ArticlePLoS computational biology2017
Computational identification of the selenocysteine tRNA (tRNASec) in genomes.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 68 citations in OpenAlex.
- The mycobacterial selenocysteine machinery: presence and expression.RNA biology · 2026Article
- Recent advances in exploring the composition and evolution of the prokaryotic selenoproteome.Applied and environmental microbiology · 2026Review
- An atlas of plant selenium metabolism.The New phytologist · 2026Review
- Evolution, structure and function of L-cysteine desulfidase, an enzyme involved in sulfur metabolism in the methanogenic archeon Methanococcus maripaludis.Communications biology · 2025Article
- Article
- Unveiling the Role of Selenium in Child Development: Impacts on Growth, Neurodevelopment and Immunity.Journal of clinical medicine · 2025Review
- Yerba mate (eLife · 2025Article
- Asgard archaea modulate potential methanogenesis substrates in wetland soil.Nature communications · 2024Article
- Article
- Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery.The ISME journal · 2024Article
- Selenoproteins in Health.Molecules (Basel, Switzerland) · 2023Review
- A homozygous mutation in the human selenocysteine tRNA gene impairs UGA recoding activity and selenoproteome regulation by selenium.Nucleic acids research · 2023Article
- Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective.Biomolecules · 2022Review
- Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution.Molecular biology and evolution · 2022Article
- Unconventional genetic code systems in archaea.Frontiers in microbiology · 2022Review
- Historical Roles of Selenium and Selenoproteins in Health and Development: The Good, the Bad and the Ugly.International journal of molecular sciences · 2021Review
- A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis.BMC genomics · 2021Article
- An Ecological Basis for Dual Genetic Code Expansion in Marine Deltaproteobacteria.Frontiers in microbiology · 2021Article
- Programmed Deviations of Ribosomes From Standard Decoding in Archaea.Frontiers in microbiology · 2021Review
- The algal selenoproteomes.BMC genomics · 2020Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.