tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote.

RNA
James R Iben, R J Maraia

Abstract

tRNA genes are interspersed throughout eukaryotic DNA, contributing to genome architecture and evolution in addition to translation of the transcriptome. Codon use correlates with tRNA gene copy number in noncomplex organisms including yeasts. Synonymous codons impact translation with various outcomes, dependent on relative tRNA abundances. Availability of whole-genome sequences allowed us to examine tRNA gene copy number variation (tgCNV) and codon use in four Schizosaccharomyces species and Saccharomyces cerevisiae. tRNA gene numbers vary from 171 to 322 in the four Schizosaccharomyces despite very high similarity in other features of their genomes. In addition, we performed whole-genome sequencing of several related laboratory strains of Schizosaccharomyces pombe and found tgCNV at a cluster of tRNA genes. We examined for the first time effects of wobble rules on correlation of tRNA gene number and codon use and showed improvement for S. cerevisiae and three of the Schizosaccharomyces species. In contrast, correlation in Schizosaccharomyces japonicus is poor due to markedly divergent tRNA gene content, and much worsened by the wobble rules. In japonicus, some tRNA iso-acceptor genes are absent and others are greatly reduced ...Continue Reading

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Oct 27, 2012·Biochimica Et Biophysica Acta·Aneeshkumar G ArimbasseriRichard J Maraia
May 30, 2013·Molecular and Cellular Biology·Tek N LamichhaneRichard J Maraia
Dec 5, 2015·RNA Biology·Aneeshkumar G Arimbasseri, Richard J Maraia
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Dec 9, 2016·BMC Genomics·Brigitte GlanzmannPaul D van Helden
Jun 18, 2014·RNA·Richard J Maraia, James R Iben

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