Selection intensity for codon bias

D. L. Hartl, E. N. Moriyama, S. A. Sawyer

Research output: Contribution to journalArticle

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Abstract

The patterns of nonrandom usage of synonymous codons (codon bias) in enteric bacteria were analyzed. Poisson random field (PRF) theory was used to derive the expected distribution of frequencies of nucleotides differing from the ancestral state at aligned sites in a set of DNA sequences. This distribution was applied to synonymous nucleotide polymorphisms and amino acid polymorphisms in the gnd and putP genes of Escherichia coli. For the gnd gene, the average intensity of selection against disfavored synonymous codons was estimated as approximately 7.3 x 10-9; this value is significantly smaller than the estimated selection intensity against selectively disfavored amino acids in observed polymorphisms (2.0 x 10-8), but it is approximately of the same order of magnitude. The selection coefficients for optimal synonymous codons estimated from PRF theory were consistent with independent estimates based on codon usage for threonine and glycine. Across 118 genes in E. coli and Salmonella typhimurium, the distribution of estimated selection coefficients, expressed as multiples of the effective population size, has a mean and standard deviation of 0.5 ± 0.4. No significant differences were found in the degree of codon bias between conserved positions and replacement positions, suggesting that translational misincorporation is not an important selective constraint among synonymous polymorphic codons in enteric bacteria. However, across the first 100 codons of the genes, conserved amino acids with identical codons have significantly greater codon bias than that of either synonymous or nonidentical codons, suggesting that there are unique selective constraints, perhaps including mRNA secondary structures, in this part of the coding region.

Original languageEnglish (US)
Pages (from-to)227-234
Number of pages8
JournalGenetics
Volume138
Issue number1
StatePublished - Jan 1 1994

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Codon
Enterobacteriaceae
Amino Acids
Genes
Nucleotides
Escherichia coli
Threonine
Salmonella typhimurium
Population Density
Glycine
Messenger RNA

ASJC Scopus subject areas

  • Genetics

Cite this

Hartl, D. L., Moriyama, E. N., & Sawyer, S. A. (1994). Selection intensity for codon bias. Genetics, 138(1), 227-234.

Selection intensity for codon bias. / Hartl, D. L.; Moriyama, E. N.; Sawyer, S. A.

In: Genetics, Vol. 138, No. 1, 01.01.1994, p. 227-234.

Research output: Contribution to journalArticle

Hartl, DL, Moriyama, EN & Sawyer, SA 1994, 'Selection intensity for codon bias', Genetics, vol. 138, no. 1, pp. 227-234.
Hartl DL, Moriyama EN, Sawyer SA. Selection intensity for codon bias. Genetics. 1994 Jan 1;138(1):227-234.
Hartl, D. L. ; Moriyama, E. N. ; Sawyer, S. A. / Selection intensity for codon bias. In: Genetics. 1994 ; Vol. 138, No. 1. pp. 227-234.
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