Nucleic Acids Research, 1989, Vol. 17, No. 13 5029-5040
© 1989
MOLECULAR BIOLOGY |
Codon usage and gene expression level in Dictyosteiium discoidtum: highly expressed genes do [prefer[ optimal codons
Department of Genetics, Trinity College Dublin 2, Ireland
Received April 14, 1989. Accepted June 12, 1989.
Codon usage patterns in the slime mould Dictyosteiium discoideum have been reexamined (a total of 58 genes have been analysed). Considering the extreme A+T-richness of this genome (G+C
22%), there is a surprising degree of codon usage variation among genes. For example, G+C content at silent sites varies from less than 10% to greater than 30%. It was previously suggested [Warrick, H.M. and Spudich, J.A. (1988) Nucleic Acids Res. 16: 6617—6635] that highly expressed genes contain fewer 'optimal' codons than genes expressed at lower levels. However, it appears that the optimal codons were misidentified. Multivariate statistical analysis shows that the greatest variation among genes is in relative usage of a particular subset of codons (about one per amino acid), many of which are C-ending. We have identified these as optimal codons, since (i) their frequency is positively correlated with gene expression level, and (ii) there is a strong mutation bias in this genome towards A and T nucleotides. Thus, codon usage in D.discoideum can be explained by a balance between the forces of mutational bias and translational selection.
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