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Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics

Decoding of all codons can be achieved by a subset of tRNAs. In bacteria, certain tRNA species are mandatory, while others are auxiliary and are variably used. It is currently unknown how this variability has evolved and whether it provides an adaptive advantage. Here we shed light on the subset of...

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Detalles Bibliográficos
Autores principales: Wald, Naama, Margalit, Hanah
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041420/
https://www.ncbi.nlm.nih.gov/pubmed/24782525
http://dx.doi.org/10.1093/nar/gku245
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author Wald, Naama
Margalit, Hanah
author_facet Wald, Naama
Margalit, Hanah
author_sort Wald, Naama
collection PubMed
description Decoding of all codons can be achieved by a subset of tRNAs. In bacteria, certain tRNA species are mandatory, while others are auxiliary and are variably used. It is currently unknown how this variability has evolved and whether it provides an adaptive advantage. Here we shed light on the subset of auxiliary tRNAs, using genomic data from 319 bacteria. By reconstructing the evolution of tRNAs we show that the auxiliary tRNAs are highly dynamic, being frequently gained and lost along the phylogenetic tree, with a clear dominance of loss events for most auxiliary tRNA species. We reveal distinct co-gain and co-loss patterns for subsets of the auxiliary tRNAs, suggesting that they are subjected to the same selection forces. Controlling for phylogenetic dependencies, we find that the usage of these tRNA species is positively correlated with GC content and may derive directly from nucleotide bias or from preference of Watson–Crick codon–anticodon interactions. Our results highlight the highly dynamic nature of these tRNAs and their complicated balance with codon usage.
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spelling pubmed-40414202014-06-11 Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics Wald, Naama Margalit, Hanah Nucleic Acids Res RNA Decoding of all codons can be achieved by a subset of tRNAs. In bacteria, certain tRNA species are mandatory, while others are auxiliary and are variably used. It is currently unknown how this variability has evolved and whether it provides an adaptive advantage. Here we shed light on the subset of auxiliary tRNAs, using genomic data from 319 bacteria. By reconstructing the evolution of tRNAs we show that the auxiliary tRNAs are highly dynamic, being frequently gained and lost along the phylogenetic tree, with a clear dominance of loss events for most auxiliary tRNA species. We reveal distinct co-gain and co-loss patterns for subsets of the auxiliary tRNAs, suggesting that they are subjected to the same selection forces. Controlling for phylogenetic dependencies, we find that the usage of these tRNA species is positively correlated with GC content and may derive directly from nucleotide bias or from preference of Watson–Crick codon–anticodon interactions. Our results highlight the highly dynamic nature of these tRNAs and their complicated balance with codon usage. Oxford University Press 2014-06-01 2014-04-29 /pmc/articles/PMC4041420/ /pubmed/24782525 http://dx.doi.org/10.1093/nar/gku245 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Wald, Naama
Margalit, Hanah
Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics
title Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics
title_full Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics
title_fullStr Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics
title_full_unstemmed Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics
title_short Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics
title_sort auxiliary trnas: large-scale analysis of trna genes reveals patterns of trna repertoire dynamics
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041420/
https://www.ncbi.nlm.nih.gov/pubmed/24782525
http://dx.doi.org/10.1093/nar/gku245
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