A role for tRNA modifications in genome structure and codon usage.

Abstract:

:Transfer RNA (tRNA) gene content is a differentiating feature of genomes that contributes to the efficiency of the translational apparatus, but the principles shaping tRNA gene copy number and codon composition are poorly understood. Here, we report that the emergence of two specific tRNA modifications shaped the structure and composition of all extant genomes. Through the analysis of more than 500 genomes, we identify two kingdom-specific tRNA modifications as major contributors that separated archaeal, bacterial, and eukaryal genomes in terms of their tRNA gene composition. We show that, contrary to prior observations, genomic codon usage and tRNA gene frequencies correlate in all kingdoms if these two modifications are taken into account and that presence or absence of these modifications explains patterns of gene expression observed in previous studies. Finally, we experimentally demonstrate that human gene expression levels correlate well with genomic codon composition if these identified modifications are considered.

journal_name

Cell

journal_title

Cell

authors

Novoa EM,Pavon-Eternod M,Pan T,Ribas de Pouplana L

doi

10.1016/j.cell.2012.01.050

subject

Has Abstract

pub_date

2012-03-30 00:00:00

pages

202-13

issue

1

eissn

0092-8674

issn

1097-4172

pii

S0092-8674(12)00212-7

journal_volume

149

pub_type

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