title: %(G+C) variation and prediction by a model of bacterial gene transfer and codon adaptation.
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.
authors.affiliation: Theoretical & Computational Biology Group, Michigan State University, East Lansing, Michigan 48824, USA. jhjacksn@msu.edu
authors.forename: Cedric O
authors.initials: CO
authors.lastname: Buckley
authors.forename: Desmond
authors.initials: D
authors.lastname: Stephens
authors.forename: Patricia A
authors.initials: PA
authors.lastname: Herring
authors.forename: Julius H
authors.initials: JH
authors.lastname: Jackson
mesh_terms: D001483:Base Sequence; D003062:Codon; D003596:Cytosine / Q000737:chemistry*; D018014:Gene Transfer Techniques; D005798:Genes, Bacterial; D005822:Genetic Vectors; D016680:Genome, Bacterial; D006147:Guanine / Q000737:chemistry*; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D012343:RNA, Transfer / Q000378:metabolism
chemical_list: D003062:Codon; D006147:Guanine; D003596:Cytosine; D012343:RNA, Transfer