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Molecular analysis of the genus Anoxybacillus based on sequence similarity of the genes recN, flaA, and ftsY

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Abstract

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies. We analyzed three genes, recN, flaA, and ftsY, for determining if these genes are useful tools for systematic analyses in the genus Anoxybacillus. The genes encoding a DNA repair and genetic recombination protein (recN), the flagellin protein (flaA), and GTPase signal docking protein (ftsY) were sequenced for ten Anoxybacillus species. The sequence comparisons revealed that recN sequence similarities range between 61% and 99% in the genus Anoxybacillus. Comparisons to other bacterial recN genes indicated that levels of similarity did not differ from the levels within genus Anoxybacillus. These data showed that recN is not a useful marker for the genus Anoxybacillus. A 550–600-bp region of the flagellin gene was amplified for all Anoxybacillus strains except for Anoxybacillus contaminans. The sequence similarity of flaA gene varies between 61% and 76%. Comparisons to other bacterial flagellin genes obtained from GenBank (Bacillus, Pectinatus, Proteus, and Vibrio) indicated that the levels of similarity were lower (3–42%). Based on these data, we concluded that the variability in this single gene makes it a particularly useful marker. Another housekeeping gene ftsY suggested to reflect the G+C (mol/mol) content of whole genome was analyzed for Anoxybacillus strains. A mean difference of 1.4% was observed between the G+C content of the gene ftsY and the G+C content of the whole genome. These results showed that the gene ftsY can be used to represent whole G+C content of the Anoxybacillus species.

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References

  • Atanassova M, Derekova A, Mandeva R, Sjøholm C, Kambourova M (2008) Anoxybacillus bogrovensis sp. nov., a novel thermophilic bacterium isolated from a hot spring in Dolni Bogrov, Bulgaria. Int J Syst Evol Microbiol 58:2359–2362

    Google Scholar 

  • Belduz AO, Dulger S, Demirbag Z (2003) Anoxybacillus gonensis sp. nov., a moderately thermophilic, xylose-utilizing, endospore-forming bacterium. Int J Syst Evol Microbiol 53:1315–1320

    Article  PubMed  CAS  Google Scholar 

  • De Clerck E, Rodrı’guez-Dıaz M, Vanhoutte T, Heyrman J, Logan NA, De Vos P (2004) Anoxybacillus contaminans sp. nov. and Bacillus gelatini sp. nov., isolated from contaminated gelatin batches. Int J Syst Evol Microbiol 54:941–946

    Article  PubMed  Google Scholar 

  • Derekova A, Sjøholm C, Mandeva R, Kambourova M (2007) Anoxybacillus rupiensis sp. nov., a novel thermophilic bacterium isolated from Rupi basin (Bulgaria). Extremophiles 11:577–583

    Google Scholar 

  • Dulger S, Demirbag Z, Belduz AO (2004) Anoxybacillus ayderensis sp. nov. and Anoxybacillus kestanbolensis sp. nov. Int J Syst Evol Microbiol 54:1499–1503

    Article  PubMed  CAS  Google Scholar 

  • Ezaki T, Saidi SM, Liu SL, Hashimoto Y, Yamamoto H, Yabuuchi E (1990) Rapid procedure to determine the DNA base composition from small amounts of gram positive bacteria. FEMS Microbiol Lett 55:127–130

    Article  PubMed  CAS  Google Scholar 

  • Fischer SH, Nachamkin I (1991) Common and variable domains of the flagellin gene, flaA in Campylobacter jejuni. Mol Microbiol 5:1151–1158

    Article  PubMed  CAS  Google Scholar 

  • Fournier PE, Suhre K, Fournous G, Raoult D (2006) Estimation of prokaryote genomic G+C content by sequencing universally conserved genes. Int J Syst Evol Microbiol 56:1025–1029

    Article  PubMed  CAS  Google Scholar 

  • Goodfellow M, Manfio GP, Chun J (1997) Towards a practical species concept for cultivable bacteria. In: Claridge MF, Dawah HA (eds) Species: the units of biodiversity. Chapman and Hall, London, pp 25–59

    Google Scholar 

  • Gray DI, Kroll RG (1995) Polymerase chain reaction amplification of the flaA gene for the rapid identification of Listeria spp. Lett Appl Microbiol 20:65–68

    Article  PubMed  CAS  Google Scholar 

  • Kacagan M, Canakci S, Sandalli C, Inan K, Colak DN, Belduz AO (2008) Characterization of a xylanase from a thermophilic strain of Anoxybacillus pushchinoensis A8. Biol Sect Cell Mol Biol 63:599–606

    CAS  Google Scholar 

  • Kevbrin V, Zengler K, Lysenko AM, Wiegel J (2005) Anoxybacillus kamchatkensis sp. nov., a novel thermophilic facultative aerobic bacterium with a broad pH optimum from the Geyser valley, Kamchatka. Extremophiles 9:391–398

    Article  PubMed  CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through compararative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  • Mandel M, Igambi L, Bergendahl J, Dodson ML Jr, Scheltgen E (1970) Correlation of melting temperature and cesium chloride buoyant density of bacterial deoxyribonucleic acid. J Bacteriol 101:333–338

    PubMed  CAS  Google Scholar 

  • Maniatis T, Fritsch EF, Sambrook J (1982) In: Molecular cloning. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

  • Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118

    Article  PubMed  CAS  Google Scholar 

  • Namsaraev ZB, Babasanova OB, Dunaevsky YE, Akimov VN, Barkhutova DD, Gorlenko VM, Namsaraev BB (2010) Anoxybacillus mongoliensis sp. nov., a novel thermophilic proteinase producing bacterium isolated from alkaline hot spring, central Mongolia. Microbiologia 79:516–523

    CAS  Google Scholar 

  • Olsen I, Moller K. (2005) Genus II Actinobacillus Brumpt 1910, 849AL. Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 2, part B: 866–883. Edited by Brenner D J, Krieg NR, Staley JT, Garrity GM. New York: Springer

  • Oyofo BA, Rollins DM (1993) Efficacy of filter types for detecting Campylobacter jejuni and Campylobacter coli in environmental water samples by polymerase chain reaction. Appl Environ Microbiol 59:4090–4095

    PubMed  CAS  Google Scholar 

  • Picken RN (1992) Polymerase chain reaction primers and probes derived from flagellin gene sequences for specific detection of the agents of Lyme disease and North American relapsing fever. J Clin Microbiol 30:99–114

    PubMed  CAS  Google Scholar 

  • Pikuta E, Lysenko A, Chuvilskaya N, Mendrock U, Hippe H, Suzina N, Nikitin D, Osipov G, Laurinavichius K (2000) Anoxybacillus pushchinensis gen. nov., sp. nov., a novel anaerobic, alkaliphilic, moderately thermophilic bacterium from manure, and description of Anoxybacillus flavithermus comb. nov. Int J Syst Evol Microbiol 50:2109–2117

    Article  PubMed  CAS  Google Scholar 

  • Poli A, Esposito E, Lama L, Orlando P, Nicolaus G, Appolonia F, Gambacorta A, Nicolaus B (2006) Anoxybacillus amylolyticus sp. nov., a thermophilic amylase producing bacterium isolated from Mount Rittmann (Antarctica). Syst Appl Microbiol 29:300–307

    Article  PubMed  CAS  Google Scholar 

  • Rasmussen HN, Olsen JE, Jorgensen K, Rasmussen OF (1996) Detection of Campylobacter jejuni and Camp. coli in chicken faecal samples by PCR. Lett Appl Microbiol 23:363–366

    Article  PubMed  CAS  Google Scholar 

  • Rossello-Mora R, Aman R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67

    Article  PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning—a laboratory manual, volume 2. Cold Spring Habour Laboratory Press, New York

    Google Scholar 

  • Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    Article  CAS  Google Scholar 

  • Stackebrandt E, Fredericksen W, Garrity GM, Grimont PAD, Kampfer P, Maiden MCJ, Nemse X, Rossello-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewinak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acid Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • Torsvik V, Daae FL, Goksoyr J (1995) In: Trevors JT, Elsas JD (eds) Nucleic acids in the environment: methods and applications. Springer, Berlin, p 29

    Chapter  Google Scholar 

  • Whittam TS (1995) Genetic population structure and pathogenicity in enteric bacteria. In Population Genetics of Bacteria (Society for General Microbiology Symposium) 52:217–245. Edited by Baumberg S, Young JPW, Wellington EMH, Saunders JR. Eds. Cambridge: Cambridge University Pres

  • Winstanley C, Morgan JA (1997) The bacterial flagellin gene as a biomarker for detection, population genetics and epidemiological analysis. Microbiology 143:3071–3084

    Article  PubMed  CAS  Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

    PubMed  CAS  Google Scholar 

  • Yumoto I, Hirota K, Kawahara T, Nodasaka Y, Okuyama H, Matsuyama H, Yokota Y, Nakajima K, Hoshino T (2004) Anoxybacillus voinovskinensis sp. nov., a moderately thermophilic bacterium from a hot spring in Kamchatka. Int J Syst Evol Microbiol 54:1239–1242

    Article  PubMed  CAS  Google Scholar 

  • Zeigler DR (2003) Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1900

    Article  PubMed  CAS  Google Scholar 

  • Zeigler DR (2005) Application of a recN sequence similarity analysis to the ıdentification of species within the bacterial genus Geobacillus. Int J Syst Evol Microbiol 55:1171–1179

    Article  PubMed  CAS  Google Scholar 

  • Zhang CM, Huang XW, Pan WZ, Zhang J, Wei KB, Klenk HP, Tang SK, Li WJ, Zhang KQ (2011) Anoxybacillus tengchongensis sp. nov. and Anoxybacillus eryuanensis sp. nov., facultatively anaerobic, alkalitolerant bacteria from hot springs. Int J Syst Evol Microbiol 61:118–122

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We would like to thank TUBITAK for the support.

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Authors and Affiliations

  1. Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey

    Dilsat Nigar Colak, Kadriye Inan, Sabriye Canakcı & Ali Osman Belduz

  2. Faculty of Fisheries and Aquatic Sciences, Rize University, 53100, Rize, Turkey

    Hakan Karaoglu

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  1. Dilsat Nigar Colak
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  2. Kadriye Inan
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  3. Hakan Karaoglu
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  4. Sabriye Canakcı
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  5. Ali Osman Belduz
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Correspondence to Ali Osman Belduz.

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Colak, D.N., Inan, K., Karaoglu, H. et al. Molecular analysis of the genus Anoxybacillus based on sequence similarity of the genes recN, flaA, and ftsY . Folia Microbiol 57, 61–69 (2012). https://doi.org/10.1007/s12223-011-0094-1

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