The nucleotide sequence has been determined for a twelve-gene operon of Escherichia coli designated the hyf operon (hyfABCDEFGHIR-focB). The hyf operon is located at 55.8-56.0 min and encodes a putative nine-subunit hydrogenase complex (hydrogenase four or Hyf), a potential formate- and σ54dependent transcriptional activator, HyfR (related to FhlA), and a possible formate transporter, FocB (related to FocA). Five of the nine Hyf-complex subunits are related to subunits of both the E. coli hydrogenase-3 complex (Hyc) and the proton-translocating NADH:quinone oxidoreductases (complex I and Nuo), whereas two Hyf subunits are related solely to NADH:quinone oxidoreductase subunits. The Hyf components include a predicted 523 residue [Ni-Fe] hydrogenase (large subunit) with an N-terminus (residues 1-170) homologous to the 30 kDa or NuoC subunit of complex I. It is proposed that Hyf, in conjunction with formate dehydrogenase H (Fdh-H), forms a hitherto unrecognized respiration-linked proton-translocating formate hydrogenlyase (FHL-2). It is likely that HyfR acts as a formate-dependent regulator of the hyf operon and that FocB provides the Hyf complex with external formate as substrate.
AndrewsS.C., HarrisonP. M.,
GuestJ. R.1991; A molecular analysis of the 53·3 minute region of the Escherichia coli linkage map.
. J Gen Microbiol 137:361–367
BallantineS.P.,
BoxerD.H.1986; Isolation and characterization of a soluble fragment of hydrogenase isoenzyme 2 from the membranes of anaerobically grown Escherichia coli.
. Eur J Biochem 156:277–284
BartoloméB.,
JubeteY.,
MartínezE.,
de la CruzF.1991; Construction and properties of a family of pACYC184-derived cloning vectors compatible with pBR322 and its derivatives.. Gene 102:75–78
BerksB. C,
PageM.D.,
RichardsonD.J.,
ReillyA.,
CavillA.,
OutenF.,
FergusonS.J.1995a; Sequence analysis of subunits of the membrane-bound nitrate reductase from a denitrifying bacterium: the integral membrane subunit provides a prototype for the dihaem electron-carrying arm of a redox loop.. Mol Microbiol 15:319–331
BerksB. C.,
FergusonS.J.,
MoirJ.W.B., RichardsonD.J.1995b; Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxy- anions. . Biochim Biophys Acta 1232:97–173
BerlynM.B.,
Brooks LowK.,
RuddK.E.1996; Linkage map of Escherichia coli K-12, edition 9. . In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edn. pp. 1715–1902NeidhardtF.C. others Washington, DC: American Society for Microbiology;
BinderU.,
MaierT.,
BöckA.1996; Nickel incorporation into hydrogenase 3 from Escherichia colirequires the precursor form of the large subunit.. Arch Microbiol 165:69–72
BöckA.,
SawersG.1996; Fermentation.. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edn. pp. 262–282NeidhardtF.C.
others Edited by Washington, DC: American Society for Microbiology;
BöhmR.,
SauterM.,
BöckA.1990; Nucleotide sequence and expression of an operon in Escherichia coliencoding formate hydrogenlyase components.. Mol Microbiol 4:231–243
BrØndstedL.,
AtlungT.1996; Effect of growth conditions on expression of the acid phosphatase (cyx-appA) operon and the appYgene, which encodes a transcriptional activator of Escherichia coli.
. J Bacteriol 178:156–1564
DarwinA.,
TormayP.,
PageL.,
GriffithsL.,
ColeJ.1993; Identification of the formate dehydrogenases and genetic determinants of formate-dependent nitrite reduction by Escherichia coli.
. J Gen Microbiol 139:1829–1840
DrummondM.,
WhittyP.,
WottonJ.1986; Sequence and domain relationships of ntrCand nifAfrom Klebsiella pneumoniae: homologies to other regulatory proteins.. EMBO J 5:441–447
EnsignS.A.,
LuddenP.W.1991; Characterization of the CO oxidation/H2evolution 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
FisherH.M.,
BrudererT.,
HenneckeH.1988; Essential and non-essential domains in the Bradyrhizobium japonicumNifA protein: identification of indispensable cysteine residues potentially involved in redox activity and/or metal binding.. Nucleic Acids Res 16:2207–2224
FoxJ.D.,
KerbyR.L.,
RobertsG.P.,
LuddenP.W.1996a; Characterization of the CO-induced, CO-tolerant hydrogenase from Rhodospirillum rubrumand the gene encoding the large subunit of the enzyme.. J Bacteriol 178:1515–1524
FoxJ.D.,
HeY.,
ShelverD.,
RobertsG.P.,
LuddenP.W.1996b; Characterization of the region encoding the CO-induced hydrogenase of Rhodospirillum rubrum.
. J Bacteriol 178:6200–6208
FriedrichT.,
SteinmoüllerK.,
WeissH.1995; The protonpumping respiratory complex I of bacteria and mitochondria and its homologue in chloroplasts.. FEBS Lett 367:107–111
GennisR.B.,
StewartV.1996; Respiration.. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edn. pp. 217–261NeidhardtF.C. others Edited by Washington, DC: American Society for Microbiology;
GollinD.J.,
MortensonL.E.,
RobsonR.L.1992; Carboxyl- terminal processing may be essential for production of active NiFe hydrogenase in Azotobacter vinelandii.
. FEBS Lett 309:371–375
GrosjeanH.,
FiersW.1982; Preferential codon usage in prokaryotic genes: optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes.. Gene 18:199–209
GuénebautV.,
VincentelliR.,
MillsD.,
WeissH.,
LeonardK.R.1997; Three-dimensional structure of NADH-dehydrogen- ase from Neurospora crassaby electron microscopy and conical tilt reconstruction.. J Mol Biol 265:409–418
HamamotoT.,
HashimotoM.,
HinoM.,
KitadaM.,
SetoY.,
KudoT.,
HorikoshiK.1994; Characterization of a gene responsible for the Na+/H+antiporter system of alkalophilic Bacillus species strain C-125. . Mol Microbiol 14:939–946
HaroldF.M.,
MaloneyP.C.1996; Energy transduction by ion currents.. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edn. pp. 283–306NeidhardtF.C. others Edited by Washington, DC: American Society for Microbiology;
HidalgoE.,
BollingerJ.M.,
BradleyT.M.,
WalshC.T.,
DempleB.1995; Binuclear [2Fe-2S] clusters in the Escherichia coliSoxR protein and role of the metal centres in transcription.. J Biol Chem 270:20908–20914
HopperS.,
BöckA.1995; Effector-mediated stimulation of ATPase activity by the σ54-dependent transcriptional activator FHLA from Escherichia coli.
. J Bacteriol 177:2798–2803
HopperS.,
KorsaI.,
BöckA.1996; The nucleotide concentration determines the specificity of in vitrotranscription activation by the σ54-dependent activator FHLA.. J Bacteriol 178:199–203
KaiserK.,
MurrayN.E.,
WhittakerP.A.1995; Construction of representative genomic DNA libraries using phage lambda replacement vectors.. In DNA Cloning: a Practical Approach pp. 37–84GloverD.M., HamesB.D.
Edited by Oxford: IRL Press;
KesslerD.,
KnappeJ.1996; Anaerobic dissimilation of pyruvate.. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edn.. pp. 199–205NeidhardtF.C. others Edited by Washington, DC: American Society for Microbiology;
KushnerS.R.1996; mRNA decay. . In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd edn.. pp. 849–860NeidhardtF.C. others Edited by Washington, DC: American Society for Microbiology;
MacDonaldH.,
PopeN.R.,
ColeJ.A.1985; Isolation, characterization and complementation analysis of nirBmutants of Escherichia colideficient only in NADH-dependent nitrite reductase activity. . J Gen Microbiol 131:2771–2782
MaierT.,
BinderU.,
BöckA.1996; Analysis of the hydAlocus of Escherichia coli: two genes (hydN and hypF) involved in formate and hydrogen metabolism.. Arch Microbiol 165:333–341
MenonN.K.,
RobbinsJ.,
PeckH.D.JRChatelusC.Y.,
ChoiE.-S.,
PrzybylaA.E.1990; Cloning and sequencing of a putative Escherichia coli[NiFe] hydrogenase-1 operon containing six open reading frames.. J Bacteriol 172:1969–1977
MorettE.,
SegoviaL.1993; The σ54bacterial enhancerbinding protein family: mechanism of action and phylogenetic relationship of their functional domains.. J Bacteriol 175:6067–6074
NielsenH.,
EngelbrechtJ.,
BrunakS.,
von HeijneG.1997; Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.. Protein Eng 10:1–6
PrickrilB.C.,
KurtzD.M.,
LeGallJ.,
VoordouwG.1991; Cloning and sequencing of the gene for rubrerythrin from Desulfovibrio vulgaris(Hildenborough). . Biochemistry 30:11118–11123
RaganC.I.,
GalanteY.M.,
HatefiY.1982; Purification of three iron-sulfur proteins from the iron-protein fragment of mitochondrial NADH-ubiquinone oxidoreductase.. Biochemistry 21:2518–2524
RossmannR.,
SawersG.,
BöckA.1991; Mechanism of regulation of the formate-hydrogenlyase pathway by oxygen, nitrate, and pH: definition of the formate regulon.. Mol Microbiol 5:2807–2814
RossmannR.,
SauterM.,
LottspeichF.,
BöckA.1994; Maturation of the large subunit (HYCE) of Escherichia colihydrogenase 3 requires nickel incorporation followed by C- terminal processing at Arg537.. Eur J Biochem 220:377–384
RossmannR.,
MaierT.,
LottspeichF.,
BöckA.1995; Characterization of a protease from Escherichia coliinvolved in hydrogenase maturation.. Eur J Biochem 227:545–550
SandfordR.A.,
UrbanceJ.W.,
TiedjeJ.M.1996; Anaerobic oxidation of formate to H2supports growth in strain FOX1, a novel sulfate reducer. General Meeting of the American Society for Microbiology, New Orleans, abstract. 0–66
SawersR.G.,
BallantineS.P.,
BoxerD.H.1985; Differential expression of hydrogenase isoenzymes in Escherichia coliK-12: evidence for a third isoenzyme. . J Bacteriol 164:1324–1331
SchlensogV.,
BöckA.1990; Identification and sequence analysis of the gene encoding the transcriptional activator of the formate hydrogenlyase system of Escherichia coli.
. Mol Microbiol 4:1319–1327
SchlensogV.,
BirkmannA.,
BöckA.1989; Mutations in transwhich affect the anaerobic expression of a formate dehydrogenase (fdhF) structural gene.. Arch Microbiol 152:83–89
SchlensogV.,
LutzS.,
BöckA.1994; Purification and DNA- binding properties of FHLA, the transcriptional activator of the formate hydrogenlyase system from Escherichia coli.
. J Biol Chem 269:19590–19596
ShineJ.,
DalgarnoL.1974; The 3ʹ-terminal sequence of Escherichia coli16S ribosomal RNA: complementarity to nonsense triplets and ribosome-binding sites.. Proc Natl Acad Sci USA 711342–1346
SuppmannB.,
SawersG.1994; Isolation and characterization of hyophosphite-resistant mutants ofEscherichia coli: identification of the FocA protein, encoded by the pfloperon, as a putative formate transporter. . Mol Microbiol 11:965–982
ThauerR.K.,
HedderichR.,
FischerR.1993; Reactions and enzymes involved in methanogenesis from CO2and H2.. In Methanogenesis pp. 209–252FerryJ.G. Edited by New York: Chapman & Hall;
VideiraA.,
AzevedoJ.E.1994; 2 nuclear-coded subunits of mitrochondrial complex I are similar to different domains of a bacterial formate hydrogenlyase subunit.. Int J Biochem 26:1391–1393
VolbedaA.,
GarcinE.,
PirasC.,
de LaceyA.L.,
FernandezV.M.,
HatchikianE.C.,
FreyM.,
Fontecilla-CampsJ.C.1996; Structure of the [NiFe] hydrogenase active site: evidence for biologically uncommon Fe ligands.. J Am Chem Soc 118:12989–12996
YamaguchiM.,
HatefiY.1993; Mitochondrial NADH:ubiquinone oxidoreductase (complex I) : proximity of the subunits of the flavoprotein and the iron-sulfur protein subcomplexes.. Biochemistry 32:1935–1939