Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis

Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined. In a neutrality analysis, the correlation between GC₁₂ and GC₃ was statistically significant, and the regression line had a relatively gradual slope (0.218). NC-plot, i.e., GC₃ vs effective number of codons (ENC), showed that most of the tyrosinase genes were below the expected curve. The codon adaptation index (CAI) values of the platyhelminth tyrosinases had a narrow distribution between 0.685/0.714 and 0.797/0.837, and were negatively correlated with their ENC. Taken together, these results suggested that CUB in the tyrosinase genes seemed to be basically governed by selection pressures rather than mutational bias, although the latter factor provided an additional force in shaping CUB of the C. sinensis and Opisthorchis viverrini genes. It was also apparent that the equilibrium point between selection pressure and mutational bias is much more inclined to selection pressure in highly expressed C. sinensis genes, than in poorly expressed genes.

Expression analysis of genes responsible for amino acid biosynthesis in halophilic bacterium Salinibacter ruber.

The degeneracy of the genetic code allows for multiple codons to encode the same amino acid. However, alternative codons and amino acids are used unevenly among genes, a phenomenon termed codon-usage bias. Genes regulating amino acid biosynthesis of Salinibacter ruber, an extremely halophilic bacterium were studied in order to determine the synonymous codon usage patterns. Factors responsible for codon usage variation among the genes were investigated using codon usage indices and multi-variate statistical approach. Overall codon usage data analysis indicated that codons ending in G and/or C were predominant among the genes. Multi-variate statistical analysis showed that there was a single major trend in the codon usage variation among the genes, which had a strong positive correlation (r = 0.93, P<0.01) with (G + C) content of the genes. Further, correlation analysis indicated that genes with higher expression level and showing a greater degree of codon usage bias were GC-rich and preferred codons with C or G nucleotides at the third position. A set of thirteen codons were identified through Chi-square test as optimal codons, which were preferred in highly expressed genes. It could be concluded that mutational bias had a profound effect on codon usage pattern. In addition, translational selections also operated with a proper balance, making the genes translationally more efficient. The frequency of these codons appeared to be correlated with the level of gene expression and might be a useful indicator in the case of genes (or open-reading-frames) whose expression levels are unknown.