Genomic Choice of Codons in 16 Microbial Species

• Published in: Journal of biomolecular structure & dynamics 2004-12, Vol.22 (3), p.315-329
• Main Authors: Mougel, F., Manichanh, C., N'Guyen, G. Duchateau, Termier, M.
• Format: Article
• Language: English
• Subjects: Archaea; Base Composition; Codon; Computational Biology - methods; Databases as Topic; DNA - metabolism; Genome, Archaeal; Genome, Bacterial; Genome, Fungal; Open Reading Frames; Software
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2004.10507003

We study the codon usage over whole set of ORFs of 16 unicellular microbial species: eight archaebacteria, seven eubacteria, and one eukarya. We first try to define, for each species, the neutral expected codon usage to better approach subsequently the influence of selection. Overlapping triplets counted from the complete DNA genomic sequence and mean amino acid composition of ORFs allow us to build satisfying expected codon usage for each species. Within species deviation from this neutral model is then studied through Correspondence Analysis and characterization with bias index, N C′ (effective number of codons reported to neutral model). Our results are compared to previously published ones for three species and let appear good agreement in spite of very different methods. We thus propose set of codons probably preferred by selection for nine other species. In the four last species, no clear preference can be evidenced. Finally, we characterize variation of codon usage over functional categories. We propose that the high degree of bias of proteins involved in translation, ribosomal structure and biogenesis has a positive influence on overexpression of the corresponding genes under optimum growth conditions and is a negative regulator of the same genes when amino acids become limited resources.