Codon bias in Escherichia coli: the influence of codon context on mutation and selection | Zendy

Otto G. Berg | Zendy; Pedro Silva | Zendy

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Codon bias in Escherichia coli: the influence of codon context on mutation and selection

Author(s) -

Otto G. Berg,

Pedro Silva

Publication year - 1997

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/25.7.1397

Subject(s) - biology , codon usage bias , genetics , escherichia coli , context (archaeology) , mutation , selection (genetic algorithm) , silent mutation , gene , genome , paleontology , missense mutation , artificial intelligence , computer science

The codon bias in Escherichia coli for all two-fold degenerate amino acids was studied as dependent on the context from the six bases in the nearest surrounding codons. By comparing the results in genes at different expression levels, effects that are due to differences in mutation rates can be distinguished from those that are due to selection. Selective effects on the codon bias is found mostly from the first neighbouring base in the 3'direction, while neighbouring bases further away influence mostly the mutational bias. In some cases it is also possible to identify specific molecular processes, repair or avoidance of frame shift, that lead to the context dependence of the bias.

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