1887

Abstract

ClpB is a member of the protein-disaggregating chaperone machinery belonging to the AAA+ superfamily. This paper describes a new gene from the halophilic methanoarchaeon , which has not been reported previously in Archaea. The partial sequence of was identified from the investigation of the salt-stress response of by differential-display RT-PCR (DDRT-PCR). Furthermore, the complete sequence (2610 nt) and its upstream genes encoding the type I chaperonin GroEL/ES were obtained through inverse PCR, Southern hybridization and sequencing. The G+C ratio of is 49.6 mol%. The predicted ClpB polypeptide contains 869 aa and possesses a long central domain and a predicted distinctly discontinuous coiled-coil motif separating two nucleotide-binding domains (NBD1 and NBD2). NBD1 has a single Walker A and two Walker B motifs and NBD2 has only one of each Walker motif, a characteristic of HSP100 proteins. Two repeated Clp amino-terminal domain motifs (ClpN) were identified in ClpB. The putative amino acid sequence shared 75.6 % identity with the predicted homologue annotated as ATPase AAA-2 of DSM 6242. Preliminary phylogenetic analysis clustered ClpB (ClpB) with the low G+C Gram-positive bacteria. Stress response analysis of by Northern blotting showed up to 1.5-fold increased transcription levels in response to both salt up-shock (from 2.1 to 3.1 M NaCl) and down-shock (from 2.1 to 0.9 M NaCl). Both and transcript levels increased when the temperature was shifted from 37 °C to 55 °C. Under heat stress transcription was repressed by the addition of the osmolyte betaine (1 mM). In conclusion, a novel AAA+ chaperone gene from a halophilic methanogen that responded to the fluctuations in temperature, salt concentration and betaine has been identified and analysed for the first time.

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2007-08-01
2019-11-15
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References

  1. Albers, S.-V., van de Vossenberg, J. L. C. M., Driessen, A. J. M. & Konings, W. N. ( 2000; ). Adaptations of the archaeal cell membrane to heat stress. Front Biosci 5, D813–D820.[CrossRef]
    [Google Scholar]
  2. Balch, W. E., Fox, G. E., Woese, C. R. & Wolfe, R. S. ( 1979; ). Methanogens: reevaluation of a biological group. Microbiol Rev 43, 260–296.
    [Google Scholar]
  3. Barnett, M. E., Zolkiewska, A. & Zolkiewski, M. ( 2000; ). Structure and activity of ClpB from Escherichia coli: role of the amino-and carboxyl terminal domains. J Biol Chem 275, 37565–37571.[CrossRef]
    [Google Scholar]
  4. Ben-Zvi, A. P. & Goloubinoff, P. ( 2001; ). Mechanism of disaggregation and refolding of stable protein aggregates by molecular chaperone. J Struct Biol 135, 84–93.[CrossRef]
    [Google Scholar]
  5. Boone, D. R., Mathrani, I. M., Liu, Y., Menaia, J. A. G. F., Mah, R. A. & Boone, J. E. ( 1993; ). Isolation and characterization of Methanohalophilus portucalensis sp. nov. and DNA reassociation study of the genus Methanohalophilus. Int J Syst Evol Microbiol 43, 430–437.
    [Google Scholar]
  6. Boonyaratanakornkit, B. B., Simpson, A. J., Whitehead, T. A., Fraser, C. M., El-Sayed, N. M. A. & Clark, D. S. ( 2005; ). Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock. Environ Microbiol 7, 789–797.[CrossRef]
    [Google Scholar]
  7. Cannio, R., Fiorentino, G., Morana, A., Rossi, M. & Bartolucci, S. ( 2000; ). Oxygen: friend or foe? Archaeal superoxide dismutases in the protection of intra- and extracellular oxidative stress. Front Biosci 5, D768–D779.[CrossRef]
    [Google Scholar]
  8. Celerin, M., Gilpin, A. A., Schisler, N. J., Ivanov, A. G., Miskiewicz, E., Krol, M. & Laudenbach, D. E. ( 1998; ). ClpB in a cyanobacterium: predicted structure, phylogenetic relationships, and regulation by light and temperature. J Bacteriol 180, 5173–5182.
    [Google Scholar]
  9. Conway de Macario, E., Maeder, D. L. & Macario, A. J. L. ( 2003; ). Breaking the mould: archaea with all four chaperoning systems. Biochem Biophys Res Commun 301, 811–812.[CrossRef]
    [Google Scholar]
  10. Deppenmeier, U., Johann, A., Hartsch, T., Merkl, R., Schmitz, R. A., Martinez-Arias, R., Henne, A., Wiezer, A., Bäumer, S. & other authors ( 2002; ). The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4, 453–461.
    [Google Scholar]
  11. Diamant, S., Eliahu, N., Rosenthal, D. & Goloubinoff, P. ( 2001; ). Chemical chaperones regulate molecular chaperones in vitro and in cells under combined salt and heat stresses. J Biol Chem 276, 39586–39591.[CrossRef]
    [Google Scholar]
  12. Diamant, S., Rosenthal, D., Azem, A., Eliahu, N., Ben-Zvi, A. P. & Goloubinoff, P. ( 2003; ). Dicarboxylic amino acids and glycine-betaine regulate chaperone-mediated protein-disaggregation under stress. Mol Microbiol 49, 401–410.[CrossRef]
    [Google Scholar]
  13. Dougan, D. A., Mogk, A., Zeth, K., Turgay, K. & Bukau, B. ( 2002; ). AAA+ proteins and substrate recognition, it all depends on their partner in crime. FEBS Lett 529, 6–10.[CrossRef]
    [Google Scholar]
  14. Galagan, J. E., Nusbaum, C., Roy, A., Endrizzi, M. G., Macdonald, P., FitzHugh, W., Calvo, S., Engels, R., Smirnov, S. & other authors ( 2002; ). The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res 12, 532–542.[CrossRef]
    [Google Scholar]
  15. Jarrell, K. F., Faguy, D., Hebert, A. M. & Kalmokoff, M. L. ( 1992; ). A general method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria). Can J Microbiol 38, 65–68.[CrossRef]
    [Google Scholar]
  16. Johnson, J. L. ( 1985; ). DNA reassociation and DNA hybridization of bacterial nucleic acids. Methods Microbiol 18, 33–74.
    [Google Scholar]
  17. Kagawa, H. K., Osipiuk, J., Maltsev, N., Overbeek, R., Quaite-Randall, E., Joachimiak, A. & Trent, J. D. ( 1995; ). The 60 kDa heat shock proteins in the hyperthermophilic archaeon Sulfolobus shibatae. J Mol Biol 253, 712–725.[CrossRef]
    [Google Scholar]
  18. Klunker, D., Haas, B., Hirtreiter, A., Figueiredo, L., Naylor, G. D., Pfeifer, J., Müller, V., Deppenmeier, U., Gottschalk, G. & other authors ( 2003; ). Coexistence of Group I and Group II chaperonins in the Archaeon Methanosarcina mazei. J Biol Chem 278, 33256–33267.[CrossRef]
    [Google Scholar]
  19. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  20. Lai, M.-C., Sowers, K. R., Robertson, D. E., Roberts, M. F. & Gunsalus, R. P. ( 1991; ). Distribution of compatible solutes in the halophilic methanogenic archaebacteria. J Bacteriol 173, 5352–5358.
    [Google Scholar]
  21. Lai, M.-C., Yang, D.-R. & Cuang, M.-J. ( 1999; ). Regulatory factors associated with synthesis of the osmolyte glycine betaine in the halophilic methanoarchaeon Methanohalophilus portucalensis. Appl Environ Microbiol 65, 828–833.
    [Google Scholar]
  22. Lai, M.-C., Hong, T.-Y. & Gunsalus, R. P. ( 2000; ). Glycine betaine transport in halophilic methanogenic archaea, Methanohalophilus portucalensis. J Bacteriol 182, 5020–5024.[CrossRef]
    [Google Scholar]
  23. Lai, M.-C., Chen, S.-C., Shu, C.-M., Chiou, M.-S., Wang, C.-C., Chuang, M.-J., Hong, T.-Y., Liu, C.-C., Lai, L.-J. & Hua, J. J. ( 2002; ). Methanocalculus taiwanensis sp. nov., isolated from an estuarine environment. Int J Syst Evol Microbiol 52, 1799–1806.[CrossRef]
    [Google Scholar]
  24. Lai, M.-C., Lin, C.-C., Yu, P.-H., Huang, Y.-F. & Chen, S.-C. ( 2004; ). Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan. Int J Syst Evol Microbiol 54, 183–189.[CrossRef]
    [Google Scholar]
  25. Lai, M.-C., Wang, C.-C., Chuang, M.-J., Wu, Y.-C. & Lee, Y.-C. ( 2006; ). The effects of substrate and potassium on betaine synthesizing enzyme glycine sarcosine dimethylglycine N-methyltransferase from a halophilic methanoarchaeon Methanohalophilus portucalensis. Res Microbiol 157, 948–955.[CrossRef]
    [Google Scholar]
  26. Laksanalamai, P., Whitehead, T. A. & Robb, F. T. ( 2004; ). Minimal protein-folding systems in hyperthermophilic archaea. Nat Rev Microbiol 2, 315–324.[CrossRef]
    [Google Scholar]
  27. Lee, S. & Tsai, F. T. F. ( 2005; ). Molecular chaperones in protein quality control. J Biochem Mol Biol 38, 259–265.[CrossRef]
    [Google Scholar]
  28. Lee, S., Sowa, M. E., Watanabe, Y.-H., Sigler, P. B., Chiu, W., Yoshida, M. & Tsai, F. T. F. ( 2003; ). The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state. Cell 115, 229–240.[CrossRef]
    [Google Scholar]
  29. Lee, S., Sowa, M. E., Choi, J.-M. & Tsai, F. T. F. ( 2004; ). The ClpB/Hsp104 molecular chaperone – a protein disaggregating machine. J Struct Biol 146, 99–105.[CrossRef]
    [Google Scholar]
  30. Lupas, A. ( 1996; ). Coiled coils: new structures and new functions. Trends Biochem Sci 21, 375–382.[CrossRef]
    [Google Scholar]
  31. Macario, A. J. L., Lange, M., Ahring, B. K. & Conway de Macario, E. ( 1999; ). Stress genes and proteins in the archaea. Microbiol Mol Biol Rev 63, 923–967.
    [Google Scholar]
  32. Macario, A. J. L., Malz, M. & Conway de Macario, E. ( 2004; ). Evolution of assisted protein folding: the distribution of the main chaperoning systems within the phylogenetic domain archaea. Front Biosci 9, 1318–1332.[CrossRef]
    [Google Scholar]
  33. Macario, A. J. L., Brocchieri, L., Shenoy, A. R. & Conway de Macario, E. ( 2006; ). Evolution of a protein-folding machine: genomic and evolutionary analyses reveal three lineages of the archaeal hsp70 (dnaK) gene. J Mol Evol 63, 74–86.[CrossRef]
    [Google Scholar]
  34. Martin, J., Gruber, M. & Lupas, A. N. ( 2004; ). Coiled coils meet the chaperone world. Trends Biochem Sci 29, 455–458.[CrossRef]
    [Google Scholar]
  35. Maruyama, T. & Furutani, M. ( 2000; ). Archaeal peptidyl prolyl cis-trans isomerases (PPIases). Front Biosci 5, D821–D836.[CrossRef]
    [Google Scholar]
  36. Mathrani, I. M. & Boone, D. R. ( 1985; ). Isolation and characterization of a moderately halophilic methanogen from a solar saltern. Appl Environ Microbiol 50, 140–143.
    [Google Scholar]
  37. Neuwald, A. F., Aravind, L., Spouge, J. L. & Koonin, E. V. ( 1999; ). AAA+: a class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res 9, 27–43.
    [Google Scholar]
  38. Ogura, T. & Wilkinson, A. J. ( 2001; ). AAA+ superfamily ATPases: common structure – diverse function. Genes Cells 6, 575–597.[CrossRef]
    [Google Scholar]
  39. Osipiuk, J. & Joachimiak, A. ( 1997; ). Cloning, sequencing, and expression of dnaK-operon proteins from the thermophilic bacterium Thermus thermophilus. Biochim Biophys Acta 1353, 253–265.[CrossRef]
    [Google Scholar]
  40. Quaite-Randall, E., Trent, J. D., Josephs, R. & Joachimiak, A. ( 1995; ). Conformational cycle of the archaeosome, a TCP1-like chaperonin from Sulfolobus shibatae. J Biol Chem 270, 28818–28823.[CrossRef]
    [Google Scholar]
  41. Queitsch, C., Hong, S. W., Vierling, E. & Lindquist, S. ( 2000; ). Heat shock protein 101 plays a crucial role in thermotolerance in Arabidopsis. Plant Cell 12, 479–492.[CrossRef]
    [Google Scholar]
  42. Roberts, M. F. ( 2000; ). Osmoadaptation and osmoregulation in archaea. Front Biosci 5, D796–D812.[CrossRef]
    [Google Scholar]
  43. Sambrook, J. & Russell, D. W. ( 2001; ). Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  44. Sanchez, Y. & Lindquist, S. ( 1990; ). Hsp104 required for induced thermotolerance. Science 248, 1112–1115.[CrossRef]
    [Google Scholar]
  45. Saunders, N. F. W., Thomas, T., Curmi, P. M. G., Mattick, J. S., Kuczek, E., Slade, R., Davis, J., Franzmann, P. D., Boone, D. & other authors ( 2003; ). Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res 13, 1580–1588.[CrossRef]
    [Google Scholar]
  46. Scandurra, R., Consalvi, V., Chiaraluce, R., Politi, L. & Engel, P. C. ( 2000; ). Protein stability in extremophilic archaea. Front Biosci 5, D787–D795.[CrossRef]
    [Google Scholar]
  47. Schirmer, E. C., Glover, J. R., Singer, M. A. & Lindquist, S. ( 1996; ). HSP100/Clp proteins: a common mechanism explains diverse functions. Trends Biochem Sci 21, 289–296.[CrossRef]
    [Google Scholar]
  48. Schlieker, C., Weibezahn, J., Patzelt, H., Tessarz, P., Strub, C., Zeth, K., Erbse, A., Schneider-Mergener, J., Chin, J. W. & other authors ( 2004; ). Substrate recognition by the AAA+ chaperone ClpB. Nat Struct Mol Biol 11, 607–615.[CrossRef]
    [Google Scholar]
  49. Singh, S. K., Grimaud, R., Hoskins, J. R., Wickner, S. & Maurizi, M. R. ( 2000; ). Unfolding and internalization of proteins by ATP-dependent protease ClpXP and ClpAP. Proc Natl Acad Sci U S A 97, 8898–8903.[CrossRef]
    [Google Scholar]
  50. Singh, S. K., Rozycki, J., Ortega, J., Ishikawa, T., Lo, J., Steven, A. C. & Maurizi, M. R. ( 2001; ). Functional domains of the ClpA and ClpX molecular chaperones identified by limited proteolysis and deletion analysis. J Biol Chem 276, 29420–29429.[CrossRef]
    [Google Scholar]
  51. Squires, C. & Squires, C. L. ( 1992; ). The Clp proteins: proteolysis regulators or molecular chaperones?. J Bacteriol 174, 1081–1085.
    [Google Scholar]
  52. Squires, C. L., Pedersen, S., Ross, B. M. & Squires, C. ( 1991; ). ClpB is the Escherichia coli heat shock protein F84.1. J Bacteriol 173, 4254–4262.
    [Google Scholar]
  53. 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.[CrossRef]
    [Google Scholar]
  54. Waldmann, T., Lupas, A. N., Kellermann, J., Peters, J. & Baumeister, W. ( 1995; ). Primary structure of the thermosome from Thermoplasma acidophilum. Biol Chem Hoppe Seyler 376, 119–126.[CrossRef]
    [Google Scholar]
  55. Woo, K. M., Kim, K. I., Goldberg, A. L., Ha, D. B. & Chung, C. H. ( 1992; ). The heat-shock protein ClpB in Escherichia coli is a protein-activated ATPase. J Biol Chem 267, 20429–20434.
    [Google Scholar]
  56. Zolkiewski, M. ( 1999; ). ClpB cooperates with DnaK, DnaJ, and GrpE in suppressing protein aggregation. A novel multi-chaperone system from Escherichia coli. J Biol Chem 274, 28083–28086.[CrossRef]
    [Google Scholar]
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vol. , part 8, pp. 2572 - 2583

Sequence alignment and secondary structure elements of ClpB/Hsp101/Hsp104. The amino acid sequences aligned were (MpClpB), (EcClpB), (MbATPase), (MhATPase), (AtHsp101), (MtClpA/B), (TtClpB) and (ScHsp104). Numbers indicate positions in the amino-acid sequence. Secondary structure elements (based on TtClpB) are shown as helices (α helices) and arrows (β strand). Identical residues are shaded. The conserved nucleotide-binding domains (NBD1 and NBD2) and two repeated Clp amino-terminal domain motifs (ClpN) are in bold boxes and thin boxes, respectively. Conserved Walker motifs (Walker A and Walker B) are indicated as star symbols and the dashed line indicates the middle region which forms the coiled-coil structure. [ PDF] (675 kb)



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