Moura GR, Pinheiro M, Freitas A, Oliveira JL, Frommlet JC, Carreto L, Soares AR, Bezerra AR, Santos MAS. Species-specific codon context rules unveil non-neutrality effects of synonymous mutations.
PLoS One 2011;
6:e26817. [PMID:
22046369 PMCID:
PMC3202573 DOI:
10.1371/journal.pone.0026817]
[Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 10/05/2011] [Indexed: 11/18/2022] Open
Abstract
Background
Codon pair usage (codon context) is a species specific gene primary structure feature whose evolutionary and functional roles are poorly understood. The data available show that codon-context has direct impact on both translation accuracy and efficiency, but one does not yet understand how it affects these two translation variables or whether context biases shape gene evolution.
Methodologies/Principal Findings
Here we study codon-context biases using a set of 72 orthologous highly conserved genes from bacteria, archaea, fungi and high eukaryotes to identify 7 distinct groups of codon context rules. We show that synonymous mutations, i.e., neutral mutations that occur in synonymous codons of codon-pairs, are selected to maintain context biases and that non-synonymous mutations, i.e., non-neutral mutations that alter protein amino acid sequences, are also under selective pressure to preserve codon-context biases.
Conclusions
Since in vivo studies provide evidence for a role of codon context on decoding fidelity in E. coli and for decoding efficiency in mammalian cells, our data support the hypothesis that, like codon usage, codon context modulates the evolution of gene primary structure and fine tunes the structure of open reading frames for high genome translational fidelity and efficiency in the 3 domains of life.
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