Skip to main content
SpringerLink
Log in

Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase

  • Original Article
  • Published:
JBIC Journal of Biological Inorganic Chemistry Aims and scope Submit manuscript

Abstract

The genome of Desulfovibrio vulgaris Hildenborough (DvH) encodes for six hydrogenases (Hases), making it an interesting organism to study the role of these proteins in sulphate respiration. In this work we address the role of the [NiFeSe] Hase, found to be the major Hase associated with the cytoplasmic membrane. The purified enzyme displays interesting catalytic properties, such as a very high H2 production activity, which is dependent on the presence of phospholipids or detergent, and resistance to oxygen inactivation since it is isolated aerobically in a Ni(II) oxidation state. Evidence was obtained that the [NiFeSe] Hase is post-translationally modified to include a hydrophobic group bound to the N-terminal, which is responsible for its membrane association. Cleavage of this group originates a soluble, less active form of the enzyme. Sequence analysis shows that [NiFeSe] Hases from Desulfovibrionacae form a separate family from the [NiFe] enzymes of these organisms, and are more closely related to [NiFe] Hases from more distant bacterial species that have a medial [4Fe4S]2+/1+ cluster, but not a selenocysteine. The interaction of the [NiFeSe] Hase with periplasmic cytochromes was investigated and is similar to the [NiFe]1 Hase, with the Type I cytochrome c 3 as the preferred electron acceptor. A model of the DvH [NiFeSe] Hase was generated based on the structure of the Desulfomicrobium baculatum enzyme. The structures of the two [NiFeSe] Hases are compared with the structures of [NiFe] Hases, to evaluate the consensual structural differences between the two families. Several conserved residues close to the redox centres were identified, which may be relevant to the higher activity displayed by [NiFeSe] Hases.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

Abbreviations

DvH:

D. vulgaris Hildenborough

Dm :

Desulfomicrobium

Hase:

Hydrogenase

[NiFeSe]m :

Membrane-bound form of the [NiFeSe] Hase

[NiFeSe]s :

Soluble form of the [NiFeSe] Hase

TpIc 3 :

Type I cytochrome c 3

TpIIc 3 :

Type II cytochrome c 3

HmcA:

16-haem high molecular weight cytochrome c

References

  1. Woodward J, Orr M, Cordray K, Greenbaum E (2000) Nature 405: 1014–1015

    Article  PubMed  CAS  Google Scholar 

  2. Hallenbeck PC, Benemann JR (2002) Int J Hydrogen Energ 27: 1185–1193

    Article  CAS  Google Scholar 

  3. Kalia VC, Lal S, Ghai R, Mandal M, Chauhan A (2003) Trends Biotechnol 21:152–156

    Article  PubMed  CAS  Google Scholar 

  4. Nandi R, Sengupta S (1998) Crit Rev Microbiol 24:61–84

    Article  PubMed  CAS  Google Scholar 

  5. Armstrong FA (2004) Curr Opin Chem Biol 8:133–140

    Article  PubMed  CAS  Google Scholar 

  6. Jones AK, Sillery E, Albracht SPJ, Armstrong FA (2002) Chem Commun 8:866–867

    Article  CAS  Google Scholar 

  7. Mertens R, Liese A (2004) Curr Opin Biotechnol 15:343–348

    Article  PubMed  CAS  Google Scholar 

  8. Schwartz E, Friedrich B (2003) In: Dworkin M et al. (ed) The prokaryotes: an evolving electronic resource for the microbiological community. Springer, Berlin Heidelberg New York. http://link.springer-ny.com/link/service/books/10125/. New York,

  9. Odom JM, Peck HD Jr (1981) FEMS Microbiol Lett 12:47–50

    Article  CAS  Google Scholar 

  10. Vignais PM, Billoud B, Meyer J (2001) FEMS Microbiol Rev 25: 455–501

    Article  PubMed  CAS  Google Scholar 

  11. Vignais PM, Colbeau A (2004) Curr Issues Mol Biol 6:159–188

    PubMed  CAS  Google Scholar 

  12. Wu LF, Mandrand MA (1993) FEMS Microbiol Rev 10:243–269

    PubMed  CAS  Google Scholar 

  13. Matias PM, Pereira IAC, Soares CM, Carrondo MA (2005) Prog Biophys Mol Biol 89:292–329

    Article  PubMed  CAS  Google Scholar 

  14. Fauque G, Peck HD Jr, Moura JJ, Huynh BH, Berlier Y, DerVartanian DV, Teixeira M, Przybyla AE, Lespinat PA, Moura I, LeGall J (1988) FEMS Microbiol Rev 4:299–344

    PubMed  CAS  Google Scholar 

  15. Frey M, Fontecilla-Camps JC, Volbeda A (2001) In: Messerschmidt A, Huber R, Wieghardt K, Poulos T (eds) Handbook of metalloproteins, Wiley, New York, pp 880–896

  16. Lemon BJ, Peters JW (2001) In: Messerschmidt A, Huber R, Wieghardt K, Poulos T (eds) Handbook of metalloproteins, Wiley, New York, pp 738–751

  17. Voordouw G, Niviere V, Ferris FG, Fedorak PM, Westlake DWS (1990) Appl Environ Microbiol 56:3748–3754

    PubMed  CAS  Google Scholar 

  18. Rossi M, Pollock WBR, Reij MW, Keon RG, Fu R, Voordouw G (1993) J Bacteriol 175:4699–4711

    PubMed  CAS  Google Scholar 

  19. Pereira IAC, Romão CV, Xavier AV, LeGall J, Teixeira M (1998) J Biol Inorg Chem 3:494–498

    Article  CAS  Google Scholar 

  20. Valente FMA, Saraiva LM, LeGall J, Xavier AV, Teixeira M, Pereira IAC (2001) ChemBioChem 2:895–905

    Article  PubMed  CAS  Google Scholar 

  21. Heidelberg J F, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou LW, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM (2004) Nat Biotechnol 22: 554–559

    Article  PubMed  CAS  Google Scholar 

  22. Rodrigues R, Valente FM, Pereira IA, Oliveira S, Rodrigues-Pousada C (2003) Biochem Biophys Res Commun 306:366–375

    Article  PubMed  CAS  Google Scholar 

  23. Hedderich R (2004) J Bioenerg Biomembr 36:65–75

    Article  PubMed  CAS  Google Scholar 

  24. Casalot L, Valette O, De Luca G, Dermoun Z, Rousset M, de Philip P (2002) FEMS Microbiol Lett 214:107–112

    Article  PubMed  CAS  Google Scholar 

  25. Casalot L, De Luca G, Dermoun Z, Rousset M, de Philip P (2002) J Bacteriol 184:853–856

    PubMed  CAS  Google Scholar 

  26. Pohorelic BK, Voordouw JK, Lojou E, Dolla A, Harder J, Voordouw G (2002) J Bacteriol 184:679–686

    Article  PubMed  CAS  Google Scholar 

  27. Romao CV, Pereira IA, Xavier AV, LeGall J, Teixeira M (1997) Biochem Biophys Res Commun 240:75–79

    Article  PubMed  CAS  Google Scholar 

  28. Lissolo T, Choi ES, LeGall J, Peck HD Jr (1986) Biochem Biophys Res Commun 139:701–708

    Article  PubMed  CAS  Google Scholar 

  29. Yagi T (1970) J Biochem (Tokyo) 68:649–657

    CAS  Google Scholar 

  30. Rieder R, Cammack R, Hall DO (1984) Eur J Biochem 145:637–643

    Article  PubMed  CAS  Google Scholar 

  31. Teixeira M, Fauque G, Moura I, Lespinat PA, Berlier Y, Prickril B, Peck HD, Xavier AV, Legall J, Moura JJG (1987) Eur J Biochem 167:47–58

    Article  PubMed  CAS  Google Scholar 

  32. Voordouw G, Menon NK, LeGall J, Choi ES, Peck HD Jr, Przybyla A E (1989) J Bacteriol 171:2894–2899

    PubMed  CAS  Google Scholar 

  33. He SH, Teixeira M, LeGall J, Patil DS, Moura I, Moura JJ, DerVartanian DV, Huynh BH, Peck HD Jr (1989) J Biol Chem 264: 2678–2682

    PubMed  CAS  Google Scholar 

  34. Pereira AS, Franco R, Feio MJ, Pinto C, Lampreia J, Reis MA, Calvete J, Moura I, Beech I, Lino AR, Moura JJ (1996) Biochem Biophys Res Commun 221:414–421

    Article  PubMed  CAS  Google Scholar 

  35. Eidsness MK, Scott RA, Prickril BC, DerVartanian DV, Legall J, Moura I, Moura JJ, Peck HD Jr (1989) Proc Natl Acad Sci USA 86: 147–151

    Article  PubMed  CAS  Google Scholar 

  36. Garcin E, Vernede X, Hatchikian EC, Volbeda A, Frey M, Fontecilla-Camps JC (1999) Structure 7:557–566

    Article  PubMed  CAS  Google Scholar 

  37. Sorgenfrei O, Duin EC, Klein A, Albracht SP (1996) J Biol Chem 271: 23799–23806

    Article  PubMed  CAS  Google Scholar 

  38. Sorgenfrei O, Duin EC, Klein A, Albracht SP (1997) Eur J Biochem 247:681–687

    Article  PubMed  CAS  Google Scholar 

  39. Legall J, Payne WJ, Chen L, Liu MY, Xavier AV (1994) Biochimie 76: 655–665

    Article  PubMed  CAS  Google Scholar 

  40. Ackrell BAC, Asato RN, Mower HF (1966) J Bacteriol 92:828–838

    PubMed  CAS  Google Scholar 

  41. Wardi AH, Michos GA (1972) Anal Biochem 49:607–609

    Article  PubMed  CAS  Google Scholar 

  42. Teixeira M, Campos AP, Aguiar AP, Costa HS, Santos H, Turner DL, Xavier AV (1993) FEBS Lett 317:233–236

    Article  PubMed  CAS  Google Scholar 

  43. Pandey A, Andersen JS, Mann M (2000) Science’s Stke 37:1–12

    Google Scholar 

  44. Gonnet F, Lemaître G, Waksman G, Tortajada J (2003) Proteome Sci 1:2

    Article  PubMed  Google Scholar 

  45. Peck HD Jr, Gest H (1956) J Bacteriol 71:70–80

    PubMed  CAS  Google Scholar 

  46. Lallamaharajh WV, Hall DO, Cammack R, Rao KK, Legall J (1983) Biochem J 209:445–454

    PubMed  CAS  Google Scholar 

  47. Bjorklof K, Zickermann V, Finel M (2000) FEBS Lett 467:105–110

    Article  PubMed  CAS  Google Scholar 

  48. Sanchez R, Sali A (1997) Curr Opin Struct Biol 7:206–214

    Article  PubMed  CAS  Google Scholar 

  49. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A (2000) Annu Rev Biophys Biomol Struct 29:291–325

    Article  PubMed  CAS  Google Scholar 

  50. Sali A, Blundell TL (1993) J Mol Biol 234:779–815

    Article  PubMed  CAS  Google Scholar 

  51. Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283–291

    Article  CAS  Google Scholar 

  52. Meuer J, Kuettner HC, Zhang JK, Hedderich R, Metcalf WW (2002) Proc Natl Acad Sci USA 99:5632–5637

    Article  PubMed  CAS  Google Scholar 

  53. Fox JD, Kerby RL, Roberts GP, Ludden PW (1996) J Bacteriol 178: 1515–1524

    PubMed  CAS  Google Scholar 

  54. Haveman SA, Brunelle V, Voordouw JK, Voordouw G, Heidelberg JF, Rabus R (2003) J Bacteriol 185:4345–4353

    Article  PubMed  CAS  Google Scholar 

  55. Hayashi S, Wu HC (1990) J Bioenerg Biomembr 22:451–471

    Article  PubMed  CAS  Google Scholar 

  56. Makula RA, Finnerty WR (1974) J Bacteriol 120:1279–1283

    PubMed  CAS  Google Scholar 

  57. Volbeda A, Martin L, Cavazza C, Matho M, Faber BW, Roseboom W, Albracht SP, Garcin E, Rousset M, Fontecilla-Camps JC (2005) J Biol Inorg Chem 10:239–249

    Article  PubMed  CAS  Google Scholar 

  58. Sebban C, Blanchard L, Bruschi M, Guerlesquin F (1995) FEMS Microbiol Lett 133:143–149

    Article  PubMed  CAS  Google Scholar 

  59. Costa C, Teixeira M, LeGall J, Moura JJG, Moura I (1997) J Biol Inorg Chem 2:198–208

    Article  CAS  Google Scholar 

  60. Pieulle L, Haladjian J, Bonicel J, Hatchikian EC (1996) Biochem Biophys Acta 1273:51–61

    Article  PubMed  Google Scholar 

  61. Matias PM, Coelho R, Pereira IAC, Coelho AV, Thompson AW, Sieker LC, LeGall J, Carrondo MA (1999) Structure 7:119–130

    Article  PubMed  CAS  Google Scholar 

  62. Aubert C, Brugna M, Dolla A, Bruschi M, Giudici-Orticoni MT (2000) Biochim Biophys Acta 1476:85–92

    PubMed  CAS  Google Scholar 

  63. Matias PM, Coelho AV, Valente FMA, Ptacido D, LeGall J, Xavier AV, Pereira IAC, Carrondo MA (2002) J Biol Chem 277:47907–47916

    Article  PubMed  CAS  Google Scholar 

  64. Frazão C, Sieker L, Sheldrick G, Lamzin V, LeGall J, Carrondo MA (1999) J Biol Inorg Chem 4:162–165

    Article  PubMed  Google Scholar 

  65. Czjzek M, Guerlesquin F, Bruschi M, Haser R (1996) Structure 4: 395–404

    Article  PubMed  CAS  Google Scholar 

  66. Peck HDJ, Lissolo T (1988) In: Cole JA, Ferguson SJ (eds) The nitrogen and sulphur cycles. Cambridge University Press, Cambridge, pp 99–132

  67. Rohde M, Furstenau U, Mayer F, Przybyla AE, Peck HD Jr, Le Gall J, Choi ES, Menon NK (1990) Eur J Biochem 191:389–396

    Article  PubMed  CAS  Google Scholar 

  68. Casalot L, Rousset M (2001) Trends Microbiol 9:228–237

    Article  PubMed  CAS  Google Scholar 

  69. Price MN, Huang KH, Alm EJ, Arkin AP (2005) Nucleic Acids Res 33: 880–892

    Article  PubMed  CAS  Google Scholar 

  70. Akoh CC, Lee GC, Liaw YC, Huang TH, Shaw JF (2004) Prog Lipid Res 43:534–552

    Article  PubMed  CAS  Google Scholar 

  71. Page CC, Moser CC, Chen X, Dutton PL (1999) Nature (London) 402: 47–52

    Article  CAS  Google Scholar 

  72. Bingemann R, Klein A (2000) Eur J Biochem 267:6612–6618

    Article  PubMed  CAS  Google Scholar 

  73. Rousset M, Montet Y, Guigliarelli B, Forget N, Asso M, Bertrand P, Fontecilla-Camps JC, Hatchikian EC (1998) Proc Natl Acad Sci USA 95:11625–11630

    Article  PubMed  CAS  Google Scholar 

  74. Higuchi Y, Yagi T, Yasuoka N (1997) Structure 5:1671–1680

    Article  PubMed  CAS  Google Scholar 

  75. Volbeda A, Charon MH, Piras C, Hatchikian EC, Frey M, Fontecilla-Camps JC (1995) Nature 373:580–587

    Article  PubMed  CAS  Google Scholar 

  76. De Gioia L, Fantucci P, Guigliarelli B, Bertrand P (1999) Int J Quantum Chem 73:187–195

    Article  CAS  Google Scholar 

  77. Matias PM, Soares CM, Saraiva LM, Coelho R, Morais J, Le Gall J, Carrondo MA (2001) J Biol Inorg Chem 6:63–81

    Article  PubMed  CAS  Google Scholar 

  78. Delano W (2003) Delano Scientific LLC, San Carlos

Download references

Acknowledgements

We would like to thank Mr. João Carita and the staff of the IBET Fermentation Plant for growing the bacterial cells, Mrs. M.Regalla for N-terminal sequence determinations, and Ms. Elisabete Pires for mass spectrometry analyses. We would also like to thank Dr. John Heidelberg from The Institute of Genomic Research for allowing us access to the DvH list of annotated genes prior to publication. This work was supported by FCT grants POCTI/ESP/44782/02 to I.A.C.P., POCTI/BME/32789/99 to C.M.S. and A.S.F.O., and POCTI/QUI/47866/02 to A.V.X. F.M.A.V. is supported by a FCT PhD grant (SFRH/BD/9187/2002).

Author information

Authors and Affiliations

  1. Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal

    Filipa M. A. Valente, A. Sofia F. Oliveira, Nicole Gnadt, Isabel Pacheco, Ana V. Coelho, António V. Xavier, Miguel Teixeira, Cláudio M. Soares & Inês A. C. Pereira

  2. Departamento de Química, Universidade de Évora, Évora, Portugal

    Ana V. Coelho

Authors
  1. Filipa M. A. Valente
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. Sofia F. Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nicole Gnadt
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Isabel Pacheco
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ana V. Coelho
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. António V. Xavier
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Miguel Teixeira
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Cláudio M. Soares
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Inês A. C. Pereira
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Inês A. C. Pereira.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Valente, F.M.A., Oliveira, A.S.F., Gnadt, N. et al. Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase. J Biol Inorg Chem 10, 667–682 (2005). https://doi.org/10.1007/s00775-005-0022-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00775-005-0022-4

Keywords

Search

Navigation