The sodium ion translocating glutaconyl-CoA decarboxylase from Acidaminococcus fermentans: Cloning and function of the genes forming a second operon

Molecular Microbiology

Volumn 31, Issue 2, 1999, Pages 473-487

  Braune, Annett ^a,b   Bendrat, Klaus ^a,c   Rospert, Sabine ^a,d   Buckel, Wolfgang ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

^b GERMAN INSTITUTE OF HUMAN NUTRITION   (Germany)

^c MEDEEA Forschungs GmbH   (Germany)

^d UNIVERSITY OF BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; AMINO ACID; BIOTIN; CARBOXYLYASE; GENE PRODUCT; LYSINE; PROLINE; PROTON; SODIUM ION; VALINE;

ALKYLATION; AMINO ACID SEQUENCE; ARCHAEOGLOBUS FULGIDUS; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CARBOXYLATION; CELL MEMBRANE; DECARBOXYLATION; ENZYME ACTIVITY; ENZYME MECHANISM; ENZYME SUBUNIT; ENZYME SYNTHESIS; ESCHERICHIA COLI; GENE FUNCTION; GENETIC TRANSCRIPTION; INTESTINE FLORA; KLEBSIELLA PNEUMONIAE; MOLECULAR CLONING; NONHUMAN; OPERON; PRIORITY JOURNAL; PROMOTER REGION; PROTON TRANSPORT; SALMONELLA TYPHIMURIUM; SEQUENCE HOMOLOGY; SODIUM TRANSPORT; VEILLONELLA;

AMINO ACID SEQUENCE; BASE SEQUENCE; BIOLOGICAL TRANSPORT; BIOTIN; CARBOXY-LYASES; CLONING, MOLECULAR; DNA, BACTERIAL; GENES, BACTERIAL; GRAM-NEGATIVE ANAEROBIC BACTERIA; IONS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; OPERON; SODIUM; TRANSCRIPTION, GENETIC;

EID: 0032956982     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.1999.01189.x     Document Type: Article

References (69)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Beatrix, B., Bendrat, K., Rospert, S., and Buckel, W. (1990) The biotin-dependent sodium ion pump glutaconyl-CoA decarboxylase from Fusobacterium nucleatum (subsp. nucleatum). Arch Microbiol 154: 362-369.
3. Bendrat, K., Berger, S., Buckel, W., Etzel, W.A., and Röhm, K.-H. (1990) Carbon-13 labelled biotin - a new probe for the study of enzyme catalyzed carboxylation and decarboxylation reactions. FEBS Lett 277: 156-158.
4. + pump glutaconyl-CoA decarboxylase from Acidaminococcus fermentans in Escherichia coli. Eur J Biochem 211: 697-702.
5. Bendrat, K., Müller, U., Klees, A.-G., and Buckel, W. (1993) Identification of the gene encoding the activator of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. FEBS Lett 329: 329-331.
6. + pump and evidence for their function. Eur J Biochem 245: 103-115.
7. 13C-spin-spin coupling. Angew Chem 108: 2259-2261; Angew Chem Int Ed Engl 35: 2132-2133.
8. 13C-spin-spin coupling. Angew Chem 108: 2259-2261; Angew Chem Int Ed Engl 35: 2132-2133.
9. Birnboim, H.C., and Doly, J. (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7: 1513-1523.
10. Both, B., Buckel, W., Kroppenstedt, R., and Stackebrandt, E. (1992) Phylogenetic and chemotaxonomic characterization of Acidaminococcus fermentans. FEMS Microbiol Lett 97: 7-12.
11. Bott, M., Pfister, K., Burda, P., Kalbermatter, O., Woelke, G., and Dimroth, P. (1997) Methylmalonyl-CoA decarboxylase from Propionigenium modestum. Cloning and sequencing of the structural genes and purification of the enzyme complex. Eur J Biochem 250: 590-599.
12. Boyer, P.D. (1997) The ATP synthase - a splendid molecular machine. Annu Rev Biochem 66: 717-749.
13. Bradford, M.M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein dye binding. Anal Biochem 72: 248-254.
14. Buckel, W. (1980) The reversible dehydration of (R)-2-hydroxyglutarate to (E)-glutaconate. Eur J Biochem 106: 439-447.
15. Buckel, W. (1986) Biotin-dependent decarboxylases as bacterial sodium pumps: purification and reconstitution of glutaconyl-CoA decarboxylase from Acidaminococcus fermentans. Methods Enzymol 125: 547-558.
16. Buckel, W., Dorn, U., and Semmler, R. (1981) Glutaconate CoA-transferase from Acidaminococcus fermentans. Eur J Biochem 118: 315-321.
17. Buckel, W., and Liedtke, H. (1986) The sodium pump glutaconyl-CoA decarboxylase from A. fermentans. Specific cleavage by n-alkanols. Eur J Biochem 156: 251-257.
18. Buckel, W., and Semmler, R. (1982) A biotin-dependent sodium pump: glutaconyl-CoA decarboxylase from Acidaminococcus fermentans. FEBS Lett 148: 35-38.
19. Buckel, W., and Semmler, R. (1983) Purification, characterization and reconstitution of glutaconyl-CoA decarboxylase, a biotin-dependent sodium pump from anaerobic bacteria. Eur J Biochem 136: 427-434.
20. Collins, M.D., Lawson, P.A., Willems, A., Cordoba, J.J., Fernandez-Garayzabal, J., Garcia, P., et al. (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Bacteriol 44: 812-826.
21. Cook, G.M., Rainey, F.A., Chen, G., Stackebrandt, E., and Russell, J.B. (1994) Emendation of the description of Acidaminococcus fermentans, a trans-aconitate and citrate-oxidizing bacterium. Int J Sys Bact 44: 576-578.
22. Cronan, J.E. Jr (1990) Biotination of proteins in vivo. J Biol Chem 265: 10327-10333.
23. Csordas, A. (1996) Butyrate, aspirin and colorectal cancer. Eur J Cancer Prevent 5: 221-231.
24. + pump and its individual subunits in Escherichia coli and analysis of their function. Eur J Biochem 231: 790-801.
25. + pump. EMBO J 15: 1842-1849.
26. Dimroth, P. (1980) A new sodium-transport system energized by the decarboxylation of oxaloacetate. FEBS Lett 122: 234-236.
27. Dimroth, P. (1997) Primary sodium ion translocating enzymes. Biochim Biophys Acta 1318: 11-51.
28. Dimroth, P., and Thomer, A. (1993) On the mechanism of sodium ion translocation by oxaloacetate decarboxylase from Klebsiella pneumoniae. Biochemistry 32: 1734-1739.
29. Dutscho, R., Wohlfarth, G., Buckel, P., and Buckel, W. (1989) Cloning and sequencing of the genes of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Eur J Biochem 181: 741-746.
30. Fall, R.R., and Vagelos, P.R. (1972) Acetyl coenzyme A carboxylase. Molecular forms and subunit composition of biotin carboxyl carrier protein. J Biol Chem 247: 8005-8015.
31. Fuller, R. (1966) Some morphological and physiological characteristics of Gram-negative anaerobic bacteria isolated from the alimentary tract of the pig. J Appl Bacteriol 29: 375-379.
32. Hager, D.A., and Burgess, R.R. (1980) Elution of proteins from sodium dodecylsulfate polyacrylamide gels, removal of SDS and renaturation of enzymatic activity: results with sigma subunit of E. coli RNA polymerase, wheat germ DNA topoisomerase and other enzymes. Anal Biochem 109: 76-86.
33. Hanahan, D. (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166: 557.
34. Härtel, U., and Buckel, W. (1996a) Fermentation of trans-aconitate via citrate, oxaloacetate and pyruvate by Acidaminococcus fermentans. Arch Microbiol 166: 342-349.
35. Härtel, U., and Buckel, W. (1996b) Sodium ion-dependent hydrogen production in Acidaminococcus fermentans. Arch Microbiol 166: 350-356.
36. Hawley, D.K., and McClure, W.R. (1983) Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res 11: 2237-2255.
37. von Heijne, G. (1986) The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J 5: 3021-3027.
38. Hilpert, W., and Dimroth, P. (1986) Sodium pump methylmalonyl-CoA decarboxylase from Veillonella parvula. Methods Enzymol 125: 540-546.
39. Huder, J.B., and Dimroth, P. (1993) Sequence of the sodium ion pump methylmalonyl-CoA decarboxylase from Veillonella parvula. J Biol Chem 268: 24564-24571.
40. Jacob, U., Mack, M., Clausen, T., Huber, R., Buckel, W., and Messerschmidt, A. (1997) Glutaconate CoA-transferase from Acidaminococcus fermentans: the crystal structure reveals homology with other CoA-transferases. Structure 5: 415-426.
41. Klenk, H.P., Clayton, R.A., Tomb, J., White, O., Nelson, K.E., Ketchum, K.A., et al. (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390: 364-370.
42. Knowles, J.R. (1989) The mechanism of biotin-dependent enzymes. Annu Rev Biochem 58: 195-221.
43. Kyte, J., and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
44. Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of the bacteriophage T4. Nature 227: 680-685.
45. Lynen, F., Knappe, J., Lorch, E., Jütting, G., Ringelmann, E., and Lachance, J.-P. (1961) Zur biochemischen Funktion des Biotins. Biochem Z 335: 123-167.
46. Mack, M., Bendrat, K., Zelder, O., Eckel, E., Linder, D., and Buckel, W. (1994) Location of the two genes encoding glutaconate coenzyme A-transferase at the beginning of the hydroxyglutarate operon in Acidaminococcus fermentans. Eur J Biochem 226: 41-51.
47. Miles, J.S., Guest, J.R., Radford, S.E., and Perham, R.H. (1988) Investigation of the mechanism of active site coupling in the pyruvate dehydrogenase multienzyme complex of Escherichia coli by protein engineering. J Mol Biol 202: 97-106.
48. Müller, U., and Buckel, W. (1995) Activation of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Eur J Biochem 230: 698-704.
49. Prasad, K.N. (1980) Butyric acid: a small fatty acid with diverse biological functions. Life Sciences 27: 1351-1358.
50. Radford, S.E., Laue, E.D., Perham, R.N., Miles, J.S., and Guest, J.R. (1987) Segmental structure and protein domains in the pyruvate dehydrogenase multienzyme complex of Escherichia coli. Genetic reconstruction in vitro and 1H-n.m.r. spectroscopy. Biochem J 247: 641-649.
51. Rogosa, M. (1969) Acidaminococcus gen. n., Acidaminococcus fermentans sp. n. anaerobic Gram-negative diplococci using amino acids as the sole energy source for growth. J Bacteriol 98: 756-766.
52. Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T., Mullis, K.B., and Erlich, H.A. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491.
53. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning. A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
54. Samols, D., Thornton, C.G., Murtif, V.L., Kumar, G.K., Haase, F.C., and Wood, H.G. (1988) Evolutionary conservation among biotin enzymes. J Mol Biol 263: 6461-6464.
55. Sanger, F., Nicklen, S., and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463-5467.
56. Schiele, U., Niedermeier, R., Stürzer, M., and Lynen, F. (1975) Investigations of the structure of 3-methylcrotonyl-CoA carboxylase from Achromobacter. Eur J Biochem 60: 256-266.
57. Schwarz, E., Oesterhelt, D., Reinke, H., Beyreuther, K., and Dimroth, P. (1988) The sodium translocating oxaloacetate decarboxylase of Klebsiella pneumoniae. Sequence of the biotin-containing α-subunit and relationship to other biotin-containing enzymes. J Biol Chem 263: 9640-9645.
58. Shine, J., and Dalgarno, L. (1975) Determinant of cistron specificity in bacterial ribosomes. Nature 254: 34-38.
59. Srere, P.A. (1966) Citrate-condensing enzyme-oxaloacetate binary complex. J Biol Chem 241: 2157-2165.
60. Stephens, P.E., Darlinson, M.G., Lewis, H.M., and Guest, J.R. (1983) The pyruvate dehydrogenase complex of Escherichia coli K12. Nucleotide sequence encoding the dihydrolipoamide acetyltransferase component. Eur J Biochem 133: 481-489.
61. Studier, F.W., and Moffatt, B.A. (1986) Use of the bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189: 113-130.
62. Takeshita, S., Sato, M., Toba, M., Masahashi, W., and Hashimoto-Gotoh, T. (1987) High-copy-number and low-copy-number plasmid vectors for lacZ α-complementation and chloramphenicol- or kanamycin-resistance selection. Gene 61: 63-74.
63. Thauer, R.K., Jungermann, K., and Decker, K. (1977) Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev 41: 100-180.
64. 2O in Ferroglobus placidus. Arch Microbiol 167: 19-23.
65. Willems, A., and Collins, M.D. (1995) Phylogenetic placement of Dialister pneumosintes (formerly Bacteroides pneumosintes) within the Sporomusa subbranch of the Clostridium subphylum of the gram-positive bacteria. Int J Syst Bacteriol 45: 403-405.
66. Woehlke, G., Wifling, K., and Dimroth, P. (1992) Sequence of the sodium ion pump oxaloacetate decarboxylase from Salmonella typhimurium. J Biol Chem 267: 22798-22803. Appendix: Woehlke, G., Laussermair, E., Schwarz, E., Oesterhelt, D., Reinke, H., Beyreuther, K. and Dimroth, P. (1992) Sequence of the β-subunit of oxaloacetate decarboxylase from Salmonella typhimurium: a correction of the C-terminal part. J Biol Chem 267: 22804-22805.
67. Woehlke, G., Wifling, K., and Dimroth, P. (1992) Sequence of the sodium ion pump oxaloacetate decarboxylase from Salmonella typhimurium. J Biol Chem 267: 22798-22803. Appendix: Woehlke, G., Laussermair, E., Schwarz, E., Oesterhelt, D., Reinke, H., Beyreuther, K. and Dimroth, P. (1992) Sequence of the β-subunit of oxaloacetate decarboxylase from Salmonella typhimurium: a correction of the C-terminal part. J Biol Chem 267: 22804-22805.
68. Woese, C.R., Kandler, O., and Wheelis, M.L. (1990) Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576-4579.
69. Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Improved M13 phage cloning vectors: nucleotide sequences of M13mp18 and pUC19 vectors. Gene 33: 103-119.