Functional divergence outlines the evolution of novel protein function in NifH/BchL protein family

Abstract

Biological nitrogen fixation is accomplished by prokaryotes through the catalytic action of complex metalloenzyme, nitrogenase. Nitrogenase is a two-protein component system comprising MoFe protein (NifD and K) and Fe protein (NifH). NifH shares structural and mechanistic similarities as well as evolutionary relationships with light-independent protochlorophyllide reductase (BchL), a photosynthesis-related metalloenzyme belonging to the same protein family. We performed a comprehensive bioinformatics analysis of the NifH/BchL family in order to elucidate the intrinsic functional diversity and the underlying evolutionary mechanism among the members. To analyse functional divergence in the NifH/ BchL family, we have conducted pair-wise estimation in altered evolutionary rates between the member proteins. We identified a number of vital amino acid sites which contribute to predicted functional diversity. We have also made use of the maximum likelihood tests for detection of positive selection at the amino acid level followed by the structure-based phylogenetic approach to draw conclusion on the ancient lineage and novel characterization of the NifH/BchL protein family. Our investigation provides ample support to the fact that NifH protein and BchL share robust structural similarities and have probably deviated from a common ancestor followed by divergence in functional properties possibly due to gene duplication.

Distribution and functional potential of photoautotrophic bacteria in alkaline hot springs

“…Lastly, nitrogen fixation and bacteriochlorophyll synthesis genes share an evolutionary history (57); therefore, we would expect that closely related species like Roseiflexus and Chloroflexus would both contain these genes. Yet, our data suggest that only Roseiflexus encode both nifH and bchL, while Chloroflexus contain only bchL genes, which is in accordance with previous work (50,52,53).…”

Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis

“…Thus, if the assumption concerning the ancestral nature of the NifH gene in comparison to the BchL and BchX sequences is not well founded or incorrect, then the results of phylogenetic analysis and CSIs-based analysis on BchL-BchX and NifH sequences could be readily reinterpreted to indicate that the BchL-B-N complex originated first, followed by the BchX-Y-Z complex, and then the nitrogenase complex. It should also be noted that this evolutionary scenario is also supported by a structure-based analysis of the NifH, MinD/ ParA, and BchL type sequences, in which the BchL protein is indicated to have evolved first from MinD/ParA-like ancestor, followed by the divergence of NifH sequences (Thakur et al 2013).…”

“…6) (Sakai et al 2001;Cordell and Lowe 2001;Leonard et al 2005). Structural similarities between the ParA/Soj/MinD and the BchL and NifH protein sequences have led to the suggestion that all of these proteins have evolved from a common ancestor and the results of structure-based phylogenetic analysis further suggest that of these proteins ParA/Soj/MinD proteins are ancestral (Thakur et al 2013). Although it is possible that the BchL protein was either originally not present in Rubrobacter, or it has been lost from Rubrobacter, in view of the predicted ancient nature of the Rubrobacter BchB and BchN homologs, the observed structural similarity of the ParA/Soj/MinD proteins to the BchL protein is of much interest.…”

“…The top BLAST hits in Rubrobacter showing marginal sequence similarity to the BchL protein were for the ParA/Soj/MinD family of ATPases, involved in chromosome partitioning and regulating/determining the positions where large structures assemble (Hester and Lutkenhaus 2007;Lutkenhaus 2012). Earlier studies have indicated that the ParA/Soj/MinD proteins are structurally related to the BchL and NifH protein sequences (Sakai et al 2001;Lutkenhaus 2012;Thakur et al 2013). Hence, we have also carried out a structural comparisons of the solved crystal structures of the BchL protein from Rhodobacter sphaeroides (PDB ID: 3FWY) (Sarma et al 2008), the ParA proteins from Thermus thermophilus (PDB ID: 1WCV) (Leonard et al 2005) and cell division regulator protein MinD (PDB ID: 1HYQ) (Cordell and Lowe 2001) from Archaeoglobus fulgidus (Fig.…”

Temperature and Geographic Location Impact the Distribution and Diversity of Photoautotrophic Gene Variants in Alkaline Yellowstone Hot Springs

“…Nitrogenase is an iron-sulfur complex containing one of three metals harbored in the active site: molybdenum (Mo), iron (Fe), or vanadium (V). Mo-nitrogenase is the most common and is encoded by nif genes ( 27 , 28 ). Several studies have assessed potential nitrogenase activity in acidic hot springs of >55ºC using the gene nifH , which encodes the iron protein (NifH) in nitrogenase ( 29 – 31 ).…”