Abstract
Induction of the CO-oxidizing system of the photosynthetic bacterium Rhodospirillum rubrum is regulated at the level of gene expression by the presence of CO. In this paper, we describe the identification of a gene that is required for CO-induced gene expression. An 11-kb deletion of the region adjacent to the previously characterized cooFSCTJ region resulted in a mutant unable to synthesize CO dehydrogenase in response to CO and unable to grow utilizing CO as an energy source. A 2.5-kb region that corresponded to a portion of the deleted region complemented this mutant for its CO regulation defect, restoring its ability to grow utilizing CO as an energy source. When the 2.5-kb region was sequenced, one open reading frame, designated cooA, predicted a product showing similarity to members of the cyclic AMP receptor protein (CRP) family of transcriptional regulators. The product, CooA, is 28% identical (51% similar) to CRP and 18% identical (45% similar) to FNR from Escherichia coli. The insertion of a drug resistance cassette into cooA resulted in a mutant that could not grow utilizing CO as an energy source. CooA contains a number of cysteine residues substituted at, or adjacent to, positions that correspond to residues that contact cyclic AMP in the crystal structure of CRP. A model based on this observation is proposed for the recognition of CO by Cooa. Adjacent to cooA are two genes, nadB and nadC, with predicted products similar to proteins in other bacteria that catalyze reactions in the de novo synthesis of NAD.(ABSTRACT TRUNCATED AT 250 WORDS)
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- Adams M. W. The mechanisms of H2 activation and CO binding by hydrogenase I and hydrogenase II of Clostridium pasteurianum. J Biol Chem. 1987 Nov 5;262(31):15054–15061. [PubMed] [Google Scholar]
- Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- Batut J., Daveran-Mingot M. L., David M., Jacobs J., Garnerone A. M., Kahn D. fixK, a gene homologous with fnr and crp from Escherichia coli, regulates nitrogen fixation genes both positively and negatively in Rhizobium meliloti. EMBO J. 1989 Apr;8(4):1279–1286. doi: 10.1002/j.1460-2075.1989.tb03502.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- 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]
- Bonam D., McKenna M. C., Stephens P. J., Ludden P. W. Nickel-deficient carbon monoxide dehydrogenase from Rhodospirillum rubrum: in vivo and in vitro activation by exogenous nickel. Proc Natl Acad Sci U S A. 1988 Jan;85(1):31–35. doi: 10.1073/pnas.85.1.31. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bonam D., Murrell S. A., Ludden P. W. Carbon monoxide dehydrogenase from Rhodospirillum rubrum. J Bacteriol. 1984 Aug;159(2):693–699. doi: 10.1128/jb.159.2.693-699.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chisholm D. A convenient moderate-scale procedure for obtaining DNA from bacteriophage lambda. Biotechniques. 1989 Jan;7(1):21–23. [PubMed] [Google Scholar]
- Dispensa M., Thomas C. T., Kim M. K., Perrotta J. A., Gibson J., Harwood C. S. Anaerobic growth of Rhodopseudomonas palustris on 4-hydroxybenzoate is dependent on AadR, a member of the cyclic AMP receptor protein family of transcriptional regulators. J Bacteriol. 1992 Sep;174(18):5803–5813. doi: 10.1128/jb.174.18.5803-5813.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ensign S. A., Bonam D., Ludden P. W. Nickel is required for the transfer of electrons from carbon monoxide to the iron-sulfur center(s) of carbon monoxide dehydrogenase from Rhodospirillum rubrum. Biochemistry. 1989 Jun 13;28(12):4968–4973. doi: 10.1021/bi00438a010. [DOI] [PubMed] [Google Scholar]
- Ensign S. A., Hyman M. R., Ludden P. W. Nickel-specific, slow-binding inhibition of carbon monoxide dehydrogenase from Rhodospirillum rubrum by cyanide. Biochemistry. 1989 Jun 13;28(12):4973–4979. doi: 10.1021/bi00438a011. [DOI] [PubMed] [Google Scholar]
- 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]
- Fawcett T. W., Bartlett G. An effective method for eliminating "artifact banding" when sequencing double-stranded DNA templates. Biotechniques. 1990 Jul;9(1):46–48. [PubMed] [Google Scholar]
- 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]
- Flachmann R., Kunz N., Seifert J., Gütlich M., Wientjes F. J., Läufer A., Gassen H. G. Molecular biology of pyridine nucleotide biosynthesis in Escherichia coli. Cloning and characterization of quinolinate synthesis genes nadA and nadB. Eur J Biochem. 1988 Aug 1;175(2):221–228. doi: 10.1111/j.1432-1033.1988.tb14187.x. [DOI] [PubMed] [Google Scholar]
- Foster J. W., Moat A. G. Nicotinamide adenine dinucleotide biosynthesis and pyridine nucleotide cycle metabolism in microbial systems. Microbiol Rev. 1980 Mar;44(1):83–105. doi: 10.1128/mr.44.1.83-105.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fujita N., Mori H., Yura T., Ishihama A. Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region. Nucleic Acids Res. 1994 May 11;22(9):1637–1639. doi: 10.1093/nar/22.9.1637. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gronenborn A. M., Sandulache R., Gärtner S., Clore G. M. Mutations in the cyclic AMP binding site of the cyclic AMP receptor protein of Escherichia coli. Biochem J. 1988 Aug 1;253(3):801–807. doi: 10.1042/bj2530801. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Henikoff S. Unidirectional digestion with exonuclease III in DNA sequence analysis. Methods Enzymol. 1987;155:156–165. doi: 10.1016/0076-6879(87)55014-5. [DOI] [PubMed] [Google Scholar]
- Holmes D. S., Quigley M. A rapid boiling method for the preparation of bacterial plasmids. Anal Biochem. 1981 Jun;114(1):193–197. doi: 10.1016/0003-2697(81)90473-5. [DOI] [PubMed] [Google Scholar]
- Hughes K. T., Dessen A., Gray J. P., Grubmeyer C. The Salmonella typhimurium nadC gene: sequence determination by use of Mud-P22 and purification of quinolinate phosphoribosyltransferase. J Bacteriol. 1993 Jan;175(2):479–486. doi: 10.1128/jb.175.2.479-486.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- 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]
- Kolb A., Busby S., Buc H., Garges S., Adhya S. Transcriptional regulation by cAMP and its receptor protein. Annu Rev Biochem. 1993;62:749–795. doi: 10.1146/annurev.bi.62.070193.003533. [DOI] [PubMed] [Google Scholar]
- Lee S. Y., Rasheed S. A simple procedure for maximum yield of high-quality plasmid DNA. Biotechniques. 1990 Dec;9(6):676–679. [PubMed] [Google Scholar]
- Lehman L. J., Roberts G. P. Identification of an alternative nitrogenase system in Rhodospirillum rubrum. J Bacteriol. 1991 Sep;173(18):5705–5711. doi: 10.1128/jb.173.18.5705-5711.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Melville S. B., Gunsalus R. P. Mutations in fnr that alter anaerobic regulation of electron transport-associated genes in Escherichia coli. J Biol Chem. 1990 Nov 5;265(31):18733–18736. [PubMed] [Google Scholar]
- Miller V. L., Mekalanos J. J. A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR. J Bacteriol. 1988 Jun;170(6):2575–2583. doi: 10.1128/jb.170.6.2575-2583.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Moore J., Kantorow M., Vanderzwaag D., McKenney K. Escherichia coli cyclic AMP receptor protein mutants provide evidence for ligand contacts important in activation. J Bacteriol. 1992 Dec;174(24):8030–8035. doi: 10.1128/jb.174.24.8030-8035.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nasu S., Wicks F. D., Gholson R. K. L-Aspartate oxidase, a newly discovered enzyme of Escherichia coli, is the B protein of quinolinate synthetase. J Biol Chem. 1982 Jan 25;257(2):626–632. [PubMed] [Google Scholar]
- Prentki P., Krisch H. M. In vitro insertional mutagenesis with a selectable DNA fragment. Gene. 1984 Sep;29(3):303–313. doi: 10.1016/0378-1119(84)90059-3. [DOI] [PubMed] [Google Scholar]
- Qiu D., Kumar M., Ragsdale S. W., Spiro T. G. Nature's carbonylation catalyst: Raman spectroscopic evidence that carbon monoxide binds to iron, not nickel, in CO dehydrogenase. Science. 1994 May 6;264(5160):817–819. doi: 10.1126/science.8171334. [DOI] [PubMed] [Google Scholar]
- Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schultz S. C., Shields G. C., Steitz T. A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science. 1991 Aug 30;253(5023):1001–1007. doi: 10.1126/science.1653449. [DOI] [PubMed] [Google Scholar]
- Schweizer H. D. Small broad-host-range gentamycin resistance gene cassettes for site-specific insertion and deletion mutagenesis. Biotechniques. 1993 Nov;15(5):831–834. [PubMed] [Google Scholar]
- Shin W., Lindahl P. A. Function and CO binding properties of the NiFe complex in carbon monoxide dehydrogenase from Clostridium thermoaceticum. Biochemistry. 1992 Dec 29;31(51):12870–12875. doi: 10.1021/bi00166a023. [DOI] [PubMed] [Google Scholar]
- Sun D., Setlow P. Cloning, nucleotide sequence, and regulation of the Bacillus subtilis nadB gene and a nifS-like gene, both of which are essential for NAD biosynthesis. J Bacteriol. 1993 Mar;175(5):1423–1432. doi: 10.1128/jb.175.5.1423-1432.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vieira J., Messing J. New pUC-derived cloning vectors with different selectable markers and DNA replication origins. Gene. 1991 Apr;100:189–194. doi: 10.1016/0378-1119(91)90365-i. [DOI] [PubMed] [Google Scholar]
- Weber I. T., Steitz T. A. Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 A resolution. J Mol Biol. 1987 Nov 20;198(2):311–326. doi: 10.1016/0022-2836(87)90315-9. [DOI] [PubMed] [Google Scholar]
- Wei T. F., Ramasubramanian T. S., Golden J. W. Anabaena sp. strain PCC 7120 ntcA gene required for growth on nitrate and heterocyst development. J Bacteriol. 1994 Aug;176(15):4473–4482. doi: 10.1128/jb.176.15.4473-4482.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wei T. F., Ramasubramanian T. S., Pu F., Golden J. W. Anabaena sp. strain PCC 7120 bifA gene encoding a sequence-specific DNA-binding protein cloned by in vivo transcriptional interference selection. J Bacteriol. 1993 Jul;175(13):4025–4035. doi: 10.1128/jb.175.13.4025-4035.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]