[{"title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"article_processing_charge":"No","author":[{"orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nagel","full_name":"Nagel, Marie-Kristin","first_name":"Marie-Kristin"},{"last_name":"Monzer","full_name":"Monzer, Aline","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria","last_name":"Hlavata","full_name":"Hlavata, Annamaria"},{"last_name":"Isono","full_name":"Isono, Erika","first_name":"Erika"},{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523."},"date_updated":"2023-12-01T13:51:06Z","status":"public","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"type":"preprint","_id":"14591","date_created":"2023-11-22T10:17:49Z","ec_funded":1,"date_published":"2023-10-10T00:00:00Z","related_material":{"record":[{"id":"14510","status":"public","relation":"dissertation_contains"}]},"doi":"10.1101/2023.10.09.561523","publication":"bioRxiv","language":[{"iso":"eng"}],"day":"10","year":"2023","publication_status":"submitted","month":"10","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2","open_access":"1"}],"oa":1,"oa_version":"Preprint","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins."}]},{"date_published":"2023-12-05T00:00:00Z","doi":"10.15479/AT:ISTA:14644","date_created":"2023-12-04T14:51:00Z","day":"05","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"We thank B. Kaczmarek and other members of the Bernecky lab for helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid. We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant P34185. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","author":[{"id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Tluckova","full_name":"Tluckova, Katarina"},{"first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P"},{"last_name":"Bernecky","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Tluckova, Katarina, et al. Mechanism of Mammalian Transcriptional Repression by Noncoding RNA. Institute of Science and Technology Austria, doi:10.15479/AT:ISTA:14644.","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:10.15479/AT:ISTA:14644","apa":"Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14644","chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. https://doi.org/10.15479/AT:ISTA:14644.","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. 10.15479/AT:ISTA:14644."},"project":[{"grant_number":"P34185","name":"Regulation of mammalian transcription by noncoding RNA","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","file":[{"creator":"dernst","date_updated":"2023-12-05T10:37:02Z","file_size":4892920,"date_created":"2023-12-05T10:37:02Z","file_name":"2023_Tluckova_etal_REx.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14646","checksum":"c45608cb97ee36d7b50ba518db8e07b0","success":1}],"language":[{"iso":"eng"}],"publication_status":"submitted","month":"12","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"file_date_updated":"2023-12-05T10:37:02Z","department":[{"_id":"CaBe"}],"ddc":["572"],"date_updated":"2023-12-05T10:37:28Z","status":"public","type":"preprint","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"_id":"14644"},{"article_number":"e202201568","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. Life Science Alliance. Life Science Alliance. https://doi.org/10.26508/lsa.202201568","ama":"Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Science Alliance. 2022;5(11). doi:10.26508/lsa.202201568","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).","ieee":"J. L. Daiß et al., “The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans,” Life Science Alliance, vol. 5, no. 11. Life Science Alliance, 2022.","mla":"Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” Life Science Alliance, vol. 5, no. 11, e202201568, Life Science Alliance, 2022, doi:10.26508/lsa.202201568.","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.","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.” Life Science Alliance. Life Science Alliance, 2022. https://doi.org/10.26508/lsa.202201568."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000972702600001"]},"article_processing_charge":"No","author":[{"full_name":"Daiß, Julia L","last_name":"Daiß","first_name":"Julia L"},{"first_name":"Michael","full_name":"Pilsl, Michael","last_name":"Pilsl"},{"first_name":"Kristina","full_name":"Straub, Kristina","last_name":"Straub"},{"first_name":"Andrea","last_name":"Bleckmann","full_name":"Bleckmann, Andrea"},{"first_name":"Mona","full_name":"Höcherl, Mona","last_name":"Höcherl"},{"last_name":"Heiss","full_name":"Heiss, Florian B","first_name":"Florian B"},{"last_name":"Abascal-Palacios","full_name":"Abascal-Palacios, Guillermo","first_name":"Guillermo"},{"full_name":"Ramsay, Ewan P","last_name":"Ramsay","first_name":"Ewan P"},{"id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","full_name":"Tluckova, Katarina","last_name":"Tluckova"},{"full_name":"Mars, Jean-Clement","last_name":"Mars","first_name":"Jean-Clement"},{"full_name":"Fürtges, Torben","last_name":"Fürtges","first_name":"Torben"},{"first_name":"Astrid","full_name":"Bruckmann, Astrid","last_name":"Bruckmann"},{"first_name":"Till","last_name":"Rudack","full_name":"Rudack, Till"},{"first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","last_name":"Bernecky"},{"full_name":"Lamour, Valérie","last_name":"Lamour","first_name":"Valérie"},{"full_name":"Panov, Konstantin","last_name":"Panov","first_name":"Konstantin"},{"first_name":"Alessandro","full_name":"Vannini, Alessandro","last_name":"Vannini"},{"first_name":"Tom","last_name":"Moss","full_name":"Moss, Tom"},{"full_name":"Engel, Christoph","last_name":"Engel","first_name":"Christoph"}],"title":"The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans","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).","oa":1,"publisher":"Life Science Alliance","quality_controlled":"1","year":"2022","has_accepted_license":"1","isi":1,"publication":"Life Science Alliance","day":"01","date_created":"2022-09-06T18:45:23Z","doi":"10.26508/lsa.202201568","date_published":"2022-09-01T00:00:00Z","_id":"12051","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"status":"public","date_updated":"2023-08-03T13:39:36Z","ddc":["570"],"department":[{"_id":"CaBe"}],"file_date_updated":"2022-09-08T06:41:14Z","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"}],"oa_version":"Published Version","intvolume":" 5","month":"09","publication_status":"published","publication_identifier":{"issn":["2575-1077"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"4201d876a3e5e8b65e319d03300014ad","file_id":"12062","success":1,"date_updated":"2022-09-08T06:41:14Z","file_size":3183129,"creator":"dernst","date_created":"2022-09-08T06:41:14Z","file_name":"2022_LifeScienceAlliance_Daiss.pdf"}],"license":"https://creativecommons.org/licenses/by/4.0/","volume":5,"issue":"11"},{"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","article_type":"original","keyword":["Cell Biology","Molecular Biology"],"status":"public","_id":"12143","file_date_updated":"2023-01-24T09:29:02Z","department":[{"_id":"CaBe"}],"date_updated":"2023-08-04T08:57:17Z","ddc":["570"],"scopus_import":"1","intvolume":" 82","month":"11","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":82,"issue":"21","publication_status":"published","publication_identifier":{"issn":["1097-2765"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12354","checksum":"999e443b54e4fdaa2542ca5a97619731","success":1,"date_updated":"2023-01-24T09:29:02Z","file_size":7368534,"creator":"dernst","date_created":"2023-01-24T09:29:02Z","file_name":"2022_MolecularCell_Zapletal.pdf"}],"external_id":{"pmid":["36332606"],"isi":["000898565300011"]},"article_processing_charge":"No","author":[{"full_name":"Zapletal, David","last_name":"Zapletal","first_name":"David"},{"first_name":"Eliska","full_name":"Taborska, Eliska","last_name":"Taborska"},{"first_name":"Josef","last_name":"Pasulka","full_name":"Pasulka, Josef"},{"full_name":"Malik, Radek","last_name":"Malik","first_name":"Radek"},{"first_name":"Karel","full_name":"Kubicek, Karel","last_name":"Kubicek"},{"last_name":"Zanova","full_name":"Zanova, Martina","first_name":"Martina"},{"first_name":"Christian","full_name":"Much, Christian","last_name":"Much"},{"first_name":"Marek","last_name":"Sebesta","full_name":"Sebesta, Marek"},{"last_name":"Buccheri","full_name":"Buccheri, Valeria","first_name":"Valeria"},{"first_name":"Filip","full_name":"Horvat, Filip","last_name":"Horvat"},{"first_name":"Irena","full_name":"Jenickova, Irena","last_name":"Jenickova"},{"last_name":"Prochazkova","full_name":"Prochazkova, Michaela","first_name":"Michaela"},{"first_name":"Jan","full_name":"Prochazka, Jan","last_name":"Prochazka"},{"full_name":"Pinkas, Matyas","last_name":"Pinkas","first_name":"Matyas"},{"full_name":"Novacek, Jiri","last_name":"Novacek","first_name":"Jiri"},{"first_name":"Diego F.","last_name":"Joseph","full_name":"Joseph, Diego F."},{"full_name":"Sedlacek, Radislav","last_name":"Sedlacek","first_name":"Radislav"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036"},{"first_name":"Dónal","last_name":"O’Carroll","full_name":"O’Carroll, Dónal"},{"first_name":"Richard","full_name":"Stefl, Richard","last_name":"Stefl"},{"full_name":"Svoboda, Petr","last_name":"Svoboda","first_name":"Petr"}],"title":"Structural and functional basis of mammalian microRNA biogenesis by Dicer","citation":{"ama":"Zapletal D, Taborska E, Pasulka J, et al. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. 2022;82(21):4064-4079.e13. doi:10.1016/j.molcel.2022.10.010","apa":"Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M., … Svoboda, P. (2022). Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2022.10.010","ieee":"D. Zapletal et al., “Structural and functional basis of mammalian microRNA biogenesis by Dicer,” Molecular Cell, vol. 82, no. 21. Elsevier, p. 4064–4079.e13, 2022.","short":"D. Zapletal, E. Taborska, J. Pasulka, R. Malik, K. Kubicek, M. Zanova, C. Much, M. Sebesta, V. Buccheri, F. Horvat, I. Jenickova, M. Prochazkova, J. Prochazka, M. Pinkas, J. Novacek, D.F. Joseph, R. Sedlacek, C. Bernecky, D. O’Carroll, R. Stefl, P. Svoboda, Molecular Cell 82 (2022) 4064–4079.e13.","mla":"Zapletal, David, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” Molecular Cell, vol. 82, no. 21, Elsevier, 2022, p. 4064–4079.e13, doi:10.1016/j.molcel.2022.10.010.","ista":"Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek J, Joseph DF, Sedlacek R, Bernecky C, O’Carroll D, Stefl R, Svoboda P. 2022. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. 82(21), 4064–4079.e13.","chicago":"Zapletal, David, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek, Martina Zanova, Christian Much, et al. “Structural and Functional Basis of Mammalian MicroRNA Biogenesis by Dicer.” Molecular Cell. Elsevier, 2022. https://doi.org/10.1016/j.molcel.2022.10.010."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We thank Kristian Vlahovicek (University of Zagreb) for support of bioinformatics analyses and Vladimir Benes (EMBL Sequencing Facility) and Genomics and Bioinformatics Core Facility at the Institute of Molecular Genetics for help with RNA sequencing. The main funding was provided by the Czech Science Foundation (EXPRO grant 20-03950X to P.S. and 22-19896S to R. Stefl). Early stages of the work were supported by European Research Council grants under the European Union’s Horizon 2020 Research and Innovation Programme (grants 647403 to P.S. and 649030 to R. Stefl). V.B., D.F.J., and F.H. were in part supported by PhD student fellowships from the Charles University; this work will be in part fulfilling requirements for a PhD degree as “school work.” Funding of D.Z. included the OP RDE project “Internal Grant Agency of Masaryk University” no. CZ.02.2.69/0.0/0.0/19_073/0016943. The Ministry of Education, Youth, and Sports of the Czech Republic (MEYS CR) provided institutional support for CEITEC 2020 project LQ1601. For technical support, we acknowledge EMBL Monterotondo’s genome engineering and transgenic core facilities, the Czech Centre for Phenogenomics at the Institute of Molecular Genetics (supported by RVO 68378050 from the Czech Academy of Sciences and LM2018126 and CZ.02.1.01/0.0/0.0/18_046/0015861 CCP Infrastructure Upgrade II from MEYS CR), the Cryo-EM and Proteomics Core Facilities (CEITEC, Masaryk University) supported by the CIISB research infrastructure (LM2018127 from MEYS CR), and support from the Scientific Service Units of ISTA through resources from the Electron Microscopy Facility. Computational resources included e-Infrastruktura CZ (LM2018140) and ELIXIR-CZ (LM2018131) projects by MEYS CR and the Croatian National Centres of Research Excellence in Personalized Healthcare (#KK.01.1.1.01.0010) and Data Science and Advanced Cooperative Systems (#KK.01.1.1.01.0009) projects funded by the European Structural and Investment Funds grants.","page":"4064-4079.e13","date_created":"2023-01-12T12:05:36Z","doi":"10.1016/j.molcel.2022.10.010","date_published":"2022-11-03T00:00:00Z","year":"2022","has_accepted_license":"1","isi":1,"publication":"Molecular Cell","day":"03"},{"date_published":"2021-10-19T00:00:00Z","doi":"10.1038/s41467-021-26360-2","date_created":"2021-10-20T14:40:32Z","day":"19","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2021","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S.","title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","author":[{"last_name":"Appel","full_name":"Appel, Lisa-Marie","first_name":"Lisa-Marie"},{"last_name":"Franke","full_name":"Franke, Vedran","first_name":"Vedran"},{"first_name":"Melania","full_name":"Bruno, Melania","last_name":"Bruno"},{"last_name":"Grishkovskaya","full_name":"Grishkovskaya, Irina","first_name":"Irina"},{"full_name":"Kasiliauskaite, Aiste","last_name":"Kasiliauskaite","first_name":"Aiste"},{"last_name":"Kaufmann","full_name":"Kaufmann, Tanja","first_name":"Tanja"},{"first_name":"Ursula E.","full_name":"Schoeberl, Ursula E.","last_name":"Schoeberl"},{"first_name":"Martin G.","full_name":"Puchinger, Martin G.","last_name":"Puchinger"},{"first_name":"Sebastian","full_name":"Kostrhon, Sebastian","last_name":"Kostrhon"},{"first_name":"Carmen","full_name":"Ebenwaldner, Carmen","last_name":"Ebenwaldner"},{"first_name":"Marek","last_name":"Sebesta","full_name":"Sebesta, Marek"},{"first_name":"Etienne","full_name":"Beltzung, Etienne","last_name":"Beltzung"},{"full_name":"Mechtler, Karl","last_name":"Mechtler","first_name":"Karl"},{"first_name":"Gen","full_name":"Lin, Gen","last_name":"Lin"},{"last_name":"Vlasova","full_name":"Vlasova, Anna","first_name":"Anna"},{"last_name":"Leeb","full_name":"Leeb, Martin","first_name":"Martin"},{"first_name":"Rushad","full_name":"Pavri, Rushad","last_name":"Pavri"},{"last_name":"Stark","full_name":"Stark, Alexander","first_name":"Alexander"},{"first_name":"Altuna","last_name":"Akalin","full_name":"Akalin, Altuna"},{"last_name":"Stefl","full_name":"Stefl, Richard","first_name":"Richard"},{"last_name":"Bernecky","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","first_name":"Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kristina","last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina"},{"last_name":"Slade","full_name":"Slade, Dea","first_name":"Dea"}],"article_processing_charge":"No","external_id":{"isi":["000709050300001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.","ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2.","short":"L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021).","ieee":"L.-M. Appel et al., “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021.","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26360-2","apa":"Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26360-2"},"article_number":"6078","related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159","relation":"earlier_version","description":"Preprint "}]},"volume":12,"issue":"1","file":[{"date_created":"2021-10-21T13:51:49Z","file_name":"2021_NatComm_Appel.pdf","creator":"cchlebak","date_updated":"2021-10-21T13:51:49Z","file_size":5111706,"checksum":"d99fcd51aebde19c21314e3de0148007","file_id":"10169","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","month":"10","intvolume":" 12","oa_version":"Published Version","abstract":[{"text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay.","lang":"eng"}],"department":[{"_id":"CaBe"}],"file_date_updated":"2021-10-21T13:51:49Z","ddc":["610"],"date_updated":"2023-08-14T08:02:31Z","status":"public","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"10163"},{"doi":"10.1038/s41598-020-58264-4","date_published":"2020-02-10T00:00:00Z","date_created":"2020-02-16T23:00:49Z","day":"10","publication":"Scientific reports","has_accepted_license":"1","isi":1,"year":"2020","publisher":"Springer Nature","quality_controlled":"1","oa":1,"title":"Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation","author":[{"full_name":"López De La Oliva, Amada R.","last_name":"López De La Oliva","first_name":"Amada R."},{"full_name":"Campos-Sandoval, José A.","last_name":"Campos-Sandoval","first_name":"José A."},{"last_name":"Gómez-García","full_name":"Gómez-García, María C.","first_name":"María C."},{"first_name":"Carolina","full_name":"Cardona, Carolina","last_name":"Cardona"},{"last_name":"Martín-Rufián","full_name":"Martín-Rufián, Mercedes","first_name":"Mercedes"},{"full_name":"Sialana, Fernando J.","last_name":"Sialana","first_name":"Fernando J."},{"last_name":"Castilla","full_name":"Castilla, Laura","first_name":"Laura"},{"full_name":"Bae, Narkhyun","last_name":"Bae","id":"3A5F7CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Narkhyun"},{"full_name":"Lobo, Carolina","last_name":"Lobo","first_name":"Carolina"},{"last_name":"Peñalver","full_name":"Peñalver, Ana","first_name":"Ana"},{"first_name":"Marina","full_name":"García-Frutos, Marina","last_name":"García-Frutos"},{"last_name":"Carro","full_name":"Carro, David","first_name":"David"},{"last_name":"Enrique","full_name":"Enrique, Victoria","first_name":"Victoria"},{"full_name":"Paz, José C.","last_name":"Paz","first_name":"José C."},{"first_name":"Raghavendra G.","last_name":"Mirmira","full_name":"Mirmira, Raghavendra G."},{"last_name":"Gutiérrez","full_name":"Gutiérrez, Antonia","first_name":"Antonia"},{"first_name":"Francisco J.","full_name":"Alonso, Francisco J.","last_name":"Alonso"},{"full_name":"Segura, Juan A.","last_name":"Segura","first_name":"Juan A."},{"last_name":"Matés","full_name":"Matés, José M.","first_name":"José M."},{"last_name":"Lubec","full_name":"Lubec, Gert","first_name":"Gert"},{"first_name":"Javier","full_name":"Márquez, Javier","last_name":"Márquez"}],"external_id":{"isi":["000560694800012"],"pmid":["32042057"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"López De La Oliva, A. R., Campos-Sandoval, J. A., Gómez-García, M. C., Cardona, C., Martín-Rufián, M., Sialana, F. J., … Márquez, J. (2020). Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-58264-4","ama":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, et al. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-58264-4","ieee":"A. R. López De La Oliva et al., “Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020.","short":"A.R. López De La Oliva, J.A. Campos-Sandoval, M.C. Gómez-García, C. Cardona, M. Martín-Rufián, F.J. Sialana, L. Castilla, N. Bae, C. Lobo, A. Peñalver, M. García-Frutos, D. Carro, V. Enrique, J.C. Paz, R.G. Mirmira, A. Gutiérrez, F.J. Alonso, J.A. Segura, J.M. Matés, G. Lubec, J. Márquez, Scientific Reports 10 (2020).","mla":"López De La Oliva, Amada R., et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” Scientific Reports, vol. 10, no. 1, 2259, Springer Nature, 2020, doi:10.1038/s41598-020-58264-4.","ista":"López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, Cardona C, Martín-Rufián M, Sialana FJ, Castilla L, Bae N, Lobo C, Peñalver A, García-Frutos M, Carro D, Enrique V, Paz JC, Mirmira RG, Gutiérrez A, Alonso FJ, Segura JA, Matés JM, Lubec G, Márquez J. 2020. Nuclear translocation of glutaminase GLS2 in human cancer cells associates with proliferation arrest and differentiation. Scientific reports. 10(1), 2259.","chicago":"López De La Oliva, Amada R., José A. Campos-Sandoval, María C. Gómez-García, Carolina Cardona, Mercedes Martín-Rufián, Fernando J. Sialana, Laura Castilla, et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-58264-4."},"article_number":"2259","issue":"1","volume":10,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41598-020-80651-0","relation":"erratum"}]},"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:59Z","file_size":4703751,"date_created":"2020-02-18T07:43:21Z","file_name":"2020_ScientificReport_Lopez.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7495","checksum":"c780bd87476a9c9e12668ff66de3dc96"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20452322"]},"publication_status":"published","month":"02","intvolume":" 10","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis playing a key role in cancer metabolic reprogramming. Humans express two types of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2 is repressed in many tumor cells and a better understanding of its function in tumorigenesis may further the development of new therapeutic approaches. We analyzed GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7 cells. We studied GLS2 expression after induction of differentiation with phorbol ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we investigated cell cycle progression and levels of p53, p21 and c-Myc proteins. Using the baculovirus system, human GLS2 protein was overexpressed, purified and analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform. We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry and subcellular fractionation gave consistent results demonstrating nuclear and mitochondrial locations, with the latter being predominant. Nuclear targeting was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins. We assessed the subnuclear location finding a widespread distribution of GLS2 in the nucleoplasm without clear overlapping with specific nuclear substructures. GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore, human GLS2 was identified as being hypusinated by MS analysis, a posttranslational modification which may be relevant for its nuclear targeting and/or function. Our studies provide evidence for a tumor suppressor role of GLS2 in certain types of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in cancer cells induced an antiproliferative response with cell cycle arrest at the G2/M phase.","lang":"eng"}],"department":[{"_id":"CaBe"}],"file_date_updated":"2020-07-14T12:47:59Z","ddc":["570"],"date_updated":"2023-08-18T06:35:13Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"7487"},{"doi":"10.1073/pnas.1921027117","date_published":"2020-03-24T00:00:00Z","date_created":"2020-03-12T05:32:26Z","page":"6504-6549","day":"24","publication":"Proceedings of the National Academy of Sciences","isi":1,"year":"2020","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"title":"Stochastic activation and bistability in a Rab GTPase regulatory network","author":[{"last_name":"Bezeljak","full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","first_name":"Urban"},{"first_name":"Hrushikesh","last_name":"Loya","full_name":"Loya, Hrushikesh"},{"full_name":"Kaczmarek, Beata M","last_name":"Kaczmarek","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Timothy E.","full_name":"Saunders, Timothy E.","last_name":"Saunders"},{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"external_id":{"isi":["000521821800040"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1921027117","ama":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 2020;117(12):6504-6549. doi:10.1073/pnas.1921027117","short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences 117 (2020) 6504–6549.","ieee":"U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic activation and bistability in a Rab GTPase regulatory network,” Proceedings of the National Academy of Sciences, vol. 117, no. 12. Proceedings of the National Academy of Sciences, pp. 6504–6549, 2020.","mla":"Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences, vol. 117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49, doi:10.1073/pnas.1921027117.","ista":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences. 117(12), 6504–6549.","chicago":"Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders, and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921027117."},"project":[{"name":"Reconstitution of cell polarity and axis determination in a cell-free system","grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425"}],"volume":117,"issue":"12","related_material":{"record":[{"id":"8341","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/","description":"News on IST Homepage"}]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","month":"03","intvolume":" 117","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/776567","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"department":[{"_id":"MaLo"},{"_id":"CaBe"}],"date_updated":"2023-09-07T13:17:06Z","status":"public","article_type":"original","type":"journal_article","_id":"7580"},{"department":[{"_id":"CaBe"}],"date_updated":"2024-03-04T10:14:44Z","status":"public","type":"journal_article","article_type":"original","_id":"15061","volume":117,"issue":"36","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","month":"09","intvolume":" 117","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.191726911"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery."}],"acknowledged_ssus":[{"_id":"LifeSc"}],"title":"Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin","author":[{"full_name":"Pinotsis, Nikos","last_name":"Pinotsis","first_name":"Nikos"},{"last_name":"Zielinska","full_name":"Zielinska, Karolina","first_name":"Karolina"},{"full_name":"Babuta, Mrigya","last_name":"Babuta","first_name":"Mrigya"},{"first_name":"Joan L.","full_name":"Arolas, Joan L.","last_name":"Arolas"},{"last_name":"Kostan","full_name":"Kostan, Julius","first_name":"Julius"},{"full_name":"Khan, Muhammad Bashir","last_name":"Khan","first_name":"Muhammad Bashir"},{"last_name":"Schreiner","full_name":"Schreiner, Claudia","first_name":"Claudia"},{"last_name":"Testa Salmazo","full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","first_name":"Anita P"},{"full_name":"Ciccarelli, Luciano","last_name":"Ciccarelli","first_name":"Luciano"},{"first_name":"Martin","last_name":"Puchinger","full_name":"Puchinger, Martin"},{"first_name":"Eirini A.","full_name":"Gkougkoulia, Eirini A.","last_name":"Gkougkoulia"},{"last_name":"Ribeiro","full_name":"Ribeiro, Euripedes de Almeida","first_name":"Euripedes de Almeida"},{"full_name":"Marlovits, Thomas C.","last_name":"Marlovits","first_name":"Thomas C."},{"full_name":"Bhattacharya, Alok","last_name":"Bhattacharya","first_name":"Alok"},{"first_name":"Kristina","last_name":"Djinovic-Carugo","full_name":"Djinovic-Carugo, Kristina"}],"external_id":{"pmid":["32848067"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117.","apa":"Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M. B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1917269117","ama":"Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117","ieee":"N. Pinotsis et al., “Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy of Sciences, pp. 22101–22112, 2020.","short":"N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan, C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia, E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings of the National Academy of Sciences 117 (2020) 22101–22112.","chicago":"Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117.","ista":"Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A, Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings of the National Academy of Sciences. 117(36), 22101–22112."},"date_published":"2020-09-08T00:00:00Z","doi":"10.1073/pnas.1917269117","date_created":"2024-03-04T10:03:52Z","page":"22101-22112","day":"08","publication":"Proceedings of the National Academy of Sciences","year":"2020","publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"We thank the staff of the macromolecular crystallography (MX) and SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss Light Source for excellent support, and the Life Sciences Facility of the Institute of Science and Technology Austria for usage of the rheometer. We thank Life Sciences editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423), Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF) Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R. ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I 2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological Macromolecules. M.B. acknowledges the University Grant Commission, India, for a senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science Engineering Research Council. "}]