Abstract
Bacillus megaterium NCT-2 is a novel bacterium that can utilize nitrate as its only nitrogen source for growth. The nitrate assimilation related genes that are involved in this process would be expected to be crucial. However, little is known about the genomic background of this bacterium, let alone the sequences of the nitrate assimilation related genes. In order to further investigate the nitrate assimilation function of the NCT-2, genome sequencing was performed. After obtaining the fine map of the NCT-2 genome, which was submitted to the NCBI GenBank (AHTF00000000), the sequences of the nitrate assimilation related genes (the nitrate reductase electron transfer subunit nasB and the nitrate reductase catalytic subunit nasC, the nitrite reductase [NAD(P)H] large subunit nasD and the nitrite reductase [NAD(P)H] small subunit nasE, and the glutamine synthetase glnA) were identified. Multiple alignments were performed to find out the sequence identities of the nitrate assimilation related genes to that of their similar species. Through KEGG signaling mapping search, the nitrate assimilation related genes were revealed to be located in the nitrogen metabolism signaling pathway. The putative 3D protein structures of these genes were modeled by SWISS MODEL, and shown to be highly similar to the nitrate assimilation related genes in the PDB database. Finally, the sequence validity of the nitrate assimilation related genes was verified by PCR with specifically designed primers.
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References
Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics 22(2):195–201. doi:10.1093/bioinformatics/bti770
Gonzalez PJ, Correia C, Moura I, Brondino CD, Moura JJG (2006) Bacterial nitrate reductases: molecular and biological aspects of nitrate reduction. J Inorg Biochem 100(5–6):1015–1023. doi:10.1016/j.jinorgbio.2005.11.024
Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18(15):2714–2723. doi:10.1002/elps.1150181505
Kanamori K, Weiss RL, Roberts JD (1987) Ammonia assimilation in Bacillus polymyxa. 15N NMR and enzymatic studies. J Biol Chem 262(23):11038–11045
Lledo B, Marhuenda-Egea FC, Martinez-Espinosa RM, Bonete MJ (2005) Identification and transcriptional analysis of nitrate assimilation genes in the halophilic archaeon Haloferax mediterranei. Gene 361:80–88. doi:10.1016/j.gene.2005.07.011
Moreno-Vivian C, Cabello P, Martinez-Luque M, Blasco R, Castillo F (1999) Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases. J Bacteriol 181(21):6573–6584
Richardson DJ (2000) Bacterial respiration: a flexible process for a changing environment. Microbiol 146:551–571
Richardson DJ, Berks BC, Russell DA, Spiro S, Taylor CJ (2001) Functional, biochemical, and genetic diversity of prokaryotic nitrate reductases. Cell Mol Life Sci 58(2):165–178. doi:10.1007/Pl00000845
Richardson DJ, Watmough NJ (1999) Inorganic nitrogen metabolism in bacteria. Curr Opin Chem Biol 3(2):207–219. doi:10.1016/S1367-5931(99)80034-9
Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31(13):3381–3385. doi:10.1093/Nar/Gkg520
Acknowledgments
This research work was supported by the National Natural Science Foundation of China (no. 31071860) and the Specialized Research Fund for the Doctoral Program of Higher Education (no. 20120073120069).
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Weiwei Shi and Wei Lu contributed equally to this work.
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Shi, W., Lu, W., Liu, Q. et al. The identification of the nitrate assimilation related genes in the novel Bacillus megaterium NCT-2 accounts for its ability to use nitrate as its only source of nitrogen. Funct Integr Genomics 14, 219–227 (2014). https://doi.org/10.1007/s10142-013-0339-y
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DOI: https://doi.org/10.1007/s10142-013-0339-y