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TBDB – A database of structurally annotated T-box riboswitch:tRNA pairs

View ORCID ProfileJorge A. Marchand, View ORCID ProfileMerrick D. Pierson Smela, View ORCID ProfileThomas H. H. Jordan, View ORCID ProfileKamesh Narasimhan, View ORCID ProfileGeorge M. Church
doi: https://doi.org/10.1101/2020.06.17.157016
Jorge A. Marchand
1Department of Genetics, Harvard Medical School, Boston, MA 02115
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Merrick D. Pierson Smela
1Department of Genetics, Harvard Medical School, Boston, MA 02115
2Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
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Thomas H. H. Jordan
3Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Kamesh Narasimhan
1Department of Genetics, Harvard Medical School, Boston, MA 02115
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  • For correspondence: kamesh_narasimhan@hms.harvard.edu gchurch@genetics.med.harvard.edu
George M. Church
1Department of Genetics, Harvard Medical School, Boston, MA 02115
4Wyss Institute for Biologically Inspired Engineering, Boston, MA, 02115 USA
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  • For correspondence: kamesh_narasimhan@hms.harvard.edu gchurch@genetics.med.harvard.edu
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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-boxes 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 advance knowledge of computational tools to annotate riboswitch secondary structure features. Here we present T-box annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,497 T-box sequences, spanning the major phyla of 3,621 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory target. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.

Competing Interest Statement

This project has been funded by DOE grant DE-FG02-02ER63445. Dr. Church is a founder of the following companies in which he has related financial interests: ReadCoor; EnEvolv; and 64-x. For a complete list of financial interests of Prof. George Church, see also http://arep [dot]med[dot]harvard[dot]edu/gmc/tech[dot]html

Footnotes

  • https://tbdb.io

  • https://github.com/mpiersonsmela/tbox/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted June 19, 2020.
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TBDB – A database of structurally annotated T-box riboswitch:tRNA pairs
Jorge A. Marchand, Merrick D. Pierson Smela, Thomas H. H. Jordan, Kamesh Narasimhan, George M. Church
bioRxiv 2020.06.17.157016; doi: https://doi.org/10.1101/2020.06.17.157016
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TBDB – A database of structurally annotated T-box riboswitch:tRNA pairs
Jorge A. Marchand, Merrick D. Pierson Smela, Thomas H. H. Jordan, Kamesh Narasimhan, George M. Church
bioRxiv 2020.06.17.157016; doi: https://doi.org/10.1101/2020.06.17.157016

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