Abstract
NrfA is the molecular marker for dissimilatory nitrate reduction to ammonium (DNRA) activity, catalysing cytochrome c nitrite reductase enzyme. However, the limited study has been made so far to understand the structural homology modeling of NrfA protein in DNRA bacteria. Therefore, three model DNRA bacteria (Escherechia coli, Wolinella succinogenes and Shewanella oneidensis) were chosen in this study for in-silico protein modeling of NrfA which roughly consists of similar length of amino acids and molecular weight and they belong to two contrasting taxonomic families (γ-proteobacteria with nrfABCDEFG and ε-proteobacteria with nrfHAIJ operon). Multiple bioinformatic tools were used to examine the primary, secondary, and tertiary structure of NrfA protein using three distinct homology modeling pipelines viz., Phyre2, Swiss model and Modeller. The results indicated that NrfA protein in E. coli, W. succinogenes and S. oneidensis was mostly periplasmic and hydrophilic. Four conserved Cys-X1-X2-Cys-His motifs, one Cys-X1-X2-Cys-Lys haem-binding motif and Ca ligand were also identified in NrfA protein irrespective of three model bacteria. Moreover, 11 identical conserved amino acids sequence was observed for the first time between serine and proline in NrfA protein. Secondary structure of NrfA revealed that α-helices were observed in 77.9%, 73.4%, and 77.4% in E. coli, W. succinogenes and S. oneidensis, respectively. Ramachandran plot showed that number of residue in favored region in E. coli, W. succinogenes and S. oneidensis was 97.03%, 97.01% and 97.25%, respectively. Our findings also revealed that among three pipelines, Modeller was considered the best in-silico tool for prediction of NrfA protein. Overall, significant findings of this study may aid in the identification of future unexplored DNRA bacteria containing cytochrome c nitrite reductase. The NrfA system, which is linked to respiratory nitrite ammonification, provides an analogous target for monitoring less studied N-retention processes, particularly in agricultural ecosystems. Furthermore, one of the challenging research tasks for the future is to determine how the NrfA protein responds to redox status in the microbial cells.
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Authors are extremely thankful to the Director, ICAR-NRRI, Cuttack, Odisha, India for providing necessary facility and web server for carrying out this work. Authors are also thankful to ICAR-Incentivizing project on “Genetic modifications to improve biological nitrogen fixation (BNF) for augmenting nitrogen needs of rice (EAP-200)” for partial financial support. The first author (Ms Megha Kaviraj) is also grateful for financial assistance as an SRF under the BNF project, which allowed her to complete a portion of her PhD work.
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ICAR-Incentivizing project on “Genetic modifications to improve biological nitrogen fixation for augmenting nitrogen needs of rice (EAP-200)” for partial financial support.
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MK and UK: contributed in conceiving and designing experiments, performed the major part of in silico experiments, analyzed data, and wrote the initial draft. UK, AKN and SNC: guided the progression of work, and proof read the manuscript. All the authors read and approved the final manuscript.
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Kaviraj, M., Kumar, U., Nayak, A.K. et al. Homology modeling and virtual characterization of cytochrome c nitrite reductase (NrfA) in three model bacteria responsible for short-circuit pathway, DNRA in the terrestrial nitrogen cycle. World J Microbiol Biotechnol 38, 168 (2022). https://doi.org/10.1007/s11274-022-03352-y
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DOI: https://doi.org/10.1007/s11274-022-03352-y