A comparative computational study of the ‘rbcL’ gene in plants and in the three prokaryotic families—Archaea, cyanobacteria and proteobacteria

The rbcL (ribulose-1,5-biphosphate carboxylase oxygenase) gene plays a crucial role in carbon fixation. Previous studies shed light on its evolutionary relationship among different Phyla. Here, authors have done a comparative study of rbcL genes among proteobacteria, archaea, cyanobacteria and plants based on their compositional variations (GC%, amino acid frequency, codon usage, etc.). In addition we have checked the mutational pressure on rbcL genes. The results indicate that the rbcL genes of cyanobacteria have a wide range of GC%. On the other hand, those of the proteobacteria have mainly higher GC%. Preferences of some amino acids usages have observed in rbcL genes among all species with an exception of plant. Analysis of RSCU (relative synonymous codon usage) values depicts GC ending codon biasness in proteobacteria, archaea and with few exceptions in cyanobacterial species. On the other hand, AU ending codon biasness has been observed for plants. The correspondence analysis shows the significant difference in codon usage pattern among the selected four groups of species. The ENc (expected effective number of codons) plot implys the choice of rbcL gene codon is constrained only by mutational biasness. Moreover, the rbcL genes’ expression ability, as predicted by CAI (codon adaptation index), is similar for most of the species from different groups.