{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T08:03:50Z","timestamp":1773475430140,"version":"3.50.1"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,9,3]],"date-time":"2020-09-03T00:00:00Z","timestamp":1599091200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-FG02-02ER63445"],"award-info":[{"award-number":["DE-FG02-02ER63445"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>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.<\/jats:p>","DOI":"10.1093\/nar\/gkaa721","type":"journal-article","created":{"date-parts":[[2020,8,21]],"date-time":"2020-08-21T15:14:29Z","timestamp":1598022869000},"page":"D229-D235","source":"Crossref","is-referenced-by-count":20,"title":["TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs"],"prefix":"10.1093","volume":"49","author":[{"given":"Jorge A","family":"Marchand","sequence":"first","affiliation":[{"name":"Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"}]},{"given":"Merrick D","family":"Pierson\u00a0Smela","sequence":"additional","affiliation":[{"name":"Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA"},{"name":"Wyss Institute for Biologically Inspired Engineering, Boston, MA\u00a002115, USA"}]},{"given":"Thomas H H","family":"Jordan","sequence":"additional","affiliation":[{"name":"Institute of Chemical Sciences and Engineering, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Lausanne, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5065-1085","authenticated-orcid":false,"given":"Kamesh","family":"Narasimhan","sequence":"additional","affiliation":[{"name":"Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3535-2076","authenticated-orcid":false,"given":"George M","family":"Church","sequence":"additional","affiliation":[{"name":"Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"Wyss Institute for Biologically Inspired Engineering, Boston, MA\u00a002115, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,9,3]]},"reference":[{"key":"2021010313110522200_B1","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1016\/j.cbpa.2005.09.016","article-title":"Riboswitches and the role of noncoding RNAs in bacterial metabolic control","volume":"9","author":"Winkler","year":"2005","journal-title":"Curr. 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Bacteriol."},{"key":"2021010313110522200_B6","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1016\/0092-8674(93)80049-K","article-title":"tRNA as a positive regulator of transcription antitermination in B. subtilis","volume":"74","author":"Grundy","year":"1993","journal-title":"Cell"},{"key":"2021010313110522200_B7","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1016\/j.bbagrm.2014.04.022","article-title":"The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand","volume":"1839","author":"Henkin","year":"2014","journal-title":"Biochim. Biophys. Acta - Gene Regul. Mech."},{"key":"2021010313110522200_B8","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1073\/pnas.1424175112","article-title":"T box riboswitches in Actinobacteria: Translational regulation via novel tRNA interactions","volume":"112","author":"Sherwood","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2021010313110522200_B9","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/j.febslet.2009.11.056","article-title":"The T box mechanism: tRNA as a regulatory molecule","volume":"584","author":"Green","year":"2010","journal-title":"FEBS Lett."},{"key":"2021010313110522200_B10","first-page":"1","article-title":"Unboxing the T-box riboswitches \u2013 a glimpse into multivalent and multimodal RNA \u2013 RNA interactions","author":"Zhang","year":"2020","journal-title":"WIREs RNA"},{"key":"2021010313110522200_B11","doi-asserted-by":"crossref","first-page":"1790","DOI":"10.1261\/rna.052712.115","article-title":"A glyS T-box riboswitch with species-specific structural features responding to both proteinogenic and nonproteinogenic tRNA Gly isoacceptors","volume":"21","author":"Apostolidi","year":"2015","journal-title":"Rna"},{"key":"2021010313110522200_B12","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/S0022-2836(02)01339-6","article-title":"Solution structure of the Bacillus subtilis T-box antiterminator RNA: Seven nucleotide bulge characterized by stacking and flexibility","volume":"326","author":"Gerdeman","year":"2003","journal-title":"J. Mol. Biol."},{"key":"2021010313110522200_B13","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.bbagrm.2008.12.004","article-title":"T box transcription antitermination riboswitch: Influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element","volume":"1789","author":"Fauzi","year":"2009","journal-title":"Biochim. Biophys. Acta - Gene Regul. Mech."},{"key":"2021010313110522200_B14","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1038\/s41594-019-0327-6","article-title":"Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators","volume":"26","author":"Battaglia","year":"2019","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2021010313110522200_B15","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1038\/s41594-019-0326-7","article-title":"Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions","volume":"26","author":"Li","year":"2019","journal-title":"Nat. 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