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. 1990 Aug;125(4):691–702. doi: 10.1093/genetics/125.4.691

Structural Genes for Nitrate-Inducible Formate Dehydrogenase in Escherichia Coli K-12

B L Berg 1, V Stewart 1
PMCID: PMC1204095  PMID: 2168848

Abstract

Formate oxidation coupled to nitrate reduction constitutes a major anaerobic respiratory pathway in Escherichia coli. This respiratory chain consists of formate dehydrogenase-N, quinone, and nitrate reductase. We have isolated a recombinant DNA clone that likely contains the structural genes, fdnGHI, for the three subunits of formate dehydrogenase-N. The fdnGHI clone produced proteins of 110, 32 and 20 kDa which correspond to the subunit sizes of purified formate dehydrogenase-N. Our analysis indicates that fdnGHI is organized as an operon. We mapped the fdn operon to 32 min on the E. coli genetic map, close to the genes for cryptic nitrate reductase (encoded by the narZ operon). Expression of φ(fdnG-lacZ) operon fusions was induced by anaerobiosis and nitrate. This induction required fnr(+) and narL(+), two regulatory genes whose products are also required for the anaerobic, nitrate-inducible activation of the nitrate reductase structural gene operon, narGHJI. We conclude that regulation of fdnGHI and narGHJI expression is mediated through common pathways.

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Selected References

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  1. Abou-Jaoudé A., Chippaux M., Pascal M. C. Formate-nitrite reduction in Escherchia coli K12. 1. Physiological study of the system. Eur J Biochem. 1979 Apr 2;95(2):309–314. doi: 10.1111/j.1432-1033.1979.tb12966.x. [DOI] [PubMed] [Google Scholar]
  2. Abou-Jaoudé A., Pascal M. C., Chippaux M. Formate-nitrite reduction in Escherichia coli K12. 2. Identification of components involved in the electron transfer. Eur J Biochem. 1979 Apr 2;95(2):315–321. doi: 10.1111/j.1432-1033.1979.tb12967.x. [DOI] [PubMed] [Google Scholar]
  3. Barrett E. L., Jackson C. E., Fukumoto H. T., Chang G. W. Formate dehydrogenase mutants of Salmonella typhimurium: a new medium for their isolation and new mutant classes. Mol Gen Genet. 1979;177(1):95–101. doi: 10.1007/BF00267258. [DOI] [PubMed] [Google Scholar]
  4. Barrett E. L., Riggs D. L. Salmonella typhimurium mutants defective in the formate dehydrogenase linked to nitrate reductase. J Bacteriol. 1982 Feb;149(2):554–560. doi: 10.1128/jb.149.2.554-560.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bell A. I., Gaston K. L., Cole J. A., Busby S. J. Cloning of binding sequences for the Escherichia coli transcription activators, FNR and CRP: location of bases involved in discrimination between FNR and CRP. Nucleic Acids Res. 1989 May 25;17(10):3865–3874. doi: 10.1093/nar/17.10.3865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Berg D. E., Schmandt M. A., Lowe J. B. Specificity of transposon Tn5 insertion. Genetics. 1983 Dec;105(4):813–828. doi: 10.1093/genetics/105.4.813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Birkmann A., Sawers R. G., Böck A. Involvement of the ntrA gene product in the anaerobic metabolism of Escherichia coli. Mol Gen Genet. 1987 Dec;210(3):535–542. doi: 10.1007/BF00327209. [DOI] [PubMed] [Google Scholar]
  8. Birkmann A., Zinoni F., Sawers G., Böck A. Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli. Arch Microbiol. 1987 Jun;148(1):44–51. doi: 10.1007/BF00429646. [DOI] [PubMed] [Google Scholar]
  9. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1006/abio.1976.9999. [DOI] [PubMed] [Google Scholar]
  10. Chamberlain J. P. Fluorographic detection of radioactivity in polyacrylamide gels with the water-soluble fluor, sodium salicylate. Anal Biochem. 1979 Sep 15;98(1):132–135. doi: 10.1016/0003-2697(79)90716-4. [DOI] [PubMed] [Google Scholar]
  11. Ciampi M. S., Roth J. R. Polarity effects in the hisG gene of salmonella require a site within the coding sequence. Genetics. 1988 Feb;118(2):193–202. doi: 10.1093/genetics/118.2.193. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Cox J. C., Edwards E. S., DeMoss J. A. Resolution of distinct selenium-containing formate dehydrogenases from Escherichia coli. J Bacteriol. 1981 Mar;145(3):1317–1324. doi: 10.1128/jb.145.3.1317-1324.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Enoch H. G., Lester R. L. The purification and properties of formate dehydrogenase and nitrate reductase from Escherichia coli. J Biol Chem. 1975 Sep 10;250(17):6693–6705. [PubMed] [Google Scholar]
  14. Enoch H. G., Lester R. L. The role of a novel cytochrome b-containing nitrate reductase and quinone in the in vitro reconstruction of formate-nitrate reductase activity of E. coli. Biochem Biophys Res Commun. 1974 Dec 23;61(4):1234–1241. doi: 10.1016/s0006-291x(74)80416-x. [DOI] [PubMed] [Google Scholar]
  15. Forchhammer K., Leinfelder W., Böck A. Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein. Nature. 1989 Nov 23;342(6248):453–456. doi: 10.1038/342453a0. [DOI] [PubMed] [Google Scholar]
  16. Groisman E. A., Casadaban M. J. Mini-mu bacteriophage with plasmid replicons for in vivo cloning and lac gene fusing. J Bacteriol. 1986 Oct;168(1):357–364. doi: 10.1128/jb.168.1.357-364.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Gunsalus R. P., Kalman L. V., Stewart R. R. Nucleotide sequence of the narL gene that is involved in global regulation of nitrate controlled respiratory genes of Escherichia coli. Nucleic Acids Res. 1989 Mar 11;17(5):1965–1975. doi: 10.1093/nar/17.5.1965. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Iuchi S., Lin E. C. The narL gene product activates the nitrate reductase operon and represses the fumarate reductase and trimethylamine N-oxide reductase operons in Escherichia coli. Proc Natl Acad Sci U S A. 1987 Jun;84(11):3901–3905. doi: 10.1073/pnas.84.11.3901. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Iuchi S., Lin E. C. arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1888–1892. doi: 10.1073/pnas.85.6.1888. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kalman L. V., Gunsalus R. P. Identification of a second gene involved in global regulation of fumarate reductase and other nitrate-controlled genes for anaerobic respiration in Escherichia coli. J Bacteriol. 1989 Jul;171(7):3810–3816. doi: 10.1128/jb.171.7.3810-3816.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kleckner N., Roth J., Botstein D. Genetic engineering in vivo using translocatable drug-resistance elements. New methods in bacterial genetics. J Mol Biol. 1977 Oct 15;116(1):125–159. doi: 10.1016/0022-2836(77)90123-1. [DOI] [PubMed] [Google Scholar]
  22. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  23. Kustu S., Santero E., Keener J., Popham D., Weiss D. Expression of sigma 54 (ntrA)-dependent genes is probably united by a common mechanism. Microbiol Rev. 1989 Sep;53(3):367–376. doi: 10.1128/mr.53.3.367-376.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lambden P. R., Guest J. R. Mutants of Escherichia coli K12 unable to use fumarate as an anaerobic electron acceptor. J Gen Microbiol. 1976 Dec;97(2):145–160. doi: 10.1099/00221287-97-2-145. [DOI] [PubMed] [Google Scholar]
  25. Leinfelder W., Forchhammer K., Zinoni F., Sawers G., Mandrand-Berthelot M. A., Böck A. Escherichia coli genes whose products are involved in selenium metabolism. J Bacteriol. 1988 Feb;170(2):540–546. doi: 10.1128/jb.170.2.540-546.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Leinfelder W., Stadtman T. C., Böck A. Occurrence in vivo of selenocysteyl-tRNA(SERUCA) in Escherichia coli. Effect of sel mutations. J Biol Chem. 1989 Jun 15;264(17):9720–9723. [PubMed] [Google Scholar]
  27. Lester R. L., DeMoss J. A. Effects of molybdate and selenite on formate and nitrate metabolism in Escherichia coli. J Bacteriol. 1971 Mar;105(3):1006–1014. doi: 10.1128/jb.105.3.1006-1014.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Li S. F., DeMoss J. A. Location of sequences in the nar promoter of Escherichia coli required for regulation by Fnr and NarL. J Biol Chem. 1988 Sep 25;263(27):13700–13705. [PubMed] [Google Scholar]
  29. MacDonald H., Pope N. R., Cole J. A. Isolation, characterization and complementation analysis of nirB mutants of Escherichia coli deficient only in NADH-dependent nitrite reductase activity. J Gen Microbiol. 1985 Oct;131(10):2771–2782. doi: 10.1099/00221287-131-10-2771. [DOI] [PubMed] [Google Scholar]
  30. Mandrand-Berthelot M. A., Couchoux-Luthaud G., Santini C. L., Giordano G. Mutants of Escherichia coli specifically deficient in respiratory formate dehydrogenase activity. J Gen Microbiol. 1988 Dec;134(12):3129–3139. doi: 10.1099/00221287-134-12-3129. [DOI] [PubMed] [Google Scholar]
  31. Newman B. M., Cole J. A. The chromosomal location and pleiotropic effects of mutations of the nirA+ gene of Escherichia coli K12: the essential role of nirA+ in nitrite reduction and in other anaerobic redox reactions. J Gen Microbiol. 1978 May;106(1):1–12. doi: 10.1099/00221287-106-1-1. [DOI] [PubMed] [Google Scholar]
  32. Nohno T., Noji S., Taniguchi S., Saito T. The narX and narL genes encoding the nitrate-sensing regulators of Escherichia coli are homologous to a family of prokaryotic two-component regulatory genes. Nucleic Acids Res. 1989 Apr 25;17(8):2947–2957. doi: 10.1093/nar/17.8.2947. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. PECK H. D., Jr, GEST H. Formic dehydrogenase and the hydrogenlyase enzyme complex in coli-aerogenes bacteria. J Bacteriol. 1957 Jun;73(6):706–721. doi: 10.1128/jb.73.6.706-721.1957. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Paveglio M. T., Tang J. S., Unger R. E., Barrett E. L. Formate-nitrate respiration in Salmonella typhimurium: studies of two rha-linked fdn genes. J Bacteriol. 1988 Jan;170(1):213–217. doi: 10.1128/jb.170.1.213-217.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Pecher A., Zinoni F., Böck A. The seleno-polypeptide of formic dehydrogenase (formate hydrogen-lyase linked) from Escherichia coli: genetic analysis. Arch Microbiol. 1985 May;141(4):359–363. doi: 10.1007/BF00428850. [DOI] [PubMed] [Google Scholar]
  36. Pope N. R., Cole J. A. Generation of a membrane potential by one of two independent pathways for nitrite reduction by Escherichia coli. J Gen Microbiol. 1982 Jan;128(1):219–222. doi: 10.1099/00221287-128-1-219. [DOI] [PubMed] [Google Scholar]
  37. 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]
  38. Rothstein S. J., Jorgensen R. A., Postle K., Reznikoff W. S. The inverted repeats of Tn5 are functionally different. Cell. 1980 Mar;19(3):795–805. doi: 10.1016/s0092-8674(80)80055-9. [DOI] [PubMed] [Google Scholar]
  39. Ruiz-Herrera J., DeMoss J. A. Nitrate reductase complex of Escherichia coli K-12: participation of specific formate dehydrogenase and cytochrome b1 components in nitrate reduction. J Bacteriol. 1969 Sep;99(3):720–729. doi: 10.1128/jb.99.3.720-729.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Shaw D. J., Guest J. R. Amplification and product identification of the fnr gene of Escherichia coli. J Gen Microbiol. 1982 Oct;128(10):2221–2228. doi: 10.1099/00221287-128-10-2221. [DOI] [PubMed] [Google Scholar]
  41. Shaw W. V., Packman L. C., Burleigh B. D., Dell A., Morris H. R., Hartley B. S. Primary structure of a chloramphenicol acetyltransferase specified by R plasmids. Nature. 1979 Dec 20;282(5741):870–872. doi: 10.1038/282870a0. [DOI] [PubMed] [Google Scholar]
  42. Stewart G. S., Lubinsky-Mink S., Jackson C. G., Cassel A., Kuhn J. pHG165: a pBR322 copy number derivative of pUC8 for cloning and expression. Plasmid. 1986 May;15(3):172–181. doi: 10.1016/0147-619x(86)90035-1. [DOI] [PubMed] [Google Scholar]
  43. Stewart V., Berg B. L. Influence of nar (nitrate reductase) genes on nitrate inhibition of formate-hydrogen lyase and fumarate reductase gene expression in Escherichia coli K-12. J Bacteriol. 1988 Oct;170(10):4437–4444. doi: 10.1128/jb.170.10.4437-4444.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Stewart V., MacGregor C. H. Nitrate reductase in Escherichia coli K-12: involvement of chlC, chlE, and chlG loci. J Bacteriol. 1982 Aug;151(2):788–799. doi: 10.1128/jb.151.2.788-799.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Stewart V., MacGregor C. H. Nitrate reductase in Escherichia coli K-12: involvement of chlC, chlE, and chlG loci. J Bacteriol. 1982 Aug;151(2):788–799. doi: 10.1128/jb.151.2.788-799.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Stewart V., Parales J., Jr, Merkel S. M. Structure of genes narL and narX of the nar (nitrate reductase) locus in Escherichia coli K-12. J Bacteriol. 1989 Apr;171(4):2229–2234. doi: 10.1128/jb.171.4.2229-2234.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Stock J. B., Ninfa A. J., Stock A. M. Protein phosphorylation and regulation of adaptive responses in bacteria. Microbiol Rev. 1989 Dec;53(4):450–490. doi: 10.1128/mr.53.4.450-490.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Studier F. W., Moffatt B. A. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol. 1986 May 5;189(1):113–130. doi: 10.1016/0022-2836(86)90385-2. [DOI] [PubMed] [Google Scholar]
  49. Winans S. C., Elledge S. J., Krueger J. H., Walker G. C. Site-directed insertion and deletion mutagenesis with cloned fragments in Escherichia coli. J Bacteriol. 1985 Mar;161(3):1219–1221. doi: 10.1128/jb.161.3.1219-1221.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Yamamoto I., Ishimoto M. Anaerobic growth of Escherichia coli on formate by reduction of nitrate, fumarate, and trimethylamine N-oxide. Z Allg Mikrobiol. 1977;17(3):235–242. doi: 10.1002/jobm.3630170309. [DOI] [PubMed] [Google Scholar]
  51. Zinoni F., Birkmann A., Leinfelder W., Böck A. Cotranslational insertion of selenocysteine into formate dehydrogenase from Escherichia coli directed by a UGA codon. Proc Natl Acad Sci U S A. 1987 May;84(10):3156–3160. doi: 10.1073/pnas.84.10.3156. [DOI] [PMC free article] [PubMed] [Google Scholar]

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