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Oxygen regulated gene expression in Escherichia coli: Control of anaerobic respiration by the FNR protein

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Abstract

Molecular oxygen is an important regulatory signal in facultative anaerobic bacteria and controles the expression of a great variety of genes positively or negatively. The expression of anaerobic respiration and of related functions of E. coli is controlled by the positive gene regulator FNR, which activates transcription in the absence of O2. The regulated genes carry a FNR consensus sequence upstream of the promoter. Under the same conditions FNR represses some of the genes of aerobic respiration. The binding to the DNA occurs by an α-helix-turn-α-helix DNA-binding domain. FNR contains 5 cysteine residues, four of which are arranged in a cluster close to the N-terminal end. For the function of FNR as a O2-dependent regulator three of the cysteine residues in the cluster and the residue outside the cluster are essential. FNR binds iron as a cofactor which most likely is involved in the O2-sensing by the protein. The experiments indicate that the cysteine residues are responsible for the binding of the iron. From the protein in vivo two functional states can be differentiated, an aerobic or metal-depleted form and an anaerobic form. Only the anaerobic form acts as a gene activator or repressor. Sensing of O2 or of positive redox potentials by the iron ion is thought to cause the conversion of the two functional states. The FNR protein in addition contains a potential nucleotide binding domain. The significance and function of this site is not clear.

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References

  • Aliabadi Z, Warren F, Mya S & Foster JW (1986) Oxygen-regulated stimulons of Salmonella typhimurium identified by Mu d (Ap lac) operon fusions. J. Bacteriol. 165: 780–786

    Google Scholar 

  • Andersson DI & Roth JR (1989) Redox regulation of the genes for cobinamide biosynthesis in Salmonella typhimurium. J. Bacteriol. 171: 6734–6739

    Google Scholar 

  • Bagg A & Neilands JB (1987) Ferric uptake regulation protein acts as a repressor, employing iron (II) as a cofactor to bind the operator of an iron transport operon in E. coli. Biochemistry 26: 5471–5477

    Google Scholar 

  • Batut J, Daveran-Mingot M-L, David M, Jacobs J, Garnerone AM & Kahn D (1989) fixK, a gene homologous with fnr and crp from E. coli, regulates nitrogen fixation genes both positively and negatively in Rhizobium meliloti. EMBO Journal 8: 1279–1286

    Google Scholar 

  • Bauer CE, Young DA & Marrs BL (1988) Analysis of the Rhodobacter capsulatus puf operon. J. Biol. Chem. 263: 4820–4827

    Google Scholar 

  • Bell AI, Gaston KL, Cole JA & Busby SJW (1989) Cloning of binding sequences for the E. coli transcription activators, FNR and CRP: location of bases involved in discrimination between FNR and CRP. Nucl. Acids Res. 17: 3865–3874

    Google Scholar 

  • Berg JM (1986) Potential metal-binding domains in nucleic acid binding proteins. Science 232: 485–487

    Google Scholar 

  • Birkmann A, Sawers RG & Böck A (1987) Involvement of the ntrA gene product in the anaerobic metabolism of E. coli. Mol. Gen. Genet. 210: 535–542

    Google Scholar 

  • Carlioz A, Ludwig ML, Stallings WC, Fee JA, Steinman HM & Touati D (1988) Iron superoxide dismutase. J. Biol. Chem. 263: 1555–1562

    Google Scholar 

  • Cherfils J, Gibrat J-F, Levin J, Batut J & Kahn D (1989) Model-building of Fnr and FixK DNA-binding domains suggests a basis for specific DNA recognition. J. Molec. Recognition 2(3): 114–121

    Google Scholar 

  • Chippaux M, Giudici D, Aboujaoude A, Casse F & Pascal M (1978) A mutation leading to the total lack of nitrite reductase activity in E. coli K-12. Mol. Gen. Genet. 182: 477–479

    Google Scholar 

  • Clark DP (1984) The number of anaerobically regulated genes in E. coli. FEMS Microbiol. Lett. 24: 251–254

    Google Scholar 

  • Colonna-Romano S, Arnold W, Schlüter A, Boistard P, Pühler A & Priefer UB (1990) An FNR-like protein encoded in Rhizobium leguminosarum biovar viciae shows structural and functional homology to Rhizobium meliloti FixK. Mol. Gen. Genet. 223: 138–147

    Google Scholar 

  • Cotter PA & Gunsalus RP (1989) Oxygen, nitrate and molybdenum regulation of dmsABC gene expression in E. coli. J. Bacteriol. 171: 3817–3823

    Google Scholar 

  • Cotter PA, Chepuri V, Gennis RB & Gunsalus R (1990) Cytochrome o (cyoABCDE) and d (cydAB) oxidase gene expression in E. coli is regulated by oxygen, pH and the fnr gene product. J. Bacteriol. 172: 6333–6338

    Google Scholar 

  • De Crombrugghe B, Busby S & Buc H (1984) Cyclic AMP receptor protein: Role in transcription activation. Science 224: 831–838

    Google Scholar 

  • Deisenhofer J & Michel H (1989) The photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis. EMBO Journal 8(8): 2149–2170

    Google Scholar 

  • Eiglmeier K, Honoré N, Iuchi S, Lin ECC & Cole ST (1989) Molecular genetic analysis of FNR-dependent promoters. Mol. Microbiol. 3(7): 869–878

    Google Scholar 

  • Filser M, Merrick M & Cannon F (1983) Cloning and characterization of the nifLA regulatory mutations from Klebsiella pneumoniae. Mol. Gen. Genet. 191: 485–491

    Google Scholar 

  • Fischer H, Bruderer T & Hennecke H (1988) Essential and non-essential domains in the Bradyrhizobium japonicum NifA protein: identification of dispensible cysteine residues potentially involved in redox reactivity and/or metal binding. Nucl. Acids Res. 16: 2207–2224

    Google Scholar 

  • Frey B, Jänel G, Michelsen U & Kersten H (1989) Mutations in the E. coli fnr and tgt genes: control of molybdate activity and the cytochrome d complex by fnr. J. Bacteriol. 171: 1524–1530

    Google Scholar 

  • Gentry RD & Burgess RR (1986) The cloning and sequence of the gene encoding the omega subunit of E. coli RNA polymerase. Gene 48: 33–40

    Google Scholar 

  • Green J, Trageser M, Six S, Unden G & Guest JR (1991) Characterization of the FNR protein of E. coli, an iron-binding transcriptional regulator (submitted)

  • Gross R, Arico B & Rappuoli R (1989) Families of bacterial signal-transducing proteins. Mol. Microbiol. 3(1): 1661–1667

    Google Scholar 

  • Gussin GN, Ronson CW & Ausubel FM (1986) Regulation of nitrogen fixation genes. Ann. Rev. Genet. 20: 567–591

    Google Scholar 

  • Hayashi M, Miyoshi T, Takashina S & Unemoto T (1989) Purification of NADH-ferricyanide dehydrogenase and NADH-quinone reductase from E. coli membranes and their roles in the respiratory chain. Biochim. Biophys. Acta 977: 62–69

    Google Scholar 

  • Henderson N, Austin S & Dixon RA (1989) Role of metal ions in negative regulation of nitrogen fixation by the nifL gene product of Klebsiella pneumoniae. Mol. Gen. Genet. 216: 484–491

    Google Scholar 

  • Herriott JR, Sieker LC, Jensen LH & Lovenberg W (1970) Structure of rubredoxin: An X-ray study to 2.5 Å resolution. J. Mol. Biol. 50: 391–406

    Google Scholar 

  • Hill S (1985) Redox regulation of enteric nif expression is independent of the fnr gene product. FEMS Microbiol. Lett. 29: 5–9

    Google Scholar 

  • Holmgren A (1981) Thioredoxin: structure and functions. Trends Biochem. Sciences: 26–29

  • Hüdig H, Stark G & Drews G (1987) The regulation of cytochrome c oxidase of Rhodobacter capsulatus by light and oxygen. Arch. Microbiol. 149: 12–18

    Google Scholar 

  • Igarashi K, Fujita N & Ishihama A (1989) Promoter selectivity of E. coli RNA polymerase: omega factor is responsible for the ppGpp sensitivity. Nucl. Acids Res. 17: 8755–8765

    Google Scholar 

  • Ingledew WJ & Poole RK (1984) The respiratory chains of Escherichia coli. Microbiol. Rev. 48: 222–271

    Google Scholar 

  • Iuchi S & Lin ECC (1988) arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc. Natl. Acad. Sci. USA 85: 1888–1892

    Google Scholar 

  • Iuchi S, Cole ST & Lin ECC (1990a) Multiple regulatory elements for the glpA operon encoding anaerobic glycerol-3-phosphate dehydrogenase and the glpD operon encoding aerobic glycerol-3-phosphate dehydrogenase in E. coli: Further characterization of respiratory control. J. Bacteriol. 172: 179–184

    Google Scholar 

  • Iuchi S, Matsuda Z, Fujiwara T & Lin ECC (1990b) The arcB gene of E. coli encodes a sensor-regulator protein for anaerobic repression of the arc modulon. Molec. Microbiol. 4(5): 715–727

    Google Scholar 

  • Jamieson DJ, Sawers RG, Rugman PA, Boxer DH & Higgins CF (1986) Effects of anaerobic regulatory mutations and catabolite repression on regulation of hydrogen metabolism and hydrogenase isoenzyme composition in Salmonella typhimurium. J. Bacteriol. 168: 405–411

    Google Scholar 

  • Jamieson DJ & Higgins CF (1986) Two genetically distinct pathways for transcriptional regulation of anaerobic gene expression in Salmonella typhimurium. J. Bacteriol. 168: 389–397

    Google Scholar 

  • Jayaraman P-S, Cole JA & Busby SJW (1989) Mutational analysis of the nucleotide sequences at the FNR-dependent nirB promoter in E. coli. Nucl. Acids Res. 17: 135–145

    Google Scholar 

  • Jayaraman P-S, Gaston KL, Cole JA & Busby SJW (1988) The nirB promoter of E. coli: Location of the nucleotide sequences essential for regulation by oxygen, the FNR protein and nitrite. Mol. Microbiol. 2(4): 527–530

    Google Scholar 

  • Jennings MP & Beacham IR (1990) Analysis of the E. coli gene encoding L-asparaginase II, ansB, and its regulation by cyclic AMP receptor and FNR proteins. J. Bacteriol. 172: 1491–1498

    Google Scholar 

  • Jerlström PG, Liu J, Beacham IR (1987) Regulation of E. coli L-asparaginase II and L-aspartase by the fnr gene product. FEMS Microbiol. Lett. 41: 127–130

    Google Scholar 

  • Jones HM & Gunsalus RP (1987) Regulation of E. coli fumarate reductase (frdABCD) operon expression by respiratory electron acceptors and the fnr gene product. J. Bacteriol. 169: 3340–3349

    Google Scholar 

  • Lambden PR & Guest JR (1976) Mutants of Escherichia coli unable to use fumarate as an anaerobic electron acceptor. J. Gen. Microbiol. 97: 145–160

    Google Scholar 

  • Lee PC, Bochner BR & Ames BN (1983) AppppA, heat-shock stress, and cell oxidation. Proc. Natl. Acad. Sci. 80: 7496–7500

    Google Scholar 

  • Li SF & DeMoss JA (1988) Location of sequences in the nar promoter of E. coli required for the regulation by Fnr and NarL. J. Biol. Chem. 263: 13700–13705

    Google Scholar 

  • MacInnes JI, Kim EJ, Lian C-J & Soltes GA (1990) Actinobacillus pleuropneumoniae hlyX gene homology with the fnr gene of E. coli. J. Bacteriol. 172: 4587–4592

    Google Scholar 

  • Matzanke BF, Müller GJ, Bill E & Trautwein AX (1989) Iron metabolism of E. coli studied by Mössbauer spectroscopy and biochemical methods. Eur. J. Biochem. 183: 371–379

    Google Scholar 

  • Maupin JA & Shanmugam KT (1990) Genetic regulation of formate hydrogenlyase of E. coli: Role of the fhlA gene product as a transcriptional activator for a new regulatory gene, fhlB. J. Bacteriol. 172: 4798–4806

    Google Scholar 

  • Melville SB & Gunsalus RP (1990) Mutations in fnr that alter anaerobic regulation of electron transport-associated genes in Escherichia coli. J. Biol. Chem. 256: 18733–18736

    Google Scholar 

  • Möller W & Amons R (1985) Phosphate-binding sequences in nucleotide-binding proteins. FEBS Lett. 186: 1–7

    Google Scholar 

  • Newman BM & Cole JA (1978) The chromosomal location and pleiotropic effects of mutations of the nirA + gene of Escherichia coli: The essential role of nirA + in nitrite reduction and in other anaerobic redox reactions. J. Gen. Microbiol. 106: 1–12

    Google Scholar 

  • Ni Bhriain N, Dorman CJ & Higgins CF (1989) An overlap between osmotic and anaerobic stress responses: a potential role for DNA supercoiling in the coordinate regulation of gene expression. Mol. Microbiol. 3: 933–942

    Google Scholar 

  • Niederhoffer EC, Naranjo CM, Bradley KL & Fee JA (1990) Control of Escherichia coli superoxide dismutase (sodA and sodB) genes by the ferric uptake regulation (fur) locus. J. Bacteriol. 172: 1930–1938

    Google Scholar 

  • Noji S & Taniguchi S (1987) Molecular oxygen controls nitrate transport of E. coli nitrate respiring cells. J. Biol. Chem. 262: 9441–9443

    Google Scholar 

  • Ohlendorf DH, Lipscomb JD & Weber PC (1988) Structure and assembly of protocatechuate-3,4-dioxygenase. Nature 336: 403–405

    Google Scholar 

  • Pabo CO & Sauer RT (1984) Protein-DNA recognition. Ann. Rev. Biochem. 53: 293–321

    Google Scholar 

  • Pao CC & Gallant J (1978) A gene involved in the metabolic control of ppGpp synthesis. Mol. Gen. Genet. 158: 271–277

    Google Scholar 

  • Pascal M-C, Bonnefoy V, Fons M & Chippaux M (1986) Use of gene fusions to study the expression of fnr, the regulatory gene of anaerobic electron transfer in E. coli. FEMS Microbiol. Lett. 36: 35–39

    Google Scholar 

  • Rödel W, Plaga W, Frank R & Knappe J (1988) Primary structures of E. coli pyruvate formate-lyase and pyruvate formatelyase-activating enzyme deduced from the DNA nucleotide sequences. Eur. J. Biochem. 177: 153–158

    Google Scholar 

  • Sawers G, Wagner AFV & Böck A (1989) Transcriptional initiation at multiple promoters of the pfl gene by δ70-dependent transcription in vitro and heterologous expression in Pseudomonas putida in vivo. J. Bacteriol. 171: 4930–4937

    Google Scholar 

  • Sawers G, Zehelein E & Böck A (1988) Two-dimensional gel electrophoretic analysis of Escherichia coli proteins: Influence of various anaerobic growth conditions and the fnr gene product on cellular protein composition. Arch. Microbiol. 149: 240–244

    Google Scholar 

  • Schäfer S, Hantke H & Braun V (1985) Nucleotide sequence of the iron regulatory gene fur. Mol. Gen. Genet. 200: 110–113

    Google Scholar 

  • Schiavone JR & Hassan HM (1988) The role of redox in the regulation of manganese-containing superoxide dismutase biosynthesis in Escherichia coli. J. Biol. Chem. 263: 4269–4273

    Google Scholar 

  • Schlensog V & Böck A (1990) Identification and sequence analysis of the gene encoding the transcriptional activator of the formate hydrogenlyase system of E. coli. Mol. Microbiol 4: 1319–1327

    Google Scholar 

  • Sharrocks AD, Green J & Guest JR (1990) In vivo and in vitro mutants of FNR, the anaerobic transcriptional regulator of E. coli. FEBS Lett. 270: 119–122

    Google Scholar 

  • Shaw DJ & Guest JR (1982a) Amplification and product identification of the fnr gene of E. coli. J. Gen. Microbiol. 128: 2221–2228

    Google Scholar 

  • (1982b) Nucleotide sequence of the fnr gene and primary structure of the FNR protein of E. coli. Nucleic Acids Res. 10: 6119–6130

    Google Scholar 

  • Shaw DJ, Rice DW & Guest JR (1983) Homology between CAP and Fnr, a regulator of anaerobic respiration in Escherichia coli. J. Mol. Biol. 166: 241–247

    Google Scholar 

  • Smith MW & Neidhardt FC (1983) Proteins induced by anaerobiosis in E. coli. J. Bacteriol. 154: 336–343

    Google Scholar 

  • Spiro S & Guest JR (1987a) Regulation and over-expression of the fnr gene of Escherichia coli. J. Gen. Microbiol. 133: 3279–3288

    Google Scholar 

  • (1987b) Activation of the lac-operon of Escherichia coli by a mutant FNR protein. Mol. Microbiol. 1: 53–58

    Google Scholar 

  • (1988) Inactivation of the FNR protein of Escherichia coli by targeted mutagenesis in the N-terminal region. Mol. Microbiol. 2: 701–707

    Google Scholar 

  • (1990) FNR and its role in oxygen-regulated gene expression in Escherichia coli. FEMS Microbiol. Rev. 75: 399–428

    Google Scholar 

  • Spiro S, Roberts RE & Guest JR (1989) FNR-dependent repression of the ndh gene of E. coli and metal ion requirement for FNR-regulated gene expression. Mol. Microbiol. 3(5): 601–608

    Google Scholar 

  • Stewart V (1988) Nitrate respiration in relation to facultative metabolism in Enterobacteria. Microbiol. Rev. 52: 190–232

    Google Scholar 

  • Strauch KL, Lenk JB, Gamble BL & Miller CG (1985) Oxygen regulation in Salmonella typhimurium. J. Bacteriol. 161: 673–680

    Google Scholar 

  • Struhl H (1989) Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eucaryotic transcriptional regulatory proteins. Trends Biochem. Sciences. 14: 137–140

    Google Scholar 

  • Taylor BL (1983) How do bacteria find the optimal concentration of oxygen. TIBS 8: 438–441

    Google Scholar 

  • Thöny B & Hennecke H (1989) The -24/-12 promoter comes of age. FEMS Microbiol. Reviews 63: 341–358

    Google Scholar 

  • Trageser M & Unden G (1989) Role of cysteine residues and metal ions in the regulatory functioning of FNR, the transcriptional regulator of anaerobic respiration in E. coli. Mol. Microbiol. 3(5): 593–599

    Google Scholar 

  • Trageser M, Spiro S, Duchêne A, Kojro E, Fahrenholtz F, Guest JR & Unden G (1990) Isolation of intact FNR protein (Mr 30000) of E. coli. Mol. Microbiol. 4(1): 21–27

    Google Scholar 

  • Unden G & Guest JR (1984) Cyclic AMP and anaerobic gene expression in E. coli. FEBS Lett. 170: 321–325

    Google Scholar 

  • (1985) Isolation and characterization of the FNR protein, the transcriptional regulator of anaerobic electron transport in E. coli. Eur. J. Biochem. 146: 193–199

    Google Scholar 

  • Unden G & Duchêne A (1987) On the role of cyclic AMP and the FNR protein in E. coli growing anaerobically. Arch. Microbiol. 147: 195–200

    Google Scholar 

  • Unden G (1988) Differential roles for menaquinone and demethyl-menaquinone in anaerobic electron transport of E. coli and their fnr-independent expression. Arch. Microbiol. 150: 499–503

    Google Scholar 

  • Unden G, Trageser M & Duchêne A (1990) Effect of positive redox potentials (>+400mV) on the expression of anaerobic respiratory enzymes in E. coli. Mol. Microbiol. 4(2): 315–319

    Google Scholar 

  • Weber JT & Steitz TA (1987) Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 Å resolution. J. Mol. Biol. 198: 311–326

    Google Scholar 

  • Wissenbach U, Kröger A & Unden G (1990) The specific functions of menaquinone and demethylmenaquinone in anaerobic respiration with fumarate, dimethylsulfoxide, trimethylamine N-oxide and nitrate by E. coli. Arch. Microbiol. 154: 60–66

    Google Scholar 

  • Woods SA & Guest JR (1987) Differential roles of the E. coli fumarases and fnr-dependent expression of fumarase B and aspartase. FEMS Microbiol. Lett. 48: 219–224

    Google Scholar 

  • Wu LF & Mandrand-Berthelot M-A (1986) Genetic and physiological characterization of new E. coli mutants unpaired in hydrogenase activity. Biochimie 68: 167–179

    Google Scholar 

  • Wu LF, Mandrand-Berthelot, Waugh R, Edmonds CJ, Holt SE & Boxer DH (1989) Nickel deficiency gives rise to the defective hydrogenase phenotype of hydC and fnr mutants in E. coli. Mol. Microbiol. 3: 1709–1718

    Google Scholar 

  • Yamamoto N & Droffner ML (1985) Mechanisms determining aerobic or anaerobic growth in the facultative anaerobic Salmonella typhimurium. Proc. Natl. Acad. Sci. USA 82: 2077–2081

    Google Scholar 

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  1. Institut für Biochemie, Gebäude 26.42, Heinrich-Heine-Universität, Universitätsstr. 1, 4000, Düsseldorf, Germany

    Gottfried Unden & Martin Trageser

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Unden, G., Trageser, M. Oxygen regulated gene expression in Escherichia coli: Control of anaerobic respiration by the FNR protein. Antonie van Leeuwenhoek 59, 65–76 (1991). https://doi.org/10.1007/BF00445650

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