Characterization of the region encoding the CO-induced hydrogenase of Rhodospirillum rubrum

Journal of Bacteriology

Volumn 178, Issue 21, 1996, Pages 6200-6208

  Fox, Jeffrey D ^a   Yiping, H E ^b   Shelver, Daniel ^b   Roberts, Gary P ^b   Ludden, Paul W ^a,b  

^a Departments of Biochemistry and Nutritional Sciences   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; CARBON MONOXIDE; CARBON MONOXIDE DEHYDROGENASE; DICYCLOHEXYLCARBODIIMIDE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE;

ARTICLE; ENZYME ISOLATION; ENZYME SUBUNIT; GENE EXPRESSION REGULATION; OPERON; PHOTOSYNTHESIS; PREDICTION; PRIORITY JOURNAL; REGULATOR GENE; RHODOSPIRILLUM RUBRUM; SEQUENCE HOMOLOGY; TRANSCRIPTION REGULATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; EUKARYOTA; PHOTOBACTERIA; PROKARYOTA; RHODOSPIRILLUM RUBRUM;

EID: 10344238576     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.178.21.6200-6208.1996     Document Type: Article

References (60)

1. Adams, M. W. W. 1990. The structure and mechanism of iron-hydrogenases. Biochim. Biophys. Acta 1020:115-145.
2. Adams, M. W. W., L. E. Mortenson, and H. S. Chen. 1981. Hydrogenase. Biochim. Biophys. Acta 594:105-176.
3. Albracht, S. P. J. 1993. Intimate relationships of the large and the small subunits of all nickel hydrogenases with two nuclear-encoded subunits of mitochondrial NADH:ubiquinone oxidoreductase. Biochim. Biophys. Acta 1144:221-224.
4. Albracht, S. P. J. 1994. Nickel hydrogenases: in search of the active site. Biochim. Biophys. Acta 1188:167-204.
5. Anderson, S., M. H. L. de Bruijn, A. R. Coulson, I. C. Eperon, F. Sanger, and I. G. Young. 1982. Complete sequence of bovine mitochondrial DNA: conserved features of the mammalian mitochondrial genome. J. Mol. Biol. 156:683-717.
6. Arizmendi, J. M., M. J. Runswick, J. M. Skehel, and J. E. Walker. 1992. NADH:ubiquinone oxidoreductase from bovine heart mitochondria. FEBS Lett. 301:237-242.
7. Bélanger, G., J. Bérard, P. Corriveau, and G. Gingras. 1988. The structural genes coding for the L and M subunits of Rhodospirillum rubrum photore-action center. J. Biol. Chem. 263:7632-7638.
8. Bóhm, R., M. Sauter, and A. Böck. 1990. Nucleotide sequence and expression of an operon in Escherichia coli coding for formate hydrogenlyase components. Mol. Microbiol. 4:231-243.
9. Bonam, D., L. Lehman, G. P. Roberts, and P. W. Ludden. 1989. Regulation of carbon monoxide dehydrogenase and hydrogenase in Rhodospirillum rubrum: effects of CO and oxygen on synthesis and activity. J. Bacteriol. 171:3102-3107.
10. Bonam, D., and P. W. Ludden. 1987. Purification and characterization of carbon monoxide dehydrogenase, a nickel, zinc, iron-sulfur protein, from Rhodospirillum rubrum. J. Biol. Chem. 262:2980-2987.
11. 2 with the phosphorylation of ADP in acetate-grown Methanosarcina barkeri. Eur. J. Biochem. 159:393-398.
12. 2 in Methanosarcina barkeri. Eur. J. Biochem. 179:469-472.
13. Champine, J. E., and R. L. Uffen. 1987. Membrane topography of anaerobic carbon monoxide oxidation in Rhodocyclus gelatinosus. J. Bacteriol. 169: 4784-4789.
14. Champine, J. E., and R. L. Uffen. 1987. Regulation of anaerobic carbon monoxide oxidation activity in Rhodocyclus gelatinosus. FEMS Microbiol. Lett. 44:307-311.
15. Chomyn, A., P. Mariottini, M. W. J. Cleeter, C. I. Ragan, A. Matsuno-Yagi, Y. Hatefi, R. F. Dooliltle, and G. Attardi. 1985. Six unidentified reading frames of human mitochondrial DNA encode components of the respiratory-chain NADH dehydrogenase. Nature (London) 314:592-597.
16. Dupuis, A., J. M. Skehel, and J. E. Walker. 1991. A homologue of a nuclearcoded iron-sulfur protein subunit of bovine mitochondrial complex I is encoded in chloroplast genomes. Biochemistry 30:2954-2960.
17. 2 evolution system of Rhodospirillum rubrum. Role of a 22-kDa iron-sulfur protein in mediating electron transfer between carbon monoxide dehydrogenase and hydrogenase. J. Biol. Chem. 266:18395-18403.
18. Ferber, D. M., B. Moy, and R. J. Maier. 1995. Bradyrhizobium japonicum hydrogen-ubiquinone oxidoreductase activity: quinone specificity, inhibition by quinone analogs, and evidence for separate sites of electron acceptor reactivity. Biochim. Biophys. Acta 1229:334-346.
19. Ferrante, A. A., J. Augliera, K. Lewis, and A. M. Klibanov. 1995. Cloning of an organic solvent-resistance gene in Escherichia coli: the unexpected role of alkylhydroperoxide reductase. Proc. Natl. Acad. Sci. USA 92:7617-7621.
20. Finel, M., J. M. Skehel, S. P. J. Albracht, I. M. Fearnley, and J. E. Walker. 1992. Resolution of NADH:ubiquinone oxidoreductase from bovine heart mitochondria into two subcomplexes, one of which contains the redox centers of the enzyme. Biochemistry 31:11425-11434.
21. Fitzmaurice, W. P., L. L. Saari, R. G. Lowery, P. W. Ludden, and G. P. Roberts. 1989. Genes coding for the reversible ADP-ribosylation system of dinitrogenase reductase from Rhodospirillum rubrum. Mol. Gen. Genet. 218: 340-347.
22. Fox, J. D., R. L. Kerby, G. P. Roberts, and P. W. Ludden. 1996. Characterization of the CO-induced, CO-tolerant hydrogenase from Rhodospirillum rubrum and the gene encoding the large subunit of the enzyme. J. Bacteriol. 178:1515-1524.
23. Friedrich, T., M. Strohdeicher, G. Hofhaus, D. Preis, H. Sahm, and H. Weiss. 1990. The same domain motif for ubiquinone reduction in mitochondrial or chloroplast NADH dehydrogenase and bacterial glucose dehydrogenase. FEBS 265:37-40.
24. Gosink, M. M., N. M. Franklin, and G. P. Roberts. 1990. The product of the Klebsiella pneumoniae nifX gene is a negative regulator of the nitrogen fixation (nif) regulon. J. Bacteriol. 172:1441-1447.
25. He, Y., D. Shelver, R. L. Kerby, and G. P. Roberts. 1996. Characterization of a CO-responsive transcriptional activator from Rhodospirillum rubrum. J. Biol. Chem. 271:120-123.
26. Jacobi, A., R. Rossman, and A. Böck. 1992. The hyp operon gene products are required for the maturation of catalytically active hydrogenase isoenzymes in Escherichia coli. Arch. Microbiol. 158:444-451.
27. Kerby, R. L., S. S. Hong, S. A. Ensign, L. J. Coppoc, P. W. Ludden, and G. P. Roberts. 1992. Genetic and physiological characterization of the Rhodospirillum rubrum carbon monoxide dehydrogenase system. J. Bacteriol. 174: 5284-5294.
28. Kerby, R. L., P. W. Ludden, and G. P. Roberts. 1995. Carbon monoxide-dependent growth of Rhodospirillum rubrum. J. Bacteriol. 177:2241-2244.
29. Kerby, R. L., P. W. Ludden, and G. P. Roberts. In vivo nickel insertion into the carbon monoxide dehydrogenase of Rhodospirillum rubrum: molecular and physiological characterization of cooCTJ. Submitted for publication.
30. Kerby, R. L., and G. P. Roberts. Unpublished data.
31. Kikuno, R., and T. Miyata. 1985. Sequence homologies among mitochondrial DNA-coded URF2, URF4 and URF5. FEBS Lett. 189:85-88.
32. Li, C., H. D. Peck, J. LeGall, and A. E. Przybyla. 1987. Cloning, characterization, and sequencing of the genes encoding the large and small subunits of the periplasmic [NiFe] hydrogenase of Desulfovibrio gigas. DNA 6:539-551.
33. Matsubara, H., K. Inoue, T. Hase, H. Hiura, T. Kakuno, J. Yamashita, and T. Horio. 1983. Structure of the extracellular ferredoxin from Rhodospirillum rubrum: close similarity to clostridial ferredoxins. J. Biochem. 93:1385-1390.
34. Nozato, N., K. Oda, K. Yamato, E. Ohta, M. Takemura, K. Akashi, H. Fukuzawa, and K. Ohyama. 1993. Cotranscriptional expression of mitochondrial genes for subunits of NADH dehydrogenase, nad5, nad4, nad2, in Marchantia polymorpha. Mol. Gen. Genet. 237:343-350.
35. O'Brien, J. M., R. H. Wolkin, T. T. Moench, J. B. Morgan, and J. G. Zeikus. 1984. Association of hydrogen metabolism with unitrophic or mixotrophic growth of Methanosarcina barkeri on carbon monoxide. J. Bacteriol. 158:373-375.
36. Oda, K., K. Yamato, E. Ohta, Y. Nakamura, M. Takemura, N. Nozato, K. Akashi, T. Kanegae, Y. Ogura, T. Kochi, and K. Ohyama. 1992. Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. J. Mol. Biol. 223:1-7.
37. Peyer, R., and G. P. Roberts. Unpublished data.
38. Pilkington, S. J., J. M. Skehel, and J. E. Walker. 1991. The 30-kilodalton subunit of bovine mitochondrial complex I is homologous to a protein coded in chloroplast DNA. Biochemistry 30:1901-1908.
39. Przybyla, A. E., J. Robbins, N. Menon, and H. D. Peck, Jr. 1992. Structure-function relationships among the nickel-containing hydrogenases. FEMS Microbiol. Rev. 88:109-136.
40. Rossman, R., T. Maier, F. Lottspeich, and A. Böck. 1995. Characterisation of a protease from Escherichia coli involved in hydrogenase maturation. Eur. J. Biochem. 227:545-550.
41. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
42. Sauter, M., R. Böhm, and A. Böck. 1992. Mutational analysis of the operon (hyc) determining hydrogenase 3 formation in Escherichia coli. Mol. Microbiol. 6:1523-1532.
43. Shelver, D., R. L. Kerby, Y. He, and G. P. Roberts. 1995. Carbon monoxide-induced activation of gene expression in Rhodospirillum rubrum requires the product of cooA, a member of the cyclic AMP receptor protein family of transcriptional regulators. J. Bacteriol. 177:2157-2163.
44. Silhavy, T. J., M. L. Berman, and L. W. Enquist. 1984. Experiments with gene fusions. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
45. Singer, T. P. 1979. Mitochondrial electron-transport inhibitors. Methods Enzymol. 55:454-462.
46. Solioz, M. 1984. Dicyclohexylcarbodiimide as a probe for proton translocating enzymes. Trends Biochem. Sci. 9:309-312.
47. Storz, G., F. S. Jacobson, L. A. Tartaglia, R. W. Morgan, L. A. Silveira, and B. N. Ames. 1989. An alkyl hydroperoxide reductase induced by oxidative stress in Salmonella typhimurium and Escherichia coli: genetic characterization and cloning of ahp. J. Bacteriol. 171:2049-2055.
48. Stultz, C. M., J. V. White, and T. F. Smith. 1993. Structural analysis based on stale-space modeling. Protein Sci. 2:305-314.
49. Tartaglia, L. A., G. Storz, M. H. Brodsky, A. Lai, and B. N. Ames. 1990. Alkyl hydroperoxide reductase from Salmonella typhimurium. J. Biol. Chem. 265: 10535-10540.
50. Terlesky, K. C., and J. G. Ferry. 1988. Ferredoxin requirement for electron transport from the carbon monoxide dehydrogenase complex to a membrane-bound hydrogenase in acetate-grown Methanosarcina thermophila. J. Biol. Chem. 263:4075-4079.
51. Volbeda, A., M.-H. Charon, C. Piras, E. C. Hatchikian, M. Frey, and J. C. Fontecilla-Camps. 1995. Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas. Nature (London) 373:580-587.
52. Voordouw, G., N. K. Menon, J. LeGall, E.-S. Choi, H. D. Peck, Jr., and A. E. Przybyla. 1989. Analysis and comparison of nucleotide sequences encoding the genes for [NiFe] and [NiFeSe] hydrogenases from Desulfovibrio gigas and Desulfovibrio baculatus. J. Bacteriol. 171:2894-2899.
53. Weidner, U., S. Geier, A. Ptock, T. Friedrich, H. Leif, and H. Weiss. 1993. The gene locus of the proton-translocating NADH:ubiquinone oxidoreductase in Escherichia coli. J. Mol. Biol. 233:109-122.
54. Weiss, H., T. Friedrich, G. Hofhaus, and D. Preis. 1991. The respiratory-chain NADH dehydrogenase (complex I) of mitochondria. Eur. J. Biochem. 197:563-576.
55. White, J. V., C. M. Stultz, and T. F. Smith. 1994. Protein classification by stochastic modeling and optimal filtering of amino-acid sequences. Math. Biosci. 119:35-75.
56. Wu, L.-F., and M. A. Mandrand. 1993. Microbial hydrogenases: primary structure, classification, signatures and phylogeny. FEMS Microbiol. Rev. 104:243-270.
57. Xu, X., A. Matsuno-Yagi, and T. Vagi. 1992. Gene cluster of the energy-transducing NADH-quinone oxidoreductase of Paracoccus denitrificans: characterization of four structural gene products. Biochemistry 31:6925-6932.
58. Xu, X., A. Matsuno-Yagi, and T. Vagi. 1993 DNA sequencing of the seven remaining structural genes of the gene cluster encoding the energy-transducing NADH-quinone oxidoreductase of Paracoccus denitrificans. Biochemistry 32:968-981.
59. Yagi, T. 1987. Inhibition of NADH-ubiquinone reductase activity by N,N-dicyclohexylcarbodiimide and correlation of this inhibition with the occurrence of energy-coupling site 1 in various organisms. Biochemistry 26:2822-2828.
60. Yagi, T., and Y. Hatefl. 1988. Identification of the dicyclohexylcarbodiimide-binding subunit of NADH-ubiquinone oxidoreductase (complex I). J. Biol. Chem. 263:16150-16155.