Substrate-dependent transcriptomic shifts in Pelotomaculum thermopropionicum grown in syntrophic co-culture with Methanothermobacter thermautotrophicus

Microbial Biotechnology

Volumn 2, Issue 5, 2009, Pages 575-584

  Kato, Souichiro ^a,b   Kosaka, Tomoyuki ^a,b   Watanabe, Kazuya ^a,b,c  

^a MARINE BIOTECHNOLOGY INSTITUTE   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL; AMINO ACID; FUMARIC ACID; LACTIC ACID; OLIGONUCLEOTIDE; PROPANOL; PROPIONIC ACID;

ARTICLE; BACTERIAL GROWTH; BACTERIUM; CATABOLISM; COCULTURE; GENE EXPRESSION REGULATION; METHANOGENESIS; METHANOGENIC ARCHAEON; MICROARRAY ANALYSIS; MONOCULTURE; NONHUMAN; OXIDATION; PELOTOMACULUM THERMOPROPIONICUM; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; UPREGULATION;

1-PROPANOL; COCULTURE TECHNIQUES; CULTURE MEDIA; ETHANOL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; LACTATES; METABOLIC NETWORKS AND PATHWAYS; METHANOBACTERIACEAE; MICROARRAY ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEPTOCOCCACEAE; PROPIONATES; STRESS, PHYSIOLOGICAL;

ARCHAEA; BACTERIA (MICROORGANISMS); METHANOTHERMOBACTER THERMAUTOTROPHICUS; PELOTOMACULUM THERMOPROPIONICUM;

EID: 77953589117     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/j.1751-7915.2009.00102.x     Document Type: Article

References (37)

1. 2 or formate uptake. Appl Environ Microbiol 55: 1735-1741.
2. Brüggemann, H., Henne, A., Hoster, F., Liesegang, H., Wiezer, A., Strittmatter, A., et al. (2005) The complete genome sequence of Propionibacterium acnes, a commensal of human skin. Science 305: 671-673.
3. Georgi, T., Engels, V., and Wendisch, V.F. (2008) Regulation of L-lactate utilization by the FadR-type regulator LldR of Corynebacterium glutamicum. J Bacteriol 190: 963-971. (Pubitemid 351170940)
4. Harmsen, H.J., Van Kuijk, B.L., Plugge, C.M., Akkermans, A.D., De Vos, W.M., and Stams, A.J. (1998) Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacteria. Int J Syst Bacteriol 48: 1383-1387.
5. Harper, S.R., and Pohland, F.G. (1986) Recent developments in hydrogen management during anaerobic biological wastewater treatment. Biotechnol Bioeng 28: 585-602.
6. Houwen, F.P., Plokker, J., Stams, A.J.M., and Zehnder, A.J.B. (1990) Enzymatic evidence for involvement of the methylmalonyl- CoA pathway in propionate oxidation by Syntrophobacter wolinii. Arch Microbiol 155: 52-55.
7. Imachi, H., Sekiguchi, Y., Kamagata, Y., Ohashi, A., and Harada, H. (2000) Cultivation and in situ detection of a thermophilic bacterium capable of oxidizing propionate in syntrophic association with hydrogenotrophic methanogens in a thermophilic methanogenic granular sludge. Appl Environ Microbiol 66: 3608-3615. (Pubitemid 30624604)
8. Imachi, H., Sekiguchi, Y., Kamagata, Y., Ohashi, A., Hanada, S., and Harada, H. (2002) Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. Int J Syst Evol Microbiol 52: 1729-1735.
9. Ishii, S., Kosaka, T., Hori, K., Hotta, Y., and Watanabe, K. (2005) Coaggregation facilitates interspecies hydrogen transfer between Pelotomaculum thermopropionicum and Methanothermobacter thermautotrophicus. Appl Environ Microbiol 71: 7838-7845. (Pubitemid 41803903)
10. Ishii, S., Shimoyama, T., Hotta, Y., and Watanabe, K. (2008) Characterization of a filamentous biofilm community established in a cellulose-fed microbial fuel cell. BMC Microbiol 8: 6. (Pubitemid 351327173)
11. Jackson, B.E., and McInerney, M.J. (2002) Anaerobic microbial metabolism can proceed close to thermodynamic limits. Nature 415: 454-456.
12. Kasper, H.F., and Wuhrmann, K. (1978a) Product inhibition in sludge digestion. Microb Ecol 4: 241-248.
13. Kasper, H.F., and Wuhrmann, K. (1978b) Kinetic parameters and relative turnovers of some important catabolic reactions in digesting sludge. Appl Environ Microbiol 36: 1-7.
14. Kato, S., Kosaka, T., and Watanabe, K. (2008) Comparative transcriptome analysis of responses of Methanothermobacter thermautotrophicus to different environmental stimuli. Environ Microbiol 10: 893-905.
15. Kosaka, T., Uchiyama, T., Ishii, S., Enoki, M., Imachi, H., Kamagata, Y., et al. (2006) Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. J Bacteriol 188: 202-210.
16. Kosaka, T., Kato, S., Shimoyama, T., Ishii, S., Abe, T., and Watanabe, K. (2008) The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota. Genome Res 18: 442-448. (Pubitemid 351347087)
17. Kremer, D.R., and Hansen, T.A. (1988) Pathway of propionate degradation in Desulfobulbus propionicus. FEMS Microbiol Lett 49: 273-277.
18. Lettinga, G. (1995) Anaerobic digestion and wastewater treatment systems. Antonie Leewenhock 67: 3-28.
19. Liu, Y., Balkwill, D.L., Aldrich, H.C., Drake, G.R., and Boone, D.R. (1999) Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov., sp. nov. and Syntrophobacter wolinii. Int J Syst Bacteriol 49: 545-556. (Pubitemid 29222342)
20. Marchler-Bauer, A., and Bryant, S.H. (2004) CD-Search: protein domain annotations on the fly. Nucleic Acids Res 32: 327-331. (Pubitemid 38997352)
21. McInerney, M.J., Struchtemeyer, C.G., Sieber, J., Mouttaki, H., Stams, A.J., Schink, B., et al. (2008) Physiology, ecology, phylogeny, and genomics of microorganisms capable of syntrophic metabolism. Ann NY Acad Sci 1125: 58-72.
22. Pellicer, M.T., Badía, J., Aguilar, J., and Baldomà, L. (1996) glc locus of Escherichia coli: characterization of genes encoding the subunits of glycolate oxidase and the glc regulator protein. J Bacteriol 178: 2051-2059. (Pubitemid 3043054)
23. Plugge, C.M., Dijkema, C., and Stams, A.J.M. (1993) Acetyl- CoA cleavage pathway in a syntrophic propionate oxidizing bacterium growing on fumarate in the absence of methanogens. FEMS Microbiol Lett 110: 71-76. (Pubitemid 23171230)
24. Plugge, C.M., Balk, M., and Stams, A.J.M. (2002) Desulfotomaculum thermobenzoicum subsp. thermosyntrophicum subsp. nov., a thermophilic, syntrophic, propionate-oxidizing, spore-forming bacterium. Int J Syst Evol Microbiol 52: 391-399. (Pubitemid 34262633)
25. Rigali, S., Derouaux, A., Giannotta, F., and Dusart, J. (2002) Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J Biol Chem 277: 12507-12515. (Pubitemid 34952608)
26. Schink, B. (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61: 262-280.
27. Schink, B., Kremer, D.R., and Hansen, T.A. (1987) Pathway of propionate formation from ethanol in Pelobacter propionicus. Arch Microbiol 147: 321-327. (Pubitemid 17103234)
28. Schmidt, J.E., and Ahring, B.K. (1993) Effects of hydrogen and formate on the degradation of propionate and butyrate in thermophilic granules from an upflow anaerobic sludge blanket reactor. Appl Environ Microbiol 59: 2546-2551. (Pubitemid 23222994)
29. Schönheit, P., Moll, J., and Thauer, R.K. (1979) Nickel, cobalt and molybdenum requirement for growth of Methanobacterium thermoautotrophicum. Arch Microbiol 123: 105-107. (Pubitemid 10248899)
30. Sekiguchi, Y., Uyeno, Y., Sunaga, A., Yoshida, H., and Kamagata, Y. (2005) Sequence-specific cleavage of 16S rRNA for rapid and quantitative detection of particular groups of anaerobes in bioreactors. Water Sci Technol 52: 107-113. (Pubitemid 41350255)
31. Stams, A.J.M. (1994) Metabolic interactions between anaerobic bacteria in methanogenic environments. Antonie Leeuwenhoek 66: 271-294.
32. Tatusov, R.L., Galperin, M.Y., Natale, D.A., and Koonin, E.V. (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28: 33-36.
33. Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., Tatusova, T.A., Shankavaram, U.T., Rao, B.S., et al. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29: 22-28.
34. Uyeno, Y., Sekiguchi, Y., Sunaga, A., Yoshida, H., and Kamagata, Y. (2004) Sequence-specific cleavage of small-subunit (SSU) rRNA with oligonucleotides and RNase H: a rapid and simple approach to SSU rRNA-based quantitative detection of microorganisms. Appl Environ Microbiol 70: 3650-3663. (Pubitemid 38745915)
35. Van Lier, J.B., Martin, J.L.S., and Lettinga, G. (1996) Effect of temperature on the anaerobic thermophilic conversion of volatile fatty acids by dispersed and granular sludge. Water Res 30: 199-207. (Pubitemid 126755402)
36. Xu, Y., Heath, R.J., Li, Z., Rock, C.O., and White, S.W. (2001) The FadR·DNA complex. Transcriptional control of fatty acid metabolism in Escherichia coli. J Biol Chem 276: 17373-17379. (Pubitemid 37411549)
37. Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J., and Speed, T.P. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic validation. Nucleic Acids Res 30: e15.