Computational identification of the selenocysteine tRNA (tRNASec) in genomes

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  • dc.contributor.author Santesmasses Ruiz, Didac, 1978-ca
  • dc.contributor.author Mariotti, Marco, 1984-ca
  • dc.contributor.author Guigó Serra, Rodericca
  • dc.date.accessioned 2017-06-20T12:05:41Z
  • dc.date.available 2017-06-20T12:05:41Z
  • dc.date.issued 2017
  • dc.description.abstract Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages. Available tRNA prediction methods fail to accurately predict tRNASec, due to its unusual structural fold. Here, we present Secmarker, a method based on manually curated covariance models capturing the specific tRNASec structure in archaea, bacteria and eukaryotes. We exploited the non-universality of Sec to build a proper benchmark set for tRNASec predictions, which is not possible for the predictions of other tRNAs. We show that Secmarker greatly improves the accuracy of previously existing methods constituting a valuable tool to identify tRNASec genes, and to efficiently determine whether a genome contains selenoproteins. We used Secmarker to analyze a large set of fully sequenced genomes, and the results revealed new insights in the biology of tRNASec, led to the discovery of a novel bacterial selenoprotein family, and shed additional light on the phylogenetic distribution of selenoprotein containing genomes. Secmarker is freely accessible for download, or online analysis through a web server at http://secmarker.crg.cat.
  • dc.description.sponsorship This work was funded by the Ministry of Economy and Competitiveness (MINECO) under the grant number BIO2011-26205. We acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017’ SEV-2012-0208 and also the support of the Agency for the Research Centres of Catalonia CERCA Programme / Generalitat de Catalunya.
  • dc.format.mimetype application/pdfca
  • dc.identifier.citation Santesmasses D, Mariotti M, Guigó Serra R. Computational identification of the selenocysteine tRNA (tRNASec) in genomes. PLoS Computational Biology. 2017;13(2):e1005383. DOI: 10.1371/journal.pcbi.1005383
  • dc.identifier.doi http://dx.doi.org/10.1371/journal.pcbi.1005383
  • dc.identifier.issn 1553-734X
  • dc.identifier.uri http://hdl.handle.net/10230/32385
  • dc.language.iso eng
  • dc.publisher Public Library of Science (PLoS)ca
  • dc.relation.ispartof PLoS Computational Biology. 2017;13(2):e1005383
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2011-26205
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV2012-0208
  • dc.rights © 2017 Santesmasses et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri https://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Invertebrate genomics
  • dc.subject.keyword Transfer RNA
  • dc.subject.keyword Sequence alignment
  • dc.subject.keyword Genomic databases
  • dc.subject.keyword Archaean biology
  • dc.subject.keyword Gene prediction
  • dc.subject.keyword Multiple alignment calculation
  • dc.subject.keyword Anticodons
  • dc.title Computational identification of the selenocysteine tRNA (tRNASec) in genomesca
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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