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. 2015 Mar 5;3(2):e00060-15. doi: 10.1128/genomeA.00060-15

Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes

Malini Kotak a, Jantiya Isanapong b, Lynne Goodwin c, David Bruce c, Amy Chen d, Cliff S Han c, Marcel Huntemann d, Natalia Ivanova d, Miriam L Land e, Matt Nolan d, Amrita Pati d, Tanja Woyke d, Jorge L M Rodrigues f,
PMCID: PMC4358385  PMID: 25744998

Abstract

The Opitutaceae bacterium strain TAV5, a member of the phylum Verrucomicrobia, was isolated from the wood-feeding termite hindgut. We report here its complete genome sequence, which contains a chromosome and a plasmid of 7,317,842 bp and 99,831 bp, respectively. The genomic analysis reveals genes for methylotrophy, lignocellulose degradation, and ammonia and sulfate assimilation.

GENOME ANNOUNCEMENT

The ability to grow on single-carbon compounds other than CO2 is a distinctive feature of methylotrophs. Among this group, members of the Verrucomicrobia have been identified as the first phylum outside of the Proteobacteria to be characterized as methanotrophs (1). The genomes of three species isolated from geographically distant but geothermally similar environments were previously sequenced and studied (24). Here, we report the complete genome of the Opitutaceae bacterium strain TAV5, a mesophilic verrucomicrobium isolated from the hindgut of the wood-feeding termite Reticulitermes flavipes (5), containing genes associated with methylotrophic competency.

The genomic DNA of TAV5 was isolated using a cetyltrimethylammonium bromide method, and the genome was sequenced using a combination of Illumina HiSeq 2000 and 454 FLX Titanium systems. The individual reads were assembled with the Newbler assembler (Roche). Prodigal (6) was used to identify the genes, and manual curation was done using the Joint Genome Institute (JGI) GenePRIMP pipeline (7). The translated protein-coding genes (coding sequences [CDSs]) were used to search the National Center for Biotechnology Information (NCBI) nonredundant, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases, and a product description for each protein was predicted. Noncoding genes and miscellaneous features were predicted using tRNAscan-SE (8), RNAmmer (9), Rfam (10), TMHMM (6), and signalP (11).

The TAV5 genome is composed of a chromosome that is 7,317,842 bp long and contains 6,000 genes, with a G+C content of 63.45%, and a plasmid that is 99,831 bp long and contains 96 genes, with a G+C content of 54.44%. Together, they contain 5,950 CDSs, 48 tRNA genes, and 1 complete rRNA operon. The number of CDSs with a predicted function is 4,086 (67.03% of the total), the number of KEGG orthologs is 1,912 (31.36%), and the number of Cluster of Orthologous Group classifications is 2,984 (48.95%). An analysis of the genome revealed the presence of enzymes for formate metabolism, such as formate dehydrogenase, a formate transporter, and enzymes of the serine pathway, like serine hydroxymethyltransferase, glycerate kinase, and phosphoenolpyruvate carboxykinase.

The TAV5 genome contains a number of glycoside hydrolases (GH) involved in the degradation of cellulose (GH 5 and 9) and hemicellulose (GH 8, 10, 26, 28, and 53), as observed for the TAV1 and TAV2 genomes (12, 13). The genome has genes for the enzymes 3-carboxymuconate cyclase (EC 5.5.1.5) and 4-carboxymuconolactone decarboxylase (EC 4.1.1.44), which are involved in the degradation of protocatechuate that is derived from lignin (14), as well as genes coding for dioxygenases and dienelactone hydrolase (EC 3.1.1.45), known for ring cleavage of aromatic compounds. These enzymes structurally modify lignin, improving the accessibility of polysaccharides to glycoside hydrolases and increasing the efficiency of degradation (15). The TAV5 genome contains the cbb3-type cytochrome oxidase gene, implying the role of TAV5 in oxygen removal. Furthermore, genes for ammonia and sulfate assimilation, the urea cycle, and nitrogen fixation were observed. The availability of this genome will allow the understanding of metabolic and physiological properties carried out by members of the phylum Verrucomicrobia present in the termite hindgut.

Nucleotide sequence accession numbers.

The complete genome sequence of the Opitutaceae bacterium TAV5 was deposited in GenBank under the accession numbers CP007053.1 (chromosome) and CP007054.1 (plasmid).

ACKNOWLEDGMENT

The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract DE-AC02-05CH11231.

Footnotes

Citation Kotak M, Isanapong J, Goodwin L, Bruce D, Chen A, Han CS, Huntemann M, Ivanova N, Land ML, Nolan M, Pati A, Woyke T, Rodrigues JLM. 2015. Complete genome sequence of the Opitutaceae bacterium strain TAV5, a potential facultative methylotroph of the wood-feeding termite Reticulitermes flavipes. Genome Announc 3(2):e00060-15. doi:10.1128/genomeA.00060-15.

REFERENCES

  • 1.Op den Camp HJ, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MS, Birkeland NK, Pol A, Dunfield PF. 2009. Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ Microbiol Rep 1:293–306. doi: 10.1111/j.1758-2229.2009.00022.x. [DOI] [PubMed] [Google Scholar]
  • 2.Dunfield PF, Yuryev A, Senin P, Smirnova AV, Stott MB, Hou S, Ly B, Saw JH, Zhou Z, Ren Y, Wang J, Mountain BW, Crowe MA, Weatherby TM, Bodelier PL, Liesack W, Feng L, Wang L, Alam M. 2007. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450:879–882. doi: 10.1038/nature06411. [DOI] [PubMed] [Google Scholar]
  • 3.Pol A, Heijmans K, Harhangi HR, Tedesco D, Jetten MS, Op den Camp HJ. 2007. Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature 450:874–878. doi: 10.1038/nature06222. [DOI] [PubMed] [Google Scholar]
  • 4.Islam T, Jensen S, Reigstad LJ, Larsen O, Birkeland NK. 2008. Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc Natl Acad Sci U S A 105:300–304. doi: 10.1073/pnas.0704162105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA. 2004. New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70:4748–4755. doi: 10.1128/AEM.70.8.4748-4755.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. doi: 10.1186/1471-2105-11-119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. 2010. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7:455–457. doi: 10.1038/nmeth.1457. [DOI] [PubMed] [Google Scholar]
  • 8.Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. doi: 10.1093/nar/25.5.0955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. doi: 10.1093/nar/gkm160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. 2003. Rfam: an RNA family database. Nucleic Acids Res 31:439–441. doi: 10.1093/nar/gkg006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Bendtsen JD, Nielsen H, von Heijne G, Brunak S. 2004. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795. doi: 10.1016/j.jmb.2004.05.028. [DOI] [PubMed] [Google Scholar]
  • 12.Isanapong J, Goodwin L, Bruce D, Chen A, Detter C, Han J, Han CS, Held B, Huntemann M, Ivanova N, Land ML, Mavromatis K, Nolan M, Pati A, Pennacchio L, Pitluck S, Szeto E, Tapia R, Woyke T, Rodrigues JL. 2012. High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes. J Bacteriol 194:2744–2745. doi: 10.1128/JB.00264-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Isanapong J, Sealy Hambright W, Willis AG, Boonmee A, Callister SJ, Burnum KE, Paša-Tolić L, Nicora CD, Wertz JT, Schmidt TM, Rodrigues JL. 2013. Development of an ecophysiological model for Diplosphaera colotermitum TAV2, a termite hindgut Verrucomicrobium. ISME J 7:1803–1813. doi: 10.1038/ismej.2013.74. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Harwood CS, Parales RE. 1996. The β-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 50:553–590. doi: 10.1146/annurev.micro.50.1.553. [DOI] [PubMed] [Google Scholar]
  • 15.Brune A. 2014. Symbiotic digestion of lignocellulose in termite guts. Nat Rev Microbiol 12:168–180. doi: 10.1038/nrmicro3182. [DOI] [PubMed] [Google Scholar]

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