The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 6, 2008, Pages 2128-2133

  Seedorf, Henning ^a   Fricke, W Florian ^b   Veith, Birgit ^b   Brüggemann, Holger ^b   Liesegang, Heiko ^b   Strittmatter, Axel ^b   Miethke, Marcus ^c   Buckel, Wolfgang ^c   Hinderberger, Julia ^a   Li, Fuli ^a   Hagemeier, Christoph ^a   Thauer, Rudolf K ^a   Gottschalk, Gerhard ^b  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

Butyryl CoA dehydrogenase; Electron transfer flavoproteins; Genome sequence; Rnf dependent energy conservation

Indexed keywords

ALCOHOL DEHYDROGENASE; ALDEHYDE DEHYDROGENASE; BUTYRYL COENZYME A DEHYDROGENASE; COENZYME A; CROTONYL COENZYME A; FERREDOXIN; FERRODOXIN OXIDOREDUCTASE; GLYCEROL; IRON; NICOTINAMIDE ADENINE DINUCLEOTIDE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; OXIDOREDUCTASE; POLYKETIDE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; SIDEROPHORE; SYNTHETASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL METABOLISM; CATALYSIS; CLOSTRIDIUM KLUYVERI; CONTROLLED STUDY; ENZYME MECHANISM; FERMENTATION; GENE SEQUENCE; GENETIC LINKAGE; GENOME; MACROMOLECULE; NONHUMAN; NONRIBOSOMAL PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN STRUCTURE;

ACETIC ACIDS; ALCOHOL DEHYDROGENASE; ALDEHYDE OXIDOREDUCTASES; CLOSTRIDIUM KLUYVERI; ETHANOL; FERMENTATION; GENOME, BACTERIAL; GLYCEROL; MOLECULAR SEQUENCE DATA; PHENOLS; SUCCINIC ACID; THIAZOLES;

CLOSTRIDIA; CLOSTRIDIUM KLUYVERI;

EID: 41149164162     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0711093105     Document Type: Article

References (56)

1. Barker HA (1937) The production of caproic and butyric acids by the methane fermentation of ethyl alcohol. Arch Mikrobiol 8:415-421.
2. Bornstein BT, Barker HA (1948) The nutrition of Clostridium kluyveri. J Bacteriol 55:223-230.
3. Barker HA, Taha SM (1942) Clostridium kluyverii, an organism concerned in the formation of caproic acid from ethyl alcohol. J Bacteriol 43:347-363.
4. Thauer RK, Jungermann K, Wenning J, Decker K (1968) Characterization of crotonate grown Clostridium kluyveri by its assimilatory metabolism. Arch Mikrobiol 64:125-129.
5. Thauer RK, Jungermann K, Henninger H, Wenning J, Decker K (1968) The energy metabolism of Clostridium kluyveri. Eur J Biochem 4:173-180.
6. Schoberth S, Gottschalk G (1969) Considerations on the energy metabolism of Clostridium kluyveri. Arch Mikrobiol 65:318-328.
7. Bryant MP, Wolin EA, Wolin MJ, Wolfe RS (1967) Methanobacillus omelianskii, a symbiotic association of two species of bacteria. Arch Mikrobiol 59:20-31.
8. Stadtman ER (1953) The coenzyme A transphorase system in Clostridium kluyveri. J Biol Chem 203:501-512.
9. Barker HA (1956) Bacterial Fermentations (Wiley, New York), pp 28-56.
10. Stadtman ER (1953) Functional group of coenzyme A, its metabolic relations, especially in the fatty acid cycle: Discussion. Fed Proc 12:692-693.
11. Wolin MJ, Miller TL (1982) Interspecies hydrogen transfer: 15 years later. Am Soc Microbiol News 48:561-565.
12. Kenealy WR, Waselefsky DM (1985) Studies on the substrate range of Clostridium kluyveri: The use of propanol and succinate. Arch Microbiol 141:187-194.
13. Thauer RK, Jungermann K, Decker K (1977) Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev 41:100-180.
14. Bader J, Simon H (1980) The activities of hydrogenase and enoate reductase in two Clostridium species, their interrelationship and dependence on growth conditions. Arch Microbiol 127:279-287.
15. Gottschalk G, Barker HA (1966) Synthesis of glutamate and citrate by Clostridium kluyveri: An new type of citrate synthase. Biochemistry 5:1125-1133.
16. Li F, Hagemeier CH, Seedorf H, Gottschalk G, Thauer RK (2007) Re-citrate synthase from Clostridium kluyveri is phylogenetically related to homocitrate synthase and isopropylmalate synthase rather than to Si-citrate synthase. J Bacteriol 189:4299-4304.
17. Thauer RK, Rupprecht E, Jungermann K (1970) The synthesis of one-carbon units from CO(2) via a new ferredoxin dependent monocarboxylic acid cycle. FEBS Lett 8:304-307.
18. Waack S, et al. (2006) Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 7:142.
19. Sebaihia M, et al. (2006) The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet 38:779-786.
20. Kanamori K, Weiss RL, Roberts JD (1989) Ammonia assimilation pathways in nitrogen-fixing Clostridium kluyverii and Clostridium butyricum. J Bacteriol 171:2148-2154.
21. Hillmer P, Gottschalk G (1972) Particulate nature of enzymes involved in the fermentation of ethanol and acetate by Clostridium kluyveri. FEBS Lett 21:351-354.
22. Lurz R, Mayer F, Gottschalk G (1979) Electron microscopic study on the quaternary structure of the isolated particulate alcohol-acetaldehyde dehydrogenase complex and on its identity with the polygonal bodies of Clostridium kuyveri. Arch Microbiol 120:255-262.
23. Penrod JT, Roth JR (2006) Conserving a volatile metabolite: A role for carboxysome-like organelles in Salmonella enterica. J Bacteriol 188:2865-2874.
24. Sliwkowski MX, Stadtman TC (1985) Incorporation and distribution of selenium into thiolase from Clostridium kluyveri. J Biol Chem 260:3140-3144.
25. Hartmanis MGN, Stadtman TC (1982) Isolation of a selenium-containing thiolase from Clostridium kluyveri: Identification of the selenium moiety as selenomethionine. Proc Natl Acad Sci USA 79:4912-4916.
26. Bertini I, Donaire A, Luchinat C, Rosato A (1997) Paramagnetic relaxation as a tool for solution structure determination: Clostridium pasteurianum ferredoxin as an example. Proteins 29:348-358.
27. Smith ET, et al. (1991) A totally synthetic histidine-2 ferredoxin: Thermal stability and redox properties. Biochemistry 30:11669-11676.
28. Peters JW, Lanzilotta WN, Lemon BJ, Seefeldt LC (1998) X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution. Science 282:1853-1858.
29. Diekert GB, Graf EG, Thauer RK (1979) Nickel requirement for carbon-monoxide dehydrogenase formation in Clostridium pasteurianum. Arch Microbiol 122:117-120.
30. Crane FL, Mii S, Hauge JG, Green DE, Beinert H (1956) On the mechanism of dehydrogenation of fatty acyl derivatives of coenzyme A. I. The general fatty acyl coenzyme A dehydrogenase. J Biol Chem 218:701-706.
31. Djordjevic S, Pace CP, Stankovich MT, Kim JJ (1995) Three-dimensional structure of butyryl-CoA dehydrogenase from Megasphaera elsdenii. Biochemistry 34:2163-2171.
32. Hetzel M, et al. (2003) Acryloyl-CoA reductase from Clostridium propionicum: An enzyme complex of propionyl-CoA dehydrogenase and electron-transferring flavoprotein. Eur J Biochem 270:902-910.
33. Herrmann G, Jayamani E, Mai G, Buckel W (November 26, 2007) Energy conservation via electron transferring flavoprotein (Etf) in anaerobic bacteria. J Bacteriol, 10.1128/JB.01422-07.
34. Schmehl M, et al. (1993) Identification of a new class of nitrogen-fixation genes in Rhodobacter capsulatus: A putative membrane complex involved in electron-transport to nitrogenase. Mol Gen Genet 241:602-615.
35. Boiangiu CD, et al. (2005) Sodium ion pumps and hydrogen production in glutamate fermenting anaerobic bacteria. J Mol Microbiol Biotechnol 10:105-119.
36. Li F, et al. (November 9, 2007) Coupled ferredoxin- and crotonyl-CoA reduction with NADH catalyzed by the butyryl-CoA dehydrogenase/Etf complex from Clostridium kluyveri. J Bacteriol, 10.1128/JB.01417-07.
37. Kim JJP, Miura R (2004) Acyl-CoA dehydrogenases and acyl-CoA oxidases: Structural basis for mechanistic similarities and differences. Eur J Biochem 271:483-493.
38. Sato K, Nishina Y, Shiga K (2003) Purification of electron-transferring flavoprotein from Megasphaera elsdenii and binding of additional FAD with an unusual absorption spectrum. J Biochem (Tokyo) 134:719-729.
39. Sato K, Nishina Y, Shiga K, Tanaka F (2003) Hydrogen-bonding dynamics of free flavins in benzene and FAD in electron-transferring flavoprotein upon excitation. J Photochem Photobiol B 70:67-73.
40. Brüggemann H, et al. (2003) The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc Natl Acad Sci USA 100:1316-1321.
41. Pfeiff B (1992) MS thesis (Philipps University, Marburg, Germany).
42. Scherf U, Söhling B, Gottschalk G, Linder D, Buckel W (1994) Succinate-ethanol fermentation in Clostridium kluyveri: Purification and characterisation of 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA delta 3-delta 2-isomerase. Arch Microbiol 161:239-245.
43. Söhling B, Gottschalk G (1996) Molecular analysis of the anaerobic succinate degradation pathway in Clostridium kluyveri. J Bacteriol 178:871-880.
44. Gerhardt A, Cinkaya I, Linder D, Huisman G, Buckel W (2000) Fermentation of 4-aminobutyrate by Clostridium aminobutyricum: Cloning of two genes involved in the formation and dehydration of 4-hydroxybutyryl-CoA. Arch Microbiol 174:189-199.
45. Tischer W, Bader J, Simon H (1979) Purification and some properties of a hitherto-unknown enzyme reducing the carbon-carbon double bond of alpha, beta-unsaturated carboxylate anions. Eur J Biochem 97:103-112.
46. Rohdich F, Wiese A, Feicht R, Simon H, Bacher A (2001) Enoate reductases of Clostridia: Cloning, sequencing, and expression. J Biol Chem 276:5779-5787.
47. Dickert S, Pierik AJ, Linder D, Buckel W (2000) The involvement of coenzyme A esters in the dehydration of (R)-phenyllactate to (E)-cinnamate by Clostridium sporogenes. Eur J Biochem 267:3874-3884.
48. Macis L, Daniel R, Gottschalk G (1998) Properties and sequence of the coenzyme B12-dependent glycerol dehydratase of Clostridium pasteurianum. FEMS Microbiol Lett 164:21-28.
49. 12. Proc Natl Acad Sci USA 44:1093-1097.
50. Quadri LE (2000) Assembly of aryl-capped siderophores by modular peptide synthetases and polyketide synthases. Mol Microbiol 37:1-12.
51. Quadri LE, Keating TA, Patel HM, Walsh CT (1999) Assembly of the Pseudomonas aeruginosa nonribosomal peptide siderophore pyochelin: In vitro reconstitution of aryl-4, 2-bisthiazoline synthetase activity from PchD, PchE, and PchF. Biochemistry 38:14941-14954.
52. Gehring AM, Mori I, Perry RD, Walsh CT (1998) The nonribosomal peptide synthetase HMWP2 forms a thiazoline ring during biogenesis of yersiniabactin, an iron-chelating virulence factor of Yersinia pestis. Biochemistry 37:11637-11650.
53. Staden R, Beal KF, Bonfield JK (2000) The Staden package, 1998. Methods Mol Biol 132:115-130.
54. Tech M, Merkl R (2003) YACOP: Enhanced gene prediction obtained by a combination of existing methods. In Silico Biol 3:441-451.
55. Marchler-Bauer A, Bryant SH (2004) CD-Search: Protein domain annotations on the fly. Nucleic Acids Res 32:W327-W331.
56. Merkl R (2004) SIGI: Score-based identification of genomic islands. BMC Bioinformatics 5:22.