%(G+C) variation and prediction by a model of bacterial gene transfer and codon adaptation

OMICS. 2002;6(3):259-72. doi: 10.1089/15362310260256918.

Abstract

The %(G + C) of bacterial genomes ranges from 25% in Mycoplasma to 75% in Micrococcus. Our model for horizontal gene flow enabled a theoretical study of the adaptation of relative codon frequency to match the pattern of the tRNA set of a new host. This study explored the dynamic relationship of %(G + C) to vectors of relative codon frequency (F(gamma)), relative amino acid coding frequency (F(alpha)), and absolute codon frequency (F(|gamma|)) in chromosomes of nine, fully sequenced bacterial genomes that varied widely in %(G + C). At constant F(alpha), the theoretical maximum average range possible was %(G + C) = 37.4 +/- 0.9%. In simulations of F(gamma) adaptation to a new host following hypothetical gene transfer, we modeled %(G + C) as a function of F(gamma) and F(alpha). The simulation revealed that %(G + C) is dependent on F(gamma) and F(alpha) in an explicit relationship described in this paper. We conclude that (1) F(gamma) and F(alpha) determine %(G + C), and (2) the degree of adaptation of %(G + C) in a transferred gene depends upon the degree of F(gamma) equilibration and the similarity of F(alpha) of the transferred gene to that of the new host.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Codon*
  • Cytosine / chemistry*
  • Gene Transfer Techniques*
  • Genes, Bacterial*
  • Genetic Vectors
  • Genome, Bacterial
  • Guanine / chemistry*
  • Models, Genetic
  • Models, Statistical
  • Molecular Sequence Data
  • RNA, Transfer / metabolism

Substances

  • Codon
  • Guanine
  • Cytosine
  • RNA, Transfer