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Reconsideration of an early dogma, saying “there is no evidence for disulfide bonds in proteins from archaea”

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Abstract

Stability and function of a large number of proteins are crucially dependent on the presence of disulfide bonds. Recent genome analysis has pointed out an important role of disulfide bonds for the structural stabilization of intracellular proteins from hyperthermophilic archaea and bacteria. These findings contradict the conventional view that disulfide bonds are rare in those proteins. A specific protein, known as protein disulfide oxidoreductase (PDO) is recognized as a potential key enzyme in intracellular disulfide-shuffling in hyperthermophiles. The structure of this protein consists of two combined thioredoxin-related units which together, in tandem-like manner, form a closed protein domain. Each of these units contains a distinct CXXC active site motif. Both sites seem to have different redox properties. A relation to eukaryotic protein disulfide isomerase is suggested by the observed structural and functional characteristics of the protein. Enzymological studies have revealed that both, the archaeal and bacterial forms of this protein show oxidative and reductive activity and are able to isomerize protein disulfides. The variety of active site disulfides found in PDO’s from hyperthermophiles is puzzling. It is assumed, that PDO enzymes in hyperthermophilic archaea and bacteria may be part of a complex system involved in the maintenance of protein disulfide bonds.

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Abbreviations

PDI:

Protein disulfide isomerase

PDO:

Protein disulfide oxido-reductase

DTT:

Dithiothreitol

GSH:

Reduced glutathione

GSSG:

Oxidized glutathione

References

  • Anfinsen CB, Haber E (1961) studies on the reduction and re-formation of protein disulfide bonds. J Biol Chem 236:1361–1363

    PubMed  CAS  Google Scholar 

  • Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223–230

    Article  PubMed  CAS  Google Scholar 

  • Aslund F, Berndt KD, Holmgren A (1997) Redox potentials of glutaredoxins and other thiol-disulfide oxidoreductases of the thioredoxin superfamily determined by direct protein-protein redox equilibria. J Biol Chem 272:30780–86

    Article  PubMed  CAS  Google Scholar 

  • Bardwell JCA, Beckwith J (1993) The bonds that tie: catalyzed disulfide bond formation. Cell 74:769–711

    Article  PubMed  CAS  Google Scholar 

  • Bardwell JC, McGovern K, Beckwith J (1991) Identification of a protein required for disulfide bond formation in vivo. Cell 67:581–589

    Article  PubMed  CAS  Google Scholar 

  • Beeby M, O’Connor BD, Ryttersgaard C, Boutz DR, Perry LJ, Yeates TO (2005) The genomics of disulfide bonding and protein stabilization in thermophiles. PloS Biol 3:1–10

    Article  CAS  Google Scholar 

  • Bönisch H, Schmidt CL, Schäfer G, Ladenstein R (2002) The structure of the soluble domain of an archaeal rieske iron–sulfur protein at 1.1 Å resolution. J Mol Biol 319:791–805

    Article  PubMed  CAS  Google Scholar 

  • Bryk R, Lima CD, Erdjument-Bromage H, Tempst P, Nathan C (2002) Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein. Science 295:1073–1077

    Article  PubMed  CAS  Google Scholar 

  • D’Ambrosio K, DeSimone G, Pedone E, Rossi M, Bartolucci S, Pedone C (2004) Crystallization and preliminary X-ray diffraction studies of a protein disulfide oxidoreductase from Aquifex aeolicus. Acta Cryst D 60:2076–2077

    Article  CAS  Google Scholar 

  • Darby NJ, Freedman RB, Creighton TE (1994) Dissecting the mechanism of protein disulfide isomerase: catalysis of disulfide bond formation in a model peptide. Biochemistry 33:7937–7947

    Article  PubMed  CAS  Google Scholar 

  • Darby NJ, Creighton TE (1995) Functional properties of the individual thioredoxin-like domains of protein disulfide isomerase. Biochemistry 34:11725–11735

    Article  PubMed  CAS  Google Scholar 

  • Darby NJ, Kemmink J, Creighton TE (1996) Identifying and characterizing a structural domain of protein disulfide isomerase. Biochemistry 35:10517–10528

    Article  PubMed  CAS  Google Scholar 

  • Derman AI, Beckwith J (1991) Escherichia coli alkaline phosphatase fails to acquire disulfide bonds when retained in the cytoplasm. J Bacteriol 173:7719–7722

    PubMed  CAS  Google Scholar 

  • Derman AI, Prinz WA, Belin D, Beckwith J (1993) Mutations that allow disulfide bond formation in the cytoplasm of Escherichia coli. Science 262:1744–1747

    Article  PubMed  CAS  Google Scholar 

  • Eklund H, Ingelman M, Söderberg BO, Uhlin T, Nordlund P, Nikkola M, Sonnerstam U, Joelson T, Petratos K (1992) Structure of oxidized bacteriophage T4 glutaredoxin (thioredoxin): refinement of native and mutant proteins. J Mol Biol 228:596–618

    Article  PubMed  CAS  Google Scholar 

  • Ellgaard L, Ruddock LW (2005) The human protein disulphide isomerase family: substrate interactions and functional properties. EMBO Rep 6:28–32

    Article  PubMed  CAS  Google Scholar 

  • Fomenko DE, Gladyshev VN (2003) Identity and functions of CXXC-derived motifs. Biochemistry 42:1214–11225

    Article  CAS  Google Scholar 

  • Freedman RB (1995) The formation of protein disulfide bonds. Curr Opin Struct Biol 5:85–91

    Article  PubMed  CAS  Google Scholar 

  • Freedman RB, Hirst TR, Tuite MF (1994) Protein disulfide isomerase: building bridges in protein folding. Trends Biochem Sci 19:331–336

    Article  PubMed  CAS  Google Scholar 

  • Guagliardi A, de Pascale D, Cannio R, Nobile V, Bartolucci S, Rossi M (1995) The purification, cloning, and high level expression of a glutaredoxin-like protein from the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem 270, 5748–5755, with a published erratum in J Biol Chem (1997) 272, 20961

    Google Scholar 

  • Holmgren A (1972) Tryptophan fluorescence study of conformational transitions of the oxidized and reduced form of thioredoxin. J Biol Chem 247:1992–1998

    PubMed  CAS  Google Scholar 

  • Holmgren A (1979) Thioredoxin catalyzes the reduction of insuline disulfides by dithiothreitol and dihydrolipoamide. J Biol Chem 254:9627–9632

    PubMed  CAS  Google Scholar 

  • Holmgren A (1995) Thioredoxin structure and mechanism: conformational changes on oxidation of the active-site sulfhydryls to a disulfide. Structure 3:239–243

    Article  PubMed  CAS  Google Scholar 

  • Holmgren A, Söderberg BO, Eklund H, Brändén CI (1975) Three-dimensional structure of Escherichia coli thioredoxin-S2 to 2.8 Å resolution. Proc Natl Acad Sci USA 72:2305–2309

    Article  PubMed  CAS  Google Scholar 

  • Huber-Wunderlich M, Glockshuber R (1998) A single dipeptide sequence determines the redox properties of a whole enzyme family. Fold Des 3:161–171

    Article  PubMed  CAS  Google Scholar 

  • Hutchinson EG, Thornton JM (1996) PROMOTIF-A program to identify and analyze structural motifs in proteins. Protein Sci 5:212–220

    Article  PubMed  CAS  Google Scholar 

  • Kadokura H, Katzen F, Beckwith J (2003) Protein disulfide bond formation in prokaryotes. Annu Rev Biochem 72:111–135

    Article  PubMed  CAS  Google Scholar 

  • Karlström M, Stokke R, Steen IH, Birkeland NK, Ladenstein R (2005) Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability. J Mol Biol 345:559–577

    Article  PubMed  CAS  Google Scholar 

  • Karshikoff A, Ladenstein R (2001) Ion pairs and the thermotolerance of proteins from hyperthermophiles: a “traffic rule” for hot roads. TiBS 26:550–556

    PubMed  CAS  Google Scholar 

  • Kashima Y, Ishikawa K (2003) A hyperthermostable novel protein-disulfide oxidoreductase is reduced by thioredoxin reductase from the hyperthermophilic archaeon Pyrococcus horikoshii. Arch Biochem Biophys 418:179–185

    Article  PubMed  CAS  Google Scholar 

  • Katti SK, LeMaster DM, Eklund H (1990) Crystal structure of thioredoxin from Escherichia coli at 1.68 Å resolution. J Mol Biol 212:167–184

    Article  PubMed  CAS  Google Scholar 

  • Katz BA, Kossiakoff A (1986) The crystallographically determined structures of atypical strained disulfides engineered into subtilisin. J Biol Chem 261:15480–15485

    PubMed  CAS  Google Scholar 

  • Kemmink J, Darby N, Dijkstra K, Nilges M, Creighton TE (1996) Structure determination of the N-terminal thioredoxin-like domain of protein disulfide isomerase using multidimensional heteronuclear 13C/15N NMR spectroscopy. Biochemistry 35:7684–7691

    Article  PubMed  CAS  Google Scholar 

  • Krause G, Lundström J, Barea JL, Delacues CP, Holmgren A (1991) Mimicking the active site of protein disulfide isomerase by substitution of proline 34 in Escherichia coli thioredoxin. J Biol Chem 266:9494–9500

    PubMed  CAS  Google Scholar 

  • Kulp MH, Frickel EM, Ellgaard L, Weissman JS (2006) Domain architecture of protein-disulfide isomerase facilitates its dual role as an oxidase and an isomerase in ero1p-mediated disulfide formation. J Biol Chem 281:876–884

    Article  PubMed  CAS  Google Scholar 

  • Lambert N, Freedman RB (1983) Kinetics and specificity of homogeneous protein disulphide-isomerase in protein disulphide isomerization and in thiol–protein–disulphide oxidoreduction. Biochem J 213:235–243

    PubMed  CAS  Google Scholar 

  • Mallick P, Boutz DR, Eisenberg D, Yeates TO (2002) Genomic evidence that the intercellular proteins of archaeal microbes contain disulfide bonds. Proc Natl Acad Sci USA 99:9679–9684

    Article  PubMed  CAS  Google Scholar 

  • Martin JL, Bardwell JCA, Kuriyan J (1993) Crystal structure of the DsbA protein required for disulfide bond formation in vivo. Nature 365:464–468

    Article  PubMed  CAS  Google Scholar 

  • Mössner E, Huber-Wunderlich M, Glockshuber R (1998) Characterization of E. coli thioredoxin variants mimicking the active sites of other thiol-disulfide oxidoreductases. Protein Science 7:1233–1244

    Article  PubMed  Google Scholar 

  • Pedone E, Ren B, Ladenstein R, Rossi M, Bartolucci S (2004) Functional properties of the protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus: a member of a novel protein family related to protein disulfide-isomerase. Eur J Biochem 271:3437–3448

    Article  PubMed  CAS  Google Scholar 

  • Pedone E, D’Ambrosio K, De Simone G, Rossi M, Pedone C, Bartolucci S (2006a) Insights on a new PDI-like family: structural and functional analysis of a protein disulfide oxidoreductase from the bacterium Aquifex aeolicus. J Mol Biol 356:155–164

    Article  PubMed  CAS  Google Scholar 

  • Pedone E, Limauro D, D’Alterio R, Rossi M, Bartolucci S (2006b) Characterization of a multifunctional protein disulfide oxidoreductase from Sulfolobus solfataricus. FEBS J 273:5407–5420

    Article  PubMed  CAS  Google Scholar 

  • Pigiet VP, Schuster BJ (1986) Thioredoxin-catalyzed refolding of disulfide-containing proteins. Proc Natl Acad Sci USA 83:7643–7647

    Article  PubMed  CAS  Google Scholar 

  • Prinz WA, Aslund F, Holmgren A, Beckwith J (1997) The role of the thioredoxin and glutaredoxin pathways in reducing disulfide bonds in the Escherichia coli cytoplasm. J Biol Chem 272:15661–15667

    Article  PubMed  CAS  Google Scholar 

  • Ren B, Tibbelin G, de Pascale D, Rossi M, Bartolucci S, Ladenstein R (1998) A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units. Nat Struct Biol 5:602–611

    Article  PubMed  CAS  Google Scholar 

  • Ren B, Haase I, Fischer M, Ladenstein R (2006) unpublished work

  • Ruddock LW, Hirst TR, Freedman RB (1996) pH dependence of the dithiol-oxidizing activity of DsbA (a periplasmic protein thiol: disulphide oxidoreductase) and protein disulphide isomerase: studies with a novel simple peptide substrate. Biochem J 315:1000–1005

    Google Scholar 

  • Tian G, Xiang S, Noiva R, Lennarz WJ, Schindelin H (2006) The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites. Cell 124:61–73

    Article  PubMed  CAS  Google Scholar 

  • Toth EA, Worby C, Dixon JE, Goedken ER, Marqusee S, Yeates TO (2000) The crystal structure of adenylosuccinate lyase from Pyrobaculum aerophilum reveals an intracellular protein with three disulfide bonds. J Mol Biol 301:433–450

    Article  PubMed  CAS  Google Scholar 

  • Vuori K, Myllylä R, Pihlajaniemi T, Kivirikko KI (1992) Expression and site-directed mutagenesis of human protein disulfide isomerase in Escherichia coli. This multifunctional polypeptide has two independently acting catalytic sites for the isomerase activity. J Biol Chem 267:7211–7214

    PubMed  CAS  Google Scholar 

  • Wang Q, Chang A (1999) Eps1, a novel PDI-related protein involved in ER quality control in yeast. EMBO J 18:5972–5982

    Article  PubMed  CAS  Google Scholar 

  • Wunderlich M, Jaenicke R, Glockshuber R (1993) The redox properties of protein disulfide isomerase (DsbA) of Escherichia coli result from a tense conformation of its oxidized form. J Mol Biol 233:559–566

    Article  PubMed  CAS  Google Scholar 

  • Zapun A, Bardwell JC, Creighton TE (1993) The reactive and destabilizing disulfide bond of DsbA, a protein required for disulfide bond formation in vivo. Biochemistry 32:5083–5092

    Article  PubMed  CAS  Google Scholar 

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Correspondence to Rudolf Ladenstein.

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Communicated by D.A. Cowan.

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Ladenstein, R., Ren, B. Reconsideration of an early dogma, saying “there is no evidence for disulfide bonds in proteins from archaea”. Extremophiles 12, 29–38 (2008). https://doi.org/10.1007/s00792-007-0076-z

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