Abstract
A sulfite reductase gene sequence database, which could facilitate analysis of metagenomic data of a functional gene from sulfate-reducing bacteria, is described. The database contains 127 aligned nucleotide sequences of a gene (dsrA), encoding a dissimilatory sulfite reductase alpha subunit, retrieved from Reference Sequence of GenBank that provides only well-annotated genome sequences. The dsrA gene sequences were screened for length and aligned using four multiple sequencing alignment programs, Mafft, Muscle, Mothur, and Clustal Omega. In addition to the dsrA gene sequences, 16S ribosomal RNA (rRNA) gene sequences for the bacterial species appearing in the database were also retrieved from the GenBank and aligned by a public database of SILVA in Mothur to examine any potential relationship between taxonomy of the bacteria and distribution of a functional gene. The aligned dsrA and 16S rRNA gene sequences were used to construct neighbor-joining phylogenetic trees for comparison of the alignments for relative agreement among the aligned sequence databases. This method of aligned reference database construction using public database can help provide better insight into microbial communities by suggesting an alternative approach of studying metagenomic analysis of functional genes involved in important ecological processes.
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References
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J et al. (2013) GenBank. Nucleic Acids Res 41, D36–42.
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72, 5069–72.
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792–7.
Fish JA, Chai B, Wang Q, Sun Y, Brown CT, and Tiedje JM (2013) FunGene: the functional gene pipeline and repository. Front Microbiol 4, 291.
Gaby JC and Buckley DH (2014) A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria. Database 2014, bau001.
Geets J, Borremans B, Diels L, Springael D, Vangronsveld J, van der Lelie D et al. (2006) DsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria. J Microbiol Methods 66, 194–205.
Katoh K, Misawa K, Kuma Ki, and Miyata T (2002) MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30, 3059–66.
Lloyd JR, Ridley J, Khizniak T, Lyalikova NN, and Macaskie LE (1999) Reduction of technetium by Desulfovibrio desulfuricans: Biocatalyst characterization and use in a flowthrough bioreactor. Appl Environ Microbiol 65, 2691–6.
Lovley DR and Phillips EJ (1988) Novel mode of microbial energy metabolism: Organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl Environ Microbiol 54, 1472–80.
Lovley DR and Phillips EJP (1992) Reduction of uranium by Desulfovibrio desulfuricans. Appl Environ Microbiol 58, 850–6.
Lovley DR and Phillips EJP (1994) Reduction of chromate by Desulfovibrio vulgaris and its c 3 cytochrome. Appl Environ Microbiol 60, 726–8.
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32, 1363–71.
Michel C, Brugna M, Aubert C, Bernadac A, and Bruschi M (2001) Enzymatic reduction of chromate: comparative studies using sulfatereducing bacteria. Key role of polyheme cytochromes c and hydrogenases. Appl Microbiol Biotechnol 55, 95–100.
Myers CR and Nealson KH (1988) Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240, 1319–21.
Payne RB, Gentry DM, Rapp-Giles BJ, Casalot L, and Wall JD (2002) Uranium reduction by Desulfovibrio desulfuricans strain G20 and a cytochrome c 3 mutant. Appl Environ Microbiol 68, 3129–32.
Postgate JR (1984) In The Sulphate-Reducing Bacteria, (2nd ed). Cambridge University Press, UK.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P et al. (2013) The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res 41, D590–6.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. (2009) Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Appl Environ Microbiol 75, 7537–41.
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W et al. (2011) Fast, scalable generation of highquality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7, 539.
Stahl DA, Fishbain S, Klein M, Baker BJ, and Wagner M (2002) Origins and diversification of sulfate-respiring microorganisms. Antonie Van Leeuwenhoek 81, 189–95.
Wagner M, Roger AJ, Flax JL, Brusseau GA, and Stahl DA (1998) Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J Bacteriol 180, 2975–82.
Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH et al. (2008) The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31, 241–50.
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Lee, JH., Kim, BA. & Ki, MG. Construction of aligned database of dsrA, a gene encoding dissimilatory sulfite reductase alpha subunit, for metagenomic studies of sulfate-reducing bacteria. J Korean Soc Appl Biol Chem 57, 419–427 (2014). https://doi.org/10.1007/s13765-014-4158-1
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DOI: https://doi.org/10.1007/s13765-014-4158-1