Skip to main content

Advertisement

Log in

[NiFe] hydrogenases from the hyperthermophilic bacterium Aquifex aeolicus: properties, function, and phylogenetics

  • Original Paper
  • Published:
Extremophiles Aims and scope Submit manuscript

Abstract

Genes potentially coding for three distinct [NiFe] hydrogenases are present in the genome of Aquifex aeolicus. We have demonstrated that all three hydrogenases are expressed under standard growth conditions of the organism. Two hydrogenases were further purified to homogeneity. A periplasmically oriented hydrogenase was obtained in two forms, i.e., as a soluble enzyme containing only the two essential subunits and as a detergent-solubilized complex additionally containing a membrane-integral b-type cytochrome. The second hydrogenase purified was identified as a soluble cytoplasmic enzyme. The isolated enzymes were characterized with respect to biochemical/biophysical parameters, activity, thermostability, and substrate specificity. The phylogenetic positioning of all three hydrogenases was analyzed. A model for the metabolic roles of the three enzymes is proposed on the basis of the obtained results.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.
Fig. 6.

Similar content being viewed by others

References

  • Ackrell BA, Asato RN, Mower HF (1966) Multiple forms of bacterial hydrogenases. J Bacteriol 92:828–838

    CAS  PubMed  Google Scholar 

  • Adams MWW (1990) The structure and mechanism of iron-hydrogenases. Biochim Biophys Acta 1020:115–145

    CAS  PubMed  Google Scholar 

  • Adams MWW (1994) Biochemical diversity among sulfur-dependent, hyperthermophilic microorganisms. FEMS Microbiol Rev 15:261–277

    CAS  PubMed  Google Scholar 

  • Adams MWW, Kelly RM (1998) Finding and using hyperthermophilic enzymes. Trends Biotechnol 16:329–332

    Article  CAS  PubMed  Google Scholar 

  • Ahlers PM, Zwicker K, Kerscher S, Brandt U (2000) Function of conserved acidic residues in the PSST homologue of complex I (NADH:ubiquinone oxidoreductase) from Yarrowia lipolytica. J Biol Chem 275:23577–23582

    Article  CAS  PubMed  Google Scholar 

  • Akagi JM (1967) Electron carries for the phosphoroclastic reaction of Desulfovibrio desulfuricans. J Biol Chem 242:2478–2483

    CAS  PubMed  Google Scholar 

  • Albracht SPJ (1993) Intimate relationships of the large and the small subunits of all nickel hydrogenases with two nuclear-encoded subunits of mitochondrial NADH: ubiquinone oxidoreductase. Biochem Biophys Acta 1144:221–224

    CAS  Google Scholar 

  • Albracht SPJ, Hedderich R (2000) Learning from hydrogenases: location of a proton pump and of a second FMN in bovine NADH--ubiquinone oxidoreductase (Complex I). FEBS Lett 485:1–6

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Amutha B, Khire JM, Khan MI (1998) Characterization of a novel exo-N-acetyl-beta-d-glucosaminidase from the thermotolerant Bacillus sp. NCIM 5120. Biochem Biophys Acta 1425:300–310

    Article  CAS  Google Scholar 

  • Baymann F, Tron P, Schoepp-Cothenet B, Aubert C, Bianco P, Stetter KO, Nitschke W, Schutz M (2001) Cytochromes c555 from the hyperthermophilic bacterium Aquifex aeolicus (VF5). 1. Characterization of two highly homologous, soluble and membranous, cytochromes c555. Biochemistry 40:13681–13689

    Article  CAS  PubMed  Google Scholar 

  • Beh M, Strauss G, Huber R, Stetter KO, Fuchs G (1993) Enzymes of the reductive citric acid cycle in the autotrophic eubacterium Aquifex pyrophilus and in the archaebacterium Thermoproteus neutrophilus. Arch Microbiol 160:306–311

    CAS  Google Scholar 

  • Bernhard M, Benelli B, Hochkoeppler A, Zannoni D, Friedrich B. (1997) Functional and structural role of the cytochrome b subunit of the membrane-bound hydrogenase complex of Alcaligenes eutrophus H16. Eur J Biochem 248:179–186

    CAS  PubMed  Google Scholar 

  • Bernhard M, Buhrke T, Bleijlevens B, De Lacey AL, Fernandez VM, Albracht SPJ, Friedrich B (2001) The H2 sensor of Ralstonia eutropha. Biochemical characteristics, spectroscopic properties, and its interaction with a histidine protein kinase. J Biol Chem 276:15592–15597

    CAS  PubMed  Google Scholar 

  • Blamey JM, Adams MWW (1993) Purification and characterization of pyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. Biochem Biophys Acta 1161:19–27

    CAS  Google Scholar 

  • Blasie JK, Erecinska M, Samuels S, Leigh JS (1978) The structure of a cytochrome oxidase-lipid model membrane. Biochim Biophys Acta 501:33–52

    CAS  PubMed  Google Scholar 

  • Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254

    Article  CAS  PubMed  Google Scholar 

  • Bryant FO, Adams MWW (1989) Characterization of hydrogenase from the hyperthermophilic archaebacterium, Pyrococcus furiosus. J Biol Chem 264:5070–5079

    CAS  PubMed  Google Scholar 

  • Cammack R, Bagyinka C, Kovacs KL (1989) Spectroscopic characterization of the nickel and iron-sulphur clusters of hydrogenase from the purple photosynthetic bacterium Thiocapsa roseopersicina. 1. Electron spin resonance spectroscopy. Eur J Biochem 182:363–366.

    CAS  PubMed  Google Scholar 

  • Charnock JS, Cook DA, Casey R (1971) The role of cations and other factors on the apparent energy of activation of (Na + + K + )-ATPase. Arch Biochem Biophys 147:323–329

    CAS  PubMed  Google Scholar 

  • Dahl C, Rakhely G, Pott-Sperling AS, Fodor B, Takacs M, Toth A, Kraeling M, Gyorfi K, Kovacs A, Tusz J, Kovacs KL (1999) Genes involved in hydrogen and sulfur metabolism in phototrophic sulfur bacteria. FEMS Microbiol Lett 180:317–324

    Article  CAS  PubMed  Google Scholar 

  • Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, Graham DE, Overbeek R, Snead MA, Keller M, Aujay M, Huber R, Feldman RA, Short JM, Olsen GJ, Swanson RV (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392:353–358

    CAS  PubMed  Google Scholar 

  • Dross F, Geisler V, Lenger R, Theis F, Krafft T, Fahrenholz F, Kojro E, Duchene A, Tripier D, Juvenal K, Kröger A (1992) The quinone-reactive Ni/Fe-hydrogenase of Wolinella succinogenes. Eur J Biochem 206:93–102

    CAS  PubMed  Google Scholar 

  • Evans MCW, Buchanan BB, Arnon DI (1966) A new ferredoxin-dependent carbon reduction cycle in a photosynthetic bacterium. Proc Natl Acad Sci USA 55:928–934

    CAS  PubMed  Google Scholar 

  • Fauque G, Peck HD, Moura JJ, Huynh BH, Berlier Y, DerVartanian DV, Teixeira M, Przybyla AE, Lespinat PA, Moura I (1988) The three classes of hydrogenases from sulfate-reducing bacteria of the genus Desulfovibrio. FEMS Microbiol Rev 4:299–344

    CAS  PubMed  Google Scholar 

  • Friedrich B, Schwartz E (1993) Molecular biology of hydrogen utilization in aerobic chemolithotrophs. Annu Rev Microbiol 47:351–383

    CAS  PubMed  Google Scholar 

  • Friedrich T, Scheide D (2000) The respiratory complex I of bacteria, archaea and eukarya and its module common with membrane-bound multisubunit hydrogenases. FEBS Lett 479:1–5

    Article  CAS  PubMed  Google Scholar 

  • Gross R, Simon J, Lancaster RD, Kröger A (1998) Identification of histidine residues in Wolinella succinogenes hydrogenase that are essential for menaquinone reduction by H2. Mol Microbiol 30:639–646

    Article  CAS  PubMed  Google Scholar 

  • Guigliarelli B, More C, Fournel A, Asso M, Hatchikian EC, Williams R, Cammack R, Bertrand P (1995) Structural organization of the Ni and (4Fe-4S) centers in the active form of Desulfovibrio gigas hydrogenase. Analysis of the magnetic interactions by electron paramagnetic resonance spectroscopy. Biochemistry 34:4781–4790

    CAS  PubMed  Google Scholar 

  • Happe T, Schutz K, Bohme H (2000) Transcriptional and mutational analysis of the uptake hydrogenase of the filamentous cyanobacterium Anabaena variabilis ATCC 29413. J Bacteriol 182:1624–1631

    CAS  PubMed  Google Scholar 

  • Huber R, Stetter KO (2001) Discovery of hyperthermophilic microorganisms. Methods Enzymol 330:11–24

    CAS  PubMed  Google Scholar 

  • Huber R, Huber H, Stetter K-O (2000) Towards the ecology of hyperthermophiles: biotopes, new isolation strategies and novel metabolic properties. FEMS Microbiol Rev 24:615–623

    CAS  PubMed  Google Scholar 

  • Ishii M, Takishita S, Iwasaki T, Peerapornpisal P, Yoshino J-I, Kodama T, Igarashi Y (2000) Purification and characterization of membrane-bound hydrogenase from Hydrogenobacter thermophilus strain TK-6, an obligately autotrophic, thermophilic, hydrogen-oxidizing bacterium. Biosci Biotechnol Biochem 64:492–502

    CAS  PubMed  Google Scholar 

  • Jensen ON, Larsen MR, Roepstorff P (1998) Mass spectrometric identification and microcharacterization of proteins from electrophoretic gels: strategies and applications. Proteins 2:74–89

    Article  Google Scholar 

  • Kelly RM, Adams MWW (1994) Metabolism in hyperthermophilic microorganisms. Antonie V. Leeuwenhoek 66:247–270.

    CAS  Google Scholar 

  • Ma K, Weiss R, Adams MWW (2000) Characterization of hydrogenase II from the hyperthermophilic archaeon Pyrococcus furiosus and assessment of its role in sulfur reduction. J Bacteriol 182:1864–1871

    Article  CAS  PubMed  Google Scholar 

  • Meek L, Arp DJ (2000) The hydrogenase cytochrome b heme ligands of Azotobacter vinelandii are required for full H(2) oxidation capability. J Bacteriol 182:3429–3436

    Article  CAS  PubMed  Google Scholar 

  • Ohnishi T (1998) Iron-sulfur clusters/semiquinones in complex I. Biochim Biophys Acta 1364:186–206

    Article  CAS  PubMed  Google Scholar 

  • Olsen GJ (1994) Microbial ecology. Archaea, Archaea, everywhere. Nature 371:657–658

    CAS  PubMed  Google Scholar 

  • Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1–6

    CAS  PubMed  Google Scholar 

  • Pereira MM, Santana M, Teixeira M (2001) A novel scenario for the evolution of haem-copper oxygen reductases. Biochim Biophys Acta 1505:185–208

    Article  CAS  PubMed  Google Scholar 

  • Pihl TD, Maier RJ (1991) Purification and characterization of the hydrogen uptake hydrogenase from the hyperthermophilic archaebacterium Pyrodictium brockii. J Bacteriol 173:1839–1844

    CAS  PubMed  Google Scholar 

  • Rákhely G, Colbeau A, Garin J, Vignais PM, Kovács KL (1998) Unusual organization of the genes coding for HydSL, the stable [NiFe]hydrogenase in the photosynthetic bacterium Thiocapsa roseopersicina BBS. J Bacteriol 180:1460–1465

    CAS  PubMed  Google Scholar 

  • Rutherford AWR, Sétif P (1990) Orientation of P700, the primary electron donor of photosystem I. Biochim Biophys Acta 1019:128–132

    CAS  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp 18.60–18.75

    Google Scholar 

  • Sapra R, Verhagen MFJM, Adams MWW (2000) Purification and characterization of a membrane-bound hydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 182:3423–3428

    Article  CAS  PubMed  Google Scholar 

  • Scheide D, Huber R, Friedrich T (2002) The proton-pumping NADH:ubiquinone oxidoreductase (complex I) of Aquifex aeolicus. FEBS Lett 512:80–84

    Article  CAS  PubMed  Google Scholar 

  • Schütz M, Brugna M, Lebrun E, Baymann F, Huber R, Stetter KO, Hauska G, Toci R, Lemesle-Meunier D, Tron P, Schmidt C, Nitschke W (2000) Early evolution of cytochrome bc complexes. J Mol Biol 300:663–675

    Article  PubMed  Google Scholar 

  • Segel IK (1993) Enzyme kinetics. Behaviour and analysis of rapid equilibrium and steady state enzyme systems. Wiley Classics Library Edition, New York

  • Snel B, Bork P, Huynen MA (1999) Genome phylogeny based on gene content. Nat Genet 21:108–110

    Article  CAS  PubMed  Google Scholar 

  • Spies M, Kil Y, Masui R, Kujo C, Ohshima T, Kuramitsu S, Lanzov V (2000) The RadA protein from a hyperthermophilic archaeon Pyrobaculum islandicum is a DNA-dependent ATPase that exhibits two disparate catalytic modes, with a transition temperature at 75 degrees C. Eur J Biochem 267:1125–1137

    Article  CAS  PubMed  Google Scholar 

  • Stetter KO (1996) Hyperthermophilic procaryotes. FEMS Microbiol Rev 18:149–158

    CAS  Google Scholar 

  • Stetter KO (1999) Extremophiles and their adaptation to hot environments. FEBS Lett 452:22–25

    CAS  PubMed  Google Scholar 

  • Surerus KK, Chen M, van der Zwaan JW, Rusnak FM, Kolk M, Duin E, Albracht SP, Münck E (1994) Further characterization of the spin coupling observed in oxidized hydrogenase from Chromatium vinosum. A Mossbauer and multifrequency EPR study. Biochemistry 33:4980–4993

    CAS  PubMed  Google Scholar 

  • Vignais PM, Billoud B, Meyer J (2001) Classification and phylogeny of hydrogenases. FEMS Microbiol Rev 25:455–501

    CAS  PubMed  Google Scholar 

  • Volbeda A, Charon MH, Piras C, Hatchikian EC, Frey M, Fontecilla-Camps JC (1995) Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas. Nature 373:580–587

    CAS  PubMed  Google Scholar 

  • Voordouw G (1993) Molecular biology of the sulfate-reducing bacteria. In: Odom JM, Singleton RJ (eds) The sulfate-reducing bacteria: contemporary perspectives. Spinger, Berlin Heidelberg New York, pp 88–130

    Google Scholar 

  • Wu LF, Mandrand MA (1993) Microbial hydrogenases: primary structure, classification, signatures and phylogeny. FEMS Microbiol Rev 104:243–270

    CAS  Google Scholar 

  • Wu LF, Chanal A, Rodrigue A (2000) Membrane targeting and translocation of bacterial hydrogenases. Arch Microbiol 173:319–324

    Article  CAS  PubMed  Google Scholar 

  • Yoon K-S, Ishi M, Igarashi Y, Kodama T (1996a) Purification and characterization of 2-oxoglutarate:ferredoxin oxidoreductase from a thermophilic, obligately chemolithoautotrophic bacterium, Hydrogenobacter thermophilus TK-6. J Bacteriol 178:3365–3368.

    CAS  PubMed  Google Scholar 

  • Yoon K-S, Ueda Y, Ishi M, Igarashi YK, Kodama T (1996b) NADH:ferredoxin reductase and NAD-reducing hydrogenase activities in Hydrogenobacter thermophilus strain TK-6. FEMS Microbiol Lett 139:139–142

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We would like to thank Prof. T. Friedrich (Freiburg, Germany) for stimulating discussions, Dr. F. Baymann and Dr. C. Aubert (Marseille, France) for critical reading of the manuscript, as well as Dr. M. Rousset (Marseille, France) for valuable comments, D. Moinier (Protein sequencing Unit, B.I.P., Marseilles, France) for proteomic experiments, and R. Lebrun (Protein sequencing Unit, B.I.P., Marseilles, France) for performing the N-terminal sequence determination. The work of KOS was financially supported by the Fonds der Chemischen Industrie, and the project on Aquifex at the BIP in Marseille benefited from financial support by the PCV program of the CNRS and by the CNES.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Marie Thérèse Giudici-Orticoni.

Additional information

Communicated by A. Driessen

Rights and permissions

Reprints and permissions

About this article

Cite this article

Brugna-Guiral, M., Tron, P., Nitschke, W. et al. [NiFe] hydrogenases from the hyperthermophilic bacterium Aquifex aeolicus: properties, function, and phylogenetics. Extremophiles 7, 145–157 (2003). https://doi.org/10.1007/s00792-002-0306-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00792-002-0306-3

Keywords

Navigation