TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs
Abstract T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no c...
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| Veröffentlicht in: | Nucleic acids research 2021-01, Vol.49 (D1), p.D229-D235 |
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| creator | Marchand, Jorge A Pierson Smela, Merrick D Jordan, Thomas H H Narasimhan, Kamesh Church, George M |
| description | Abstract
T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA. |
| doi_str_mv | 10.1093/nar/gkaa721 |
| format | Article |
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T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkaa721</identifier><identifier>PMID: 32882008</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Bacteria - genetics ; Bacteria - metabolism ; Base Pairing ; Base Sequence ; Database Issue ; Databases, Nucleic Acid ; Internet ; Molecular Sequence Annotation ; Nucleic Acid Conformation ; Riboswitch ; RNA, Transfer - chemistry ; RNA, Transfer - genetics ; RNA, Transfer - metabolism ; Software</subject><ispartof>Nucleic acids research, 2021-01, Vol.49 (D1), p.D229-D235</ispartof><rights>The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2021</rights><rights>The Author(s) 2020. 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-c439t-a17a799c02015cbdfdd3a7013cf4965e8067de305d7905ed8d4b72bfc6a3106e3</citedby><cites>FETCH-LOGICAL-c439t-a17a799c02015cbdfdd3a7013cf4965e8067de305d7905ed8d4b72bfc6a3106e3</cites><orcidid>0000-0002-5065-1085 ; 0000-0003-3535-2076 ; 0000000250651085 ; 0000000335352076</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/PMC7778990/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778990/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32882008$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1657648$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Marchand, Jorge A</creatorcontrib><creatorcontrib>Pierson Smela, Merrick D</creatorcontrib><creatorcontrib>Jordan, Thomas H H</creatorcontrib><creatorcontrib>Narasimhan, Kamesh</creatorcontrib><creatorcontrib>Church, George M</creatorcontrib><title>TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.</description><subject>Bacteria - genetics</subject><subject>Bacteria - metabolism</subject><subject>Base Pairing</subject><subject>Base Sequence</subject><subject>Database Issue</subject><subject>Databases, Nucleic Acid</subject><subject>Internet</subject><subject>Molecular Sequence Annotation</subject><subject>Nucleic Acid Conformation</subject><subject>Riboswitch</subject><subject>RNA, Transfer - chemistry</subject><subject>RNA, Transfer - genetics</subject><subject>RNA, Transfer - metabolism</subject><subject>Software</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kc1rFDEYh4Modq2evMvgQQQZ-2aSyUcPQlutCkVB1nN4J8l0o7OTNcmo_e-N7Fr04imHPDzvAz9CHlN4SUGzkxnTyfVXRNnRO2RFmeharkV3l6yAQd9S4OqIPMj5CwDltOf3yRHrlOoA1Ipcrs9fn5822DgsOGD2TRybXNJiy5Jwmm4anOdYsHjXrNsh_mxSGGL-EYrdnJZPH86aHYaUH5J7I07ZPzq8x-Tz5Zv1xbv26uPb9xdnV63lTJcWqUSptYUOaG8HNzrHUAJldqzJvVcgpPO12kkNvXfK8UF2w2gFMgrCs2Pyau_dLcPWO-vnUivNLoUtphsTMZh_f-awMdfxu5FSKq2hCp7uBTGXYLINxduNjfPsbTFU9FJwVaHnhyspflt8LmYbsvXThLOPSzYd58CFVr2o6Is9alPMOfnxtoWC-T2PqfOYwzyVfvJ3_i37Z48KPDvkLbv_mn4BGiWZSg</recordid><startdate>20210108</startdate><enddate>20210108</enddate><creator>Marchand, Jorge A</creator><creator>Pierson Smela, Merrick D</creator><creator>Jordan, Thomas H H</creator><creator>Narasimhan, Kamesh</creator><creator>Church, George M</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>7X8</scope><scope>OTOTI</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-5065-1085</orcidid><orcidid>https://orcid.org/0000-0003-3535-2076</orcidid><orcidid>https://orcid.org/0000000250651085</orcidid><orcidid>https://orcid.org/0000000335352076</orcidid></search><sort><creationdate>20210108</creationdate><title>TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs</title><author>Marchand, Jorge A ; Pierson Smela, Merrick D ; Jordan, Thomas H H ; Narasimhan, Kamesh ; Church, George M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c439t-a17a799c02015cbdfdd3a7013cf4965e8067de305d7905ed8d4b72bfc6a3106e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Bacteria - genetics</topic><topic>Bacteria - metabolism</topic><topic>Base Pairing</topic><topic>Base Sequence</topic><topic>Database Issue</topic><topic>Databases, Nucleic Acid</topic><topic>Internet</topic><topic>Molecular Sequence Annotation</topic><topic>Nucleic Acid Conformation</topic><topic>Riboswitch</topic><topic>RNA, Transfer - chemistry</topic><topic>RNA, Transfer - genetics</topic><topic>RNA, Transfer - metabolism</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Marchand, Jorge A</creatorcontrib><creatorcontrib>Pierson Smela, Merrick D</creatorcontrib><creatorcontrib>Jordan, Thomas H H</creatorcontrib><creatorcontrib>Narasimhan, Kamesh</creatorcontrib><creatorcontrib>Church, George M</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</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>Marchand, Jorge A</au><au>Pierson Smela, Merrick D</au><au>Jordan, Thomas H H</au><au>Narasimhan, Kamesh</au><au>Church, George M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2021-01-08</date><risdate>2021</risdate><volume>49</volume><issue>D1</issue><spage>D229</spage><epage>D235</epage><pages>D229-D235</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>32882008</pmid><doi>10.1093/nar/gkaa721</doi><orcidid>https://orcid.org/0000-0002-5065-1085</orcidid><orcidid>https://orcid.org/0000-0003-3535-2076</orcidid><orcidid>https://orcid.org/0000000250651085</orcidid><orcidid>https://orcid.org/0000000335352076</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Bacteria - genetics Bacteria - metabolism Base Pairing Base Sequence Database Issue Databases, Nucleic Acid Internet Molecular Sequence Annotation Nucleic Acid Conformation Riboswitch RNA, Transfer - chemistry RNA, Transfer - genetics RNA, Transfer - metabolism Software |
| title | TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs |
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