Email this article Genes of NAD+-Dependent Formate Dehydrogenases in Taxonomy of Aerobic Methylotrophic Bacteria of the Genus Ancylobacter
- Authors: Chemodurova A.A.1, Reshetnikov A.S.1, Agafonova N.V.1, Doronina N.V.1
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Affiliations:
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences
- Issue: Vol 92, No 1 (2023)
- Pages: 98-102
- Section: КРАТКИЕ СООБЩЕНИЯ
- URL: https://journals.rcsi.science/0026-3656/article/view/138176
- DOI: https://doi.org/10.31857/S002636562260047X
- EDN: https://elibrary.ru/NOFTGB
- ID: 138176
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Abstract
Abstract—Comparative phylogenetic analysis of NAD+-dependent formate dehydrogenases (NAD+–FDH) genes, which have been detected in all available genomes of methylotrophs of the genera Ancylobacter, Starkeya and Angulomicrobium, as well as in other members of the family Xanthobacteraceae (Xanthobacter, Aquabacter, Azorhizobium), was carried out. The position of Xanthobacteraceae on the tree constructed based on comparison of NAD+–FDH amino acid sequences was found to correlate with the 16S rRNA gene-based phylogeny. The sequences of the NAD+–FDH proteins of the genera Ancylobacter, Starkeya, and Angulomicrobium exhibited 87.8–98.3% identity, indicating that this protein is very conservative within this group of methylotrophs. For the first time, analysis of the NAD+–FDH functional genes is recommended as a supplementary criterion for interspecies differentiation between methylotrophic bacteria of the genus Ancylobacter.
About the authors
A. A. Chemodurova
Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences
Email: doronina@ibpm.pushchino.ru
Russia, 142290, Pushchino
A. S. Reshetnikov
Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences
Email: doronina@ibpm.pushchino.ru
Russia, 142290, Pushchino
N. V. Agafonova
Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences
Email: doronina@ibpm.pushchino.ru
Russia, 142290, Pushchino
N. V. Doronina
Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences
Author for correspondence.
Email: doronina@ibpm.pushchino.ru
Russia, 142290, Pushchino
References
- Троценко Ю.А., Доронина Н.В., Торгонская М.Л. Аэробные метилобактерии. Пущино: ОНТИ ПНЦ РАН, 2010. 325 с.
- Trotsenko Y.A., Doronina N.V., Torgonskaya M.L. Aerobic Methylobacteria. Pushchino: ONTI PSC RAS, 2010. 325 р.
- Alekseeva A.A., Savin S.S., Tishkov V.I. NAD+-dependent formate dehydrogenase from plants // Acta Naturae. 2011. V. 3. № 4(11). P. 38–54.
- Chistoserdova L. Modularity of methylotrophy, revisited // Environ. Microbiol. 2011. V. 13. P. 2603–2622.
- Chun J., Oren A., Ventosa A., Christensen H., Arahal D.R., da Costa M.S., Rooney A.P., Yi H., Xu X.-W., De Meyer S., Trujillo M.E. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes // Int. J. Syst. Evol. Microbiol. 2018. V. 68. P. 461–466.
- Egorov A.M., Avilova T.V., Dikov M.M., Popov V.O., Rodionov Y.V., Berezin I.V. NAD-dependent formate dehydrogenase from methylotrophic bacterium, strain 1: purification and characterization // Eur. J. Biochem. 1979. V. 99. P. 569–576.
- Filippova E.V., Filippova E.V., Polyakov K.M., Tikhonova T.V., Boiko K.M., Tishkov V.I., Popov V.O. Crystal structures of complexes of NAD+-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate // Crystallography Reports. 2006. V. 51. № 4. P. 627–631.
- Hatrongjit R., Packdibamrung K. A novel NADP+-dependent formate dehydrogenase from Burkholderia stabilis 15516: screening, purification and characterization // Enzyme and Microbial Technology. 2010. V. 46. №. 7. P. 557–561.
- Keltjens J.T., Pol A., Reimann J., Op den Camp H.J. PQQ-dependent methanol dehydrogenases: rareearth elements make a difference // Appl. Microbiol. Biotechnol. 2014. V. 98. P. 6163–6183.
- McDonald I.R., Murrell J.C. The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs // Appl. Environ. Microbiol. 1997. V. 63. P. 3218–3224.
- Meier-Kolthoff J.P., Auch A.F., Klenk H.-P., Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions // BMC Bioinformatics. 2013. V. 14. P. 1–14.
- Nanba H., Takaoka Y., Hasegawa J. Purification and characterization of formate dehydrogenase from Ancylobacter aquaticus strain KNK607M, and cloning of the gene // Bioscience, Biotechnology, and Biochemistry. 2003. V. 67. № 4. P. 720–728.
- Ramachandran A., Walsch D.A. Investigation of XoxF methanol dehydrogenases reveals new methylotrophic bacteria in pelagic marine and freshwater ecosystems // FEMS Microbiol. Ecol. 2015. V. 91. P. fiv105.
- Richter M., Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition // Proc. Natl. Acad. Sci. USA. 2009. V. 106. P. 19126–19131.
- Shabalin I.G., Serov A.E., Skirgello O.E., Timofeev V.I., Samygina V.R., Popov V.O., Tishkov V.I., Kuranova I.P. Recombinant formate dehydrogenase from Arabidopsis thaliana: preparation, crystal growth in microgravity, and preliminary X-ray diffraction study // Crystallography Reports. 2010. V. 55. № 5. P. 806–810.
- Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods // Mol. Biol. Evol. 2011. V. 28. P. 2731–2739.
- Taubert M., Grob C., Howat A.M., Burns O.J., Dixon J.L., Chen Y., Murrell J.C. XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments // Environ. Microbiol. 2015. V. 17. P. 3937–3948.
- Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools // Nucleic Acids Res. 1997. V. 25. P. 4876–4882.
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