Codon usage profiling and analysis of intergenic association of Frankia EuIK1 nif genes.

Frankia is an actinomycete that makes symbiotic association with a number of woody dicotyledonous plants. It has the ability to fix atmospheric nitrogen and the most important genes for nitrogen fixation are the nif genes located in the nif operon. Here, we report the codon preference and mutational response index in 12 characterized nif genes of Frankia EuIK1. It was found that the genes are highly biased and this is due to both mutational pressure and translational selection. Correspondence analysis of the RSCU values for the nif genes revealed that the GC3 compositional bias plays an important role in the codon usage variation among them. The codon preference in the nif genes of Frankia were compared with the nif genes of symbiotic nitrogen fixing bacteria Bradyrhizobium japonicum. B. japonicum nif genes had relatively low codon preferences than Frankia which was found to be due to low G+C content in its genomic constitution. Besides, unlike Frankia, codon preference of B. japonicum was due to translational selection and not due to mutational pressure.