Analysis of the codon bias in E. coli sequences

Journal of Biomolecular Structure & Dynamics
R D Blake, P W Hinds

Abstract

Fifty-three gene sequences from E. coli containing 18,288 reading frame triplets have been characterized according to the nature and level of average codon preference. The distribution of average preferences is bimodal, with approximately half the genes using an average of only 36 codons, and the remainder just 42 codons. There is a high correlation between the level of codon bias, the tRNA population and the abundance of protein product, indicating biased patterns are exploited by the cell for the production of widely different levels of gene product. This relationship is especially striking in genes involved in the production of components for transcription and translation. Overall, the genes for these processes generate some five-fold more protein than the average in the genome, and use about five fewer codons. The very high codon bias found in the RNA polymerase gene thus provides a simple, autogenous mechanism for the coordinate synthesis of these components and RNA polymerase. A surprisingly high level of codon probability is also found in triplets of the complement of coding sequences. This is apparently due to the evolutionary dispersion of coding sequences and/or the requirement for increased levels of secondary struct...Continue Reading

References

May 24, 1978·Biochimica Et Biophysica Acta·T TakagiS Iwanaga
Jul 29, 1976·Nature·G T RobillardH J Berendsen
Jun 1, 1966·Journal of Cellular Physiology·H A Itano
Apr 29, 1982·Biochemical and Biophysical Research Communications·H KanazawaM Futai
Jan 1, 1983·Journal of Molecular Evolution·R HolmquistJ Czelusniak
Jan 11, 1984·Nucleic Acids Research·R Staden
Sep 16, 1981·Biochemical and Biophysical Research Communications·K MabuchiM Futai
Nov 25, 1982·Nucleic Acids Research·M Gouy, C Gautier
Mar 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·J C Shepherd
Jan 11, 1982·Nucleic Acids Research·R Staden, A D McLachlan
Sep 11, 1982·Nucleic Acids Research·J W Fickett
Jan 10, 1981·Nucleic Acids Research·R GranthamR Mercier
Jan 1, 1984·Computers & Graphics·J T EganR D MacElroy
Jan 25, 1959·The Journal of Biophysical and Biochemical Cytology·G ZUBAY, M R WATSON

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Citations

Apr 1, 1992·Journal of Molecular Evolution·M A HuynenP Hogeweg
Jan 1, 1986·Progress in Biophysics and Molecular Biology·A Wada, A Suyama
Apr 11, 1986·Nucleic Acids Research·L Holm
Jul 20, 2006·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Géraldine PascalAntoine Danchin
Oct 1, 1986·Journal of Biomolecular Structure & Dynamics·R D Blake, S Earley
Feb 1, 1986·Journal of Biomolecular Structure & Dynamics·A S Kolaskar, B V Reddy
Dec 1, 1985·Journal of Biomolecular Structure & Dynamics·P W Hinds, R D Blake
Dec 20, 1991·Journal of Molecular Biology·C MédigueA Danchin
Sep 1, 1993·Microbiological Reviews·C MédigueA Danchin
Jan 7, 1987·Journal of Theoretical Biology·H Liljenström, G von Heijne

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