DOI QR코드

DOI QR Code

Molecular Chaperones in Protein Quality Control

  • Lee, Suk-Yeong (Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine) ;
  • Tsai, Francis T.F. (Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine)
  • Published : 2005.05.31

Abstract

Proteins must fold into their correct three-dimensional conformation in order to attain their biological function. Conversely, protein aggregation and misfolding are primary contributors to many devastating human diseases, such as prion-mediated infections, Alzheimer's disease, type II diabetes and cystic fibrosis. While the native conformation of a polypeptide is encoded within its primary amino acid sequence and is sufficient for protein folding in vitro, the situation in vivo is more complex. Inside the cell, proteins are synthesized or folded continuously; a process that is greatly assisted by molecular chaperones. Molecular chaperones re a group of structurally diverse and mechanistically distinct proteins that either promote folding or prevent the aggregation of other proteins. With our increasing understanding of the proteome, it is becoming clear that the number of proteins that can be classified as molecular chaperones is increasing steadily. Many of these proteins have novel but essential cellular functions that differ from that of more 'conventional' chaperones, such as Hsp70 and the GroE system. This review focuses on the emerging role of molecular chaperones in protein quality control, i.e. the mechanism that rids the cell of misfolded or incompletely synthesized polypeptides that otherwise would interfere with normal cellular function.

Keywords

References

  1. Anfinsen, C. B. (1973) Principles that govern the folding of protein chains. Science 181, 223-230 https://doi.org/10.1126/science.181.4096.223
  2. Beuron, F., Maurizi, M. R., Belnap, D. M., Kocsis, E., Booy, F. P., Kessel, M. and Steven, A. C. (1998) At sixes and sevens: characterization of the symmetry mismatch of the ClpAP chaperone-assisted protease. J. Struct. Biol. 123, 248-259 https://doi.org/10.1006/jsbi.1998.4039
  3. Beyer, A. (1997) Sequence analysis of the AAA protein family. Protein Sci. 6, 2043-2058 https://doi.org/10.1002/pro.5560061001
  4. Bochtler, M., Hartmann, C., Song, H. K., Bourenkov, G. P., Bartunik, H. D. and Huber, R. (2000) The structures of HslU and the ATP-dependent protease HslU-HslV. Nature 403, 800- 805 https://doi.org/10.1038/35001629
  5. Braun, B. C., Glickman, M., Kraft, R., Dahlmann, B., Kloetzel, P. M., Finley, D. and Schmidt, M. (1999) The base of the proteasome regulatory particle exhibits chaperone-like activity. Nat. Cell Biol. 1, 221-226 https://doi.org/10.1038/12043
  6. Cashikar, A. G., Schirmer, E. C., Hattendorf, D. A., Glover, J. R., Ramakrishnan, M. S., Ware, D. M. and Lindquist, S. L. (2002) Defining a pathway of communication from the C-terminal peptide binding domain to the N-terminal ATPase domain in a AAA protein. Mol. Cell 9, 751-760 https://doi.org/10.1016/S1097-2765(02)00499-9
  7. Deuerling, E. and Bukau, B. (2004) Chaperone-assisted folding of newly synthesized proteins in the cytosol. Crit. Rev. Biochem. Mol. Biol. 39, 261-277 https://doi.org/10.1080/10409230490892496
  8. Ferbitz, L., Maier, T., Patzelt, H., Bukau, B., Deuerling, E. and Ban, N. (2004) Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature 431, 590- 596 https://doi.org/10.1038/nature02899
  9. Flanagan, J. M., Wall, J. S., Capel, M. S., Schneider, D. K. and Shanklin, J. (1995) Scanning transmission electron microscopy and small-angle scattering provide evidence that native Escherichia coli ClpP is a tetradecamer with an axial pore. Biochemistry 34, 10910-10917 https://doi.org/10.1021/bi00034a025
  10. Glickman, M. H., Rubin, D. M., Coux, O., Wefes, I., Pfeifer, G., Cjeka, Z., Baumeister, W., Fried, V. A. and Finley, D. (1998) A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9- signalosome and eIF3. Cell 94, 615-623 https://doi.org/10.1016/S0092-8674(00)81603-7
  11. Glover, J. R. and Lindquist, S. (1998) Hsp104, Hsp70, and Hsp40: a novel chaperone system that rescues previously aggregated proteins. Cell 94, 73-82 https://doi.org/10.1016/S0092-8674(00)81223-4
  12. Goloubinoff, P., Mogk, A., Zvi, A. P., Tomoyasu, T. and Bukau, B. (1999) Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network. Proc. Natl. Acad. Sci. USA 96, 13732-13737 https://doi.org/10.1073/pnas.96.24.13732
  13. Gottesman, S., Roche, E., Zhou, Y. and Sauer, R. T. (1998) The ClpXP and ClpAP proteases degrade proteins with carboxyterminal peptide tails added by the SsrA-tagging system. Genes Dev. 12, 1338-1347 https://doi.org/10.1101/gad.12.9.1338
  14. Gribun, A., Kimber, M. S., Ching, R., Sprangers, R., Fiebig, K. M. and Houry, W. A. (2005) The ClpP double-ring tetradecameric protease exhibits plastic ring-ring interactions and the N-termini of Its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation. J. Biol. Chem. 280, 16185-16196 https://doi.org/10.1074/jbc.M414124200
  15. Groll, M., Bochtler, M., Brandstetter, H., Clausen, T. and Huber, R. (2005) Molecular machines for protein degradation. Chembiochem. 6, 222-256 https://doi.org/10.1002/cbic.200400313
  16. Groll, M., Ditzel, L., Lowe, J., Stock, D., Bochtler, M., Bartunik, H. D. and Huber, R. (1997) Structure of 20S proteasome from yeast at 2.4 A resolution. Nature 386, 463-471 https://doi.org/10.1038/386463a0
  17. Guo, F., Maurizi, M. R., Esser, L. and Xia, D. (2002) Crystal structure of ClpA, an HSP100 chaperone and regulator of ClpAP protease. J. Biol. Chem. 277, 46743-46752 https://doi.org/10.1074/jbc.M207796200
  18. Harrison, C. J., Hayer-Hartl, M., Di Liberto, M., Hartl, F. and Kuriyan, J. (1997) Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK. Science 276, 431-435 https://doi.org/10.1126/science.276.5311.431
  19. Hartl, F. U. and Hayer-Hartl, M. (2002) Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295, 1852-1858 https://doi.org/10.1126/science.1068408
  20. Hegerl, R., Pfeifer, G., Puhler, G., Dahlmann, B. and Baumeister, W. (1991) The three-dimensional structure of proteasomes from Thermoplasma acidophilum as determined by electron microscopy using random conical tilting. FEBS Lett. 283, 117- 121 https://doi.org/10.1016/0014-5793(91)80567-M
  21. Horwich, A. L., Weber-Ban, E. U. and Finley, D. (1999) Chaperone rings in protein folding and degradation. Proc. Natl. Acad. Sci. USA 96, 11033-11040 https://doi.org/10.1073/pnas.96.20.11033
  22. Ikai, A., Nishigai, M., Tanaka, K. and Ichihara, A. (1991) Electron microscopy of 26 S complex containing 20 S proteasome. FEBS Lett. 292, 21-24 https://doi.org/10.1016/0014-5793(91)80824-M
  23. Joshi, S. A., Hersch, G. L., Baker, T. A. and Sauer, R. T. (2004) Communication between ClpX and ClpP during substrate processing and degradation. Nat. Struct. Mol. Biol. 11, 404-411 https://doi.org/10.1038/nsmb752
  24. Kessel, M., Maurizi, M. R., Kim, B., Kocsis, E., Trus, B. L., Singh, S. K. and Steven, A. C. (1995) Homology in structural organization between E. coli ClpAP protease and the eukaryotic 26 S proteasome. J. Mol. Biol. 250, 587-594 https://doi.org/10.1006/jmbi.1995.0400
  25. Kim, D. Y. and Kim, K. K. (2003) Crystal structure of ClpX molecular chaperone from Helicobacter pylori. J. Biol. Chem. 278, 50664-50670 https://doi.org/10.1074/jbc.M305882200
  26. Kim, K. K., Kim, R. and Kim, S. H. (1998) Crystal structure of a small heat-shock protein. Nature 394, 595-599 https://doi.org/10.1038/29106
  27. Kim, Y.-I., Levchenko, I., Fraczkowska, K., Woodruff, R. V., Sauer, R. T. and Baker, T. A. (2001) Molecular determinants of complex formation between Clp/Hsp100 ATPases and the ClpP peptidase. Nat. Struct. Biol. 8, 230-233 https://doi.org/10.1038/84967
  28. Lee, S., Hisayoshi, M., Yoshida, M. and Tsai, F. T. F. (2003a) Crystallization and preliminary X-ray crystallographic analysis of the Hsp100 chaperone ClpB from Thermus thermophilus. Acta Crystallogr. D 59, 2334-2336 https://doi.org/10.1107/S0907444903023266
  29. Lee, S., Sowa, M. E., Choi, J. M. and Tsai, F. T. F. (2004) The ClpB/Hsp104 molecular chaperone-a protein disaggregating machine. J. Struct. Biol. 146, 99-105 https://doi.org/10.1016/j.jsb.2003.11.016
  30. Lee, S., Sowa, M. E., Watanabe, Y., Sigler, P. B., Chiu, W., Yoshida, M. and Tsai, F. T. F. (2003b) The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state. Cell 115, 229-240 https://doi.org/10.1016/S0092-8674(03)00807-9
  31. Levchenko, I., Luo, L. and Baker, T. A. (1995) Disassembly of the Mu transposase tetramer by the ClpX chaperone. Genes Dev. 9, 2399-2408 https://doi.org/10.1101/gad.9.19.2399
  32. Lowe, J., Stock, D., Jap, B., Zwickl, P., Baumeister, W. and Huber, R. (1995) Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution. Science 268, 533-539 https://doi.org/10.1126/science.7725097
  33. Ludlam, A. V., Moore, B. A. and Xu, Z. (2004) The crystal structure of ribosomal chaperone trigger factor from Vibrio cholerae. Proc. Natl. Acad. Sci. USA 101, 13436-13441 https://doi.org/10.1073/pnas.0405868101
  34. Meyer, P., Prodromou, C., Hu, B., Vaughan, C., Roe, S. M., Panaretou, B., Piper, P. W. and Pearl, L. H. (2003) Structural and functional analysis of the middle segment of Hsp90: implications for ATP hydrolysis and client protein and cochaperone interactions. Mol. Cell 11, 647-658 https://doi.org/10.1016/S1097-2765(03)00065-0
  35. Mogk, A., Schlieker, C., Strub, C., Rist, W., Weibezahn, J. and Bukau, B. (2003) Roles of individual domains and conserved motifs of the AAA+ chaperone ClpB in oligomerization, ATP hydrolysis, and chaperone activity. J. Biol. Chem. 278, 17615- 17624 https://doi.org/10.1074/jbc.M209686200
  36. Mogk, A., Tomoyasu, T., Goloubinoff, P., Rüdiger, S., Röder, D., Langen, H. and Bukau, B. (1999) Identification of thermolabile Escherichia coli proteins: prevention and reversion of aggregation by DnaK and ClpB. EMBO J. 18, 6934-6949 https://doi.org/10.1093/emboj/18.24.6934
  37. Motohashi, K., Watanabe, Y., Yohda, M. and Yoshida, M. (1999) Heat-inactivated proteins are rescued by the DnaK.J-GrpE set and ClpB chaperones. Proc. Natl. Acad. Sci. USA 96, 7184-7189 https://doi.org/10.1073/pnas.96.13.7184
  38. Neuwald, A. F., Aravind, L., Spouge, J. L. and 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
  39. Ogura, T. and Wilkinson, A. J. (2001) AAA+ superfamily ATPases: common structure-diverse function. Genes Cells 6, 575-597 https://doi.org/10.1046/j.1365-2443.2001.00447.x
  40. Parsell, D. A., Kowal, A. S., Singer, M. A. and Lindquist, S. (1994) Protein disaggregation mediated by heat-shock protein Hsp104. Nature 372, 475-478 https://doi.org/10.1038/372475a0
  41. Pickart, C. M. (2004) Back to the future with ubiquitin. Cell 116, 181-190 https://doi.org/10.1016/S0092-8674(03)01074-2
  42. Sanchez, Y. and Lindquist, S. (1990) Hsp104 required for induced thermotolerance. Science 248, 1112-1115 https://doi.org/10.1126/science.2188365
  43. Sanchez, Y., Taulien, J., Borkovich, K. A. and Lindquist, S. (1992) Hsp104 is required for tolerance to many forms of stress. EMBO J. 11, 2357-2364
  44. Sauer, R. T., Bolon, D. N., Burton, B. M., Burton, R. E., Flynn, J. M., Grant, R. A., Hersch, G. L., Joshi, S. A., Kenniston, J. A., Levchenko, I., Neher, S. B., Oakes, E. S. C., Siddiqui, S. M., Wah, D. A. and Baker, T. A. (2004) Sculpting the proteome with AAA(+) proteases and disassembly machines. Cell 119, 9- 18 https://doi.org/10.1016/j.cell.2004.09.020
  45. Schirmer, E. C., Glover, J. R., Singer, M. A. and Lindquist, S. (1996) Hsp100/Clp proteins: a common mechanism explains diverse functions. Trends Biochem. Sci. 21, 289-296 https://doi.org/10.1016/0968-0004(96)10038-4
  46. Sousa, M. C., Trame, C. B., Tsuruta, H., Wilbanks, S. M., Reddy, V. S. and McKay, D. B. (2000) Crystal and solution structure of an HslUV protease-chaperone complex. Cell 103, 633-643 https://doi.org/10.1016/S0092-8674(00)00166-5
  47. Squires, C. and Squires, C. L. (1992) The Clp proteins: proteolysis regulators of molecular chaperones? J. Bacteriol. 174, 1081-1085
  48. Squires, C. L., Pedersen, S., Ross, B. M. and Squires, C. (1991) ClpB is the Escherichia coli heat shock protein F84.1. J. Bacteriol. 173, 4254-4262
  49. Unno, M., Mizushima, T., Morimoto, Y., Tomisugi, Y., Tanaka, K., Yasuoka, N. and Tsukihara, T. (2002) The structure of the mammalian 20S proteasome at 2.75 A resolution. Structure 10, 609-618 https://doi.org/10.1016/S0969-2126(02)00748-7
  50. Vale, R. D. (2000) AAA proteins: Lords of the ring. J. Cell Biol. 150, 13-19 https://doi.org/10.1083/jcb.150.1.13
  51. Walter, S. and Buchner, J. (2002) Molecular chaperones-cellular machines for protein folding. Angew. Chem. Int. Ed. Engl. 41, 1098-1113 https://doi.org/10.1002/1521-3773(20020402)41:7<1098::AID-ANIE1098>3.0.CO;2-9
  52. Wang, J., Hartling, J. A. and Flanagan, J. M. (1997) The structure of ClpP at 2.3 A resolution suggests a model for ATPdependent proteolysis. Cell 91, 447-456 https://doi.org/10.1016/S0092-8674(00)80431-6
  53. Wang, Q., Song, C. and Li, C. C. (2004) Molecular perspectives on p97-VCP: progress in understanding its structure and diverse biological functions. J. Struct. Biol. 146, 44-57 https://doi.org/10.1016/j.jsb.2003.11.014
  54. Wawrzynow, A., Wojtkowiak, D., Marszalek, J., Banecki, B., Jonsen, M., Graves, B., Georgopoulos, C. and Zylicz, M. (1995) The ClpX heat-shock protein of Escherichia coli, the ATP-dependent substrate specificity component of the ClpPClpX protease, is a novel molecular chaperone. EMBO J. 14, 1867-1877
  55. Weibezahn, J., Tessarz, P., Schlieker, C., Zahn, R., Maglica, Z., Lee, S., Zentgraf, H., Weber-Ban, E. U., Dougan, D. A., Tsai, F. T. F., Mogk, A. and Bukau, B. (2004) Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB. Cell 119, 653- 665 https://doi.org/10.1016/j.cell.2004.11.027
  56. Whitby, F. G., Masters, E. I., Kramer, L., Knowlton, J. R., Yao, Y., Wang, C. C. and Hill, C. P. (2000) Structural basis for the activation of 20S proteasomes by 11S regulators. Nature 408, 115-120 https://doi.org/10.1038/35040607
  57. Wickner, S., Gottesman, S., Skowyra, D., Hoskins, J., McKenney, K. and Maurizi, M. R. (1994) A molecular chaperone, ClpA, functions like DnaK and DnaJ. Proc. Natl. Acad. Sci. USA 91, 12218-12222 https://doi.org/10.1073/pnas.91.25.12218
  58. Xu, Z., Horwich, A. L. and Sigler, P. B. (1997) The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Nature 388, 741-750 https://doi.org/10.1038/41944
  59. Young, J. C., Agashe, V. R., Siegers, K. and Hartl, F. U. (2004) Pathways of chaperone-mediated protein folding in the cytosol. Nat. Rev. Mol. Cell Biol. 5, 781-791 https://doi.org/10.1038/nrm1492
  60. Zolkiewski, M. (1999) ClpB cooperates with DnaK, DnaJ, and GrpE in suppressing protein aggregation. J. Biol. Chem. 274, 28083-28086 https://doi.org/10.1074/jbc.274.40.28083

Cited by

  1. Effect of W62G mutation of hen lysozyme on the folding in vivo vol.338, pp.2, 2005, https://doi.org/10.1016/j.bbrc.2005.10.009
  2. Multi-faceted role of HSP40 in cancer vol.26, pp.6, 2009, https://doi.org/10.1007/s10585-009-9255-x
  3. Molecular chaperones vol.36, pp.1, 2010, https://doi.org/10.1134/S1068162010010012
  4. The Biochemistry of Disease: Desperately Seeking Syzygy vol.78, pp.1, 2009, https://doi.org/10.1146/annurev-biochem-120108-082254
  5. Synergistic coordination of polyethylene glycol with ClpB/DnaKJE bichaperone for refolding of heat-denatured malate dehydrogenase vol.25, pp.4, 2009, https://doi.org/10.1002/btpr.175
  6. Self-Assembly of Fibers and Fibrils vol.45, pp.44, 2006, https://doi.org/10.1002/anie.200602001
  7. Selbstorganisation von Fasern und Fibrillen vol.118, pp.44, 2006, https://doi.org/10.1002/ange.200602001
  8. The association of SNPs in Hsp90β gene 5′ flanking region with thermo tolerance traits and tissue mRNA expression in two chicken breeds vol.40, pp.9, 2013, https://doi.org/10.1007/s11033-013-2630-3
  9. KSHV Reactivation and Novel Implications of Protein Isomerization on Lytic Switch Control vol.7, pp.1, 2015, https://doi.org/10.3390/v7010072
  10. Examination of ClpB Quaternary Structure and Linkage to Nucleotide Binding vol.55, pp.12, 2016, https://doi.org/10.1021/acs.biochem.6b00122
  11. Synergism between the chaperone-like activity of the stress regulated ASR1 protein and the osmolyte glycine-betaine vol.227, pp.6, 2008, https://doi.org/10.1007/s00425-008-0693-5
  12. Molecular mechanisms underlying chemical liver injury vol.14, 2012, https://doi.org/10.1017/S1462399411002110
  13. The role of protein quality control in mitochondrial protein homeostasis under oxidative stress vol.10, pp.7, 2010, https://doi.org/10.1002/pmic.200800619
  14. Understanding protein folding from globular to amyloid state vol.48, pp.11, 2013, https://doi.org/10.1016/j.procbio.2013.08.011
  15. Stress Chaperones, Mortalin, and Pex19p Mediate 5-Aza-2' Deoxycytidine-Induced Senescence of Cancer Cells by DNA Methylation-Independent Pathway vol.62, pp.3, 2007, https://doi.org/10.1093/gerona/62.3.246
  16. Mitochondrial ATP-independent chaperones vol.61, pp.9, 2009, https://doi.org/10.1002/iub.235
  17. Thermodynamics of protein folding: a random matrix formulation vol.22, pp.41, 2010, https://doi.org/10.1088/0953-8984/22/41/415106
  18. Ubiquitin proteasome system as a pharmacological target in neurodegeneration vol.6, pp.9, 2006, https://doi.org/10.1586/14737175.6.9.1337
  19. Rethinking peptide supply to MHC class I molecules vol.7, pp.5, 2007, https://doi.org/10.1038/nri2077
  20. The implications of gene heterozygosity for protein folding and protein turnover vol.265, pp.4, 2010, https://doi.org/10.1016/j.jtbi.2010.05.023
  21. Role of α-helical domains in functioning of ATP-dependent Lon protease of Escherichia coli vol.40, pp.6, 2014, https://doi.org/10.1134/S106816201406003X
  22. Protein Quality Control in Neurodegeneration: Walking the Tight Rope Between Health and Disease vol.34, pp.1, 2008, https://doi.org/10.1007/s12031-007-0013-8
  23. Structural Elements Regulating AAA+ Protein Quality Control Machines vol.4, 2017, https://doi.org/10.3389/fmolb.2017.00027
  24. Charge-Rich Regions Modulate the Anti-Aggregation Activity of Hsp90 vol.401, pp.5, 2010, https://doi.org/10.1016/j.jmb.2010.06.066