SurR regulates hydrogen production in Pyrococcus furiosus by a sulfur-dependent redox switch

Molecular Microbiology

Volumn 77, Issue 5, 2010, Pages 1111-1122

  Yang, Hua ^a,d   Lipscomb, Gina L ^a   Keese, Annette M ^c   Schut, Gerrit J ^a   Thomm, Michael ^c   Adams, Michael W W ^a   Wang, Bi Cheng ^a   Scott, Robert A ^a,b  

^a University of Georgia   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c UNIVERSITY OF REGENSBURG   (Germany)

^d CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CYSTEINE; HYDROGENASE; PROTEIN SURR; SULFUR; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; DNA BINDING; NONHUMAN; OXIDATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; PYROCOCCUS FURIOSUS;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; GENE EXPRESSION REGULATION, ARCHAEAL; HYDROGEN; HYDROGEN SULFIDE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; PYROCOCCUS FURIOSUS; SULFUR; TRANSCRIPTION FACTORS;

ARCHAEA; PYROCOCCUS FURIOSUS;

EID: 77956136587     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2010.07275.x     Document Type: Article

References (56)

1. Aravind, L., Anantharaman, V., Balaji, S., Babu, M.M. Iyer, L.M. (2005) The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol Rev 29 : 231 262.
2. Bartlett, M.S. (2005) Determinants of transcription initiation by archaeal RNA polymerase. Curr Opin Microbiol 8 : 677 684.
3. Bell, S.D. (2005) Archaeal transcriptional regulation - variation on a bacterial theme? Trends Microbiol 13 : 262 265.
4. Bell, S.D., Cairns, S.S., Robson, R.L. Jackson, S.P. (1999) Transcriptional regulation of an archaeal operon in vivo and in vitro. Mol Cell 4 : 971 982.
5. Blumentals, I.I., Itoh, M., Olson, G.J. Kelly, R.M. (1990) Role of polysulfides in reduction of elemental sulfur by the hyperthermophilic archaebacterium Pyrococcus furiosus. Appl Environ Microbiol 56 : 1255 1262.
6. Brinkman, A.B., Bell, S.D., Lebbink, R.J., de Vos, W.M. van der Oost, J. (2002) The Sulfolobus solfataricus Lrp-like protein LysM regulates lysine biosynthesis in response to lysine availability. J Biol Chem 277 : 29537 29549.
7. Busenlehner, L.S., Pennella, M.A. Giedroc, D.P. (2003) The SmtB/ArsR family of metalloregulatory transcriptional repressors: structural insights into prokaryotic metal resistance. FEMS Microbiol Rev 27 : 131 143.
8. Choi, H., Kim, S., Mukhopadhyay, P., Cho, S., Woo, J., Storz, G. Ryu, S. (2001) Structural basis of the redox switch in the OxyR transcription factor. Cell 105 : 103 113.
9. Coulocheri, S.A., Pigis, D.G., Papavassiliou, K.A. Papavassiliou, A.G. (2007) Hydrogen bonds in protein-DNA complexes: where geometry meets plasticity. Biochimie 89 : 1291 1303.
10. Cowtan, K.D. Zhang, K.Y. (1999) Density modification for macromolecular phase improvement. Prog Biophys Mol Biol 72 : 245 270.
11. Crankshaw, M.W. Grant, G.A. (1996) Modification of Cysteine. In Current Protocols in Protein Science. Coligan, J.E. (ed.). Brooklyn, NY : Wiley, pp. 15.1.1 15.1.16.
12. Darcy, A., Elmore, C., Stihle, M. Johnston, J.E. (1996) A novel approach to crystallising proteins under oil. J Cryst Growth 168 : 175 180.
13. Declercq, J.P., Evrard, C., Clippe, A., Stricht, D.V., Bernard, A. Knoops, B. (2001) Crystal structure of human peroxiredoxin 5, a novel type of mammalian peroxiredoxin at 1.5 A resolution. J Mol Biol 311 : 751 759.
14. Emsley, P. Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60 : 2126 2132.
15. Fiala, G. Stetter, K.O. (1986) Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100-degrees C. Arch Microbiol 145 : 56 61.
16. Fomenko, D.E. Gladyshev, V.N. (2003) Identity and functions of CxxC-derived motifs. Biochemistry 42 : 11214 11225.
17. Galas, D.J. Schmitz, A. (1978) DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 5 : 3157 3170.
18. Geiduschek, E.P. Ouhammouch, M. (2005) Archaeal transcription and its regulators. Mol Microbiol 56 : 1397 1407.
19. Gibrat, J.F., Madej, T. Bryant, S.H. (1996) Surprising similarities in structure comparison. Curr Opin Struct Biol 6 : 377 385.
20. Hedderich, R., Klimmek, O., Kroger, A., Dirmeier, R., Keller, M. Stetter, K.O. (1998) Anaerobic respiration with elemental sulfur and with disulfides. FEMS Microbiol Rev 22 : 353 381.
21. Hethke, C., Geerling, A.C., Hausner, W., de Vos, W.M. Thomm, M. (1996) A cell-free transcription system for the hyperthermophilic archaeon Pyrococcus furiosus. Nucleic Acids Res 24 : 2369 2376.
22. Holm, L. Park, J. (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16 : 566 567.
23. Holm, L. Sander, C. (1996) Mapping the protein universe. Science 273 : 595 603.
24. Jones, S., van Heyningen, P., Berman, H.M. Thornton, J.M. (1999) Protein-DNA interactions: a structural analysis. J Mol Biol 287 : 877 896.
25. Kim, S.O., Merchant, K., Nudelman, R., Beyer, W.F., Jr., Keng, T., DeAngelo, J., et al. (2002) OxyR: a molecular code for redox-related signaling. Cell 109 : 383 396.
26. Kleinjan, W.E., de Keizer, A. Janssen, J.H. (2003) Biologically produced sulfur. Top Curr Chem 230 : 167 188.
27. Kleinjan, W.E., de Keizer, A. Janssen, A.J. (2005) Kinetics of the chemical oxidation of polysulfide anions in aqueous solution. Water Res 39 : 4093 4100.
28. Koonin, E.V. Wolf, Y.I. (2008) Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36 : 6688 6719.
29. Kosower, N.S. Kosower, E.M. (1995) Diamide: an oxidant probe for thiols. Methods Enzymol 251 : 123 133.
30. Lee, S.J., Engelmann, A., Horlacher, R., Qu, Q., Vierke, G., Hebbeln, C., et al. (2003) TrmB, a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter from the hyperthermophilic archaeon Thermococcus litoralis. J Biol Chem 278 : 983 990.
31. Lee, S.J., Moulakakis, C., Koning, S.M., Hausner, W., Thomm, M. Boos, W. (2005) TrmB, a sugar sensing regulator of ABC transporter genes in Pyrococcus furiosus exhibits dual promoter specificity and is controlled by different inducers. Mol Micro 57 : 1797 1807.
32. Lie, T.J., Wood, G.E. Leigh, J.A. (2005) Regulation of nif expression in Methanococcus maripaludis- roles of the euryarchaeal repressor NrpR, 2-oxoglutarate, and two operators. J Biol Chem 280 : 5236 5241.
33. Lipscomb, G.L., Keese, A.M., Cowart, D.M., Schut, G.J., Thomm, M., Adams, M.W. Scott, R.A. (2009) SurR: a transcriptional activator and repressor controlling hydrogen and elemental sulphur metabolism in Pyrococcus furiosus. Mol Microbiol 71 : 332 349.
34. Liu, W., Vierke, G., Wenke, A.K., Thomm, M. Ladenstein, R. (2007) Crystal structure of the archaeal heat shock regulator from Pyrococcus furiosus: a molecular chimera representing eukaryal and bacterial features. J Mol Biol 369 : 474 488.
35. Liu, Z.J., Lin, D., Tempel, W., Praissman, J.L., Rose, J.P. Wang, B.C. (2005) Parameter-space screening: a powerful tool for high-throughput crystal structure determination. Acta Crystallogr D Biol Crystallogr 61 : 520 527.
36. Lovell, S.C., Davis, I.W., Arendall, W.B., 3rd., de Bakker, P.I., Word, J.M., Prisant, M.G., et al. (2003) Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50 : 437 450.
37. McCoy, A.J. (2007) Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr D Biol Crystallogr 63 : 32 41.
38. Madej, T., Gibrat, J.F. Bryant, S.H. (1995) Threading a database of protein cores. Proteins 23 : 356 369.
39. Murshudov, G.N., Vagin, A.A. Dodson, E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53 : 240 255.
40. Nakano, S., Erwin, K.N., Ralle, M. Zuber, P. (2005) Redox-sensitive transcriptional control by a thiol/disulphide switch in the global regulator, Spx. Mol Microbiol 55 : 498 510.
41. Newberry, K.J., Nakano, S., Zuber, P. Brennan, R.G. (2005) Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the alpha C-terminal domain of RNA polymerase. Proc Natl Acad Sci USA 102 : 15839 15844.
42. Otwinowski, Z. Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276 : 307 326.
43. Paget, M.S. Buttner, M.J. (2003) Thiol-based regulatory switches. Annu Rev Genet 37 : 91 121.
44. 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.
45. Perrakis, A., Morris, R. Lamzin, V.S. (1999) Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6 : 458 463.
46. Potterton, E., Briggs, P., Turkenburg, M. Dodson, E. (2003) A graphical user interface to the CCP4 program suite. Acta Crystallogr D Biol Crystallogr 59 : 1131 1137.
47. 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.
48. Schut, G.J., Bridger, S.L. Adams, M.W. (2007) Insights into the metabolism of elemental sulfur by the hyperthermophilic archaeon Pyrococcus furiosus: characterization of a coenzyme A- dependent NAD(P)H sulfur oxidoreductase. J Bacteriol 189 : 4431 4441.
49. Storz, G., Tartaglia, L.A. Ames, B.N. (1990) Transcriptional regulator of oxidative stress-inducible genes: direct activation by oxidation. Science 248 : 189 194.
50. Studier, F.W. (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41 : 207 234.
51. Terwilliger, T.C. (2000) Maximum-likelihood density modification. Acta Crystallogr D Biol Crystallogr 56 : 965 972.
52. Terwilliger, T.C. (2002) Automated structure solution, density modification and model building. Acta Crystallogr D Biol Crystallogr 58 : 1937 1940.
53. Terwilliger, T.C. Berendzen, J. (1999) Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 55 : 849 861.
54. Thompson, J.D., Higgins, D.G. Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 : 4673 4680.
55. Vierke, G., Engelmann, A., Hebbeln, C. Thomm, M. (2003) A novel archaeal transcriptional regulator of heat shock response. J Biol Chem 278 : 18 26.
56. Wilson, D.O., Johnson, P. McCord, B.R. (2001) Nonradiochemical DNase I footprinting by capillary electrophoresis. Electrophoresis 22 : 1979 1986.