Statistical Analysis of codon usage in extremely halophilic bacterium, Salinibacterruber DSM 13855

Abstract

Sanjukta RK, Farooqi MS, Sharma N, Rai N, Mishra DC, Rai A, Singh DP, Chaturvedi KK., Statistical Analysis of codon usage in extremely halophilic bacterium, Salinibacter ruber DSM 13855, Online J Bioinform., 14(1): 15-31, 2013. Synonymous codons are randomly distributed among genes, a phenomenon termed as codon usage bias. Understanding the extent and pattern of codon bias; the forces affecting codon usage are the key steps towards elucidating the adaptive choice of codon at the level of individual genes. Herein, trends in codon usage bias in a set of 1450 genes in Salinibacter ruber, an extremely halophilic bacterium have been evaluated. Notably, synonymous codon usage varies considerably among genes of this bacterium. Base composition (mutational bias) particularly C- and G-ending codons predominate with greater preference of ‘C’ at synonymously variable sites. The effect of natural selection acting at the level of translation has been observed. Certain genes with a high codon bias have been identified by multivariate statistical approach and investigations through various codon bias indices. These genes appearto be highly expressed, and their codon usage seems to have been shaped by selection favouring a limited number of translationally optimal codons. A subset of 27 optimal codons seems to be preferentially used in highly expressed genes. The frequency of these codons appears to be correlated with the level of gene expression, and may be a useful indicator in the case of genes (or open reading frames) whose expression levels are unknown.