Subarna Thakur1, Asim K Bothra2, Arnab Sen1
1NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri 734013, India.
2Bioinformatics Chemoinformatics Laboratory, Department of Chemistry, Raiganj College, Raiganj, India.
The ability to fix nitrogen is found in most major groups of bacteria and in some methanogenic archaea. The emergence and evolution of nitrogen ﬁxation ability (diazotrophy) among Prokaryotes is complex and has not yet been fully elucidated. All N 2 -fixing organisms depend on nitrogenase for the conversion of atmospheric nitrogen to ammonia. The nitrogenase enzyme is a two-component system that consists of the iron protein (Fe-protein or NifH) and molybdenum-iron protein (MoFe-protein) working in tandem to effect nitrogen reduction. A number of proteins have structural and mechanistic similarities as well as evolutionary relationships with the NifH protein, notable among them being the light independent protochlorophyllidae reducatse (Bchl) which belong to the same superfamily of metalloproteins. In order to elucidate intrinsic functional diversity, and underlying evolutionary mechanism among NifH protein, we performed comprehensive bioinformatics analysis NifH/Bchl family. To estimate functional divergence in the NifH/Bchl family, we have conducted pair-wise functional divergence analysis between nifH paralogous genes using DIVERGE program. Our results show that NifH protein paralogs evolved from several gene duplication events followed by functional divergence. We identified a number of protein domains, and amino acid residues which contribute to predicted functional divergence. We have also made use of the maximum likelihood tests for detection of positive selection at the amino acid level. The structure based phylogenetic approach was also applied to draw conclusion on the ancient divergence and novel characterization of the NifH/Bchl protein family. The 3D structure based phylogenetic tree suggests that NifH protein and ChlL (FywA) share maximum similarities and have probably diverged most recently compared to others. It also suggests that both NifH and ChlL could have evolved from a MinD protein like ancestor. Read more…