Bioinformatic Analysis of Codon Usage Patterns in a Free Living Diazotroph, Azotobacter vinelandii

Synonymous codon usage analysis of the protein coding genes, nitrogen fixation related genes and ribosomal protein genes of Azotobacter vinelandii were performed and potentially highly expressed genes were detected. Codon usage was highly biased. Genes in the genome exhibited considerable amount of heterogeneity. However, unlike ribosomal protein genes, which were governed by translational selection, those genes associated with nitrogen fixation were affected by mutational pressure. Using the Codon Adaptation Index (CAI) as a numerical estimator of gene expression level, highly expressed genes in Azotobacter were predicted with ribosomal protein genes as a reference. Highly expressed genes are affluent in of GC rich codons. We have identified 503 potentially highly expressed genes having diverse functions. PHX genes present in the COG groups were identified. Most of them are associated with major metabolic functions. Ten PHX genes linked to the nitrogen fixing mechanism has also been identified. These results specify the capability of the bacterium to survive in a free-living state, compete with other soil bacteria and fix nitrogen in a manner somewhat different from the conventional.