Chaperone Biology and Protein-folding Diseases

Protein-folding Diseases and Chaperone Biology

We have developed yeast models of protein folding diseases and used them to investigate mechanisms of cytotoxicity and to screen for novel therapeutic targets.

Strong evidence links the misfolding of alpha-synuclein (a-syn ) to Parkinson’s Disease (PD). Cellular toxicity depends on the level of a-syn expression and is associated with cytoplasmic inclusions. Our yeast a-syn overexpression model recapitulates many features of a-syn-related pathology, including the inhibition of phospholipase D, the production of reactive oxygen species, and problems in vesicle trafficking. The earliest defect following a-syn induction in yeast was a block in vesicle trafficking from the endoplasmic reticulum (ER) to the Golgi. To identify relevant biochemical pathways and targets we screened an expression library for genetic enhancers and suppressors of a-syn toxicity. The largest class of toxicity modifiers includes proteins functioning at this same trafficking step, including the Rab GTPase Ypt1p, which is also associated with cytoplasmic a-syn inclusions. Elevated expression of Rab1, the mammalian YPT1 homolog, protects against a-syn-induced dopaminergic neuron loss in whole-animal models of PD, and in cultures of rat midbrain, demonstrating the relevance of results obtained in yeast to mammalian neurons.

MIT TechTV Documentary about our lab's yeast a-synuclein model:
(4 minutes, 53 seconds)

Left: yeast cells expressing one copy of fluorescent green-tagged human alpha-synuclein; Right: yeast cells expressing two copies. Overexpression of alpha-synuclein causes formation of protein foci and kills the cells.

We have expanded our efforts to screen for toxicity enhancers and suppressors in a yeast Huntington’s Disease model expressing human huntingtin exon I. Our work presents a paradigm for how toxicity is the result of the interaction of particular disease-associated proteins with eukaryotic cell biology and not merely a non-specific response to protein misfolding. The specific pathways elucidated by our yeast models provide new targets for therapeutic intervention.

Lindquist discusses her Science paper, "{alpha}-Synuclein Blocks ER-Golgi Traffic and Rab1 Rescues Neuron Loss in Parkinson’s Models," (Abstract) (Reprint) on Morning Edition and Science Friday

Yeast for Thought (HHMI Bulletin)

Folding Proteins, Michael J. Fox and Parkinson's Disease. What do they have in common?
(What a Year! by the Massachusetts Society for Medical Research)

Parkinson's disease process may be curtailed by regenerative processes in yeast, fruit flies
(MIT News Office)

Traffic Report (Whitehead's Paradigm Magazine)

Discovery Offers New Insight Into Parkinson's (New York Times)

Brain 'traffic jams' drive Parkinson's symptoms (Nature)

Parkinson's traits reversed in rat brain cells (New Scientist)

Protecting Neurons from Parkinson's Disease (Technology Review)

Selected Publications on Protein-folding Diseases

Su LJ, Auluck PK, Outeiro TF, Yeger-Lotem E, Kritzer JA, Tardiff DF, Strathearn KE, Liu F,Cao S, Hamamichi S, Hill KJ, Caldwell KA, Bell GW, Fraenkel E, Cooper AA, Caldwell GA, Michael McCaffery JM, Rochet J-C, Lindquist S, 2009. Compounds from an unbiased chemical screen reverse both ER-to-Golgi trafficking defects and mitochondrial dysfunction in Parkinson disease models Dis Model Mech in press.

Kritzer JA, Hamamichi S, McCaffery JM, Santagata S, Naumann TA, Caldwell KA, Caldwell GA, Lindquist S, 2009. Rapid Selection of Cyclic Peptides that Reduce Alpha-Synuclein Toxicity in Yeast and Animal Models. Nat Chem Biol 5(9): 655-63. PMCID: 2729362

Yeger-Lotem E, Riva L, Su LJ, Gitler AD, Cashikar A, King OD, Auluck PK, Geddie ML, Valastyan JS, Karger DR, Lindquist S, Fraenkel E, 2009. Bridging the gap between high-throughput genetic and transcriptional data reveals cellular pathways responding to alpha-synuclein toxicity. Nat Genet, 41(3): 316-23. [PDF 3.1 MB]

Calculating gene and protein connections in a Parkinson's Model (WIBR press release)

Gitler AD, Chesi A, Geddie ML, Strathearn KE, Hamamichi S, Hill KJ, Caldwell KA, Caldwell GA,
Cooper AA, Rochet J-C, Lindquist S, 2009. ?-Synuclein is part of a diverse and highly conserved interaction network that includes PARK9 and manganese toxicity. Nat Genet, 41(3): 308-15. [PDF 2.5 MB]

Study reveals connection between genetic and environmental causes of Parkinson's disease (WIBR press release)
Discovery Of Link Between Parkinson's Disease Genes And Manganese Poisoning (Medical News Today)

Rappley I, Gitler AD, Selvy PE, LaVoie MJ, Levy BD, Brown HA, Lindquist S, Selkoe DJ, 2009. Evidence that alpha-synuclein does not inhibit phospholipase D. Biochemistry, 48(5): 1077-83. [PDF 332 KB]

Duennwald ML, Lindquist S, 2008. Impaired ERAD and ER stress are early and specific events in polyglutamine toxicity. Genes Dev 22(23): 3308-19. [PDF 1 MB]

New clue emerges for cellular damage in Huntington's Disease (WIBR press release)

Lo Bianco C, Shorter J, Régulier E, Lashuel H, Iwatsubo T, Lindquist S, Aebischer P, 2008. Hsp104 Antagonizes a-Synuclein Aggregation and Reduces Dopaminergic Degeneration in a Rat Model of Parkinson’s Disease. J Clin Invest, 118(9): 3087-97. [PDF 1.43 MB]

Johnson BS, McCaffery JM, Lindquist S, Gitler AD, 2008. A yeast TDP-43 proteinopathy model: Exploring the molecular determinants of TDP-43 aggregation and cellular toxicity. PNAS, 105(17): 6439-6444. [PDF 627 KB]

Fleming J, Outiero TF, Slack M, Lindquist SL and Bulawa CE, 2008. Detection of compounds that rescue rab1-synuclein toxicity. Methods Enzymol, 439: 339-51. [PDF 181 KB]

Gitler AD, Bevis BJ, Shorter J, Strathearn KE, Hamamichi S, Su LJ, Caldwell KA, Caldwell GA, Rochet JC, McCaffery JM, Barlowe C and Lindquist S, 2008. The Parkinson’s Disease Protein Alpha-Synuclein Disrupts Cellular Rab Homeostasis. Proc Natl Acad Sci USA 105(1): 145-50. [PDF 832 KB]

Alberti S, Gitler AD and Lindquist S, 2007. A suite of Gateway™ cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae. Yeast 24(10):913-19. [PDF 972 KB]

Cooper AA, Gitler AD, Cashikar A, Haynes CM, Hill KJ, Bhullar B, Liu K, Xu K, Strathearn KE, Liu F, Cao S, Caldwell KA, Caldwell GA, Marsischky G, Kolodner RD, LaBaer J, Rochet J-C, Bonini NM and Lindquist S, 2006. alpha-Synuclein Blocks ER-Golgi Traffic and Rab1 Rescues Neuron Loss in Parkinson’s Models. Science 313(5785): 324-8. [PDF Link]

Duennwald ML, Jagadish S, Muchowski PJ and Lindquist S, 2006. Flanking sequences profoundly alter polyglutamine toxicity in yeast. Proc Natl Acad Sci USA 103(29): 11045-50. [PDF 1.29 MB]

Duennwald ML, Jagadish S, Giorgini F, Muchowski PJ and Lindquist S, 2006. A network of protein interactions determines polyglutamine toxicity. Proc Natl Acad Sci USA103(29): 11051-56. [PDF 1.46 MB]

Outeiro TF and Lindquist S, 2003. Yeast Cells Provide Insight into Alpha-Synuclein Biology and Pathobiology. Science 302:1772-75. [PDF Link]

Krobitsch S and Lindquist S, 2000. 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: 1589-94. [PDF 493 KB]

To obtain reagents described in Cooper et al. (2006) or Outeiro and Lindquist (2003), please download and fill out an MTA from the Request Materials page.

Chaperone Biology and Protein Disaggregation

Heat-shock proteins (Hsps) are molecular chaperones that are induced when organisms are exposed to high temperatures and other stresses. These stresses cause proteins to unfold and potentially aggregate, thereby creating a protein-folding crisis in the cell. Hsp chaperones help the cell cope with this crisis by binding different types of folding intermediates and interacting with them in different ways. One, Hsp104, has a unique ability to promote the disaggregation of aggregated proteins. This biochemical function is in keeping with its biological function: Hsp104 is not required for normal growth but is required for survival under extreme stress. Homologues of Hsp104 have been found in other fungi, bacteria and plants and appear to function in a similar way.

Hsp104 is a member of the important AAA family of proteins. AAA-proteins function to remodel other cellular proteins and thus affect a multitude of biological processes. Their power to remodel substrates lies in their capacity to couple substrate binding to conformational change. Hsp104’s ability to remodel protein structures also plays a critical role in protein conformation-based inheritance. In order to understand how Hsp104 functions in this capacity, we are employing a variety of biochemical and genetic approaches.

Deconstruction of Sup35 prion fibers by Hsp104

Selected Publications on Chaperone Biology

Sénéchal P, Arseneault G, Leroux A, Susan Lindquist S, Rokeach LA, 2009. The Schizosaccharomyces pombe Hsp104 disaggregase is unable to propagate the [PSI+] prion. PLoS ONE 4(9): e6939. PMCID: 2736384

Wendler P, Shorter J, Snead D, Plisson C, Clare DK, Lindquist S, Saibil HR, 2009. Motor mechanism for protein threading through Hsp104. Mol Cell 34(1): 81-92. PMCID: PMC2689388

Beauregard PB, Guérin R, Turcotte C, Lindquist S, Rokeach LA, 2009. A nucleolar protein allows viability in the absence of the essential ER chaperone calnexin. J Cell Sci 122: 1342-1351.

Shorter J, Lindquist S, 2008. Hsp104, Hsp70 and Hsp40 interplay regulates formation, growth and elimination of Sup35 prions. EMBO J 27(20): 2712-24. [PDF 2.1 MB]

Sadlish H, Rampelt H, Shorter J, Wegrzyn RD, Andreasson C, Lindquist S, and Bukau B, 2008. Hsp110 Chaperones Regulate Prion Formation and Propagation in S. cerevisiaeby Two Discrete Activities. PLoS ONE, 3(3): e1763. [PDF 737 KB]

Wang H, Duennwald ML, Roberts BE, Rozeboom LM, Zhang YL, Steele AD, Krishnan R, Su LJ, Griffin D, Mukhopadhyay S, Hennessy EJ, Weigele P, Blanchard BJ, King J, Deniz AA, Buchwald SL, Ingram VM, Lindquist S, Shorter J, 2008. Direct and selective elimination of specific prions and amyloids by 4,5-dianilinophthalimide and analogs. Proc Natl Acad Sci USA 105(20): 7159-64. [PDF 1.37 MB]

Doyle SM, Shorter J, Zolkiewski M, Hoskins JR, Lindquist S, Wickner S, 2007. Asymmetric deceleration of ClpB or Hsp104 ATPase activity unleashes protein- remodeling activity. Nat. Struct. Mol. Biol. 14(2): 114-22. [PDF 480 KB]

Wendler P, Shorter J, Plisson C, Cashikar AG, Lindquist S Saibil HR, 2007. Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104. Cell 131(7): 1366-77. [PDF 1.7 MB]

Shorter J, Lindquist S, 2006. Destruction or potentiation of different prions catalyzed by similar Hsp104 remodeling activities. Mol Cell 23(3): 425-38. [PDF 1.2MB]

Cashikar AG, Duennwald M, Lindquist SL, 2005. A chaperone pathway in protein disaggregation: Hsp26 alters the nature of protein aggregates to facilitate reactivation by hsp104. J Biol Chem 280:23869-75. [PDF 1.2MB]

Shorter J, Lindquist S, 2004. Hsp104 Catalyzes Formation and Elimination of Self-Replicating Sup35 Prion Conformers. Science 304:1793-97. [PD FLink]

Hattendorf DA, Lindquist S, 2002. Cooperative kinetics of both Hsp104 ATPase domains and interdomain communication revealed by AAA sensor-1 mutants. EMBO J21: 12-21.[PDF 344 KB]

Schirmer EC, Ware DM, Queitsch C, Kowal AS, Lindquist S, 2001. Subunit interactions influence the biochemical and biological properties of Hsp104. Proc Natl Acad Sci USA 98: 914-19. [PDF 236 KB]

Queitsch C, Hong S-W, Vierling E, Lindquist S, 2000. Hsp101 plays a crucial role in thermotolerance in Arabidopsis. The Plant Cell 12: 479-92.[PDF 656 KB]

Glover JR, Lindquist S, 1998. Hsp104, Hsp70 and Hsp40: a novel chaperone system that rescues previously aggregated proteins. Cell 94:73-82.

Lindquist S, 1981. Regulation of protein synthesis during heat shock. Nature 293: 311-14. [PDF 852 KB]

McKenzie SL, Henikoff S, Meselson M, 1975. Localization of RNA from heat-induced polysomes at puff sites in Drosophila melanogaster. Proc Natl Acad Sci USA 72: 1117-11. [PDF 2.5 MB]

Who's Working on Protein-folding Diseases and Chaperone Biology

Ambar Mehta Brooke Bevis Chee-Yeun Chung Chris Pacheco Dan Tardiff Dan Termine Gabriela Caraveo Julie Valastyan Kent Matlack Lera Baru Melissa Geddie Pavan Auluck Richard Manfready Vik Khurana Yelena Freyzon