The close proximity ofEscherichia coli genes: Consequences for stop codon and synonymous codon use (original) (raw)
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Abstract
It is shown that synonymous codon usage is less biased in favor of those codons preferred by highly expressed genes at the end of_Escherichia coli_ genes than in the middle. This appears to be due to the close proximity of many_E. coli_ genes. It is shown that a substantial number of genes overlap either the Shine-Dalgarno sequence or the coding sequence of the next gene on the chromosome and that the codons that overlap have lower synonymous codon bias than those which do not. It is also shown that there is an increase in the frequency of A-ending codons, and a decrease in the frequency of G-ending codons at the end of_E. coli_ genes that lie close to another gene. It is suggested that these trends in composition could be associated with selection against the formation of mRNA secondary structure near the start of the next gene on the chromosome. Stop codon use is also affected by the close proximity of genes; many genes are forced to use TGA and TAG stop codons because they terminate either within the Shine-Dalgarno or coding sequence of the next gene on the chromosome. The implications these results have for the evolution of synonymous codon use are discussed.
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- Adam Eyre-Walker
Present address: Department of Plant Science, Foran Hall, Cook Campus, Rutgers University, 08903, New Brunswick, NJ, USA
Authors and Affiliations
- Department of Biological Sciences, Rutgers University, 08855-1059, Piscataway, NJ, USA
Adam Eyre-Walker
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Eyre-Walker, A. The close proximity of_Escherichia coli_ genes: Consequences for stop codon and synonymous codon use.J Mol Evol 42, 73–78 (1996). https://doi.org/10.1007/BF02198830
- Received: 17 February 1995
- Accepted: 15 September 1995
- Issue date: February 1996
- DOI: https://doi.org/10.1007/BF02198830