Codon and base biases after the initiation codon of the open reading frames in the Escherichia coli genome and their influence on the translation efficiency

Toru Sato, Mahito Terabe, Hidemi Watanabe, Takashi Gojobori, Chie Hori-Takemoto, Kin Ichiro Miura*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

44 Scopus citations

Abstract

Nucleotide sequences around the boundaries of all open reading frames in the Escherichia coli whole genome were analyzed. Characteristic base biases were observed after the initiation codon and before the termination codon. We examined the effect of the base sequence after the initiation codon on the translation efficiency, by introducing mutations after the initiation codon of the E. coli dihydrofolate reductase (DHFR) gene, considering codon and base biases, and using in vitro and in vivo translation systems. In both assay systems, the two most frequent second codons, AAA and AAU, enhanced the translation efficiency compared with the wild type, whereas the effects of lower frequency codons were not significant. Experiments using 16S rRNA variants with mutations in the putative complementary sequence to the region downstream of the initiation codon showed that the translation efficiency of none of the DHFR mutants was affected. These results demonstrate that the statistically most frequent sequences for the second codon enhance translation efficiency, and this effect seems to be independent of base pairing between mRNA and 16S rRNA.

Original languageEnglish (US)
Pages (from-to)851-860
Number of pages10
JournalJournal of Biochemistry
Volume129
Issue number6
DOIs
StatePublished - 2001
Externally publishedYes

Keywords

  • 16S rRNA
  • Codon and base biases
  • Escherichia coli
  • Second codon
  • Translation efficiency

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry
  • Molecular Biology

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