_name":"Ding","first_name":"Yiliang"},{"first_name":"Qianwen","last_name":"Sun","full_name":"Sun, Qianwen"},{"full_name":"Kang, Hunseung","last_name":"Kang","first_name":"Hunseung"},{"full_name":"Ariel, Federico D","first_name":"Federico D","last_name":"Ariel"},{"full_name":"Crespi, Martin","last_name":"Crespi","first_name":"Martin"},{"full_name":"Giudicatti, Axel J","first_name":"Axel J","last_name":"Giudicatti"},{"first_name":"Qiang","last_name":"Cai","full_name":"Cai, Qiang"},{"last_name":"Jin","first_name":"Hailing","full_name":"Jin, Hailing"},{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"first_name":"Yijun","last_name":"Qi","full_name":"Qi, Yijun"},{"full_name":"Pikaard, Craig S","last_name":"Pikaard","first_name":"Craig S"}],"issue":"6","publication_status":"published","department":[{"_id":"XiFe"}],"date_created":"2023-02-23T09:14:59Z","article_processing_charge":"No","title":"Beyond transcription: compelling open questions in plant RNA biology","intvolume":"        35"},{"publisher":"Life Science Alliance","article_type":"original","quality_controlled":"1","file_date_updated":"2022-09-08T06:41:14Z","department":[{"_id":"CaBe"}],"date_created":"2022-09-06T18:45:23Z","article_processing_charge":"No","publication_status":"published","intvolume":"         5","title":"The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans","_id":"12051","issue":"11","author":[{"full_name":"Daiß, Julia L","last_name":"Daiß","first_name":"Julia L"},{"full_name":"Pilsl, Michael","first_name":"Michael","last_name":"Pilsl"},{"last_name":"Straub","first_name":"Kristina","full_name":"Straub, Kristina"},{"first_name":"Andrea","last_name":"Bleckmann","full_name":"Bleckmann, Andrea"},{"first_name":"Mona","last_name":"Höcherl","full_name":"Höcherl, Mona"},{"full_name":"Heiss, Florian B","first_name":"Florian B","last_name":"Heiss"},{"full_name":"Abascal-Palacios, Guillermo","first_name":"Guillermo","last_name":"Abascal-Palacios"},{"first_name":"Ewan P","last_name":"Ramsay","full_name":"Ramsay, Ewan P"},{"last_name":"Tluckova","first_name":"Katarina","full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mars, Jean-Clement","first_name":"Jean-Clement","last_name":"Mars"},{"full_name":"Fürtges, Torben","first_name":"Torben","last_name":"Fürtges"},{"full_name":"Bruckmann, Astrid","first_name":"Astrid","last_name":"Bruckmann"},{"full_name":"Rudack, Till","first_name":"Till","last_name":"Rudack"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky"},{"full_name":"Lamour, Valérie","last_name":"Lamour","first_name":"Valérie"},{"first_name":"Konstantin","last_name":"Panov","full_name":"Panov, Konstantin"},{"full_name":"Vannini, Alessandro","last_name":"Vannini","first_name":"Alessandro"},{"last_name":"Moss","first_name":"Tom","full_name":"Moss, Tom"},{"first_name":"Christoph","last_name":"Engel","full_name":"Engel, Christoph"}],"volume":5,"acknowledgement":"The authors especially thank Philip Gunkel for his contribution. We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research Center 960 (TP-A8 to C Engel).","ddc":["570"],"day":"01","doi":"10.26508/lsa.202201568","abstract":[{"text":"Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.","lang":"eng"}],"citation":{"apa":"Daiß, J. L., Pilsl, M., Straub, K., Bleckmann, A., Höcherl, M., Heiss, F. B., … Engel, C. (2022). The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>","ama":"Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. 2022;5(11). doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>","chicago":"Daiß, Julia L, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl, Florian B Heiss, Guillermo Abascal-Palacios, et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>. Life Science Alliance, 2022. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>.","ieee":"J. L. Daiß <i>et al.</i>, “The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans,” <i>Life Science Alliance</i>, vol. 5, no. 11. Life Science Alliance, 2022.","short":"J.L. Daiß, M. Pilsl, K. Straub, A. Bleckmann, M. Höcherl, F.B. Heiss, G. Abascal-Palacios, E.P. Ramsay, K. Tluckova, J.-C. Mars, T. Fürtges, A. Bruckmann, T. Rudack, C. Bernecky, V. Lamour, K. Panov, A. Vannini, T. Moss, C. Engel, Life Science Alliance 5 (2022).","mla":"Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>, vol. 5, no. 11, e202201568, Life Science Alliance, 2022, doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>.","ista":"Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tluckova K, Mars J-C, Fürtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C. 2022. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Science Alliance. 5(11), e202201568."},"year":"2022","date_updated":"2023-08-03T13:39:36Z","external_id":{"isi":["000972702600001"]},"isi":1,"keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"language":[{"iso":"eng"}],"oa_version":"Published Version","article_number":"e202201568","month":"09","has_accepted_license":"1","publication":"Life Science Alliance","file":[{"file_id":"12062","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2022-09-08T06:41:14Z","file_name":"2022_LifeScienceAlliance_Daiss.pdf","content_type":"application/pdf","date_created":"2022-09-08T06:41:14Z","checksum":"4201d876a3e5e8b65e319d03300014ad","file_size":3183129}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2575-1077"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-09-01T00:00:00Z"},{"publication_identifier":{"issn":["1674-2052"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-10-03T00:00:00Z","type":"journal_article","file":[{"date_created":"2023-01-30T07:46:51Z","file_size":2307251,"checksum":"04d5c12490052d03e4dc4412338a43dd","date_updated":"2023-01-30T07:46:51Z","content_type":"application/pdf","file_name":"2022_MolecularPlant_Johnson.pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12435","creator":"dernst"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa_version":"Published Version","project":[{"_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"month":"10","publication":"Molecular Plant","has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["Plant Science","Molecular Biology"],"doi":"10.1016/j.molp.2022.09.003","day":"03","abstract":[{"lang":"eng","text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs."}],"date_updated":"2023-08-04T09:39:24Z","year":"2022","citation":{"ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>.","ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>.","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., &#38; Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>"},"isi":1,"external_id":{"pmid":["36081349"],"isi":["000882769800009"]},"acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","volume":15,"ddc":["580"],"publication_status":"published","date_created":"2023-01-16T09:51:49Z","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","intvolume":"        15","pmid":1,"_id":"12239","scopus_import":"1","author":[{"last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","first_name":"Tommaso","last_name":"Costanzo"},{"full_name":"Dahhan, Dana A.","first_name":"Dana A.","last_name":"Dahhan"},{"first_name":"Sebastian Y.","last_name":"Bednarek","full_name":"Bednarek, Sebastian Y."},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"issue":"10","publisher":"Elsevier","article_type":"original","page":"1533-1542","quality_controlled":"1","file_date_updated":"2023-01-30T07:46:51Z"},{"main_file_link":[{"url":"https://doi.org/10.1111/jipb.13422","open_access":"1"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-12-07T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["1672-9072"],"eissn":["1744-7909"]},"oa":1,"language":[{"iso":"eng"}],"keyword":["Plant Science","General Biochemistry","Genetics and Molecular Biology","Biochemistry"],"publication":"Journal of Integrative Plant Biology","oa_version":"Published Version","month":"12","volume":64,"extern":"1","date_updated":"2023-05-08T10:59:00Z","year":"2022","citation":{"ama":"He S, Feng X. DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. 2022;64(12):2240-2251. doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>","apa":"He, S., &#38; Feng, X. (2022). DNA methylation dynamics during germline development. <i>Journal of Integrative Plant Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>","chicago":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jipb.13422\">https://doi.org/10.1111/jipb.13422</a>.","ieee":"S. He and X. Feng, “DNA methylation dynamics during germline development,” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12. Wiley, pp. 2240–2251, 2022.","mla":"He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.” <i>Journal of Integrative Plant Biology</i>, vol. 64, no. 12, Wiley, 2022, pp. 2240–51, doi:<a href=\"https://doi.org/10.1111/jipb.13422\">10.1111/jipb.13422</a>.","short":"S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.","ista":"He S, Feng X. 2022. DNA methylation dynamics during germline development. Journal of Integrative Plant Biology. 64(12), 2240–2251."},"external_id":{"pmid":["36478632"]},"doi":"10.1111/jipb.13422","day":"07","abstract":[{"text":"DNA methylation plays essential homeostatic functions in eukaryotic genomes. In animals, DNA methylation is also developmentally regulated and, in turn, regulates development. In the past two decades, huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development, especially during sexual reproduction. The power of whole-genome sequencing and cell isolation techniques, as well as bioinformatics tools, have enabled recent studies to reveal dynamic changes in DNA methylation during germline development. Furthermore, the combination of these technological advances with genetics, developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines. In this review, we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.","lang":"eng"}],"page":"2240-2251","quality_controlled":"1","publisher":"Wiley","article_type":"review","pmid":1,"_id":"12670","scopus_import":"1","author":[{"first_name":"Shengbo","last_name":"He","full_name":"He, Shengbo"},{"last_name":"Feng","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"}],"issue":"12","publication_status":"published","article_processing_charge":"No","date_created":"2023-02-23T09:15:57Z","department":[{"_id":"XiFe"}],"title":"DNA methylation dynamics during germline development","intvolume":"        64"},{"_id":"8931","pmid":1,"scopus_import":"1","author":[{"orcid":"0000-0003-4783-1752","full_name":"Gelová, Zuzana","first_name":"Zuzana","last_name":"Gelová","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"last_name":"Gallei","first_name":"Michelle C","full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pernisová, Markéta","last_name":"Pernisová","first_name":"Markéta"},{"full_name":"Brunoud, Géraldine","first_name":"Géraldine","last_name":"Brunoud"},{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","full_name":"Zhang, Xixi","first_name":"Xixi","last_name":"Zhang"},{"full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","last_name":"Glanc","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"first_name":"Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"id":"483727CA-F248-11E8-B48F-1D18A9856A87","first_name":"Jaroslav","last_name":"Michalko","full_name":"Michalko, Jaroslav"},{"last_name":"Pavlovicova","first_name":"Zlata","full_name":"Pavlovicova, Zlata"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin"},{"id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny","first_name":"Jakub","full_name":"Hajny, Jakub","orcid":"0000-0003-2140-7195"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild"},{"last_name":"Čovanová","first_name":"Milada","full_name":"Čovanová, Milada"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"first_name":"Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","first_name":"Matyas","last_name":"Fendrych"},{"full_name":"Xu, Tongda","last_name":"Xu","first_name":"Tongda"},{"first_name":"Teva","last_name":"Vernoux","full_name":"Vernoux, Teva"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"JiFr"},{"_id":"Bio"}],"date_created":"2020-12-09T14:48:28Z","title":"Developmental roles of auxin binding protein 1 in Arabidopsis thaliana","intvolume":"       303","ec_funded":1,"quality_controlled":"1","file_date_updated":"2021-02-04T07:49:25Z","publisher":"Elsevier","article_type":"original","date_updated":"2024-10-29T10:22:43Z","citation":{"chicago":"Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>.","ieee":"Z. Gelová <i>et al.</i>, “Developmental roles of auxin binding protein 1 in Arabidopsis thaliana,” <i>Plant Science</i>, vol. 303. Elsevier, 2021.","apa":"Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M., … Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">https://doi.org/10.1016/j.plantsci.2020.110750</a>","ama":"Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. <i>Plant Science</i>. 2021;303. doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>","ista":"Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.","short":"Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L. Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild, M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml, Plant Science 303 (2021).","mla":"Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis Thaliana.” <i>Plant Science</i>, vol. 303, 110750, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110750\">10.1016/j.plantsci.2020.110750</a>."},"year":"2021","isi":1,"external_id":{"pmid":["33487339"],"isi":["000614154500001"]},"doi":"10.1016/j.plantsci.2020.110750","day":"01","abstract":[{"lang":"eng","text":"Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.\r\nHere we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy."}],"acknowledgement":"We would like to acknowledge Bioimaging and Life Science Facilities at IST Austria for continuous support and also the Plant Sciences Core Facility of CEITEC Masaryk University for their support with obtaining a part of the scientific data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct design. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program [grant agreement no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship of the Austrian Academy of Sciences to L.L.; the European Structural and Investment Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“ [CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738] to M. Č.","volume":303,"ddc":["580"],"publication":"Plant Science","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa_version":"Published Version","project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"month":"02","article_number":"110750","language":[{"iso":"eng"}],"keyword":["Agronomy and Crop Science","Plant Science","Genetics","General Medicine"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2021-02-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0168-9452"]},"oa":1,"file":[{"success":1,"access_level":"open_access","relation":"main_file","file_id":"9083","creator":"dernst","date_created":"2021-02-04T07:49:25Z","checksum":"a7f2562bdca62d67dfa88e271b62a629","file_size":12563728,"date_updated":"2021-02-04T07:49:25Z","file_name":"2021_PlantScience_Gelova.pdf","content_type":"application/pdf"}],"status":"public","related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"10083"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"department":[{"_id":"XiFe"}],"date_created":"2023-01-16T09:14:35Z","article_processing_charge":"No","publication_status":"published","intvolume":"        72","title":"Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors","scopus_import":"1","_id":"12186","pmid":1,"issue":"22","author":[{"full_name":"Ding, Pingtao","first_name":"Pingtao","last_name":"Ding"},{"full_name":"Sakai, Toshiyuki","first_name":"Toshiyuki","last_name":"Sakai"},{"full_name":"Krishna Shrestha, Ram","last_name":"Krishna Shrestha","first_name":"Ram"},{"full_name":"Manosalva Perez, Nicolas","first_name":"Nicolas","last_name":"Manosalva Perez"},{"full_name":"Guo, Wenbin","last_name":"Guo","first_name":"Wenbin"},{"full_name":"Ngou, Bruno Pok Man","last_name":"Ngou","first_name":"Bruno Pok Man"},{"full_name":"He, Shengbo","first_name":"Shengbo","last_name":"He"},{"last_name":"Liu","first_name":"Chang","full_name":"Liu, Chang"},{"first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"first_name":"Runxuan","last_name":"Zhang","full_name":"Zhang, Runxuan"},{"full_name":"Vandepoele, Klaas","last_name":"Vandepoele","first_name":"Klaas"},{"full_name":"MacLean, Dan","first_name":"Dan","last_name":"MacLean"},{"last_name":"Jones","first_name":"Jonathan D G","full_name":"Jones, Jonathan D G"}],"publisher":"Oxford University Press","article_type":"original","quality_controlled":"1","page":"7927-7941","day":"13","doi":"10.1093/jxb/erab373","abstract":[{"lang":"eng","text":"Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems."}],"year":"2021","citation":{"chicago":"Ding, Pingtao, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/jxb/erab373\">https://doi.org/10.1093/jxb/erab373</a>.","ieee":"P. Ding <i>et al.</i>, “Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors,” <i>Journal of Experimental Botany</i>, vol. 72, no. 22. Oxford University Press, pp. 7927–7941, 2021.","ama":"Ding P, Sakai T, Krishna Shrestha R, et al. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. <i>Journal of Experimental Botany</i>. 2021;72(22):7927-7941. doi:<a href=\"https://doi.org/10.1093/jxb/erab373\">10.1093/jxb/erab373</a>","apa":"Ding, P., Sakai, T., Krishna Shrestha, R., Manosalva Perez, N., Guo, W., Ngou, B. P. M., … Jones, J. D. G. (2021). Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erab373\">https://doi.org/10.1093/jxb/erab373</a>","ista":"Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. 2021. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. 72(22), 7927–7941.","short":"P. Ding, T. Sakai, R. Krishna Shrestha, N. Manosalva Perez, W. Guo, B.P.M. Ngou, S. He, C. Liu, X. Feng, R. Zhang, K. Vandepoele, D. MacLean, J.D.G. Jones, Journal of Experimental Botany 72 (2021) 7927–7941.","mla":"Ding, Pingtao, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” <i>Journal of Experimental Botany</i>, vol. 72, no. 22, Oxford University Press, 2021, pp. 7927–41, doi:<a href=\"https://doi.org/10.1093/jxb/erab373\">10.1093/jxb/erab373</a>."},"date_updated":"2023-05-08T11:01:18Z","external_id":{"pmid":["34387350"]},"volume":72,"acknowledgement":"We thank the Gatsby Foundation (UK) for funding to the JDGJ laboratory. PD acknowledges support from the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodowska Curie Actions (grant agreement: 656243) and a Future Leader Fellowship from the Biotechnology and Biological Sciences Research Council (BBSRC) (grant agreement: BB/R012172/1). TS, RKS, DM, and JDGJ were supported by the Gatsby Foundation funding to the\r\nSainsbury Laboratory. NMP and KV were supported by a BOF grant from Ghent University (grant agreement: BOF24Y2019001901). WG and RZ were supported by the Scottish Government Rural and Environment Science and Analytical Services division (RESAS), and RZ also acknowledges the support from a BBSRC Bioinformatics and Biological Resources Fund (grant agreement: BB/S020160/1).BPMN was supported by the Norwich Research Park (NRP) Biosciences Doctoral Training Partnership (DTP) funded by the BBSRC (grant agreement: BB/M011216/1). SH and XF were supported by a BBSRC Responsive Mode grant (grant agreement: BB/S009620/1) and a European Research Council Starting grant ‘SexMeth’ (grant agreement: 804981). CL was supported by Deutsche Forschungsgemeinschaft (grant agreement: LI 2862/4). ","extern":"1","oa_version":"None","month":"08","publication":"Journal of Experimental Botany","keyword":["Plant Science","Physiology"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-0957","1460-2431"]},"type":"journal_article","date_published":"2021-08-13T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"extern":"1","ddc":["570"],"volume":3,"abstract":[{"text":"Nucleoporin 93 (Nup93) expression inversely correlates with the survival of triple-negative breast cancer patients. However, our knowledge of Nup93 function in breast cancer besides its role as structural component of the nuclear pore complex is not understood. Combination of functional assays and genetic analyses suggested that chromatin interaction of Nup93 partially modulates the expression of genes associated with actin cytoskeleton remodeling and epithelial to mesenchymal transition, resulting in impaired invasion of triple-negative, claudin-low breast cancer cells. Nup93 depletion induced stress fiber formation associated with reduced cell migration/proliferation and impaired expression of mesenchymal-like genes. Silencing LIMCH1, a gene responsible for actin cytoskeleton remodeling and up-regulated upon Nup93 depletion, partially restored the invasive phenotype of cancer cells. Loss of Nup93 led to significant defects in tumor establishment/propagation in vivo, whereas patient samples revealed that high Nup93 and low LIMCH1 expression correlate with late tumor stage. Our approach identified Nup93 as contributor of triple-negative, claudin-low breast cancer cell invasion and paves the way to study the role of nuclear envelope proteins during breast cancer tumorigenesis.","lang":"eng"}],"doi":"10.26508/lsa.201900623","day":"01","external_id":{"pmid":["31959624"]},"date_updated":"2022-07-18T08:31:20Z","citation":{"ieee":"S. Bersini, N. K. Lytle, R. Schulte, L. Huang, G. M. Wahl, and M. Hetzer, “Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling,” <i>Life Science Alliance</i>, vol. 3, no. 1. Life Science Alliance, 2020.","chicago":"Bersini, Simone, Nikki K Lytle, Roberta Schulte, Ling Huang, Geoffrey M Wahl, and Martin Hetzer. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” <i>Life Science Alliance</i>. Life Science Alliance, 2020. <a href=\"https://doi.org/10.26508/lsa.201900623\">https://doi.org/10.26508/lsa.201900623</a>.","apa":"Bersini, S., Lytle, N. K., Schulte, R., Huang, L., Wahl, G. M., &#38; Hetzer, M. (2020). Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.201900623\">https://doi.org/10.26508/lsa.201900623</a>","ama":"Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. <i>Life Science Alliance</i>. 2020;3(1). doi:<a href=\"https://doi.org/10.26508/lsa.201900623\">10.26508/lsa.201900623</a>","ista":"Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer M. 2020. Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. Life Science Alliance. 3(1), e201900623.","short":"S. Bersini, N.K. Lytle, R. Schulte, L. Huang, G.M. Wahl, M. Hetzer, Life Science Alliance 3 (2020).","mla":"Bersini, Simone, et al. “Nup93 Regulates Breast Tumor Growth by Modulating Cell Proliferation and Actin Cytoskeleton Remodeling.” <i>Life Science Alliance</i>, vol. 3, no. 1, e201900623, Life Science Alliance, 2020, doi:<a href=\"https://doi.org/10.26508/lsa.201900623\">10.26508/lsa.201900623</a>."},"year":"2020","article_type":"original","publisher":"Life Science Alliance","file_date_updated":"2022-04-08T07:33:01Z","quality_controlled":"1","title":"Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling","intvolume":"         3","publication_status":"published","date_created":"2022-04-07T07:44:18Z","article_processing_charge":"No","author":[{"full_name":"Bersini, Simone","last_name":"Bersini","first_name":"Simone"},{"last_name":"Lytle","first_name":"Nikki K","full_name":"Lytle, Nikki K"},{"first_name":"Roberta","last_name":"Schulte","full_name":"Schulte, Roberta"},{"last_name":"Huang","first_name":"Ling","full_name":"Huang, Ling"},{"last_name":"Wahl","first_name":"Geoffrey M","full_name":"Wahl, Geoffrey M"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W"}],"issue":"1","_id":"11058","pmid":1,"scopus_import":"1","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","file":[{"relation":"main_file","access_level":"open_access","success":1,"file_id":"11137","creator":"dernst","date_created":"2022-04-08T07:33:01Z","file_size":2653960,"checksum":"3bf33e7e93bef7823287807206b69b38","date_updated":"2022-04-08T07:33:01Z","file_name":"2020_LifeScienceAlliance_Bersini.pdf","content_type":"application/pdf"}],"oa":1,"publication_identifier":{"issn":["2575-1077"]},"date_published":"2020-01-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"month":"01","article_number":"e201900623","oa_version":"Published Version","publication":"Life Science Alliance","has_accepted_license":"1"},{"volume":18,"extern":"1","day":"06","doi":"10.1186/s12915-019-0733-6","abstract":[{"text":"Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins.","lang":"eng"}],"year":"2020","citation":{"mla":"Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” <i>BMC Biology</i>, vol. 18, 2, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1186/s12915-019-0733-6\">10.1186/s12915-019-0733-6</a>.","short":"H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou, M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).","ista":"Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 18, 2.","ama":"Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. <i>BMC Biology</i>. 2020;18. doi:<a href=\"https://doi.org/10.1186/s12915-019-0733-6\">10.1186/s12915-019-0733-6</a>","apa":"Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C., … Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. <i>BMC Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12915-019-0733-6\">https://doi.org/10.1186/s12915-019-0733-6</a>","ieee":"H. Rampelt <i>et al.</i>, “The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments,” <i>BMC Biology</i>, vol. 18. Springer Nature, 2020.","chicago":"Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil, Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” <i>BMC Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1186/s12915-019-0733-6\">https://doi.org/10.1186/s12915-019-0733-6</a>."},"date_updated":"2021-01-12T08:19:02Z","external_id":{"pmid":["31907035"]},"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","article_processing_charge":"No","date_created":"2020-09-17T10:26:53Z","publication_status":"published","intvolume":"        18","title":"The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments","_id":"8402","pmid":1,"author":[{"first_name":"Heike","last_name":"Rampelt","full_name":"Rampelt, Heike"},{"first_name":"Iva","last_name":"Sucec","full_name":"Sucec, Iva"},{"last_name":"Bersch","first_name":"Beate","full_name":"Bersch, Beate"},{"first_name":"Patrick","last_name":"Horten","full_name":"Horten, Patrick"},{"first_name":"Inge","last_name":"Perschil","full_name":"Perschil, Inge"},{"last_name":"Martinou","first_name":"Jean-Claude","full_name":"Martinou, Jean-Claude"},{"full_name":"van der Laan, Martin","last_name":"van der Laan","first_name":"Martin"},{"last_name":"Wiedemann","first_name":"Nils","full_name":"Wiedemann, Nils"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Pfanner","first_name":"Nikolaus","full_name":"Pfanner, Nikolaus"}],"main_file_link":[{"url":"https://doi.org/10.1186/s12915-019-0733-6","open_access":"1"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1741-7007"]},"oa":1,"type":"journal_article","date_published":"2020-01-06T00:00:00Z","keyword":["Biotechnology","Plant Science","General Biochemistry","Genetics and Molecular Biology","Developmental Biology","Cell Biology","Physiology","Ecology","Evolution","Behavior and Systematics","Structural Biology","General Agricultural and Biological Sciences"],"language":[{"iso":"eng"}],"oa_version":"Published Version","article_number":"2","month":"01","publication":"BMC Biology"},{"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2024-02-28T12:39:56Z","content_type":"application/pdf","file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","date_created":"2024-02-28T12:39:56Z","checksum":"c538a5008f7827f62d17d40a3bfabe65","file_size":3089212,"file_id":"15038","creator":"dernst","access_level":"open_access","relation":"main_file","success":1}],"oa":1,"publication_identifier":{"issn":["1674-2052"]},"date_published":"2020-05-04T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"keyword":["Plant Science","Molecular Biology"],"month":"05","oa_version":"Published Version","publication":"Molecular Plant","has_accepted_license":"1","ddc":["580"],"volume":13,"abstract":[{"lang":"eng","text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants."}],"doi":"10.1016/j.molp.2020.02.012","day":"04","external_id":{"pmid":["32087370"]},"date_updated":"2024-02-28T12:41:52Z","citation":{"apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">https://doi.org/10.1016/j.molp.2020.02.012</a>","ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. <i>Molecular Plant</i>. 2020;13(5):717-731. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">10.1016/j.molp.2020.02.012</a>","ieee":"J. Moulinier-Anzola <i>et al.</i>, “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” <i>Molecular Plant</i>, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” <i>Molecular Plant</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">https://doi.org/10.1016/j.molp.2020.02.012</a>.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” <i>Molecular Plant</i>, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.02.012\">10.1016/j.molp.2020.02.012</a>.","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731."},"year":"2020","article_type":"original","publisher":"Elsevier","file_date_updated":"2024-02-28T12:39:56Z","page":"717-731","quality_controlled":"1","title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","intvolume":"        13","publication_status":"published","date_created":"2024-02-28T08:55:56Z","article_processing_charge":"No","department":[{"_id":"EvBe"}],"author":[{"full_name":"Moulinier-Anzola, Jeanette","last_name":"Moulinier-Anzola","first_name":"Jeanette"},{"first_name":"Maximilian","last_name":"Schwihla","full_name":"Schwihla, Maximilian"},{"full_name":"De-Araújo, Lucinda","first_name":"Lucinda","last_name":"De-Araújo"},{"id":"45DF286A-F248-11E8-B48F-1D18A9856A87","first_name":"Christina","last_name":"Artner","full_name":"Artner, Christina"},{"full_name":"Jörg, Lisa","first_name":"Lisa","last_name":"Jörg"},{"first_name":"Nataliia","last_name":"Konstantinova","full_name":"Konstantinova, Nataliia"},{"last_name":"Luschnig","first_name":"Christian","full_name":"Luschnig, Christian"},{"first_name":"Barbara","last_name":"Korbei","full_name":"Korbei, Barbara"}],"issue":"5","_id":"15037","pmid":1},{"quality_controlled":"1","ec_funded":1,"page":"2367-2378","article_type":"original","publisher":"Oxford University Press","issue":"9","author":[{"full_name":"Moturu, Taraka Ramji","last_name":"Moturu","first_name":"Taraka Ramji"},{"full_name":"Thula, Sravankumar","last_name":"Thula","first_name":"Sravankumar"},{"last_name":"Singh","first_name":"Ravi Kumar","full_name":"Singh, Ravi Kumar"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"first_name":"Radka Svobodová","last_name":"Vařeková","full_name":"Vařeková, Radka Svobodová"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu"}],"scopus_import":"1","pmid":1,"_id":"10881","intvolume":"        69","title":"Molecular evolution and diversification of the SMXL gene family","department":[{"_id":"JiFr"}],"date_created":"2022-03-18T12:43:22Z","article_processing_charge":"No","publication_status":"published","volume":69,"acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. ","external_id":{"isi":["000430727000016"],"pmid":["29538714"]},"isi":1,"citation":{"ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. 2018;69(9):2367-2378. doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>","apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., &#38; Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>","chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>.","ieee":"T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of the SMXL gene family,” <i>Journal of Experimental Botany</i>, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>.","short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.","ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378."},"year":"2018","date_updated":"2025-05-07T11:12:33Z","abstract":[{"lang":"eng","text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants."}],"day":"13","doi":"10.1093/jxb/ery097","keyword":["Plant Science","Physiology"],"language":[{"iso":"eng"}],"publication":"Journal of Experimental Botany","month":"04","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","type":"journal_article","date_published":"2018-04-13T00:00:00Z","publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]}},{"publisher":"Oxford University Press","article_type":"original","quality_controlled":"1","page":"1616-1623","date_created":"2023-01-16T09:20:22Z","department":[{"_id":"XiFe"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        56","title":"The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity","scopus_import":"1","pmid":1,"_id":"12196","issue":"8","author":[{"full_name":"Johnson, Kaeli C.M.","first_name":"Kaeli C.M.","last_name":"Johnson"},{"last_name":"Xia","first_name":"Shitou","full_name":"Xia, Shitou"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"},{"last_name":"Li","first_name":"Xin","full_name":"Li, Xin"}],"volume":56,"acknowledgement":"This work was supported by the National Sciences and Engineering Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles Copeland for critical reading of the manuscript.","extern":"1","doi":"10.1093/pcp/pcv087","abstract":[{"lang":"eng","text":"SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity."}],"year":"2015","citation":{"chicago":"Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/pcp/pcv087\">https://doi.org/10.1093/pcp/pcv087</a>.","ieee":"K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity,” <i>Plant and Cell Physiology</i>, vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.","apa":"Johnson, K. C. M., Xia, S., Feng, X., &#38; Li, X. (2015). The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcv087\">https://doi.org/10.1093/pcp/pcv087</a>","ama":"Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. <i>Plant and Cell Physiology</i>. 2015;56(8):1616-1623. doi:<a href=\"https://doi.org/10.1093/pcp/pcv087\">10.1093/pcp/pcv087</a>","ista":"Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.","mla":"Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” <i>Plant and Cell Physiology</i>, vol. 56, no. 8, Oxford University Press, 2015, pp. 1616–23, doi:<a href=\"https://doi.org/10.1093/pcp/pcv087\">10.1093/pcp/pcv087</a>.","short":"K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015) 1616–1623."},"date_updated":"2023-05-08T11:03:23Z","external_id":{"pmid":["26063389"]},"keyword":["Cell Biology","Plant Science","Physiology","General Medicine"],"language":[{"iso":"eng"}],"oa_version":"None","month":"08","publication":"Plant and Cell Physiology","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0032-0781","1471-9053"]},"type":"journal_article","date_published":"2015-08-01T00:00:00Z"},{"page":"650-675","quality_controlled":"1","file_date_updated":"2022-03-21T12:12:56Z","publisher":"MDPI","article_type":"original","_id":"10895","pmid":1,"scopus_import":"1","author":[{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"issue":"4","publication_status":"published","department":[{"_id":"JiFr"}],"date_created":"2022-03-21T07:13:49Z","article_processing_charge":"No","title":"Calcium: The missing link in auxin action","intvolume":"         2","volume":2,"ddc":["580"],"date_updated":"2022-03-21T12:15:29Z","year":"2013","citation":{"ama":"Vanneste S, Friml J. Calcium: The missing link in auxin action. <i>Plants</i>. 2013;2(4):650-675. doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>","apa":"Vanneste, S., &#38; Friml, J. (2013). Calcium: The missing link in auxin action. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>","chicago":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>. MDPI, 2013. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>.","ieee":"S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” <i>Plants</i>, vol. 2, no. 4. MDPI, pp. 650–675, 2013.","mla":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>.","short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675.","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675."},"external_id":{"pmid":["27137397"]},"doi":"10.3390/plants2040650","day":"21","abstract":[{"lang":"eng","text":"Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. "}],"language":[{"iso":"eng"}],"keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"publication":"Plants","has_accepted_license":"1","oa_version":"Published Version","month":"10","file":[{"date_created":"2022-03-21T12:12:56Z","file_size":670188,"checksum":"fb4ff2e820e344e253c9197544610be6","date_updated":"2022-03-21T12:12:56Z","content_type":"application/pdf","file_name":"2013_Plants_Vanneste.pdf","success":1,"relation":"main_file","access_level":"open_access","file_id":"10916","creator":"dernst"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"date_published":"2013-10-21T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["2223-7747"]},"oa":1}]