DrLLPS: a data resource of liquid–liquid phase separation in eukaryotes
Abstract Here, we presented an integrative database named DrLLPS (http://llps.biocuckoo.cn/) for proteins involved in liquid–liquid phase separation (LLPS), which is a ubiquitous and crucial mechanism for spatiotemporal organization of various biochemical reactions, by creating membraneless organell...
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Veröffentlicht in: | Nucleic acids research 2020-01, Vol.48 (D1), p.D288-D295 |
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creator | Ning, Wanshan Guo, Yaping Lin, Shaofeng Mei, Bin Wu, Yu Jiang, Peiran Tan, Xiaodan Zhang, Weizhi Chen, Guowei Peng, Di Chu, Liang Xue, Yu |
description | Abstract
Here, we presented an integrative database named DrLLPS (http://llps.biocuckoo.cn/) for proteins involved in liquid–liquid phase separation (LLPS), which is a ubiquitous and crucial mechanism for spatiotemporal organization of various biochemical reactions, by creating membraneless organelles (MLOs) in eukaryotic cells. From the literature, we manually collected 150 scaffold proteins that are drivers of LLPS, 987 regulators that contribute in modulating LLPS, and 8148 potential client proteins that might be dispensable for the formation of MLOs, which were then categorized into 40 biomolecular condensates. We searched potential orthologs of these known proteins, and in total DrLLPS contained 437 887 known and potential LLPS-associated proteins in 164 eukaryotes. Furthermore, we carefully annotated LLPS-associated proteins in eight model organisms, by using the knowledge integrated from 110 widely used resources that covered 16 aspects, including protein disordered regions, domain annotations, post-translational modifications (PTMs), genetic variations, cancer mutations, molecular interactions, disease-associated information, drug-target relations, physicochemical property, protein functional annotations, protein expressions/proteomics, protein 3D structures, subcellular localizations, mRNA expressions, DNA & RNA elements, and DNA methylations. We anticipate DrLLPS can serve as a helpful resource for further analysis of LLPS. |
doi_str_mv | 10.1093/nar/gkz1027 |
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Here, we presented an integrative database named DrLLPS (http://llps.biocuckoo.cn/) for proteins involved in liquid–liquid phase separation (LLPS), which is a ubiquitous and crucial mechanism for spatiotemporal organization of various biochemical reactions, by creating membraneless organelles (MLOs) in eukaryotic cells. From the literature, we manually collected 150 scaffold proteins that are drivers of LLPS, 987 regulators that contribute in modulating LLPS, and 8148 potential client proteins that might be dispensable for the formation of MLOs, which were then categorized into 40 biomolecular condensates. We searched potential orthologs of these known proteins, and in total DrLLPS contained 437 887 known and potential LLPS-associated proteins in 164 eukaryotes. Furthermore, we carefully annotated LLPS-associated proteins in eight model organisms, by using the knowledge integrated from 110 widely used resources that covered 16 aspects, including protein disordered regions, domain annotations, post-translational modifications (PTMs), genetic variations, cancer mutations, molecular interactions, disease-associated information, drug-target relations, physicochemical property, protein functional annotations, protein expressions/proteomics, protein 3D structures, subcellular localizations, mRNA expressions, DNA & RNA elements, and DNA methylations. We anticipate DrLLPS can serve as a helpful resource for further analysis of LLPS.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkz1027</identifier><identifier>PMID: 31691822</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Database Issue ; Databases, Factual ; Eukaryota ; Genome ; Intrinsically Disordered Proteins - chemistry ; Intrinsically Disordered Proteins - metabolism ; Organelles ; Protein Processing, Post-Translational ; Proteins - chemistry ; Proteins - metabolism ; User-Computer Interface</subject><ispartof>Nucleic acids research, 2020-01, Vol.48 (D1), p.D288-D295</ispartof><rights>The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019</rights><rights>The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c412t-9e26e1cbf51e276af4b16ecf377a0a8e159fc61d63a662d7831be10135e9eca3</citedby><cites>FETCH-LOGICAL-c412t-9e26e1cbf51e276af4b16ecf377a0a8e159fc61d63a662d7831be10135e9eca3</cites><orcidid>0000-0002-9403-6869</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145660/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145660/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1603,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31691822$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ning, Wanshan</creatorcontrib><creatorcontrib>Guo, Yaping</creatorcontrib><creatorcontrib>Lin, Shaofeng</creatorcontrib><creatorcontrib>Mei, Bin</creatorcontrib><creatorcontrib>Wu, Yu</creatorcontrib><creatorcontrib>Jiang, Peiran</creatorcontrib><creatorcontrib>Tan, Xiaodan</creatorcontrib><creatorcontrib>Zhang, Weizhi</creatorcontrib><creatorcontrib>Chen, Guowei</creatorcontrib><creatorcontrib>Peng, Di</creatorcontrib><creatorcontrib>Chu, Liang</creatorcontrib><creatorcontrib>Xue, Yu</creatorcontrib><title>DrLLPS: a data resource of liquid–liquid phase separation in eukaryotes</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
Here, we presented an integrative database named DrLLPS (http://llps.biocuckoo.cn/) for proteins involved in liquid–liquid phase separation (LLPS), which is a ubiquitous and crucial mechanism for spatiotemporal organization of various biochemical reactions, by creating membraneless organelles (MLOs) in eukaryotic cells. From the literature, we manually collected 150 scaffold proteins that are drivers of LLPS, 987 regulators that contribute in modulating LLPS, and 8148 potential client proteins that might be dispensable for the formation of MLOs, which were then categorized into 40 biomolecular condensates. We searched potential orthologs of these known proteins, and in total DrLLPS contained 437 887 known and potential LLPS-associated proteins in 164 eukaryotes. Furthermore, we carefully annotated LLPS-associated proteins in eight model organisms, by using the knowledge integrated from 110 widely used resources that covered 16 aspects, including protein disordered regions, domain annotations, post-translational modifications (PTMs), genetic variations, cancer mutations, molecular interactions, disease-associated information, drug-target relations, physicochemical property, protein functional annotations, protein expressions/proteomics, protein 3D structures, subcellular localizations, mRNA expressions, DNA & RNA elements, and DNA methylations. We anticipate DrLLPS can serve as a helpful resource for further analysis of LLPS.</description><subject>Database Issue</subject><subject>Databases, Factual</subject><subject>Eukaryota</subject><subject>Genome</subject><subject>Intrinsically Disordered Proteins - chemistry</subject><subject>Intrinsically Disordered Proteins - metabolism</subject><subject>Organelles</subject><subject>Protein Processing, Post-Translational</subject><subject>Proteins - chemistry</subject><subject>Proteins - metabolism</subject><subject>User-Computer Interface</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kM9Kw0AQhxdRbK2evMuevEjszm6ySTwIUv8VAgr2vmySSRtbs3E3EfTkO_iGPomR1KIXTzMw3_xm-Ag5BHYKLBbjStvxfPkGjIdbZAhCcs-PJd8mQyZY4AHzowHZc-6RMfAh8HfJQICMIeJ8SKaXNknuH86oprluNLXoTGszpKagq_K5LfPP94--ofVCO6QOa211U5qKlhXFdqntq2nQ7ZOdQq8cHqzriMyur2aTWy-5u5lOLhIv84E3XoxcImRpEQDyUOrCT0FiVogw1ExHCEFcZBJyKbSUPA8jASkCAxFgjJkWI3Lex9Zt-oR5hlVj9UrVtnzqHlFGl-rvpCoXam5eVAh-ICXrAk76gMwa5ywWm11g6luo6oSqtdCOPvp9bsP-GOyA4x4wbf1v0hfnYIHx</recordid><startdate>20200108</startdate><enddate>20200108</enddate><creator>Ning, Wanshan</creator><creator>Guo, Yaping</creator><creator>Lin, Shaofeng</creator><creator>Mei, Bin</creator><creator>Wu, Yu</creator><creator>Jiang, Peiran</creator><creator>Tan, Xiaodan</creator><creator>Zhang, Weizhi</creator><creator>Chen, Guowei</creator><creator>Peng, Di</creator><creator>Chu, Liang</creator><creator>Xue, Yu</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-9403-6869</orcidid></search><sort><creationdate>20200108</creationdate><title>DrLLPS: a data resource of liquid–liquid phase separation in eukaryotes</title><author>Ning, Wanshan ; Guo, Yaping ; Lin, Shaofeng ; Mei, Bin ; Wu, Yu ; Jiang, Peiran ; Tan, Xiaodan ; Zhang, Weizhi ; Chen, Guowei ; Peng, Di ; Chu, Liang ; Xue, Yu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c412t-9e26e1cbf51e276af4b16ecf377a0a8e159fc61d63a662d7831be10135e9eca3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Database Issue</topic><topic>Databases, Factual</topic><topic>Eukaryota</topic><topic>Genome</topic><topic>Intrinsically Disordered Proteins - chemistry</topic><topic>Intrinsically Disordered Proteins - metabolism</topic><topic>Organelles</topic><topic>Protein Processing, Post-Translational</topic><topic>Proteins - chemistry</topic><topic>Proteins - metabolism</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ning, Wanshan</creatorcontrib><creatorcontrib>Guo, Yaping</creatorcontrib><creatorcontrib>Lin, Shaofeng</creatorcontrib><creatorcontrib>Mei, Bin</creatorcontrib><creatorcontrib>Wu, Yu</creatorcontrib><creatorcontrib>Jiang, Peiran</creatorcontrib><creatorcontrib>Tan, Xiaodan</creatorcontrib><creatorcontrib>Zhang, Weizhi</creatorcontrib><creatorcontrib>Chen, Guowei</creatorcontrib><creatorcontrib>Peng, Di</creatorcontrib><creatorcontrib>Chu, Liang</creatorcontrib><creatorcontrib>Xue, Yu</creatorcontrib><collection>Oxford University Press Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ning, Wanshan</au><au>Guo, Yaping</au><au>Lin, Shaofeng</au><au>Mei, Bin</au><au>Wu, Yu</au><au>Jiang, Peiran</au><au>Tan, Xiaodan</au><au>Zhang, Weizhi</au><au>Chen, Guowei</au><au>Peng, Di</au><au>Chu, Liang</au><au>Xue, Yu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DrLLPS: a data resource of liquid–liquid phase separation in eukaryotes</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2020-01-08</date><risdate>2020</risdate><volume>48</volume><issue>D1</issue><spage>D288</spage><epage>D295</epage><pages>D288-D295</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
Here, we presented an integrative database named DrLLPS (http://llps.biocuckoo.cn/) for proteins involved in liquid–liquid phase separation (LLPS), which is a ubiquitous and crucial mechanism for spatiotemporal organization of various biochemical reactions, by creating membraneless organelles (MLOs) in eukaryotic cells. From the literature, we manually collected 150 scaffold proteins that are drivers of LLPS, 987 regulators that contribute in modulating LLPS, and 8148 potential client proteins that might be dispensable for the formation of MLOs, which were then categorized into 40 biomolecular condensates. We searched potential orthologs of these known proteins, and in total DrLLPS contained 437 887 known and potential LLPS-associated proteins in 164 eukaryotes. Furthermore, we carefully annotated LLPS-associated proteins in eight model organisms, by using the knowledge integrated from 110 widely used resources that covered 16 aspects, including protein disordered regions, domain annotations, post-translational modifications (PTMs), genetic variations, cancer mutations, molecular interactions, disease-associated information, drug-target relations, physicochemical property, protein functional annotations, protein expressions/proteomics, protein 3D structures, subcellular localizations, mRNA expressions, DNA & RNA elements, and DNA methylations. We anticipate DrLLPS can serve as a helpful resource for further analysis of LLPS.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>31691822</pmid><doi>10.1093/nar/gkz1027</doi><orcidid>https://orcid.org/0000-0002-9403-6869</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Database Issue Databases, Factual Eukaryota Genome Intrinsically Disordered Proteins - chemistry Intrinsically Disordered Proteins - metabolism Organelles Protein Processing, Post-Translational Proteins - chemistry Proteins - metabolism User-Computer Interface |
title | DrLLPS: a data resource of liquid–liquid phase separation in eukaryotes |
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