Format

Send to

Choose Destination
See comment in PubMed Commons below
J Biomed Biotechnol. 2010;2010:202918. doi: 10.1155/2010/202918. Epub 2010 Jun 7.

Features of recent codon evolution: a comparative polymorphism-fixation study.

Author information

1
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. zhongming.zhao@vanderbilt.edu

Abstract

Features of amino-acid and codon changes can provide us important insights on protein evolution. So far, investigators have often examined mutation patterns at either interspecies fixed substitution or intraspecies nucleotide polymorphism level, but not both. Here, we performed a unique analysis of a combined set of intra-species polymorphisms and inter-species substitutions in human codons. Strong difference in mutational pattern was found at codon positions 1, 2, and 3 between the polymorphism and fixation data. Fixation had strong bias towards increasing the rarest codons but decreasing the most frequently used codons, suggesting that codon equilibrium has not been reached yet. We detected strong CpG effect on CG-containing codons and subsequent suppression by fixation. Finally, we detected the signature of purifying selection against Amid R:U dinucleotides at synonymous dicodon boundaries. Overall, fixation process could effectively and quickly correct the volatile changes introduced by polymorphisms so that codon changes could be gradual and directional and that codon composition could be kept relatively stable during evolution.

PMID:
20622912
PMCID:
PMC2896653
DOI:
10.1155/2010/202918
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Hindawi Publishing Corporation Icon for PubMed Central
    Loading ...
    Support Center