Large Scale Comparative Codon-Pair Context Analysis Unveils General Rules that Fine-Tune Evolution of mRNA Primary Structure
Open Access
- 5 September 2007
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 2 (9), e847
- https://doi.org/10.1371/journal.pone.0000847
Abstract
Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.This publication has 53 references indexed in Scilit:
- The frequency of translational misreading errors in E. coli is largely determined by tRNA competitionRNA, 2006
- Polymorphisms associated with the DAZ genes on the human Y chromosomeGenomics, 2005
- Gardening the genome: DNA methylation in Arabidopsis thalianaNature Reviews Genetics, 2005
- A Genomic Basis for the Evolution of Vertebrate Transcription Factors Containing Amino Acid RunsGenetics, 2004
- Tandem Repeats in Protein Coding Regions of Primate GenesGenome Research, 2002
- Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiaeJournal of Molecular Biology, 1997
- Codon contextCellular and Molecular Life Sciences, 1990
- Rates of aminoacyl-tRNA selection at 29 sense codons in vivoJournal of Molecular Biology, 1989
- Codon context effects in missense suppressionJournal of Molecular Biology, 1984
- Codon—anticodon pairing: The wobble hypothesisJournal of Molecular Biology, 1966