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

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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&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

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Acknowledgements

The authors are grateful to the Department of Biotechnology, India, for providing financial help in setting up Bioinformatics Centre, in the Department of Botany, University of North Bengal. ST would like to thank the CSIR for providing the CSIR-SRF research fellowship.

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Authors and Affiliations

  1. NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, India

    Subarna Thakur & Arnab Sen

  2. Bioinformatics Chemoinformatics Laboratory, Department of Chemistry, Raiganj College, Raiganj, India

    Asim K Bothra

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  1. Subarna Thakur
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  2. Asim K Bothra
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  3. Arnab Sen
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Correspondence to Arnab Sen.

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[Thakur S, Bothra AK and Sen A 2013 Functional divergence outlines the evolution of novel protein function in NifH/BchL protein family. J. Biosci. 38 1–8] DOI

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Thakur, S., Bothra, A.K. & Sen, A. Functional divergence outlines the evolution of novel protein function in NifH/BchL protein family. J Biosci 38, 733–740 (2013). https://doi.org/10.1007/s12038-013-9360-5

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