Yeast Chaperone Melts Protein Aggregates

Rejiggered chaperones untangle aggregates and refold mutant proteins associated with amyotrophic lateral sclerosis, frontotemporal dementia, and Parkinson’s disease, according to a paper in the July 25 Disease Models & Mechanisms online. The altered chaperones, variants of heat shock protein 104 (Hsp104), reverse toxicity of mutant α-synuclein, TDP-43, FUS, and TAF15 in yeast cells. “Nothing else is known that can do this,” commented senior author James Shorter of the Perelman School of Medicine at the University of Pennsylvania in Philadelphia, in an email to Alzforum. 

Other experts praised the basic science. “As a proof of principle I think it is very exciting. It means that it may be possible to make designer proteins that can specifically clear pathogenic aggregates without interfering with the normal chaperone mechanisms of the cell,” commented Gregory Petsko of Weill Cornell Medical College, New York. However, Petsko and others found it difficult to envision this specific mechanism translating directly into people, since humans have no Hsp104 homolog. “I would be astounded if it ever became a therapy,” said Petsko.

Shorter and first author Meredith Jackrel selected Hsp104 as a potential aggregate-buster because it was already known to dissolve both amyloid fibrils and soluble oligomers (DeSantis et al., 2012). They used error-prone polymerase chain reaction to randomly sprinkle mutations throughout the Hsp104 gene and screened for variants that allowed yeast to survive TDP-43 toxicity. Jackrel came up with several effective Hsp104 mutants, and earlier this year she reported that they destroyed aggregates of wild-type TDP-43, FUS, and α-synuclein (Jackrel et al., 2014). Wild-type Hsp104, in contrast, does not disassemble those protein aggregates. The authors continue to combine and shuffle the individual mutations to figure out which create the ideal disaggregase. Different variants may work best for different target aggregates, they suspect. “There is no one ‘best’ variant yet,” Shorter explained.

Because mutations in TDP-43, FUS, or α-synuclein cause a range of inherited neurodegenerative diseases, Shorter and Jackrel tested Hsp104 variants against these mutant proteins, as they report in the current manuscript. They co-expressed eight different Hsp104 versions, individually, with one of three TDP-43 variants, two FUS variants, and two α-synuclein variants. Jackrel linked the transgenes to a promoter activated by galactose and tested how well each double-mutant strain grew on galactose medium. While the mutant TDP-43, FUS, and α-synuclein alone were toxic to the yeast, also expressing the Hsp104 variants allowed the cells to survive. In addition, Jackrel observed via fluorescence microscopy that aggregates of the toxic proteins dissolved in strains that co-expressed Hsp104 variants alanine-503-valine (A503V) or valine-426-leucine, but not wild-type Hsp104 (see image).

Yeast expressing mutant FUS and wild-type Hsp104 contains FUS aggregates (green, left), which disappeared in the presence of an Hsp104 variant (right). [Image courtesy of Jackrel and Shorter, 2014.]

Next, Jackrel tested the Hsp104 disaggregases against FUS’ close relatives, TAF15 and EWS. Mutations in these proteins have also been linked to ALS and FTD, and they aggregate in patient tissues or model systems (Couthouis et al., 2012; Couthouis et al., 2012). An Hsp104 A503S variant worked against TAF15, but none of the Hsp104 variants worked on EWS. In fact, several of the modified chaperones made EWS more toxic. “We suspect that for [EWS], the Hsp104 variants exacerbate the misfolding rather than reverse it,” Shorter wrote. “We do not understand why.” The results indicate that the Hsp104 variants are not general disaggregates attacking any unfolded protein, but possess some substrate specificity.

How do the chaperone variants select their substrates, then? To investigate this, Jackrel used purified Hsp104 to unfold green fluorescent protein (GFP) until it had lost its fluorescence. She attached six histidine residues to the GFP to act as a short, unfolded hook onto which the chaperone could latch. Wild-type Hsp104 unfolded GFP a little, but the A503V variant unraveled it more. Neither wild-type nor variant Hsp104 disassembled GFP if the histidine tag was missing. “Hsp104-A503V is a more powerful unfoldase that recognizes even very short unfolded regions of substrates with greater precision than Hsp104 wild type,” the authors wrote.

Aaron Gitler of Stanford University in Palo Alto, California, who was not involved in the study, commented that these findings will help the authors develop Hsp104 variants that are specific for different substrates, such as TDP-43 or FUS. Should this evolve into a clinical treatment, doctors would want to avoid harming natural, beneficial amyloids, he noted.

“We have uncovered a powerful biochemical activity to reverse protein misfolding," Shorter wrote to Alzforum. "The challenge is to get it to where it is needed in human disease.” Dagmar Ringe of Brandeis University agreed. “I think it is a phenomenal study. It is amazing that you can take a heat shock protein and tailor it to recognize different proteins,” she said. “My concern is, how do you get from there to the clinic?” The altered chaperones would have to reach the nervous system, which is not easy, she noted.

Shorter and colleagues are testing their variants in nematodes, fruit flies, mice, and rats. In the previous study, Jackrel expressed the Hsp104 variants in a Caenorhabditis elegans model of Parkinson’s; that removed wild-type α-synuclein from aggregates, put it back where it belonged, and protected dopaminergic neurons. Wild-type Hsp104 minimized aggregates and protected neurons in a rat model of PD (Lo Bianco et al., 2008).

Shorter plans to tweak human chaperones to coax disaggregase activity against specific disease proteins. As potential therapeutic strategies, he suggested gene delivery by a virus, or direct injection of protein into the brain for transient disaggregation and to avoid off-target effects of an immune response to the yeast protein.—Amber Dance

Comments

  1. This manuscript by Jackrel and Shorter is an extension of the tour de force Cell paper published by these authors earlier this year (Jackrel et al., 2014). In that manuscript, they engineered the protein disaggregase Hsp104,which normally has no activity against neurodegenerative disease associated amyloid aggregates, to possess a remarkable ability to attack diverse human disease protein aggregates, including α-synuclein, TDP-43, and FUS. These enhanced Hsp104 variants now open up the possibility for harnessing Hsp104’s protein disaggregase function as a therapeutic approach.

    This manuscript represents an important extension to the previous work because it makes three critical advances:

    It demonstrates that the enhanced Hsp104 variants also possess disaggregase activity against the disease-linked mutant versions of the disease proteins α-synuclein, TDP-43, FUS, and TAF15. Since these mutants enhance aggregation of the proteins, it was possible that Hsp104 would not be able to disaggregate them. But now the authors report that their enhanced-activity Hsp104 variants do indeed function robustly against these mutants.

    Secondly, they report that enhanced Hsp104 variants do not suppress aggregation or toxicity of EWSR1, a FUS-related protein linked to ALS and FTLD. This is intriguing given the similarity of EWSR1 and FUS. The finding indicates that these Hsp104 variants possess some substrate specificity. This point was not clear from the original manuscript.

    Lastly, the authors now provide in vitro studies to show mechanistically how Hsp104 recognizes substrates and how their enhanced variants do so differently. These findings are important because they represent a path forward to understanding how the variants might be harnessed to become more substrate-specific (e.g., to only work on certain disease proteins).
     

    References:

    Jackrel ME, DeSantis ME, Martinez BA, Castellano LM, Stewart RM, Caldwell KA, Caldwell GA, Shorter J. Potentiated Hsp104 variants antagonize diverse proteotoxic misfolding events. Cell. 2014 Jan 16;156(1-2):170-82. PubMed.

    View all comments by Aaron Gitler

  2. The new findings by Jackrel and Shorter are an important and exciting extension of their previous work published earlier this year. They had previously engineered a variant of Hsp104 to reverse aggregation of misfolded proteins associated with Parkinson's disease and ALS, including synuclein and RNA-binding protein TDP43. Their new findings show that the potentiated Hsp104 can, in fact, reverse aggregation of a broader array of disease proteins, including mutant forms of RNA-binding proteins. These findings show the broad utility of potentiated Hsp104. More importantly, they show that potentiated Hsp104 can correct the mislocalization of mutant TDP43 and FUS and retarget these proteins back to the nucleus where they belong. Mislocalization of these proteins has previously been shown by the Finkbeiner lab to be a tight predictor of their toxicity and, consistent with that, Jackrel and Shorter find that potentiated Hsp104 reduces toxicity of these proteins in yeast and worm models of disease. It will be exciting to see how potentiated Hsp104 behaves in other models of neurodegeneration, including iPS cell-derived neurons from patients who carry mutations in these genes and also sporadic ALS patients who do not carry these known mutations. Their engineered Hsp104 has great therapeutic potential for many neurodegenerative diseases, although many challenges still remain, including a mechanism for delivery.

    View all comments by Ashkan Javaherian

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References

Paper Citations

  1. DeSantis ME, Leung EH, Sweeny EA, Jackrel ME, Cushman-Nick M, Neuhaus-Follini A, Vashist S, Sochor MA, Knight MN, Shorter J. Operational plasticity enables hsp104 to disaggregate diverse amyloid and nonamyloid clients. Cell. 2012 Nov 9;151(4):778-93. PubMed.
  2. Jackrel ME, DeSantis ME, Martinez BA, Castellano LM, Stewart RM, Caldwell KA, Caldwell GA, Shorter J. Potentiated Hsp104 variants antagonize diverse proteotoxic misfolding events. Cell. 2014 Jan 16;156(1-2):170-82. PubMed.
  3. Couthouis J, Hart MP, Shorter J, Dejesus-Hernandez M, Erion R, Oristano R, Liu AX, Ramos D, Jethava N, Hosangadi D, Epstein J, Chiang A, Diaz Z, Nakaya T, Ibrahim F, Kim HJ, Solski JA, Williams KL, Mojsilovic-Petrovic J, Ingre C, Boylan K, Graff-Radford NR, Dickson DW, Clay-Falcone D, Elman L, McCluskey L, Greene R, Kalb RG, Lee VM, Trojanowski JQ, Ludolph A, Robberecht W, Andersen PM, Nicholson GA, Blair IP, King OD, Bonini NM, Van Deerlin V, Rademakers R, Mourelatos Z, Gitler AD. Feature Article: From the Cover: A yeast functional screen predicts new candidate ALS disease genes. Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):20881-90. PubMed. Correction.
  4. Couthouis J, Hart MP, Erion R, King OD, Diaz Z, Nakaya T, Ibrahim F, Kim HJ, Mojsilovic-Petrovic J, Panossian S, Kim CE, Frackelton EC, Solski JA, Williams KL, Clay-Falcone D, Elman L, McCluskey L, Greene R, Hakonarson H, Kalb RG, Lee VM, Trojanowski JQ, Nicholson GA, Blair IP, Bonini NM, Van Deerlin VM, Mourelatos Z, Shorter J, Gitler AD. Evaluating the role of the FUS/TLS-related gene EWSR1 in amyotrophic lateral sclerosis. Hum Mol Genet. 2012 Jul 1;21(13):2899-911. Epub 2012 Mar 27 PubMed.
  5. Lo Bianco C, Shorter J, Régulier E, Lashuel H, Iwatsubo T, Lindquist S, Aebischer P. Hsp104 antagonizes alpha-synuclein aggregation and reduces dopaminergic degeneration in a rat model of Parkinson disease. J Clin Invest. 2008 Sep;118(9):3087-97. PubMed.

External Citations

  1. TDP-43
  2. FUS
  3. TAF15
  4. EWS

Further Reading

Papers

  1. Jackrel ME, Shorter J. Reversing deleterious protein aggregation with re-engineered protein disaggregases. Cell Cycle. 2014 May 1;13(9):1379-83. Epub 2014 Apr 2 PubMed.
  2. King OD, Gitler AD, Shorter J. The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease. Brain Res. 2012 Jun 26;1462:61-80. Epub 2012 Jan 21 PubMed.
  3. Kim Y, Park JH, Jang JY, Rhim H, Kang S. Characterization and Hsp104-induced artificial clearance of familial ALS-related SOD1 aggregates. Biochem Biophys Res Commun. 2013 May 10;434(3):521-6. PubMed.
  4. Helsen CW, Glover JR. Insight into molecular basis of curing of [PSI+] prion by overexpression of 104-kDa heat shock protein (Hsp104). J Biol Chem. 2012 Jan 2;287(1):542-56. PubMed.
  5. Sweeny EA, Desantis ME, Shorter J. Purification of hsp104, a protein disaggregase. J Vis Exp. 2011;(55) PubMed.
  6. Doyle SM, Genest O, Wickner S. Protein rescue from aggregates by powerful molecular chaperone machines. Nat Rev Mol Cell Biol. 2013 Oct;14(10):617-29. PubMed.

Primary Papers

  1. Jackrel ME, Shorter J. Potentiated Hsp104 variants suppress toxicity of diverse neurodegenerative disease-linked proteins. Dis Model Mech. 2014 Oct;7(10):1175-84. Epub 2014 Jul 25 PubMed.

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