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Misfolded proteins partition between two distinct quality control compartments

Abstract

The accumulation of misfolded proteins in intracellular amyloid inclusions, typical of many neurodegenerative disorders including Huntington’s and prion disease, is thought to occur after failure of the cellular protein quality control mechanisms. Here we examine the formation of misfolded protein inclusions in the eukaryotic cytosol of yeast and mammalian cell culture models. We identify two intracellular compartments for the sequestration of misfolded cytosolic proteins. Partition of quality control substrates to either compartment seems to depend on their ubiquitination status and aggregation state. Soluble ubiquitinated misfolded proteins accumulate in a juxtanuclear compartment where proteasomes are concentrated. In contrast, terminally aggregated proteins are sequestered in a perivacuolar inclusion. Notably, disease-associated Huntingtin and prion proteins are preferentially directed to the perivacuolar compartment. Enhancing ubiquitination of a prion protein suffices to promote its delivery to the juxtanuclear inclusion. Our findings provide a framework for understanding the preferential accumulation of amyloidogenic proteins in inclusions linked to human disease.

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Figure 1: A panel of quality control substrates defines two distinct compartments for the sequestration of misfolded cytosolic proteins.
Figure 2: Amyloidogenic proteins are preferentially directed to a single inclusion.
Figure 3: Mammalian cells differentially sequester misfolded proteins in two distinct compartments.
Figure 4: Differential solubility of misfolded substrates in the distinct quality control compartments.
Figure 6: Partitioning between JUNQ and IPOD is regulated by ubiquitination.
Figure 5: The JUNQ and IPOD are defined subcellular compartments.

References

  1. Bence, N. F., Sampat, R. M. & Kopito, R. R. Impairment of the ubiquitin-proteasome system by protein aggregation. Science 292, 1552–1555 (2001)

    Article  ADS  CAS  Google Scholar 

  2. Chiti, F. & Dobson, C. M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75, 333–366 (2006)

    Article  CAS  Google Scholar 

  3. Gidalevitz, T., Ben-Zvi, A., Ho, K. H., Brignull, H. R. & Morimoto, R. I. Progressive disruption of cellular protein folding in models of polyglutamine diseases. Science 311, 1471–1474 (2006)

    Article  ADS  CAS  Google Scholar 

  4. Muchowski, P. J. & Wacker, J. L. Modulation of neurodegeneration by molecular chaperones. Nature Rev. Neurosci. 6, 11–22 (2005)

    Article  CAS  Google Scholar 

  5. Outeiro, T. F. & Lindquist, S. Yeast cells provide insight into α-synuclein biology and pathobiology. Science 302, 1772–1775 (2003)

    Article  ADS  CAS  Google Scholar 

  6. Schaffar, G. et al. Cellular toxicity of polyglutamine expansion proteins: mechanism of transcription factor deactivation. Mol. Cell 15, 95–105 (2004)

    Article  CAS  Google Scholar 

  7. Lesne, S. et al. A specific amyloid-β protein assembly in the brain impairs memory. Nature 440, 352–357 (2006)

    Article  ADS  CAS  Google Scholar 

  8. Rubinsztein, D. C. The roles of intracellular protein-degradation pathways in neurodegeneration. Nature 443, 780–786 (2006)

    Article  ADS  CAS  Google Scholar 

  9. Iwata, A. et al. Increased susceptibility of cytoplasmic over nuclear polyglutamine aggregates to autophagic degradation. Proc. Natl Acad. Sci. USA 102, 13135–13140 (2005)

    Article  ADS  CAS  Google Scholar 

  10. Taylor, J. P. et al. Aggresomes protect cells by enhancing the degradation of toxic polyglutamine-containing protein. Hum. Mol. Genet. 12, 749–757 (2003)

    Article  CAS  Google Scholar 

  11. Rideout, H. J., Lang-Rollin, I. & Stefanis, L. Involvement of macroautophagy in the dissolution of neuronal inclusions. Int. J. Biochem. Cell Biol. 36, 2551–2562 (2004)

    Article  CAS  Google Scholar 

  12. Yorimitsu, T. & Klionsky, D. J. Autophagy: molecular machinery for self-eating. Cell Death Differ. 12 (Suppl 2). 1542–1552 (2005)

    Article  CAS  Google Scholar 

  13. Matsumoto, G., Kim, S. & Morimoto, R. I. Huntingtin and mutant SOD1 form aggregate structures with distinct molecular properties in human cells. J. Biol. Chem. 281, 4477–4485 (2006)

    Article  CAS  Google Scholar 

  14. Bucciantini, M. et al. Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 416, 507–511 (2002)

    Article  ADS  CAS  Google Scholar 

  15. Sherman, M. Y. & Goldberg, A. L. Cellular defenses against unfolded proteins: a cell biologist thinks about neurodegenerative diseases. Neuron 29, 15–32 (2001)

    Article  CAS  Google Scholar 

  16. Matsumoto, G., Stojanovic, A., Holmberg, C. I., Kim, S. & Morimoto, R. I. Structural properties and neuronal toxicity of amyotrophic lateral sclerosis-associated Cu/Zn superoxide dismutase 1 aggregates. J. Cell Biol. 171, 75–85 (2005)

    Article  CAS  Google Scholar 

  17. Krobitsch, S. & Lindquist, S. Aggregation of huntingtin in yeast varies with the length of the polyglutamine expansion and the expression of chaperone proteins. Proc. Natl Acad. Sci. USA 97, 1589–1594 (2000)

    Article  ADS  CAS  Google Scholar 

  18. Kamhi-Nesher, S. et al. A novel quality control compartment derived from the endoplasmic reticulum. Mol. Biol. Cell 12, 1711–1723 (2001)

    Article  CAS  Google Scholar 

  19. Huyer, G. et al. A striking quality control subcompartment in Saccharomyces cerevisiae: the endoplasmic reticulum-associated compartment. Mol. Biol. Cell 15, 908–921 (2004)

    Article  CAS  Google Scholar 

  20. Kopito, R. R. Aggresomes, inclusion bodies and protein aggregation. Trends Cell Biol. 10, 524–530 (2000)

    Article  CAS  Google Scholar 

  21. Kruse, K. B., Brodsky, J. L. & McCracken, A. A. Characterization of an ERAD gene as VPS30/ATG6 reveals two alternative and functionally distinct protein quality control pathways: one for soluble Z variant of human α-1 proteinase inhibitor (A1PiZ) and another for aggregates of A1PiZ. Mol. Biol. Cell 17, 203–212 (2006)

    Article  CAS  Google Scholar 

  22. McClellan, A. J., Tam, S., Kaganovich, D. & Frydman, J. Protein quality control: chaperones culling corrupt conformations. Nature Cell Biol. 7, 736–741 (2005)

    Article  CAS  Google Scholar 

  23. Betting, J. & Seufert, W. A yeast Ubc9 mutant protein with temperature-sensitive in vivo function is subject to conditional proteolysis by a ubiquitin- and proteasome-dependent pathway. J. Biol. Chem. 271, 25790–25796 (1996)

    Article  CAS  Google Scholar 

  24. Tongaonkar, P., Beck, K., Shinde, U. P. & Madura, K. Characterization of a temperature-sensitive mutant of a ubiquitin-conjugating enzyme and its use as a heat-inducible degradation signal. Anal. Biochem. 272, 263–269 (1999)

    Article  CAS  Google Scholar 

  25. McClellan, A. J., Scott, M. D. & Frydman, J. Folding and quality control of the VHL tumor suppressor proceed through distinct chaperone pathways. Cell 121, 739–748 (2005)

    Article  CAS  Google Scholar 

  26. Vang, S. et al. Actin mutations in hypertrophic and dilated cardiomyopathy cause inefficient protein folding and perturbed filament formation. FEBS J. 272, 2037–2049 (2005)

    Article  CAS  Google Scholar 

  27. Feldman, D. E., Thulasiraman, V., Ferreyra, R. G. & Frydman, J. Formation of the VHL-elongin BC tumor suppressor complex is mediated by the chaperonin TRiC. Mol. Cell 4, 1051–1061 (1999)

    Article  CAS  Google Scholar 

  28. Mateus, C. & Avery, S. V. Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry. Yeast 16, 1313–1323 (2000)

    Article  CAS  Google Scholar 

  29. Duennwald, M. L., Jagadish, S., Giorgini, F., Muchowski, P. J. & Lindquist, S. A network of protein interactions determines polyglutamine toxicity. Proc. Natl Acad. Sci. USA 103, 11051–11056 (2006)

    Article  ADS  CAS  Google Scholar 

  30. Lippincott-Schwartz, J. & Patterson, G. H. Development and use of fluorescent protein markers in living cells. Science 300, 87–91 (2003)

    Article  ADS  CAS  Google Scholar 

  31. Rujano, M. A. et al. Polarised asymmetric inheritance of accumulated protein damage in higher eukaryotes. PLoS Biol. 4, e417 (2006)

    Article  Google Scholar 

  32. Erjavec, N. & Nystrom, T. Sir2p-dependent protein segregation gives rise to a superior reactive oxygen species management in the progeny of Saccharomyces cerevisiae . Proc. Natl Acad. Sci. USA 104, 10877–10881 (2007)

    Article  ADS  CAS  Google Scholar 

  33. Enenkel, C., Lehmann, A. & Kloetzel, P. M. Subcellular distribution of proteasomes implicates a major location of protein degradation in the nuclear envelope-ER network in yeast. EMBO J. 17, 6144–6154 (1998)

    Article  CAS  Google Scholar 

  34. Tkach, J. M. & Glover, J. R. Amino acid substitutions in the C-terminal AAA+ module of Hsp104 prevent substrate recognition by disrupting oligomerization and cause high temperature inactivation. J. Biol. Chem. 279, 35692–35701 (2004)

    Article  CAS  Google Scholar 

  35. Sarkar, S. et al. Small molecules enhance autophagy and reduce toxicity in Huntington's disease models. Nature Chem. Biol. 3, 331–338 (2007)

    Article  CAS  Google Scholar 

  36. Szeto, J. et al. ALIS are stress-induced protein storage compartments for substrates of the proteasome and autophagy. Autophagy 2, 189–199 (2006)

    Article  CAS  Google Scholar 

  37. Kuma, A., Matsui, M. & Mizushima, N. LC3, an autophagosome marker, can be incorporated into protein aggregates independent of autophagy: caution in the interpretation of LC3 localization. Autophagy 3, 323–328 (2007)

    Article  CAS  Google Scholar 

  38. Pankiv, S. et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J. Biol. Chem. 282, 24131–24145 (2007)

    Article  CAS  Google Scholar 

  39. Swaminathan, S., Amerik, A. Y. & Hochstrasser, M. The Doa4 deubiquitinating enzyme is required for ubiquitin homeostasis in yeast. Mol. Biol. Cell 10, 2583–2594 (1999)

    Article  CAS  Google Scholar 

  40. Balch, W. E., Morimoto, R. I., Dillin, A. & Kelly, J. W. Adapting proteostasis for disease intervention. Science 319, 916–919 (2008)

    Article  ADS  CAS  Google Scholar 

  41. Siegel, S. J., Bieschke, J., Powers, E. T. & Kelly, J. W. The oxidative stress metabolite 4-hydroxynonenal promotes Alzheimer protofibril formation. Biochemistry 46, 1503–1510 (2007)

    Article  CAS  Google Scholar 

  42. Cohen, E., Bieschke, J., Perciavalle, R. M., Kelly, J. W. & Dillin, A. Opposing activities protect against age-onset proteotoxicity. Science 313, 1604–1610 (2006)

    Article  ADS  CAS  Google Scholar 

  43. Webb, J. L., Ravikumar, B., Atkins, J., Skepper, J. N. & Rubinsztein, D. C. α-Synuclein is degraded by both autophagy and the proteasome. J. Biol. Chem. 278, 25009–25013 (2003)

    Article  CAS  Google Scholar 

  44. Kruse, K. B., Brodsky, J. L. & McCracken, A. A. Autophagy: an ER protein quality control process. Autophagy 2, 135–137 (2006)

    Article  CAS  Google Scholar 

  45. Arrasate, M., Mitra, S., Schweitzer, E. S., Segal, M. R. & Finkbeiner, S. Inclusion body formation reduces levels of mutant huntingtin and the risk of neuronal death. Nature 431, 805–810 (2004)

    Article  ADS  CAS  Google Scholar 

  46. Barral, J. M., Broadley, S. A., Schaffar, G. & Hartl, F. U. Roles of molecular chaperones in protein misfolding diseases. Semin. Cell Dev. Biol. 15, 17–29 (2004)

    Article  CAS  Google Scholar 

  47. Tam, S., Geller, R., Spiess, C. & Frydman, J. The chaperonin TRiC controls polyglutamine aggregation and toxicity through subunit-specific interactions. Nature Cell Biol. 8, 1155–1162 (2006)

    Article  CAS  Google Scholar 

  48. Melville, M. W., McClellan, A. J., Meyer, A. S., Darveau, A. & Frydman, J. The Hsp70 and TRiC/CCT chaperone systems cooperate in vivo to assemble the von Hippel-Lindau tumor suppressor complex. Mol. Cell. Biol. 23, 3141–3151 (2003)

    Article  CAS  Google Scholar 

  49. Adams, A., Gottschling, D., Kaiser, C. & Stearns, T. Methods in Yeast Genetics (Cold Spring Harbor Laboratory Press, 1997)

    Google Scholar 

  50. Shaner, N. C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nature Biotechnol. 22, 1567–1572 (2004)

    Article  CAS  Google Scholar 

  51. Prinz, A., Hartmann, E. & Kalies, K. U. Sec61p is the main ribosome receptor in the endoplasmic reticulum of Saccharomyces cerevisiae . Biol. Chem. 381, 1025–1029 (2000)

    Article  CAS  Google Scholar 

  52. Ghislain, M., Udvardy, A. & Mann, C. S. cerevisiae 26S protease mutants arrest cell division in G2/metaphase. Nature 366, 358–362 (1993)

    Article  ADS  CAS  Google Scholar 

  53. Chen, P., Johnson, P., Sommer, T., Jentsch, S. & Hochstrasser, M. Multiple ubiquitin-conjugating enzymes participate in the in vivo degradation of the yeast MAT α 2 repressor. Cell 74, 357–369 (1993)

    Article  CAS  Google Scholar 

  54. Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999)

    Article  CAS  Google Scholar 

  55. Mulholland, J. et al. Ultrastructure of the yeast actin cytoskeleton and its association with the plasma membrane. J Cell Biol. 125, 381–391 (1994)

    Article  CAS  Google Scholar 

  56. Wright, R. & Rine, J. Transmission electron microscopy and immunocytochemical studies of yeast: analysis of HMG-CoA reductase overproduction by electron microscopy. Methods in cell biology 31, 473–512 (1989)

    Article  CAS  Google Scholar 

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Acknowledgements

We thank R. Tsien, S. Michaelis, J. Glover, C. Enenkel and V. Albanese for reagents; J. Mulholland for electron microscopy and deconvolution microscopy help; S. Yamada and W. J. Nelson for help with the live cell microscopy. We thank R. Andino, W. Burkholder, J. England, R. Geller, M. Kaganovich, E. Bennett, J. Nelson and members of the Frydman laboratory for discussions and comments on the manuscript. This work was supported by grants from NIH to R.K. and J.F.

Author Contributions J.F. directed the project; D.K. and J.F. designed and interpreted all experiments; R.K. participated in the initial fluorescence microscopy experiments; D.K. performed all experiments. D.K. and J.F. wrote the paper.

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Correspondence to Judith Frydman.

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Kaganovich, D., Kopito, R. & Frydman, J. Misfolded proteins partition between two distinct quality control compartments. Nature 454, 1088–1095 (2008). https://doi.org/10.1038/nature07195

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