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

Naama Wald, Hanah Margalit*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

Abstract

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.

Original languageAmerican English
Pages (from-to)6552-6566
Number of pages15
JournalNucleic Acids Research
Volume42
Issue number10
DOIs
StatePublished - 2 Jun 2014

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