Investigation of the molecular evolution of nitrogen fixation using nucleotide triplet based condensed matrix method

Abstract

Evolutionary history of nitrogen fixation has been retraced by analyzing nif H, D and K genes, and whole genomes from cyanobacteria, proteobacteria, clostridia, actinobacteria, green sulfur bacteria and archaea using condensed matrix method. This novel technique determines the resemblance among DNA sequences using the invariants, to infer upon characteristics of the DNA primary sequence. Qualitative and quantitative differences between DNA sequences at intraspecific and interspecific level are recognized. Our findings indicate that structural properties of DNA sequences are guided by different descriptors and invariants. Results support evidence for polyphyletic origin, horizontal gene transfer and gene duplication events as potent evolutionary forces. Duplications in portions of genes, operons or stretches of nucleotide sequences occurred during transformation of primitive nitrogenase to the present form, playing a crucial role in producing genes with similar properties. There is agreement on nif H, D and K phylogenies, with respect to horizontal gene transfer and gene duplication events. High degree of heterogeneity present among nif genes implied action of mutation and selection pressures with unlike intensities. Our work throws light on better understanding of the diversity of nitrogen fixation and the technique employs the power of categorization of DNA sequences by invariants to recognize the qualitative and quantitative properties.