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. 1996 Nov;178(21):6200–6208. doi: 10.1128/jb.178.21.6200-6208.1996

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

J D Fox 1, Y He 1, D Shelver 1, G P Roberts 1, P W Ludden 1
PMCID: PMC178490  PMID: 8892819

Abstract

In the photosynthetic bacterium Rhodospirillum rubrum, the presence of carbon monoxide (CO) induces expression of several proteins. These include carbon monoxide dehydrogenase (CODH) and a CO-tolerant hydrogenase. Together these enzymes catalyze the following conversion: CO + H2O --> CO2 + H2. This system enables R. rubrum to grow in the dark on CO as the sole energy source. Expression of this system has been shown previously to be regulated at the transcriptional level by CO. We have now identified the remainder of the CO-regulated genes encoded in a contiguous region of the R. rubrum genome. These genes, cooMKLXU, apparently encode proteins related to the function of the CO-induced hydrogenase. As seen before with the gene for the large subunit of the CO-induced hydrogenase (cooH), most of the proteins predicted by these additional genes show significant sequence similarity to subunits of Escherichia coli hydrogenase 3. In addition, all of the newly identified coo gene products show similarity to subunits of NADH-quinone oxidoreductase (energy-conserving NADH dehydrogenase I) from various eukaryotic and prokaryotic organisms. We have found that dicyclohexylcarbodiimide, an inhibitor of mitochondrial NADH dehydrogenase I (also called complex I), inhibits the CO-induced hydrogenase as well. We also show that expression of the cooMKLXUH operon is regulated by CO and the transcriptional activator CooA in a manner similar to that of the cooFSCTJ operon that encodes the subunits of CODH and related proteins.

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Selected References

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  1. Adams M. W., Mortenson L. E., Chen J. S. Hydrogenase. Biochim Biophys Acta. 1980 Dec;594(2-3):105–176. doi: 10.1016/0304-4173(80)90007-5. [DOI] [PubMed] [Google Scholar]
  2. Adams M. W. The structure and mechanism of iron-hydrogenases. Biochim Biophys Acta. 1990 Nov 5;1020(2):115–145. doi: 10.1016/0005-2728(90)90044-5. [DOI] [PubMed] [Google Scholar]
  3. Albracht S. P. 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. 1993 Sep 13;1144(2):221–224. doi: 10.1016/0005-2728(93)90176-g. [DOI] [PubMed] [Google Scholar]
  4. Albracht S. P. Nickel hydrogenases: in search of the active site. Biochim Biophys Acta. 1994 Dec 30;1188(3):167–204. doi: 10.1016/0005-2728(94)90036-1. [DOI] [PubMed] [Google Scholar]
  5. Anderson S., de Bruijn M. H., Coulson A. R., Eperon I. C., Sanger F., Young I. G. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J Mol Biol. 1982 Apr 25;156(4):683–717. doi: 10.1016/0022-2836(82)90137-1. [DOI] [PubMed] [Google Scholar]
  6. Arizmendi J. M., Runswick M. J., Skehel J. M., Walker J. E. NADH: ubiquinone oxidoreductase from bovine heart mitochondria. A fourth nuclear encoded subunit with a homologue encoded in chloroplast genomes. FEBS Lett. 1992 Apr 27;301(3):237–242. doi: 10.1016/0014-5793(92)80248-f. [DOI] [PubMed] [Google Scholar]
  7. Bonam D., Lehman L., Roberts G. P., Ludden P. W. Regulation of carbon monoxide dehydrogenase and hydrogenase in Rhodospirillum rubrum: effects of CO and oxygen on synthesis and activity. J Bacteriol. 1989 Jun;171(6):3102–3107. doi: 10.1128/jb.171.6.3102-3107.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bonam D., Ludden P. W. Purification and characterization of carbon monoxide dehydrogenase, a nickel, zinc, iron-sulfur protein, from Rhodospirillum rubrum. J Biol Chem. 1987 Mar 5;262(7):2980–2987. [PubMed] [Google Scholar]
  9. Bott M., Eikmanns B., Thauer R. K. Coupling of carbon monoxide oxidation to CO2 and H2 with the phosphorylation of ADP in acetate-grown Methanosarcina barkeri. Eur J Biochem. 1986 Sep 1;159(2):393–398. doi: 10.1111/j.1432-1033.1986.tb09881.x. [DOI] [PubMed] [Google Scholar]
  10. Bott M., Thauer R. K. Proton translocation coupled to the oxidation of carbon monoxide to CO2 and H2 in Methanosarcina barkeri. Eur J Biochem. 1989 Feb 1;179(2):469–472. doi: 10.1111/j.1432-1033.1989.tb14576.x. [DOI] [PubMed] [Google Scholar]
  11. Bélanger G., Bérard J., Corriveau P., Gingras G. The structural genes coding for the L and M subunits of Rhodospirillum rubrum photoreaction center. J Biol Chem. 1988 Jun 5;263(16):7632–7638. [PubMed] [Google Scholar]
  12. Böhm R., Sauter M., Böck A. Nucleotide sequence and expression of an operon in Escherichia coli coding for formate hydrogenlyase components. Mol Microbiol. 1990 Feb;4(2):231–243. doi: 10.1111/j.1365-2958.1990.tb00590.x. [DOI] [PubMed] [Google Scholar]
  13. Champine J. E., Uffen R. L. Membrane topography of anaerobic carbon monoxide oxidation in Rhodocyclus gelatinosus. J Bacteriol. 1987 Oct;169(10):4784–4789. doi: 10.1128/jb.169.10.4784-4789.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Chomyn A., Mariottini P., Cleeter M. W., Ragan C. I., Matsuno-Yagi A., Hatefi Y., Doolittle R. F., Attardi G. Six unidentified reading frames of human mitochondrial DNA encode components of the respiratory-chain NADH dehydrogenase. Nature. 1985 Apr 18;314(6012):592–597. doi: 10.1038/314592a0. [DOI] [PubMed] [Google Scholar]
  15. Dupuis A., Skehel J. M., Walker J. E. A homologue of a nuclear-coded iron-sulfur protein subunit of bovine mitochondrial complex I is encoded in chloroplast genomes. Biochemistry. 1991 Mar 19;30(11):2954–2960. doi: 10.1021/bi00225a032. [DOI] [PubMed] [Google Scholar]
  16. Ensign S. A., Ludden P. W. Characterization of the CO oxidation/H2 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. 1991 Sep 25;266(27):18395–18403. [PubMed] [Google Scholar]
  17. Ferrante A. A., Augliera J., Lewis K., Klibanov A. M. Cloning of an organic solvent-resistance gene in Escherichia coli: the unexpected role of alkylhydroperoxide reductase. Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7617–7621. doi: 10.1073/pnas.92.17.7617. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Finel M., Skehel J. M., Albracht S. P., Fearnley I. M., Walker J. E. Resolution of NADH:ubiquinone oxidoreductase from bovine heart mitochondria into two subcomplexes, one of which contains the redox centers of the enzyme. Biochemistry. 1992 Nov 24;31(46):11425–11434. doi: 10.1021/bi00161a022. [DOI] [PubMed] [Google Scholar]
  19. Fitzmaurice W. P., Saari L. L., Lowery R. G., Ludden P. W., Roberts G. P. Genes coding for the reversible ADP-ribosylation system of dinitrogenase reductase from Rhodospirillum rubrum. Mol Gen Genet. 1989 Aug;218(2):340–347. doi: 10.1007/BF00331287. [DOI] [PubMed] [Google Scholar]
  20. Fox J. D., Kerby R. L., Roberts G. P., Ludden P. W. Characterization of the CO-induced, CO-tolerant hydrogenase from Rhodospirillum rubrum and the gene encoding the large subunit of the enzyme. J Bacteriol. 1996 Mar;178(6):1515–1524. doi: 10.1128/jb.178.6.1515-1524.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Friedrich T., Strohdeicher M., Hofhaus G., Preis D., Sahm H., Weiss H. The same domain motif for ubiquinone reduction in mitochondrial or chloroplast NADH dehydrogenase and bacterial glucose dehydrogenase. FEBS Lett. 1990 Jun 4;265(1-2):37–40. doi: 10.1016/0014-5793(90)80878-m. [DOI] [PubMed] [Google Scholar]
  22. Gosink M. M., Franklin N. M., Roberts G. P. The product of the Klebsiella pneumoniae nifX gene is a negative regulator of the nitrogen fixation (nif) regulon. J Bacteriol. 1990 Mar;172(3):1441–1447. doi: 10.1128/jb.172.3.1441-1447.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. He Y., Shelver D., Kerby R. L., Roberts G. P. Characterization of a CO-responsive transcriptional activator from Rhodospirillum rubrum. J Biol Chem. 1996 Jan 5;271(1):120–123. doi: 10.1074/jbc.271.1.120. [DOI] [PubMed] [Google Scholar]
  24. Jacobi A., Rossmann R., Böck A. The hyp operon gene products are required for the maturation of catalytically active hydrogenase isoenzymes in Escherichia coli. Arch Microbiol. 1992;158(6):444–451. doi: 10.1007/BF00276307. [DOI] [PubMed] [Google Scholar]
  25. Kerby R. L., Hong S. S., Ensign S. A., Coppoc L. J., Ludden P. W., Roberts G. P. Genetic and physiological characterization of the Rhodospirillum rubrum carbon monoxide dehydrogenase system. J Bacteriol. 1992 Aug;174(16):5284–5294. doi: 10.1128/jb.174.16.5284-5294.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Kerby R. L., Ludden P. W., Roberts G. P. Carbon monoxide-dependent growth of Rhodospirillum rubrum. J Bacteriol. 1995 Apr;177(8):2241–2244. doi: 10.1128/jb.177.8.2241-2244.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kikuno R., Miyata T. Sequence homologies among mitochondrial DNA-coded URF2, URF4 and URF5. FEBS Lett. 1985 Sep 9;189(1):85–88. doi: 10.1016/0014-5793(85)80847-4. [DOI] [PubMed] [Google Scholar]
  28. Li C., Peck H. D., Jr, LeGall J., Przybyla A. E. Cloning, characterization, and sequencing of the genes encoding the large and small subunits of the periplasmic [NiFe]hydrogenase of Desulfovibrio gigas. DNA. 1987 Dec;6(6):539–551. doi: 10.1089/dna.1987.6.539. [DOI] [PubMed] [Google Scholar]
  29. Matsubara H., Inoue K., Hase T., Hiura H., Kakuno T., Yamashita J., Horio T. Structure of the extracellular ferredoxin from Rhodospirillum rubrum: close similarity to clostridial ferredoxins. J Biochem. 1983 May;93(5):1385–1390. doi: 10.1093/oxfordjournals.jbchem.a134273. [DOI] [PubMed] [Google Scholar]
  30. Nozato N., Oda K., Yamato K., Ohta E., Takemura M., Akashi K., Fukuzawa H., Ohyama K. Cotranscriptional expression of mitochondrial genes for subunits of NADH dehydrogenase, nad5, nad4, nad2, in Marchantia polymorpha. Mol Gen Genet. 1993 Mar;237(3):343–350. doi: 10.1007/BF00279437. [DOI] [PubMed] [Google Scholar]
  31. O'Brien J. M., Wolkin R. H., Moench T. T., Morgan J. B., Zeikus J. G. Association of hydrogen metabolism with unitrophic or mixotrophic growth of Methanosarcina barkeri on carbon monoxide. J Bacteriol. 1984 Apr;158(1):373–375. doi: 10.1128/jb.158.1.373-375.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Oda K., Yamato K., Ohta E., Nakamura Y., Takemura M., Nozato N., Akashi K., Kanegae T., Ogura Y., Kohchi T. Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome. J Mol Biol. 1992 Jan 5;223(1):1–7. doi: 10.1016/0022-2836(92)90708-r. [DOI] [PubMed] [Google Scholar]
  33. Pilkington S. J., Skehel J. M., Walker J. E. The 30-kilodalton subunit of bovine mitochondrial complex I is homologous to a protein coded in chloroplast DNA. Biochemistry. 1991 Feb 19;30(7):1901–1908. doi: 10.1021/bi00221a024. [DOI] [PubMed] [Google Scholar]
  34. Przybyla A. E., Robbins J., Menon N., Peck H. D., Jr Structure-function relationships among the nickel-containing hydrogenases. FEMS Microbiol Rev. 1992 Feb;8(2):109–135. doi: 10.1111/j.1574-6968.1992.tb04960.x. [DOI] [PubMed] [Google Scholar]
  35. Rossmann R., Maier T., Lottspeich F., Böck A. Characterisation of a protease from Escherichia coli involved in hydrogenase maturation. Eur J Biochem. 1995 Jan 15;227(1-2):545–550. doi: 10.1111/j.1432-1033.1995.tb20422.x. [DOI] [PubMed] [Google Scholar]
  36. Sauter M., Böhm R., Böck A. Mutational analysis of the operon (hyc) determining hydrogenase 3 formation in Escherichia coli. Mol Microbiol. 1992 Jun;6(11):1523–1532. doi: 10.1111/j.1365-2958.1992.tb00873.x. [DOI] [PubMed] [Google Scholar]
  37. Shelver D., Kerby R. L., He Y., Roberts G. P. 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. 1995 Apr;177(8):2157–2163. doi: 10.1128/jb.177.8.2157-2163.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Singer T. P. Mitochondrial electron-transport inhibitors. Methods Enzymol. 1979;55:454–462. doi: 10.1016/0076-6879(79)55059-9. [DOI] [PubMed] [Google Scholar]
  39. Storz G., Jacobson F. S., Tartaglia L. A., Morgan R. W., Silveira L. A., Ames B. N. An alkyl hydroperoxide reductase induced by oxidative stress in Salmonella typhimurium and Escherichia coli: genetic characterization and cloning of ahp. J Bacteriol. 1989 Apr;171(4):2049–2055. doi: 10.1128/jb.171.4.2049-2055.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Stultz C. M., White J. V., Smith T. F. Structural analysis based on state-space modeling. Protein Sci. 1993 Mar;2(3):305–314. doi: 10.1002/pro.5560020302. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Tartaglia L. A., Storz G., Brodsky M. H., Lai A., Ames B. N. Alkyl hydroperoxide reductase from Salmonella typhimurium. Sequence and homology to thioredoxin reductase and other flavoprotein disulfide oxidoreductases. J Biol Chem. 1990 Jun 25;265(18):10535–10540. [PubMed] [Google Scholar]
  42. Terlesky K. C., Ferry J. G. Ferredoxin requirement for electron transport from the carbon monoxide dehydrogenase complex to a membrane-bound hydrogenase in acetate-grown Methanosarcina thermophila. J Biol Chem. 1988 Mar 25;263(9):4075–4079. [PubMed] [Google Scholar]
  43. Volbeda A., Charon M. H., Piras C., Hatchikian E. C., Frey M., Fontecilla-Camps J. C. Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas. Nature. 1995 Feb 16;373(6515):580–587. doi: 10.1038/373580a0. [DOI] [PubMed] [Google Scholar]
  44. Voordouw G., Menon N. K., LeGall J., Choi E. S., Peck H. D., Jr, Przybyla A. E. Analysis and comparison of nucleotide sequences encoding the genes for [NiFe] and [NiFeSe] hydrogenases from Desulfovibrio gigas and Desulfovibrio baculatus. J Bacteriol. 1989 May;171(5):2894–2899. doi: 10.1128/jb.171.5.2894-2899.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Weidner U., Geier S., Ptock A., Friedrich T., Leif H., Weiss H. The gene locus of the proton-translocating NADH: ubiquinone oxidoreductase in Escherichia coli. Organization of the 14 genes and relationship between the derived proteins and subunits of mitochondrial complex I. J Mol Biol. 1993 Sep 5;233(1):109–122. doi: 10.1006/jmbi.1993.1488. [DOI] [PubMed] [Google Scholar]
  46. Weiss H., Friedrich T., Hofhaus G., Preis D. The respiratory-chain NADH dehydrogenase (complex I) of mitochondria. Eur J Biochem. 1991 May 8;197(3):563–576. doi: 10.1111/j.1432-1033.1991.tb15945.x. [DOI] [PubMed] [Google Scholar]
  47. White J. V., Stultz C. M., Smith T. F. Protein classification by stochastic modeling and optimal filtering of amino-acid sequences. Math Biosci. 1994 Jan;119(1):35–75. doi: 10.1016/0025-5564(94)90004-3. [DOI] [PubMed] [Google Scholar]
  48. Wu L. F., Mandrand M. A. Microbial hydrogenases: primary structure, classification, signatures and phylogeny. FEMS Microbiol Rev. 1993 Apr;10(3-4):243–269. doi: 10.1111/j.1574-6968.1993.tb05870.x. [DOI] [PubMed] [Google Scholar]
  49. Xu X., Matsuno-Yagi A., Yagi T. DNA sequencing of the seven remaining structural genes of the gene cluster encoding the energy-transducing NADH-quinone oxidoreductase of Paracoccus denitrificans. Biochemistry. 1993 Jan 26;32(3):968–981. doi: 10.1021/bi00054a030. [DOI] [PubMed] [Google Scholar]
  50. Xu X., Matsuno-Yagi A., Yagi T. Gene cluster of the energy-transducing NADH-quinone oxidoreductase of Paracoccus denitrificans: characterization of four structural gene products. Biochemistry. 1992 Aug 4;31(30):6925–6932. doi: 10.1021/bi00145a009. [DOI] [PubMed] [Google Scholar]
  51. Yagi T., Hatefi Y. Identification of the dicyclohexylcarbodiimide-binding subunit of NADH-ubiquinone oxidoreductase (Complex I). J Biol Chem. 1988 Nov 5;263(31):16150–16155. [PubMed] [Google Scholar]
  52. Yagi T. 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. 1987 May 19;26(10):2822–2828. doi: 10.1021/bi00384a025. [DOI] [PubMed] [Google Scholar]

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