title: Computational identification of the selenocysteine tRNA (tRNASec) in genomes.
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.
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.|Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.
authors.forename: Didac
authors.identifier: 0000-0003-3398-8943
authors.initials: D
authors.lastname: Santesmasses
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.|Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.|Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Marco
authors.identifier: 0000-0002-7411-4161
authors.initials: M
authors.lastname: Mariotti
authors.affiliation: Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.|Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.
authors.forename: Roderic
authors.identifier: 0000-0002-5738-4477
authors.initials: R
authors.lastname: Guigó
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D005819:Genetic Markers / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D040481:Genome Components / Q000235:genetics; D057166:High-Throughput Screening Assays / Q000379:methods*; D012345:RNA, Transfer, Amino Acid-Specific / Q000235:genetics*; D012346:RNA, Transfer, Amino Acyl / Q000235:genetics*; D017279:Selenocysteine
chemical_list: D005819:Genetic Markers; D012345:RNA, Transfer, Amino Acid-Specific; D012346:RNA, Transfer, Amino Acyl; C112705:selenocysteinyl-tRNA; C036928:tRNA, selenocysteine-; D017279:Selenocysteine