Logo of narLink to Publisher's site
Nucleic Acids Res. 1993 Sep 25; 21(19): 4599–4603.
PMCID: PMC311196

Reduced synonymous substitution rate at the start of enterobacterial genes.

Abstract

Synonymous codon usage is less biased at the start of Escherichia coli genes than elsewhere. The rate of synonymous substitution between E.coli and Salmonella typhimurium is substantially reduced near the start of the gene, which suggests the presence of an additional selection pressure which competes with the selection for codons which are most rapidly translated. Possible competing sources of selection are the presence of secondary ribosome binding sites downstream from the start codon, the avoidance of mRNA secondary structure near the start of the gene and the use of sub-optimal codons to regulate gene expression. We provide evidence against the last of these possibilities. We also show that there is a decrease in the frequency of A, and an increase in the frequency of G along the E.coli genes at all three codon positions. We argue that these results are most consistent with selection to avoid mRNA secondary structure.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (893K), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 1985 Jan;2(1):13–34. [PubMed]
  • Pedersen S. Escherichia coli ribosomes translate in vivo with variable rate. EMBO J. 1984 Dec 1;3(12):2895–2898. [PMC free article] [PubMed]
  • Sørensen MA, Kurland CG, Pedersen S. Codon usage determines translation rate in Escherichia coli. J Mol Biol. 1989 May 20;207(2):365–377. [PubMed]
  • Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics. 1991 Nov;129(3):897–907. [PMC free article] [PubMed]
  • Kurland CG. Codon bias and gene expression. FEBS Lett. 1991 Jul 22;285(2):165–169. [PubMed]
  • Bulmer M. Codon usage and intragenic position. J Theor Biol. 1988 Jul 8;133(1):67–71. [PubMed]
  • Chen GF, Inouye M. Suppression of the negative effect of minor arginine codons on gene expression; preferential usage of minor codons within the first 25 codons of the Escherichia coli genes. Nucleic Acids Res. 1990 Mar 25;18(6):1465–1473. [PMC free article] [PubMed]
  • Konigsberg W, Godson GN. Evidence for use of rare codons in the dnaG gene and other regulatory genes of Escherichia coli. Proc Natl Acad Sci U S A. 1983 Feb;80(3):687–691. [PMC free article] [PubMed]
  • Petersen GB, Stockwell PA, Hill DF. Messenger RNA recognition in Escherichia coli: a possible second site of interaction with 16S ribosomal RNA. EMBO J. 1988 Dec 1;7(12):3957–3962. [PMC free article] [PubMed]
  • Sprengart ML, Fatscher HP, Fuchs E. The initiation of translation in E. coli: apparent base pairing between the 16srRNA and downstream sequences of the mRNA. Nucleic Acids Res. 1990 Apr 11;18(7):1719–1723. [PMC free article] [PubMed]
  • Faxén M, Plumbridge J, Isaksson LA. Codon choice and potential complementarity between mRNA downstream of the initiation codon and bases 1471-1480 in 16S ribosomal RNA affects expression of glnS. Nucleic Acids Res. 1991 Oct 11;19(19):5247–5251. [PMC free article] [PubMed]
  • Gold L. Posttranscriptional regulatory mechanisms in Escherichia coli. Annu Rev Biochem. 1988;57:199–233. [PubMed]
  • de Smit MH, van Duin J. Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Proc Natl Acad Sci U S A. 1990 Oct;87(19):7668–7672. [PMC free article] [PubMed]
  • Vellanoweth RL, Rabinowitz JC. The influence of ribosome-binding-site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo. Mol Microbiol. 1992 May;6(9):1105–1114. [PubMed]
  • Devereux J, Haeberli P, Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. [PMC free article] [PubMed]
  • Sharp PM, Li WH. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987 Feb 11;15(3):1281–1295. [PMC free article] [PubMed]
  • Sharp PM. Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J Mol Evol. 1991 Jul;33(1):23–33. [PubMed]
  • Sharp PM, Li WH. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res. 1986 Oct 10;14(19):7737–7749. [PMC free article] [PubMed]
  • Stormo GD, Schneider TD, Gold LM. Characterization of translational initiation sites in E. coli. Nucleic Acids Res. 1982 May 11;10(9):2971–2996. [PMC free article] [PubMed]
  • Schneider TD, Stormo GD, Gold L, Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J Mol Biol. 1986 Apr 5;188(3):415–431. [PubMed]
  • Kozak M. Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles. Microbiol Rev. 1983 Mar;47(1):1–45. [PMC free article] [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...