Table of Contents Author Guidelines Submit a Manuscript
Archaea
Volume 2017 (2017), Article ID 4097425, 9 pages
https://doi.org/10.1155/2017/4097425
Research Article

The Draft Genome of the Non-Host-Associated Methanobrevibacter arboriphilus Strain DH1 Encodes a Large Repertoire of Adhesin-Like Proteins

1Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
2Temasek Life Sciences Laboratory, Singapore
3Department of Biological Sciences, National University of Singapore, Singapore 117604

Correspondence should be addressed to Henning Seedorf

Received 20 January 2017; Accepted 22 March 2017; Published 28 May 2017

Academic Editor: Stefan Spring

Copyright © 2017 Anja Poehlein et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. K. Thauer, A. K. Kaster, H. Seedorf, W. Buckel, and R. Hedderich, “Methanogenic archaea: ecologically relevant differences in energy conservation,” Nature Reviews Microbiology, vol. 6, no. 8, pp. 579–591, 2008. View at Publisher · View at Google Scholar · View at Scopus
  2. A. K. Kaster, M. Goenrich, H. Seedorf et al., “More than 200 genes required for methane formation from H2 and CO2 and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus,” Archaea, vol. 2011, 23 pages, 2011. View at Publisher · View at Google Scholar · View at Scopus
  3. R. K. Thauer, “Biochemistry of methanogenesis: a tribute to Marjory Stephenson: 1998 Marjory Stephenson prize lecture,” Microbiology, vol. 144, no. 9, pp. 2377–2406, 1998. View at Publisher · View at Google Scholar
  4. P. H. Janssen and M. Kirs, “Structure of the archaeal community of the rumen,” Applied and Environmental Microbiology, vol. 74, no. 12, pp. 3619–3625, 2008. View at Publisher · View at Google Scholar · View at Scopus
  5. H. Seedorf, S. Kittelmann, G. Henderson, and P. H. Janssen, “RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments,” PeerJ, vol. 2, no. e494, 2014. View at Publisher · View at Google Scholar · View at Scopus
  6. B. Dridi, M. Henry, A. El Khechine, D. Raoult, and M. Drancourt, “High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol,” PloS One, vol. 4, no. 9, article e7063, 2009. View at Publisher · View at Google Scholar · View at Scopus
  7. T. L. Miller and M. J. Wolin, “Enumeration of Methanobrevibacter smithii in human feces,” Archives of Microbiology, vol. 131, no. 1, pp. 14–18, 1982. View at Publisher · View at Google Scholar · View at Scopus
  8. F. Ng, S. Kittelmann, M. L. Patchett et al., “An adhesin from hydrogen-utilizing rumen methanogen Methanobrevibacter ruminantium M1 binds a broad range of hydrogen-producing microorganisms,” Environmental Microbiology, vol. 18, no. 9, pp. 3010–3021, 2016. View at Publisher · View at Google Scholar · View at Scopus
  9. T. L. Miller, “Methanobrevibacter,” in Bergey's Manual of Systematics of Archaea and Bacteria, pp. 218–226, Springer Verlag, New York, 2001. View at Publisher · View at Google Scholar
  10. J. Zeikus and D. L. Henning, “Methanobacterium arbophilicum sp. nov. an obligate anaerobe isolated from wetwood of living trees,” Antonie van Leeuwenhoek, vol. 41, no. 4, pp. 543–552, 1975. View at Publisher · View at Google Scholar · View at Scopus
  11. A. J. Zehnder and K. Wuhrmann, “Physiology of a Methanobacterium strain AZ,” Archives of Microbiology, vol. 111, no. 3, pp. 199–205, 1977. View at Publisher · View at Google Scholar · View at Scopus
  12. S. Asakawa, H. Morii, M. Akagawa-Matsuhita, Y. Koga, and K. Hayano, “Characterization of Methanobrevibacter arboriphilicus SA isolated from a paddy field soil and DNA-DNA hybridization among M. arboriphilicus strains,” International Journal of Systematic and Evolutionary Microbiology, vol. 43, no. 4, pp. 683–686, 1993. View at Google Scholar
  13. S. Khelaifia, M. Garibal, C. Robert, D. Raoult, and M. Drancourt, “Draft genome sequence of a human-associated isolate of Methanobrevibacter arboriphilicus, the lowest-G+C-content archaeon,” Genome Announcements, vol. 2, no. 1, article e01181-13, 2014. View at Publisher · View at Google Scholar
  14. J. R. Leadbetter and J. A. Breznak, “Physiological ecology of Methanobrevibacter cuticularis sp. nov. and Methanobrevibacter curvatus sp. nov., isolated from the hindgut of the termite Reticulitermes flavipes,” Applied and Environmental Microbiology, vol. 62, no. 10, pp. 3620–3631, 1996. View at Google Scholar
  15. S. Shima, M. Sordel-Klippert, A. Brioukhanov, A. Netrusov, D. Linder, and R. K. Thauer, “Characterization of a heme-dependent catalase from Methanobrevibacter arboriphilus,” Applied and Environmental Microbiology, vol. 67, no. 7, pp. 3041–3045, 2001. View at Publisher · View at Google Scholar · View at Scopus
  16. W. F. Fricke, H. Seedorf, A. Henne et al., “The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis,” Journal of Bacteriology, vol. 188, no. 2, pp. 642–658, 2006. View at Publisher · View at Google Scholar · View at Scopus
  17. W. J. Kelly, D. Li, S. C. Lambie et al., “Draft genome sequence of the rumen methanogen Methanobrevibacter olleyae YLM1,” Genome Announcements, vol. 4, no. 2, article e00232-16, 2016. View at Publisher · View at Google Scholar
  18. S. Khelaifia, M. Garibal, C. Robert, D. Raoult, and M. Drancourt, “Draft genome sequencing of Methanobrevibacter oralis strain JMR01, isolated from the human intestinal microbiota,” Genome Announcements, vol. 2, no. 1, article e00073-14, 2014. View at Publisher · View at Google Scholar
  19. S. C. Leahy, W. J. Kelly, E. Altermann et al., “The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions,” PloS One, vol. 5, no. 1, article e8926, 2010. View at Publisher · View at Google Scholar
  20. S. C. Leahy, W. J. Kelly, D. Li et al., “The complete genome sequence of Methanobrevibacter sp. AbM4,” Standards in Genomic Sciences, vol. 8, no. 2, pp. 215–227, 2013. View at Publisher · View at Google Scholar · View at Scopus
  21. J.-H. Lee, M. S. Rhee, S. Kumar et al., “Genome sequence of Methanobrevibacter sp. strain JH1, isolated from rumen of Korean native cattle,” Genome Announcements, vol. 1, no. 1, article e00002-13, 2013. View at Publisher · View at Google Scholar · View at Scopus
  22. B. S. Samuel, E. E. Hansen, J. K. Manchester et al., “Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut,” Proceedings of the National Academy of Sciences, vol. 104, no. 25, pp. 10643–10648, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. S. Kittelmann, C. S. Pinares-Patiño, H. Seedorf et al., “Two different bacterial community types are linked with the low-methane emission trait in sheep,” PloS One, vol. 9, no. 7, article e103171, 2014. View at Publisher · View at Google Scholar · View at Scopus
  24. A. Rius, S. Kittelmann, K. Macdonald, G. Waghorn, P. Janssen, and E. Sikkema, “Nitrogen metabolism and rumen microbial enumeration in lactating cows with divergent residual feed intake fed high-digestibility pasture,” Journal of Dairy Science, vol. 95, no. 9, pp. 5024–5034, 2012. View at Publisher · View at Google Scholar · View at Scopus
  25. A. M. Bolger, M. Lohse, and B. Usadel, “Trimmomatic: a flexible trimmer for Illumina sequence data,” Bioinformatics, vol. 30, no. 15, pp. 2114–2120, 2014. View at Publisher · View at Google Scholar · View at Scopus
  26. B. Chevreux, T. Wetter, and S. Suhai, “Genome sequence assembly using trace signals and additional sequence information,” German Conference on Bioinformatics, vol. 99, pp. 45–56, 1999. View at Google Scholar
  27. F. García-Alcalde, K. Okonechnikov, J. Carbonell et al., “Qualimap: evaluating next-generation sequencing alignment data,” Bioinformatics, vol. 28, no. 20, pp. 2678-2679, 2012. View at Publisher · View at Google Scholar · View at Scopus
  28. D. H. Parks, M. Imelfort, C. T. Skennerton, P. Hugenholtz, and G. W. Tyson, “CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes,” Genome Research, vol. 25, no. 7, pp. 1043–1055, 2015. View at Publisher · View at Google Scholar · View at Scopus
  29. V. M. Markowitz, K. Mavromatis, N. N. Ivanova, I.-M. A. Chen, K. Chu, and N. C. Kyrpides, “IMG ER: a system for microbial genome annotation expert review and curation,” Bioinformatics, vol. 25, pp. 2271–2278, 2009. View at Publisher · View at Google Scholar · View at Scopus
  30. J. Besemer and M. Borodovsky, “GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses,” Nucleic Acids Research, vol. 33, Supplement 2, pp. W451–W454, 2005. View at Publisher · View at Google Scholar · View at Scopus
  31. S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at Publisher · View at Google Scholar · View at Scopus
  32. A. Stamatakis, “RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models,” Bioinformatics, vol. 22, no. 21, pp. 2688–2690, 2006. View at Publisher · View at Google Scholar · View at Scopus
  33. M. Lechner, S. Findeiß, L. Steiner, M. Marz, P. F. Stadler, and S. J. Prohaska, “Proteinortho: detection of (co-) orthologs in large-scale analysis,” BMC Bioinformatics, vol. 12, no. 1, p. 124, 2011. View at Publisher · View at Google Scholar · View at Scopus
  34. D. Schwarzer, R. Finking, and M. A. Marahiel, “Nonribosomal peptides: from genes to products,” Natural Product Reports, vol. 20, no. 3, pp. 275–287, 2003. View at Publisher · View at Google Scholar · View at Scopus
  35. A.-K. Kaster, J. Moll, K. Parey, and R. K. Thauer, “Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea,” Proceedings of the National Academy of Sciences, vol. 108, no. 7, pp. 2981–2986, 2011. View at Publisher · View at Google Scholar · View at Scopus
  36. R. K. Thauer, “The Wolfe cycle comes full circle,” Proceedings of the National Academy of Sciences, vol. 109, no. 39, pp. 15084-15085, 2012. View at Publisher · View at Google Scholar · View at Scopus
  37. N. Reeve, J. Nölling, R. M. Morgan, and D. R. Smith, “Methanogenesis: genes, genomes, and who’s on first?” Journal of Bacteriology, vol. 179, no. 19, p. 5975, 1997. View at Publisher · View at Google Scholar
  38. A. Poehlein and H. Seedorf, “Draft genome sequences of Methanobrevibacter curvatus DSM11111, Methanobrevibacter cuticularis DSM11139, Methanobrevibacter filiformis DSM11501, and Methanobrevibacter oralis DSM7256,” Genome Announcements, vol. 4, no. 3, article e00617-16, 2016. View at Publisher · View at Google Scholar
  39. E. C. Hoedt, P. Ó. Cuív, P. N. Evans et al., “Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids,” The ISME Journal, vol. 10, no. 10, pp. 2376–2388, 2016. View at Publisher · View at Google Scholar · View at Scopus
  40. M. Bryant, S. Tzeng, I. Robinson, and A. Joyner Jr, Nutrient Requirements of Methanogenic Bacteria, ACS Publications, United States, 1971.
  41. P. S. Alban and N. R. Krieg, “A hydrogen peroxide resistant mutant of Spirillum volutans has NADH peroxidase activity but no increased oxygen tolerance,” Canadian Journal of Microbiology, vol. 44, no. 1, pp. 87–91, 1998. View at Publisher · View at Google Scholar
  42. H. Seedorf, A. Dreisbach, R. Hedderich, S. Shima, and R. K. Thauer, “F420H2 oxidase (FprA) from Methanobrevibacter arboriphilus, a coenzyme F420-dependent enzyme involved in O2 detoxification,” Archives of Microbiology, vol. 182, no. 2-3, pp. 126–137, 2004. View at Publisher · View at Google Scholar · View at Scopus
  43. H. Seedorf, C. H. Hagemeier, S. Shima, R. K. Thauer, E. Warkentin, and U. Ermler, “Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic archaea catalyzing the reduction of O2 to H2O,” FEBS Journal, vol. 274, no. 6, pp. 1588–1599, 2007. View at Publisher · View at Google Scholar · View at Scopus
  44. H. Seedorf, J. Kahnt, A. J. Pierik, and R. K. Thauer, “Si-face stereospecificity at C5 of coenzyme F420 for F420H2 oxidase from methanogenic archaea as determined by mass spectrometry,” FEBS Journal, vol. 272, no. 20, pp. 5337–5342, 2005. View at Publisher · View at Google Scholar · View at Scopus
  45. H. Liesegang, A. K. Kaster, A. Wiezer et al., “Complete genome sequence of Methanothermobacter marburgensis, a methanoarchaeon model organism,” Journal of Bacteriology, vol. 192, no. 21, pp. 5850-5851, 2010. View at Publisher · View at Google Scholar · View at Scopus
  46. D. R. Smith, L. A. Doucette-Stamm, C. Deloughery et al., “Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics,” Journal of Bacteriology, vol. 179, no. 22, pp. 7135–7155, 1997. View at Publisher · View at Google Scholar
  47. O. Pilak, Kristallstruktur von [Fe]-Hydrogenase Hmd, Universitätsbibliothek, Marburg, 2007.
  48. C. Afting, E. Kremmer, C. Brucker, A. Hochheimer, and R. K. Thauer, “Regulation of the synthesis of H 2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) and of HmdII and HmdIII in Methanothermobacter marburgensis,” Archives of Microbiology, vol. 174, no. 4, pp. 225–232, 2000. View at Publisher · View at Google Scholar · View at Scopus
  49. E. L. Hendrickson and J. A. Leigh, “Roles of coenzyme F420-reducing hydrogenases and hydrogen-and F420-dependent methylenetetrahydromethanopterin dehydrogenases in reduction of F420 and production of hydrogen during methanogenesis,” Journal of Bacteriology, vol. 190, no. 14, pp. 4818–4821, 2008. View at Publisher · View at Google Scholar · View at Scopus
  50. E. E. Hansen, C. A. Lozupone, F. E. Rey et al., “Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins,” Proceedings of the National Academy of Sciences, vol. 108, Supplement 1, pp. 4599–4606, 2011. View at Publisher · View at Google Scholar · View at Scopus
  51. B. V. Jones, M. Begley, C. Hill, C. G. Gahan, and J. R. Marchesi, “Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome,” Proceedings of the National Academy of Sciences, vol. 105, no. 36, pp. 13580–13585, 2008. View at Publisher · View at Google Scholar · View at Scopus
  52. T. Carver, N. Thomson, A. Bleasby, M. Berriman, and J. Parkhill, “DNAPlotter: circular and linear interactive genome visualization,” Bioinformatics, vol. 25, no. 1, pp. 119-120, 2009. View at Publisher · View at Google Scholar · View at Scopus