Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do prefer optimal codons

• Published in: Nucleic acids research Vol. 17; no. 13; pp. 5029 - 5039
• Main Authors: SHARP, P. M, DEVINE, K. M
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 11.07.1989
• Subjects: Biological and medical sciences; Codon - genetics; Dictyostelium - genetics; Dictyostelium discoideum; Fundamental and applied biological sciences. Psychology; Gene expression; Genes; Genes, Fungal; Information Systems; Molecular and cellular biology; Molecular genetics; RNA, Messenger - genetics; Transcription, Genetic; Dictyostelium discoideum; Protozoa; Codon; Nucleotide sequence; DNA; Use; Multivariate analysis; Gene expression; Mycetozoa
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/17.13.5029

Codon usage patterns in the slime mould Dictyostelium discoideum have been re-examined (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.