THE CLOSE PROXIMITY OF ESCHERICHIA-COLI GENES - CONSEQUENCES FOR STOPCODON AND SYNONYMOUS CODON USE

It is shown that synonymous codon usage is less biased in favor of tho se codons preferred by highly expressed genes at the end of Escherichi a coli genes than in the middle. This appears to be due to the close p roximity of many E. coli genes. It is shown that a substantial number of genes overlap either the Shine-Dalgarno sequence or the coding sequ ence of the next gene on the chromosome and that the codons that overl ap have lower synonymous codon bias than those which do not. It is als o 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. c oli genes that lie close to another gene. It is suggested that these t rends in composition could be associated with selection against the fo rmation of mRNA secondary structure near the start of the next gene on the chromosome. Stop codon use is also affected by the close proximit y of genes; many genes are forced to use TGA and TAG stop codons becau se they terminate either within the Shine-Dalgarno or coding sequence of the next gene on the chromosome. The implications these results hav e for the evolution of synonymous codon use are discussed.