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Lin J, Carman PJ, Gambogi CW, Kendsersky NM, Chuang E, Gates SN, Yokom AL, Rizo AN, Southworth DR, Shorter J. Design principles to tailor Hsp104 therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591398. [PMID: 38712168 PMCID: PMC11071516 DOI: 10.1101/2024.04.26.591398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The hexameric AAA+ disaggregase, Hsp104, collaborates with Hsp70 and Hsp40 via its autoregulatory middle domain (MD) to solubilize aggregated protein conformers. However, how ATP- or ADP-specific MD configurations regulate Hsp104 hexamers remains poorly understood. Here, we define an ATP-specific network of interprotomer contacts between nucleotide-binding domain 1 (NBD1) and MD helix L1, which tunes Hsp70 collaboration. Manipulating this network can: (a) reduce Hsp70 collaboration without enhancing activity; (b) generate Hsp104 hypomorphs that collaborate selectively with class B Hsp40s; (c) produce Hsp70-independent potentiated variants; or (d) create species barriers between Hsp104 and Hsp70. Conversely, ADP-specific intraprotomer contacts between MD helix L2 and NBD1 restrict activity, and their perturbation frequently potentiates Hsp104. Importantly, adjusting the NBD1:MD helix L1 rheostat via rational design enables finely tuned collaboration with Hsp70 to safely potentiate Hsp104, minimize off-target toxicity, and counteract FUS proteinopathy in human cells. Thus, we establish important design principles to tailor Hsp104 therapeutics.
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Affiliation(s)
- JiaBei Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Peter J. Carman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Craig W. Gambogi
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Nathan M. Kendsersky
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Edward Chuang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Stephanie N. Gates
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
- Current address: Department of Biochemistry, University of Missouri, Columbia, MO 65211. U.S.A
| | - Adam L. Yokom
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
- Current address: Department of Biochemistry, University of Missouri, Columbia, MO 65211. U.S.A
| | - Alexandrea N. Rizo
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
| | - Daniel R. Southworth
- Department of Biochemistry and Biophysics and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158. U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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Ribes JM, Patel MP, Halim HA, Berretta A, Tooze SA, Klöhn PC. Prion protein conversion at two distinct cellular sites precedes fibrillisation. Nat Commun 2023; 14:8354. [PMID: 38102121 PMCID: PMC10724300 DOI: 10.1038/s41467-023-43961-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
The self-templating nature of prions plays a central role in prion pathogenesis and is associated with infectivity and transmissibility. Since propagation of proteopathic seeds has now been acknowledged a principal pathogenic process in many types of dementia, more insight into the molecular mechanism of prion replication is vital to delineate specific and common disease pathways. By employing highly discriminatory anti-PrP antibodies and conversion-tolerant PrP chimera, we here report that de novo PrP conversion and formation of fibril-like PrP aggregates are distinct in mechanistic and kinetic terms. De novo PrP conversion occurs within minutes after infection at two subcellular locations, while fibril-like PrP aggregates are formed exclusively at the plasma membrane, hours after infection. Phenotypically distinct pools of abnormal PrP at perinuclear sites and the plasma membrane show differences in N-terminal processing, aggregation state and fibril formation and are linked by exocytic transport via synaptic and large-dense core vesicles.
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Affiliation(s)
- Juan Manuel Ribes
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, W1W 7FF, UK
| | - Mitali P Patel
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, W1W 7FF, UK
| | - Hazim A Halim
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, W1W 7FF, UK
| | - Antonio Berretta
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, W1W 7FF, UK
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Laboratory, the Francis Crick Institute, London, NW1 1BF, UK
| | - Peter-Christian Klöhn
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, W1W 7FF, UK.
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Elsana H, Bruck‐Haimson R, Zhu H, Siddiqui AA, Zaretsky A, Cohen I, Boocholez H, Roitenberg N, Moll L, Plaschkes I, Naor D, Cohen E. A short peptide protects from age-onset proteotoxicity. Aging Cell 2023; 22:e14013. [PMID: 37897137 PMCID: PMC10726816 DOI: 10.1111/acel.14013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/08/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Aberrant protein aggregation jeopardizes cellular functionality and underlies the development of a myriad of late-onset maladies including Alzheimer's disease (AD) and Huntington's disease (HD). Accordingly, molecules that mitigate the toxicity of hazardous protein aggregates are of great interest as potential future therapeutics. Here we asked whether a small peptide, composed of five amino acids (5MER peptide) that was derived from the human pro-inflammatory CD44 protein, could protect model nematodes from the toxicity of aggregative proteins that underlie the development of neurodegenerative disorders in humans. We found that the 5MER peptide mitigates the toxicity that stems from both; the AD-causing Aβ peptide and a stretch of poly-glutamine that is accountable for the development of several disorders including HD, while minimally affecting lifespan. This protection was dependent on the activity of aging-regulating transcription factors and associated with enhanced Aβ and polyQ35-YFP aggregation. A transcriptomic analysis unveiled that the peptide modifies signaling pathways, thereby modulating the expression of various genes, including these, which are known as protein homeostasis (proteostasis) regulators such as txt-13 and modifiers of proteasome activity. The knockdown of txt-13 protects worms from proteotoxicity to the same extent as the 5MER peptide, suggesting that the peptide activates the transcellular chaperone signaling to promote proteostasis. Together, our results propose that the 5MER peptide should be considered as a component of future therapeutic cocktails for the treatment of neurodegenerative maladies.
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Affiliation(s)
- Hassan Elsana
- The Lautenberg Center of Immunology and Cancer ResearchThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Reut Bruck‐Haimson
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Huadong Zhu
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Atif Ahmed Siddiqui
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Adam Zaretsky
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Irit Cohen
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Hana Boocholez
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Noa Roitenberg
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Lorna Moll
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Inbar Plaschkes
- Info‐COREBioinformatics Unit of the I‐CORE, The Hebrew UniversityJerusalemIsrael
| | - David Naor
- The Lautenberg Center of Immunology and Cancer ResearchThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Ehud Cohen
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
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Ghosh S, Tugarinov V, Clore GM. Quantitative NMR analysis of the mechanism and kinetics of chaperone Hsp104 action on amyloid-β42 aggregation and fibril formation. Proc Natl Acad Sci U S A 2023; 120:e2305823120. [PMID: 37186848 PMCID: PMC10214214 DOI: 10.1073/pnas.2305823120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
The chaperone Hsp104, a member of the Hsp100/Clp family of translocases, prevents fibril formation of a variety of amyloidogenic peptides in a paradoxically substoichiometric manner. To understand the mechanism whereby Hsp104 inhibits fibril formation, we probed the interaction of Hsp104 with the Alzheimer's amyloid-β42 (Aβ42) peptide using a variety of biophysical techniques. Hsp104 is highly effective at suppressing the formation of Thioflavin T (ThT) reactive mature fibrils that are readily observed by atomic force (AFM) and electron (EM) microscopies. Quantitative kinetic analysis and global fitting was performed on serially recorded 1H-15N correlation spectra to monitor the disappearance of Aβ42 monomers during the course of aggregation over a wide range of Hsp104 concentrations. Under the conditions employed (50 μM Aβ42 at 20 °C), Aβ42 aggregation occurs by a branching mechanism: an irreversible on-pathway leading to mature fibrils that entails primary and secondary nucleation and saturating elongation; and a reversible off-pathway to form nonfibrillar oligomers, unreactive to ThT and too large to be observed directly by NMR, but too small to be visualized by AFM or EM. Hsp104 binds reversibly with nanomolar affinity to sparsely populated Aβ42 nuclei present in nanomolar concentrations, generated by primary and secondary nucleation, thereby completely inhibiting on-pathway fibril formation at substoichiometric ratios of Hsp104 to Aβ42 monomers. Tight binding to sparsely populated nuclei likely constitutes a general mechanism for substoichiometric inhibition of fibrillization by a variety of chaperones. Hsp104 also impacts off-pathway oligomerization but to a much smaller degree initially reducing and then increasing the rate of off-pathway oligomerization.
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Affiliation(s)
- Shreya Ghosh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
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Zhao X, Stanford K, Ahearn J, Masison DC, Greene LE. Hsp70 Binding to the N-terminal Domain of Hsp104 Regulates [ PSI+] Curing by Hsp104 Overexpression. Mol Cell Biol 2023; 43:157-173. [PMID: 37099734 PMCID: PMC10153015 DOI: 10.1080/10985549.2023.2198181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 04/28/2023] Open
Abstract
Hsp104 propagates the yeast prion [PSI+], the infectious form of Sup35, by severing the prion seeds, but when Hsp104 is overexpressed, it cures [PSI+] in a process that is not yet understood but may be caused by trimming, which removes monomers from the ends of the amyloid fibers. This curing was shown to depend on both the N-terminal domain of Hsp104 and the expression level of various members of the Hsp70 family, which raises the question as to whether these effects of Hsp70 are due to it binding to the Hsp70 binding site that was identified in the N-terminal domain of Hsp104, a site not involved in prion propagation. Investigating this question, we now find, first, that mutating this site prevents both the curing of [PSI+] by Hsp104 overexpression and the trimming activity of Hsp104. Second, we find that depending on the specific member of the Hsp70 family binding to the N-terminal domain of Hsp104, both trimming and the curing caused by Hsp104 overexpression are either increased or decreased in parallel. Therefore, the binding of Hsp70 to the N-terminal domain of Hsp104 regulates both the rate of [PSI+] trimming by Hsp104 and the rate of [PSI+] curing by Hsp104 overexpression.
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Affiliation(s)
- Xiaohong Zhao
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Katherine Stanford
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph Ahearn
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniel C. Masison
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lois E. Greene
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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Mahapatra S, Sarbahi A, Punia N, Joshi A, Avni A, Walimbe A, Mukhopadhyay S. ATP modulates self-perpetuating conformational conversion generating structurally distinct yeast prion amyloids that limit autocatalytic amplification. J Biol Chem 2023; 299:104654. [PMID: 36990219 PMCID: PMC10149227 DOI: 10.1016/j.jbc.2023.104654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/07/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Prion-like self-perpetuating conformational conversion of proteins into amyloid aggregates is associated with both transmissible neurodegenerative diseases and non-Mendelian inheritance. The cellular energy currency ATP is known to indirectly regulate the formation, dissolution, or transmission of amyloid-like aggregates by providing energy to the molecular chaperones that maintain protein homeostasis. In this work, we demonstrate that ATP molecules, independent of any chaperones, modulate the formation and dissolution of amyloids from a yeast prion domain (NM domain of Saccharomyces cerevisiae Sup35) and restricts autocatalytic amplification by controlling the amount of fragmentable and seeding-competent aggregates. ATP, at (high) physiological concentrations in the presence of Mg2+, kinetically accelerates NM aggregation. Interestingly, ATP also promotes phase-separation-mediated aggregation of a human protein harboring a yeast prion-like domain. We also show that ATP disaggregates preformed NM fibrils in a dose-independent manner. Our results indicate that ATP-mediated disaggregation, unlike the disaggregation by the disaggregase Hsp104, yields no oligomers that are considered one of the critical species for amyloid transmission. Furthermore, high concentrations of ATP delimited the number of seeds by giving rise to compact, ATP-bound NM fibrils that exhibited nominal fragmentation by either free ATP or Hsp104 disaggregase to generate lower molecular weight amyloids. Additionally, (low) pathologically relevant ATP concentrations restricted autocatalytic amplification by forming structurally distinct amyloids which are found seeding-inefficient due to their reduced β-content. Our results provide key mechanistic underpinnings of concentration-dependent chemical chaperoning by ATP against prion-like transmissions of amyloids.
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Affiliation(s)
- Sayanta Mahapatra
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
| | - Anusha Sarbahi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Neha Punia
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Anamika Avni
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Anuja Walimbe
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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Asgarkhani L, Khandakar I, Pakan R, Swayne TC, Emtage L. Threshold inclusion size triggers conversion of huntingtin to prion-like state that is reversible in newly born cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528394. [PMID: 36824970 PMCID: PMC9949074 DOI: 10.1101/2023.02.13.528394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Aggregation of mutant Huntingtin protein (mHtt) leads to neuronal cell death and human disease. We investigated the effect of inclusion formation on yeast cells. Previous work indicates that mHtt protein moves both in and out of inclusions, potentially undergoing refolding in the inclusion. However, the sustained influx of unfolded protein into an inclusion leads to a dramatic change from a phase-separated body to an irregular, less soluble form at a threshold inclusion size. Altered morphology was associated with a prion-like seeding that accelerated inclusion growth despite loss of soluble cytoplasmic protein. The structural change abolished exchange of material between the inclusion and the cytosol and resulted in early cell death. Affected cells continued to divide occasionally, giving rise to daughters with a similar phenotype. Most newly born cells were able to reverse the prion-like aggregation, restoring both soluble cytoplasmic protein and a normal inclusion structure.
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Knier AS, Davis EE, Buchholz HE, Dorweiler JE, Flannagan LE, Manogaran AL. The yeast molecular chaperone, Hsp104, influences transthyretin aggregate formation. Front Mol Neurosci 2022; 15:1050472. [PMID: 36590917 PMCID: PMC9802906 DOI: 10.3389/fnmol.2022.1050472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/19/2022] [Indexed: 12/23/2022] Open
Abstract
Patients with the fatal disorder Transthyretin Amyloidosis (ATTR) experience polyneuropathy through the progressive destruction of peripheral nervous tissue. In these patients, the transthyretin (TTR) protein dissociates from its functional tetrameric structure, misfolds, and aggregates into extracellular amyloid deposits that are associated with disease progression. These aggregates form large fibrillar structures as well as shorter oligomeric aggregates that are suspected to be cytotoxic. Several studies have shown that these extracellular TTR aggregates enter the cell and accumulate intracellularly, which is associated with increased proteostasis response. However, there are limited experimental models to study how proteostasis influences internalized TTR aggregates. Here, we use a humanized yeast system to recapitulate intracellular TTR aggregating protein in vivo. The yeast molecular chaperone Hsp104 is a disaggregase that has been shown to fragment amyloidogenic aggregates associated with certain yeast prions and reduce protein aggregation associated with human neurogenerative diseases. In yeast, we found that TTR forms both SDS-resistant oligomers and SDS-sensitive large molecular weight complexes. In actively dividing cultures, Hsp104 has no impact on oligomeric or large aggregate populations, yet overexpression of Hsp104 is loosely associated with an increase in overall aggregate size. Interestingly, a potentiating mutation in the middle domain of Hsp104 consistently results in an increase in overall TTR aggregate size. These data suggest a novel approach to aggregate management, where the Hsp104 variant shifts aggregate populations away from toxic oligomeric species to more inert larger aggregates. In aged cultures Hsp104 overexpression has no impact on TTR aggregation profiles suggesting that these chaperone approaches to shift aggregate populations are not effective with age, possibly due to proteostasis decline.
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10
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Phase separation and other forms of α-Synuclein self-assemblies. Essays Biochem 2022; 66:987-1000. [DOI: 10.1042/ebc20220055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022]
Abstract
Abstract
α-Synuclein (α-Syn) is a natively unstructured protein, which self-assembles into higher-order aggregates possessing serious pathophysiological implications. α-Syn aberrantly self-assembles into protein aggregates, which have been widely implicated in Parkinson’s disease (PD) pathogenesis and other synucleinopathies. The self-assembly of α-Syn involves the structural conversion of soluble monomeric protein into oligomeric intermediates and eventually fibrillar aggregates of amyloids with cross-β-sheet rich conformation. These aggregated α-Syn species majorly constitute the intraneuronal inclusions, which is a hallmark of PD neuropathology. Self-assembly/aggregation of α-Syn is not a single-state conversion process as unfolded protein can access multiple conformational states through the formation of metastable, transient pre-fibrillar intermediate species. Recent studies have indicated that soluble oligomers are the potential neurotoxic species responsible for cell death in PD pathogenesis. The heterogeneous and transient nature of oligomers formed during the early stage of aggregation pathway limit their detailed study in understanding the structure–toxicity relationship. Moreover, the precise molecular events occurring in the early stage of α-Syn aggregation process majorly remain unsolved. Recently, liquid–liquid phase separation (LLPS) of α-Syn has been designated as an alternate nucleation mechanism, which occurs in the early lag phase of the aggregation pathway leading to the formation of dynamic supramolecular assemblies. The stronger self-association among the protein molecules triggers the irreversible liquid-to-solid transition of these supramolecular assemblies into the amyloid-like hydrogel, which may serve as a reservoir entrapping toxic oligomeric intermediates and fibrils. This review strives to provide insights into different modes of α-Syn self-assemblies including LLPS-mediated self-assembly and its recent advancements.
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11
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Differential contributions of the proteasome, autophagy, and chaperones to the clearance of arsenite-induced protein aggregates in yeast. J Biol Chem 2022; 298:102680. [PMID: 36356902 PMCID: PMC9723941 DOI: 10.1016/j.jbc.2022.102680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
The poisonous metalloid arsenite induces widespread misfolding and aggregation of nascent proteins in vivo, and this mode of toxic action might underlie its suspected role in the pathology of certain protein misfolding diseases. Evolutionarily conserved protein quality-control systems protect cells against arsenite-mediated proteotoxicity, and herein, we systematically assessed the contribution of the ubiquitin-proteasome system, the autophagy-vacuole pathway, and chaperone-mediated disaggregation to the clearance of arsenite-induced protein aggregates in Saccharomyces cerevisiae. We show that the ubiquitin-proteasome system is the main pathway that clears aggregates formed during arsenite stress and that cells depend on this pathway for optimal growth. The autophagy-vacuole pathway and chaperone-mediated disaggregation both contribute to clearance, but their roles appear less prominent than the ubiquitin-proteasome system. Our in vitro assays with purified components of the yeast disaggregating machinery demonstrated that chaperone binding to aggregates formed in the presence of arsenite is impaired. Hsp104 and Hsp70 chaperone activity was unaffected by arsenite, suggesting that this metalloid influences aggregate structure, making them less accessible for chaperone-mediated disaggregation. We further show that the defect in chaperone-mediated refolding of a model protein was abrogated in a cysteine-free version of the substrate, suggesting that arsenite directly modifies cysteines in non-native target proteins. In conclusion, our study sheds novel light on the differential contributions of protein quality-control systems to aggregate clearance and cell proliferation and extends our understanding of how these systems operate during arsenite stress.
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12
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Buell AK. Stability matters, too - the thermodynamics of amyloid fibril formation. Chem Sci 2022; 13:10177-10192. [PMID: 36277637 PMCID: PMC9473512 DOI: 10.1039/d1sc06782f] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/30/2022] [Indexed: 12/26/2022] Open
Abstract
Amyloid fibrils are supramolecular homopolymers of proteins that play important roles in biological functions and disease. These objects have received an exponential increase in attention during the last few decades, due to their role in the aetiology of a range of severe disorders, most notably some of a neurodegenerative nature. While an overwhelming number of experimental studies exist that investigate how, and how fast, amyloid fibrils form and how their formation can be inhibited, a much more limited body of experimental work attempts to answer the question as to why these types of structures form (i.e. the thermodynamic driving force) and how stable they actually are. In this review, I attempt to give an overview of the types of experiments that have been performed to-date to answer these questions, and to summarise our current understanding of amyloid thermodynamics.
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Affiliation(s)
- Alexander K Buell
- Technical University of Denmark, Department of Biotechnology and Biomedicine Søltofts Plads, Building 227 2800 Kgs. Lyngby Denmark
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13
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Sakunthala A, Datta D, Navalkar A, Gadhe L, Kadu P, Patel K, Mehra S, Kumar R, Chatterjee D, Devi J, Sengupta K, Padinhateeri R, Maji SK. Direct Demonstration of Seed Size-Dependent α-Synuclein Amyloid Amplification. J Phys Chem Lett 2022; 13:6427-6438. [PMID: 35816132 DOI: 10.1021/acs.jpclett.2c01650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The size of amyloid seeds is known to modulate their autocatalytic amplification and cellular toxicity. However, the seed size-dependent secondary nucleation mechanism, toxicity, and disease-associated biological processes mediated by α-synuclein (α-Syn) fibrils are largely unknown. Using the cellular model and in vitro reconstitution, we showed that the size of α-Syn fibril seeds dictates not only their cellular internalization and associated cell death but also the distinct mechanisms of fibril amplification pathways involved in the pathological conformational change of α-Syn. Specifically, small fibril seeds showed elongation possibly through monomer addition at the fibril termini, whereas longer fibrils template the fibril amplification by surface-mediated nucleation as demonstrated by super-resolution microscopy. The distinct mechanism of fibril amplification and cellular uptake along with toxicity suggest that breakage of fibrils into seeds of different sizes determines the underlying pathological outcome of synucleinopathies.
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Affiliation(s)
- Arunima Sakunthala
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Debdeep Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Jyoti Devi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Kundan Sengupta
- Chromosome Biology Lab, Indian Institute of Science Education and Research, Pune 411008, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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14
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Dorweiler JE, Lyke DR, Lemoine NP, Guereca S, Buchholz HE, Legan ER, Radtke CM, Manogaran AL. Implications of the Actin Cytoskeleton on the Multi-Step Process of [PSI+] Prion Formation. Viruses 2022; 14:v14071581. [PMID: 35891561 PMCID: PMC9321047 DOI: 10.3390/v14071581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/27/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022] Open
Abstract
Yeast prions are self-perpetuating misfolded proteins that are infectious. In yeast, [PSI+] is the prion form of the Sup35 protein. While the study of [PSI+] has revealed important cellular mechanisms that contribute to prion propagation, the underlying cellular factors that influence prion formation are not well understood. Prion formation has been described as a multi-step process involving both the initial nucleation and growth of aggregates, followed by the subsequent transmission of prion particles to daughter cells. Prior evidence suggests that actin plays a role in this multi-step process, but actin’s precise role is unclear. Here, we investigate how actin influences the cell’s ability to manage newly formed visible aggregates and how actin influences the transmission of newly formed aggregates to future generations. At early steps, using 3D time-lapse microscopy, several actin mutants, and Markov modeling, we find that the movement of newly formed aggregates is random and actin independent. At later steps, our prion induction studies provide evidence that the transmission of newly formed prion particles to daughter cells is limited by the actin cytoskeletal network. We suspect that this limitation is because actin is used to possibly retain prion particles in the mother cell.
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Affiliation(s)
- Jane E. Dorweiler
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Douglas R. Lyke
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Nathan P. Lemoine
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI 53233, USA
| | - Samantha Guereca
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Hannah E. Buchholz
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Emily R. Legan
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Claire M. Radtke
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
| | - Anita L. Manogaran
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA; (J.E.D.); (D.R.L.); (N.P.L.); (S.G.); (H.E.B.); (E.R.L.); (C.M.R.)
- Correspondence:
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15
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Wang M, Wang X, Cheng Z. Heterologous overexpression of Sup35 in Escherichia coli leads to both monomer and complex states. Proteins 2022; 90:1468-1473. [PMID: 35194850 DOI: 10.1002/prot.26327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 11/08/2022]
Abstract
The heterologous overexpression states of prion proteins play a critical role in understanding the mechanisms of prion-related diseases. We report herein the identification of soluble monomer and complex states for a bakers' yeast prion, Sup35, when expressed in Escherichia coli. Two peaks are apparent with the elution of His-tagged Sup35 by imidazole from a Ni2+ affinity column. Peak I contains Sup35 in both monomer and aggregated states. Sup35 aggregate is abbreviated as C-aggregate and includes a non-fibril complex comprising Sup35 aggregate-HSP90-Dna K, ATP synthase β unit (chain D), 30S ribosome subunit, and Omp F. The purified monomer and C-aggregate can remain stable for an extended period of time. Peak II contains Sup35 also in both monomer and aggregated (abbreviated as S-aggregate) states, but the aggregated states are caused by the formation of inter-Sup35 disulfide bonds. This study demonstrates that further assembly of Sup35 non-fibril C-aggregate can be interrupted by the chaperone repertoire system in E. coli.
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Affiliation(s)
- Mingyang Wang
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Xiao Wang
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Zhenyun Cheng
- Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Clinical Laboratory of Henan Province, Zhengzhou, China
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16
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Mahapatra S, Sarbahi A, Madhu P, Swasthi HM, Sharma A, Singh P, Mukhopadhyay S. Sub-stoichiometric Hsp104 regulates the genesis and persistence of self-replicable amyloid seeds of Sup35 prion domain. J Biol Chem 2022; 298:102143. [PMID: 35714774 PMCID: PMC9304785 DOI: 10.1016/j.jbc.2022.102143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/21/2022] Open
Abstract
Prion-like self-perpetuating conformational conversion of proteins is involved in both transmissible neurodegenerative diseases in mammals and non-Mendelian inheritance in yeast. The transmissibility of amyloid-like aggregates is dependent on the stoichiometry of chaperones such as heat shock proteins (Hsps), including disaggregases. To provide the mechanistic underpinnings of the formation and persistence of prefibrillar amyloid seeds, we investigated the role of substoichiometric Hsp104 on the in vitro amyloid aggregation of the prion domain (NM-domain) of Saccharomyces cerevisiae Sup35. At low substoichiometric concentrations, we show Hsp104 exhibits a dual role: it considerably accelerates the formation of prefibrillar species by shortening the lag phase but also prolongs their persistence by introducing unusual kinetic halts and delaying their conversion into mature amyloid fibers. Additionally, Hsp104-modulated amyloid species displayed a better seeding capability compared to NM-only amyloids. Using biochemical and biophysical tools coupled with site-specific dynamic readouts, we characterized the distinct structural and dynamical signatures of these amyloids. We reveal that Hsp104-remodeled amyloidogenic species are compositionally diverse in prefibrillar aggregates and are packed in a more ordered fashion compared to NM-only amyloids. Finally, we show these Hsp104-remodeled, conformationally distinct NM aggregates display an enhanced autocatalytic self-templating ability that might be crucial for phenotypic outcomes. Taken together, our results demonstrate that substoichiometric Hsp104 promotes compositional diversity and conformational modulations during amyloid formation, yielding effective prefibrillar seeds that are capable of driving prion-like Sup35 propagation. Our findings underscore the key functional and pathological roles of substoichiometric chaperones in prion-like propagation.
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Affiliation(s)
- Sayanta Mahapatra
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences
| | - Anusha Sarbahi
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences
| | - Priyanka Madhu
- Centre for Protein Science, Design and Engineering; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Hema M Swasthi
- Centre for Protein Science, Design and Engineering; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Abhishek Sharma
- CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Priyanka Singh
- CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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17
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Taylor AIP, Staniforth RA. General Principles Underpinning Amyloid Structure. Front Neurosci 2022; 16:878869. [PMID: 35720732 PMCID: PMC9201691 DOI: 10.3389/fnins.2022.878869] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Amyloid fibrils are a pathologically and functionally relevant state of protein folding, which is generally accessible to polypeptide chains and differs fundamentally from the globular state in terms of molecular symmetry, long-range conformational order, and supramolecular scale. Although amyloid structures are challenging to study, recent developments in techniques such as cryo-EM, solid-state NMR, and AFM have led to an explosion of information about the molecular and supramolecular organization of these assemblies. With these rapid advances, it is now possible to assess the prevalence and significance of proposed general structural features in the context of a diverse body of high-resolution models, and develop a unified view of the principles that control amyloid formation and give rise to their unique properties. Here, we show that, despite system-specific differences, there is a remarkable degree of commonality in both the structural motifs that amyloids adopt and the underlying principles responsible for them. We argue that the inherent geometric differences between amyloids and globular proteins shift the balance of stabilizing forces, predisposing amyloids to distinct molecular interaction motifs with a particular tendency for massive, lattice-like networks of mutually supporting interactions. This general property unites previously characterized structural features such as steric and polar zippers, and contributes to the long-range molecular order that gives amyloids many of their unique properties. The shared features of amyloid structures support the existence of shared structure-activity principles that explain their self-assembly, function, and pathogenesis, and instill hope in efforts to develop broad-spectrum modifiers of amyloid function and pathology.
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18
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Lin J, Shorter J, Lucius AL. AAA+ proteins: one motor, multiple ways to work. Biochem Soc Trans 2022; 50:895-906. [PMID: 35356966 PMCID: PMC9115847 DOI: 10.1042/bst20200350] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/15/2022]
Abstract
Numerous ATPases associated with diverse cellular activities (AAA+) proteins form hexameric, ring-shaped complexes that function via ATPase-coupled translocation of substrates across the central channel. Cryo-electron microscopy of AAA+ proteins processing substrate has revealed non-symmetric, staircase-like hexameric structures that indicate a sequential clockwise/2-residue step translocation model for these motors. However, for many of the AAA+ proteins that share similar structural features, their translocation properties have not yet been experimentally determined. In the cases where translocation mechanisms have been determined, a two-residue translocation step-size has not been resolved. In this review, we explore Hsp104, ClpB, ClpA and ClpX as examples to review the experimental methods that have been used to examine, in solution, the translocation mechanisms employed by AAA+ motor proteins. We then ask whether AAA+ motors sharing similar structural features can have different translocation mechanisms. Finally, we discuss whether a single AAA+ motor can adopt multiple translocation mechanisms that are responsive to different challenges imposed by the substrate or the environment. We suggest that AAA+ motors adopt more than one translocation mechanism and are tuned to switch to the most energetically efficient mechanism when constraints are applied.
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Affiliation(s)
- JiaBei Lin
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Aaron L. Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, U.S.A
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19
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Mapping SP-C co-chaperone binding sites reveals molecular consequences of disease-causing mutations on protein maturation. Nat Commun 2022; 13:1821. [PMID: 35383173 PMCID: PMC8983781 DOI: 10.1038/s41467-022-29478-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 03/11/2022] [Indexed: 01/16/2023] Open
Abstract
BiP co-chaperones ERdj4, ERdj5, and GRP170 associate in cells with peptides predicted to be aggregation prone. Here, extending these findings to a full-length protein, we examine two Interstitial Lung Disease-associated mutants (ILD) of surfactant protein C (SP-C). The TANGO algorithm, which identifies sequences prone to formation of β strand aggregates, found three such regions in SP-C: the N-terminal transmembrane (TM) domain and two sites in the intermolecular chaperone BRICHOS domain. We show the ILD mutants disrupt di-sulfide bond formation in the BRICHOS domain and expose the aggregation-prone peptides leading to binding of ERdj4, ERdj5, and GRP170. The destabilized mutant BRICHOS domain fails to properly insert its TM region in the ER membrane, exposing part of the N-terminal TM domain site. Our studies with ILD-associated mutant proteins provide insights into the specificity of ERdj4, ERdj5, and GRP170, identify context-dependent differences in their binding, and reveal molecular consequences of disease-associated mutants on folding. Interstitial Lung Disease (ILD)-associated mutations in surfactant protein C (SP-C) render the protein prone to aggregation. Here, the authors reveal their impact on protein maturation, provide insights into recognition of aggregation prone regions by chaperones, and address the autosomal dominant nature of ILD mutants.
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20
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Nakagawa Y, Shen HCH, Komi Y, Sugiyama S, Kurinomaru T, Tomabechi Y, Krayukhina E, Okamoto K, Yokoyama T, Shirouzu M, Uchiyama S, Inaba M, Niwa T, Sako Y, Taguchi H, Tanaka M. Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system. Nat Chem Biol 2022; 18:321-331. [PMID: 35177839 DOI: 10.1038/s41589-021-00951-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 11/23/2021] [Indexed: 01/17/2023]
Abstract
Disaggregation of amyloid fibrils is a fundamental biological process required for amyloid propagation. However, due to the lack of experimental systems, the molecular mechanism of how amyloid is disaggregated by cellular factors remains poorly understood. Here, we established a robust in vitro reconstituted system of yeast prion propagation and found that heat-shock protein 104 (Hsp104), Ssa1 and Sis1 chaperones are essential for efficient disaggregation of Sup35 amyloid. Real-time imaging of single-molecule fluorescence coupled with the reconstitution system revealed that amyloid disaggregation is achieved by ordered, timely binding of the chaperones to amyloid. Remarkably, we uncovered two distinct prion strain conformation-dependent modes of disaggregation, fragmentation and dissolution. We characterized distinct chaperone dynamics in each mode and found that transient, repeated binding of Hsp104 to the same site of amyloid results in fragmentation. These findings provide a physical foundation for otherwise puzzling in vivo observations and for therapeutic development for amyloid-associated neurodegenerative diseases.
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Affiliation(s)
- Yoshiko Nakagawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan
| | - Howard C-H Shen
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Komi
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan
| | - Shinju Sugiyama
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan
| | | | - Yuri Tomabechi
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | | | - Kenji Okamoto
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Susumu Uchiyama
- Research Department, U-Medico Inc., Suita, Japan.,Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan.,Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Japan
| | - Megumi Inaba
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tatsuya Niwa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan. .,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
| | - Motomasa Tanaka
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan. .,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
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21
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Yoo H, Bard JA, Pilipenko E, Drummond DA. Chaperones directly and efficiently disperse stress-triggered biomolecular condensates. Mol Cell 2022; 82:741-755.e11. [PMID: 35148816 PMCID: PMC8857057 DOI: 10.1016/j.molcel.2022.01.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/30/2021] [Accepted: 01/06/2022] [Indexed: 12/28/2022]
Abstract
Stresses such as heat shock trigger the formation of protein aggregates and the induction of a disaggregation system composed of molecular chaperones. Recent work reveals that several cases of apparent heat-induced aggregation, long thought to be the result of toxic misfolding, instead reflect evolved, adaptive biomolecular condensation, with chaperone activity contributing to condensate regulation. Here we show that the yeast disaggregation system directly disperses heat-induced biomolecular condensates of endogenous poly(A)-binding protein (Pab1) orders of magnitude more rapidly than aggregates of the most commonly used misfolded model substrate, firefly luciferase. Beyond its efficiency, heat-induced condensate dispersal differs from heat-induced aggregate dispersal in its molecular requirements and mechanistic behavior. Our work establishes a bona fide endogenous heat-induced substrate for long-studied heat shock proteins, isolates a specific example of chaperone regulation of condensates, and underscores needed expansion of the proteotoxic interpretation of the heat shock response to encompass adaptive, chaperone-mediated regulation.
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Affiliation(s)
- Haneul Yoo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jared A.M. Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Evgeny Pilipenko
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - D. Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA,Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA,Lead Contact,Correspondence: (D.A.D.)
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22
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Differential Interactions of Molecular Chaperones and Yeast Prions. J Fungi (Basel) 2022; 8:jof8020122. [PMID: 35205876 PMCID: PMC8877571 DOI: 10.3390/jof8020122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
Baker’s yeast Saccharomyces cerevisiae is an important model organism that is applied to study various aspects of eukaryotic cell biology. Prions in yeast are self-perpetuating heritable protein aggregates that can be leveraged to study the interaction between the protein quality control (PQC) machinery and misfolded proteins. More than ten prions have been identified in yeast, of which the most studied ones include [PSI+], [URE3], and [PIN+]. While all of the major molecular chaperones have been implicated in propagation of yeast prions, many of these chaperones differentially impact propagation of different prions and/or prion variants. In this review, we summarize the current understanding of the life cycle of yeast prions and systematically review the effects of different chaperone proteins on their propagation. Our analysis clearly shows that Hsp40 proteins play a central role in prion propagation by determining the fate of prion seeds and other amyloids. Moreover, direct prion-chaperone interaction seems to be critically important for proper recruitment of all PQC components to the aggregate. Recent results also suggest that the cell asymmetry apparatus, cytoskeleton, and cell signaling all contribute to the complex network of prion interaction with the yeast cell.
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23
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Dennis EM, Garcia DM. Biochemical Principles in Prion-Based Inheritance. EPIGENOMES 2022; 6:4. [PMID: 35225957 PMCID: PMC8883993 DOI: 10.3390/epigenomes6010004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/13/2022] [Accepted: 01/20/2022] [Indexed: 12/14/2022] Open
Abstract
Prions are proteins that can stably fold into alternative structures that frequently alter their activities. They can self-template their alternate structures and are inherited across cell divisions and generations. While they have been studied for more than four decades, their enigmatic nature has limited their discovery. In the last decade, we have learned just how widespread they are in nature, the many beneficial phenotypes that they confer, while also learning more about their structures and modes of inheritance. Here, we provide a brief review of the biochemical principles of prion proteins, including their sequences, characteristics and structures, and what is known about how they self-template, citing examples from multiple organisms. Prion-based inheritance is the most understudied segment of epigenetics. Here, we lay a biochemical foundation and share a framework for how to define these molecules, as new examples are unearthed throughout nature.
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Affiliation(s)
- Emily M. Dennis
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA;
| | - David M. Garcia
- Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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24
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Wyszkowski H, Janta A, Sztangierska W, Obuchowski I, Chamera T, Kłosowska A, Liberek K. Class-specific interactions between Sis1 J-domain protein and Hsp70 chaperone potentiate disaggregation of misfolded proteins. Proc Natl Acad Sci U S A 2021; 118:e2108163118. [PMID: 34873058 PMCID: PMC8670446 DOI: 10.1073/pnas.2108163118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2021] [Indexed: 12/18/2022] Open
Abstract
Protein homeostasis is constantly being challenged with protein misfolding that leads to aggregation. Hsp70 is one of the versatile chaperones that interact with misfolded proteins and actively support their folding. Multifunctional Hsp70s are harnessed to specific roles by J-domain proteins (JDPs, also known as Hsp40s). Interaction with the J-domain of these cochaperones stimulates ATP hydrolysis in Hsp70, which stabilizes substrate binding. In eukaryotes, two classes of JDPs, Class A and Class B, engage Hsp70 in the reactivation of aggregated proteins. In most species, excluding metazoans, protein recovery also relies on an Hsp100 disaggregase. Although intensely studied, many mechanistic details of how the two JDP classes regulate protein disaggregation are still unknown. Here, we explore functional differences between the yeast Class A (Ydj1) and Class B (Sis1) JDPs at the individual stages of protein disaggregation. With real-time biochemical tools, we show that Ydj1 alone is superior to Sis1 in aggregate binding, yet it is Sis1 that recruits more Ssa1 molecules to the substrate. This advantage of Sis1 depends on its ability to bind to the EEVD motif of Hsp70, a quality specific to most of Class B JDPs. This second interaction also conditions the Hsp70-induced aggregate modification that boosts its subsequent dissolution by the Hsp104 disaggregase. Our results suggest that the Sis1-mediated chaperone assembly at the aggregate surface potentiates the entropic pulling, driven polypeptide disentanglement, while Ydj1 binding favors the refolding of the solubilized proteins. Such subspecialization of the JDPs across protein reactivation improves the robustness and efficiency of the disaggregation machinery.
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Affiliation(s)
- Hubert Wyszkowski
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk 80-307, Poland
| | - Anna Janta
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk 80-307, Poland
| | - Wiktoria Sztangierska
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk 80-307, Poland
| | - Igor Obuchowski
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk 80-307, Poland
| | - Tomasz Chamera
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk 80-307, Poland
| | - Agnieszka Kłosowska
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk 80-307, Poland
| | - Krzysztof Liberek
- Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk 80-307, Poland
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25
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Gadhe L, Sakunthala A, Mukherjee S, Gahlot N, Bera R, Sawner AS, Kadu P, Maji SK. Intermediates of α-synuclein aggregation: Implications in Parkinson's disease pathogenesis. Biophys Chem 2021; 281:106736. [PMID: 34923391 DOI: 10.1016/j.bpc.2021.106736] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/27/2021] [Accepted: 11/27/2021] [Indexed: 12/11/2022]
Abstract
Cytoplasmic deposition of aberrantly misfolded α-synuclein (α-Syn) is a common feature of synucleinopathies, including Parkinson's disease (PD). However, the precise pathogenic mechanism of α-Syn in synucleinopathies remains elusive. Emerging evidence has suggested that α-Syn may contribute to PD pathogenesis in several ways; wherein the contribution of fibrillar species, for exerting toxicity and disease transmission, cannot be neglected. Further, the oligomeric species could be the most plausible neurotoxic species causing neuronal cell death. However, understanding the structural and molecular insights of these oligomers are very challenging due to the heterogeneity and transient nature of the species. In this review, we discuss the recent advancements in understanding the formation and role of α-Syn oligomers in PD pathogenesis. We also summarize the different types of α-Syn oligomeric species and potential mechanisms to exert neurotoxicity. Finally, we address the possible ways to target α-Syn as a promising approach against PD and the possible future directions.
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Affiliation(s)
- Laxmikant Gadhe
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Arunima Sakunthala
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Semanti Mukherjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Nitisha Gahlot
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Riya Bera
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Ajay Singh Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India.
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26
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Fassler JS, Skuodas S, Weeks DL, Phillips BT. Protein Aggregation and Disaggregation in Cells and Development. J Mol Biol 2021; 433:167215. [PMID: 34450138 PMCID: PMC8530975 DOI: 10.1016/j.jmb.2021.167215] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/01/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
Protein aggregation is a feature of numerous neurodegenerative diseases. However, regulated, often reversible, formation of protein aggregates, also known as condensates, helps control a wide range of cellular activities including stress response, gene expression, memory, cell development and differentiation. This review presents examples of aggregates found in biological systems, how they are used, and cellular strategies that control aggregation and disaggregation. We include features of the aggregating proteins themselves, environmental factors, co-aggregates, post-translational modifications and well-known aggregation-directed activities that influence their formation, material state, stability and dissolution. We highlight the emerging roles of biomolecular condensates in early animal development, and disaggregation processing proteins that have recently been shown to play key roles in gametogenesis and embryogenesis.
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Affiliation(s)
- Jan S Fassler
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States.
| | - Sydney Skuodas
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States. https://twitter.com/@sskuodas
| | - Daniel L Weeks
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Bryan T Phillips
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States. https://twitter.com/@bt4phillips
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27
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Garcia DM, Campbell EA, Jakobson CM, Tsuchiya M, Shaw EA, DiNardo AL, Kaeberlein M, Jarosz DF. A prion accelerates proliferation at the expense of lifespan. eLife 2021; 10:e60917. [PMID: 34545808 PMCID: PMC8455135 DOI: 10.7554/elife.60917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/12/2021] [Indexed: 12/23/2022] Open
Abstract
In fluctuating environments, switching between different growth strategies, such as those affecting cell size and proliferation, can be advantageous to an organism. Trade-offs arise, however. Mechanisms that aberrantly increase cell size or proliferation-such as mutations or chemicals that interfere with growth regulatory pathways-can also shorten lifespan. Here we report a natural example of how the interplay between growth and lifespan can be epigenetically controlled. We find that a highly conserved RNA-modifying enzyme, the pseudouridine synthase Pus4/TruB, can act as a prion, endowing yeast with greater proliferation rates at the cost of a shortened lifespan. Cells harboring the prion grow larger and exhibit altered protein synthesis. This epigenetic state, [BIG+] (better in growth), allows cells to heritably yet reversibly alter their translational program, leading to the differential synthesis of dozens of proteins, including many that regulate proliferation and aging. Our data reveal a new role for prion-based control of an RNA-modifying enzyme in driving heritable epigenetic states that transform cell growth and survival.
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Affiliation(s)
- David M Garcia
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Edgar A Campbell
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Christopher M Jakobson
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Mitsuhiro Tsuchiya
- Department of Pathology, University of Washington, Seattle, United States
| | - Ethan A Shaw
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Acadia L DiNardo
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, United States
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, United States
| | - Daniel F Jarosz
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, United States
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States
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28
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Threshold concentration and random collision determine the growth of the huntingtin inclusion from a stable core. Commun Biol 2021; 4:971. [PMID: 34400761 PMCID: PMC8368079 DOI: 10.1038/s42003-021-02460-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 07/14/2021] [Indexed: 12/03/2022] Open
Abstract
The processes underlying formation and growth of unfolded protein inclusions are relevant to neurodegenerative diseases but poorly characterized in living cells. In S. cerevisiae, inclusions formed by mutant huntingtin (mHtt) have some characteristics of biomolecular condensates but the physical nature and growth mechanisms of inclusion bodies remain unclear. We have probed the relationship between concentration and inclusion growth in vivo and find that growth of mHtt inclusions in living cells is triggered at a cytoplasmic threshold concentration, while reduction in cytoplasmic mHtt causes inclusions to shrink. The growth rate is consistent with incorporation of new material through collision and coalescence. A small remnant of the inclusion is relatively long-lasting, suggesting that it contains a core that is structurally distinct, and which may serve to nucleate it. These observations support a model in which aggregative particles are incorporated by random collision into a phase-separated condensate composed of a particle-rich mixture. Pei et al. explore the mechanism underlying growth of mutant huntingtin inclusions in yeast cells and show that growth occurs through random collision and incorporation of mutant huntingtin aggregates into a phase-separated condensate. They show that there is a small inner core which is structurally distinct, and may serve to nucleate the inclusion.
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29
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Sprunger ML, Jackrel ME. Prion-Like Proteins in Phase Separation and Their Link to Disease. Biomolecules 2021; 11:biom11071014. [PMID: 34356638 PMCID: PMC8301953 DOI: 10.3390/biom11071014] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/28/2021] [Accepted: 07/06/2021] [Indexed: 02/01/2023] Open
Abstract
Aberrant protein folding underpins many neurodegenerative diseases as well as certain myopathies and cancers. Protein misfolding can be driven by the presence of distinctive prion and prion-like regions within certain proteins. These prion and prion-like regions have also been found to drive liquid-liquid phase separation. Liquid-liquid phase separation is thought to be an important physiological process, but one that is prone to malfunction. Thus, aberrant liquid-to-solid phase transitions may drive protein aggregation and fibrillization, which could give rise to pathological inclusions. Here, we review prions and prion-like proteins, their roles in phase separation and disease, as well as potential therapeutic approaches to counter aberrant phase transitions.
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30
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Creekmore BC, Chang YW, Lee EB. The Cryo-EM Effect: Structural Biology of Neurodegenerative Disease Proteostasis Factors. J Neuropathol Exp Neurol 2021; 80:494-513. [PMID: 33860329 PMCID: PMC8177850 DOI: 10.1093/jnen/nlab029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative diseases are characterized by the accumulation of misfolded proteins. This protein aggregation suggests that abnormal proteostasis contributes to aging-related neurodegeneration. A better fundamental understanding of proteins that regulate proteostasis may provide insight into the pathophysiology of neurodegenerative disease and may perhaps reveal novel therapeutic opportunities. The 26S proteasome is the key effector of the ubiquitin-proteasome system responsible for degrading polyubiquitinated proteins. However, additional factors, such as valosin-containing protein (VCP/p97/Cdc48) and C9orf72, play a role in regulation and trafficking of substrates through the normal proteostasis systems of a cell. Nonhuman AAA+ ATPases, such as the disaggregase Hsp104, also provide insights into the biochemical processes that regulate protein aggregation. X-ray crystallography and cryo-electron microscopy (cryo-EM) structures not bound to substrate have provided meaningful information about the 26S proteasome, VCP, and Hsp104. However, recent cryo-EM structures bound to substrate have provided new information about the function and mechanism of these proteostasis factors. Cryo-EM and cryo-electron tomography data combined with biochemical data have also increased the understanding of C9orf72 and its role in maintaining proteostasis. These structural insights provide a foundation for understanding proteostasis mechanisms with near-atomic resolution upon which insights can be gleaned regarding the pathophysiology of neurodegenerative diseases.
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Affiliation(s)
- Benjamin C Creekmore
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yi-Wei Chang
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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31
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Kabir MT, Uddin MS, Abdeen A, Ashraf GM, Perveen A, Hafeez A, Bin-Jumah MN, Abdel-Daim MM. Evidence Linking Protein Misfolding to Quality Control in Progressive Neurodegenerative Diseases. Curr Top Med Chem 2021; 20:2025-2043. [PMID: 32552649 DOI: 10.2174/1568026620666200618114924] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/25/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022]
Abstract
Several proteolytic systems including ubiquitin (Ub)-proteasome system (UPS), chaperonemediated autophagy (CMA), and macroautophagy are used by the mammalian cells to remove misfolded proteins (MPs). UPS mediates degradation of most of the MPs, where Ub-conjugated substrates are deubiquitinated, unfolded, and passed through the proteasome's narrow chamber, and eventually break into smaller peptides. It has been observed that the substrates that show a specific degradation signal, the KFERQ sequence motif, can be delivered to and go through CMA-mediated degradation in lysosomes. Macroautophagy can help in the degradation of substrates that are prone to aggregation and resistant to both the CMA and UPS. In the aforesaid case, cargoes are separated into autophagosomes before lysosomal hydrolase-mediated degradation. Even though the majority of the aggregated and MPs in the human proteome can be removed via cellular protein quality control (PQC), some mutant and native proteins tend to aggregate into β-sheet-rich oligomers that exhibit resistance to all identified proteolytic processes and can, therefore, grow into extracellular plaques or inclusion bodies. Indeed, the buildup of protease-resistant aggregated and MPs is a usual process underlying various protein misfolding disorders, including neurodegenerative diseases (NDs) for example Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and prion diseases. In this article, we have focused on the contribution of PQC in the degradation of pathogenic proteins in NDs.
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Affiliation(s)
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh.,Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
| | - Ahmed Abdeen
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Saharanpur, India
| | - Abdul Hafeez
- Glocal School of Pharmacy, Glocal University, Saharanpur, India
| | - May N Bin-Jumah
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11474, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt.,Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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32
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Chen YR, Ziv I, Swaminathan K, Elias JE, Jarosz DF. Protein aggregation and the evolution of stress resistance in clinical yeast. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200127. [PMID: 33866806 DOI: 10.1098/rstb.2020.0127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Protein aggregation, particularly in its prion-like form, has long been thought to be detrimental. However, recent studies have identified multiple instances where protein aggregation is important for normal physiological functions. Combining mass spectrometry and cell biological approaches, we developed a strategy for the identification of protein aggregates in cell lysates. We used this approach to characterize prion-based traits in pathogenic strains of the yeast Saccharomyces cerevisiae isolated from immunocompromised human patients. The proteins that we found, including the metabolic enzyme Cdc19, the translation elongation factor Yef3 and the fibrillarin homologue Nop1, are known to assemble under certain physiological conditions. Yet, such assemblies have not been reported to be stable or heritable. Our data suggest that some proteins which aggregate in response to stress have the capacity to acquire diverse assembled states, certain ones of which can be propagated across generations in a form of protein-based epigenetics. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Yiwen R Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Kavya Swaminathan
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.,Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
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33
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Mutuku CN, Bateta R, Rono MK, Njunge JM, Awuoche EO, Ndung'u K, Mang'era CM, Akoth MO, Adung'a VO, Ondigo BN, Mireji PO. Physiological and proteomic profiles of Trypanosoma brucei rhodesiense parasite isolated from suramin responsive and non-responsive HAT patients in Busoga, Uganda. Int J Parasitol Drugs Drug Resist 2021; 15:57-67. [PMID: 33588295 PMCID: PMC7895675 DOI: 10.1016/j.ijpddr.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 11/17/2022]
Abstract
Human African Trypanosomiasis (HAT) is a disease of major economic importance in Sub-Saharan Africa. The HAT is caused by Trypanosoma brucei rhodesiense (Tbr) parasite in eastern and southern Africa, with suramin as drug of choice for treatment of early stage of the disease. Suramin treatment failures has been observed among HAT patients in Tbr foci in Uganda. In this study, we assessed Tbr parasite strains isolated from HAT patients responsive (Tbr EATRO-232) and non-responsive (Tbr EATRO-734) to suramin treatment in Busoga, Uganda for 1) putative role of suramin resistance in the treatment failure 2) correlation of suramin resistance with Tbr pathogenicity and 3) proteomic pathways underpinning the potential suramin resistance phenotype in vivo. We first assessed suramin response in each isolate by infecting male Swiss white mice followed by treatment using a series of suramin doses. We then assessed relative pathogenicity of the two Tbr isolates by assessing changes pathogenicity indices (prepatent period, survival and mortality). We finally isolated proteins from mice infected by the isolates, and assessed their proteomic profiles using mass spectrometry. We established putative resistance to 2.5 mg/kg suramin in the parasite Tbr EATRO-734. We established that Tbr EATRO-734 proliferated slower and has significantly enriched pathways associated with detoxification and metabolism of energy and drugs relative to Tbr EATRO-232. The Tbr EATRO-734 also has more abundantly expressed mitochondrion proteins and enzymes than Tbr EATRO-232. The suramin treatment failure may be linked to the relatively higher resistance to suramin in Tbr EATRO-734 than Tbr EATRO-232, among other host and parasite specific factors. However, the Tbr EATRO-734 appears to be less pathogenic than Tbr EATRO-232, as evidenced by its lower rate of parasitaemia. The Tbr EATRO-734 putatively surmount suramin challenges through induction of energy metabolism pathways. These cellular and molecular processes may be involved in suramin resistance in Tbr.
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Affiliation(s)
- Catherine N Mutuku
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 362, Kikuyu, Kenya; Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Njoro, Kenya
| | - Rosemary Bateta
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 362, Kikuyu, Kenya.
| | - Martin K Rono
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, PO Box 230-80108 Kilifi, Kenya
| | - James M Njunge
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, PO Box 230-80108 Kilifi, Kenya
| | - Erick O Awuoche
- Department of Biological Sciences, School of Pure and Applied Science, Meru University of Science and Technology, Meru, Kenya
| | - Kariuki Ndung'u
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 362, Kikuyu, Kenya
| | - Clarence M Mang'era
- Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Njoro, Kenya
| | - Modesta O Akoth
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 362, Kikuyu, Kenya; Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Njoro, Kenya
| | - Vincent O Adung'a
- Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Njoro, Kenya
| | - Bartholomew N Ondigo
- Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Njoro, Kenya
| | - Paul O Mireji
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 362, Kikuyu, Kenya; Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, PO Box 230-80108 Kilifi, Kenya.
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34
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March ZM, Sweeney K, Kim H, Yan X, Castellano LM, Jackrel ME, Lin J, Chuang E, Gomes E, Willicott CW, Michalska K, Jedrzejczak RP, Joachimiak A, Caldwell KA, Caldwell GA, Shalem O, Shorter J. Therapeutic genetic variation revealed in diverse Hsp104 homologs. eLife 2020; 9:e57457. [PMID: 33319748 PMCID: PMC7785292 DOI: 10.7554/elife.57457] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
The AAA+ protein disaggregase, Hsp104, increases fitness under stress by reversing stress-induced protein aggregation. Natural Hsp104 variants might exist with enhanced, selective activity against neurodegenerative disease substrates. However, natural Hsp104 variation remains largely unexplored. Here, we screened a cross-kingdom collection of Hsp104 homologs in yeast proteotoxicity models. Prokaryotic ClpG reduced TDP-43, FUS, and α-synuclein toxicity, whereas prokaryotic ClpB and hyperactive variants were ineffective. We uncovered therapeutic genetic variation among eukaryotic Hsp104 homologs that specifically antagonized TDP-43 condensation and toxicity in yeast and TDP-43 aggregation in human cells. We also uncovered distinct eukaryotic Hsp104 homologs that selectively antagonized α-synuclein condensation and toxicity in yeast and dopaminergic neurodegeneration in C. elegans. Surprisingly, this therapeutic variation did not manifest as enhanced disaggregase activity, but rather as increased passive inhibition of aggregation of specific substrates. By exploring natural tuning of this passive Hsp104 activity, we elucidated enhanced, substrate-specific agents that counter proteotoxicity underlying neurodegeneration.
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Affiliation(s)
- Zachary M March
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Department of Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Katelyn Sweeney
- Department of Genetics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Hanna Kim
- Department of Biological Sciences, The University of AlabamaTuscaloosaUnited States
| | - Xiaohui Yan
- Department of Biological Sciences, The University of AlabamaTuscaloosaUnited States
| | - Laura M Castellano
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Pharmacology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Meredith E Jackrel
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - JiaBei Lin
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Edward Chuang
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Pharmacology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Edward Gomes
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - Corey W Willicott
- Department of Biological Sciences, The University of AlabamaTuscaloosaUnited States
| | - Karolina Michalska
- Structural Biology Center, X-ray Science Division, Argonne National LaboratoryArgonneUnited States
- Department of Biochemistry and Molecular Biology, University of ChicagoChicagoUnited States
| | - Robert P Jedrzejczak
- Structural Biology Center, X-ray Science Division, Argonne National LaboratoryArgonneUnited States
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National LaboratoryArgonneUnited States
- Department of Biochemistry and Molecular Biology, University of ChicagoChicagoUnited States
| | - Kim A Caldwell
- Department of Biological Sciences, The University of AlabamaTuscaloosaUnited States
| | - Guy A Caldwell
- Department of Biological Sciences, The University of AlabamaTuscaloosaUnited States
| | - Ophir Shalem
- Department of Genetics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of PhiladelphiaPhiladelphiaUnited States
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Department of Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Pharmacology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
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35
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Wilfling F, Lee CW, Erdmann PS, Zheng Y, Sherpa D, Jentsch S, Pfander B, Schulman BA, Baumeister W. A Selective Autophagy Pathway for Phase-Separated Endocytic Protein Deposits. Mol Cell 2020; 80:764-778.e7. [PMID: 33207182 PMCID: PMC7721475 DOI: 10.1016/j.molcel.2020.10.030] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/20/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022]
Abstract
Autophagy eliminates cytoplasmic content selected by autophagy receptors, which link cargo to the membrane-bound autophagosomal ubiquitin-like protein Atg8/LC3. Here, we report a selective autophagy pathway for protein condensates formed by endocytic proteins in yeast. In this pathway, the endocytic protein Ede1 functions as a selective autophagy receptor. Distinct domains within Ede1 bind Atg8 and mediate phase separation into condensates. Both properties are necessary for an Ede1-dependent autophagy pathway for endocytic proteins, which differs from regular endocytosis and does not involve other known selective autophagy receptors but requires the core autophagy machinery. Cryo-electron tomography of Ede1-containing condensates, at the plasma membrane and in autophagic bodies, shows a phase-separated compartment at the beginning and end of the Ede1-mediated selective autophagy route. Our data suggest a model for autophagic degradation of macromolecular protein complexes by the action of intrinsic autophagy receptors.
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Affiliation(s)
- Florian Wilfling
- Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - Chia-Wei Lee
- Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Philipp S Erdmann
- Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - Yumei Zheng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Dawafuti Sherpa
- Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Stefan Jentsch
- Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Boris Pfander
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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Zhu G, Harischandra DS, Ghaisas S, Zhang P, Prall W, Huang L, Maghames C, Guo L, Luna E, Mack KL, Torrente MP, Luk KC, Shorter J, Yang X. TRIM11 Prevents and Reverses Protein Aggregation and Rescues a Mouse Model of Parkinson's Disease. Cell Rep 2020; 33:108418. [PMID: 33264628 PMCID: PMC7906527 DOI: 10.1016/j.celrep.2020.108418] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 07/15/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022] Open
Abstract
Neurodegenerative diseases are characterized by the formation and propagation of protein aggregates, especially amyloid fibrils. However, what normally suppresses protein misfolding and aggregation in metazoan cells remains incompletely understood. Here, we show that TRIM11, a member of the metazoan tripartite motif (TRIM) family, both prevents the formation of protein aggregates and dissolves pre-existing protein deposits, including amyloid fibrils. These molecular chaperone and disaggregase activities are ATP independent. They enhance folding and solubility of normal proteins and cooperate with TRIM11 SUMO ligase activity to degrade aberrant proteins. TRIM11 abrogates α-synuclein fibrillization and restores viability in cell models of Parkinson's disease (PD). Intracranial adeno-associated viral delivery of TRIM11 mitigates α-synuclein-mediated pathology, neurodegeneration, and motor impairments in a PD mouse model. Other TRIMs can also function as ATP-independent molecular chaperones and disaggregases. Thus, we define TRIMs as a potent and multifunctional protein quality-control system in metazoa, which might be applied to treat neurodegenerative diseases.
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Affiliation(s)
- Guixin Zhu
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dilshan S Harischandra
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shivani Ghaisas
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pengfei Zhang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wil Prall
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Liangqian Huang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chantal Maghames
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lili Guo
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Esteban Luna
- Department of Pathology and Laboratory Medicine and Center for Neurodegenerative Disease Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Korrie L Mack
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariana P Torrente
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kelvin C Luk
- Department of Pathology and Laboratory Medicine and Center for Neurodegenerative Disease Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaolu Yang
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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37
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Oamen HP, Lau Y, Caudron F. Prion-like proteins as epigenetic devices of stress adaptation. Exp Cell Res 2020; 396:112262. [DOI: 10.1016/j.yexcr.2020.112262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/26/2020] [Accepted: 08/30/2020] [Indexed: 01/03/2023]
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38
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He W, Zhang J, Sachsenhauser V, Wang L, Bardwell JCA, Quan S. Increased surface charge in the protein chaperone Spy enhances its anti-aggregation activity. J Biol Chem 2020; 295:14488-14500. [PMID: 32817055 PMCID: PMC7573262 DOI: 10.1074/jbc.ra119.012300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
Chaperones are essential components of the protein homeostasis network. There is a growing interest in optimizing chaperone function, but exactly how to achieve this aim is unclear. Here, using a model chaperone, the bacterial protein Spy, we demonstrate that substitutions that alter the electrostatic potential of Spy's concave, client-binding surface enhance Spy's anti-aggregation activity. We show that this strategy is more efficient than one that enhances the hydrophobicity of Spy's surface. Our findings thus challenge the traditional notion that hydrophobic interactions are the major driving forces that guide chaperone-substrate binding. Kinetic data revealed that both charge- and hydrophobicity-enhanced Spy variants release clients more slowly, resulting in a greater "holdase" activity. However, increasing short-range hydrophobic interactions deleteriously affected Spy's ability to capture substrates, thus reducing its in vitro chaperone activity toward fast-aggregating substrates. Our strategy in chaperone surface engineering therefore sought to fine-tune the different molecular forces involved in chaperone-substrate interactions rather than focusing on enhancing hydrophobic interactions. These results improve our understanding of the mechanistic basis of chaperone-client interactions and illustrate how protein surface-based mutational strategies can facilitate the rational improvement of molecular chaperones.
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Affiliation(s)
- Wei He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Jiayin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
| | - Veronika Sachsenhauser
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lili Wang
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - James C A Bardwell
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, China
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39
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Beal DM, Tournus M, Marchante R, Purton TJ, Smith DP, Tuite MF, Doumic M, Xue WF. The Division of Amyloid Fibrils: Systematic Comparison of Fibril Fragmentation Stability by Linking Theory with Experiments. iScience 2020; 23:101512. [PMID: 32920487 PMCID: PMC7492994 DOI: 10.1016/j.isci.2020.101512] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/31/2020] [Accepted: 08/26/2020] [Indexed: 01/22/2023] Open
Abstract
The division of amyloid protein fibrils is required for the propagation of the amyloid state and is an important contributor to their stability, pathogenicity, and normal function. Here, we combine kinetic nanoscale imaging experiments with analysis of a mathematical model to resolve and compare the division stability of amyloid fibrils. Our theoretical results show that the division of any type of filament results in self-similar length distributions distinct to each fibril type and the conditions applied. By applying these theoretical results to profile the dynamical stability toward breakage for four different amyloid types, we reveal particular differences in the division properties of disease-related amyloid formed from α-synuclein when compared with non-disease associated model amyloid, the former showing lowered intrinsic stability toward breakage and increased likelihood of shedding smaller particles. Our results enable the comparison of protein filaments' intrinsic dynamic stabilities, which are key to unraveling their toxic and infectious potentials.
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Affiliation(s)
- David M. Beal
- Kent Fungal Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Magali Tournus
- Centrale Marseille, I2M, UMR 7373, CNRS, Aix-Marseille Univ., Marseille 13453, France
| | - Ricardo Marchante
- Kent Fungal Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Tracey J. Purton
- Kent Fungal Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK
| | - David P. Smith
- Biomolecular Research Centre, Sheffield Hallam University, Sheffield, UK
| | - Mick F. Tuite
- Kent Fungal Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Marie Doumic
- INRIA Rocquencourt, équipe-projet BANG, Domaine de Voluceau, BP 105, 78153 Rocquencourt, France
- Wolfgang Pauli Institute, University of Vienna, Vienna, Austria
| | - Wei-Feng Xue
- Kent Fungal Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK
- INRIA Rocquencourt, équipe-projet BANG, Domaine de Voluceau, BP 105, 78153 Rocquencourt, France
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40
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From Seeds to Fibrils and Back: Fragmentation as an Overlooked Step in the Propagation of Prions and Prion-Like Proteins. Biomolecules 2020; 10:biom10091305. [PMID: 32927676 PMCID: PMC7563560 DOI: 10.3390/biom10091305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/13/2022] Open
Abstract
Many devastating neurodegenerative diseases are driven by the misfolding of normal proteins into a pathogenic abnormal conformation. Examples of such protein misfolding diseases include Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, amyotrophic lateral sclerosis, and prion diseases. The misfolded proteins involved in these diseases form self-templating oligomeric assemblies that recruit further correctly folded protein and induce their conversion. Over time, this leads to the formation of high molecular and mostly fibrillar aggregates that are increasingly inefficient at converting normal protein. Evidence from a multitude of in vitro models suggests that fibrils are fragmented to form new seeds, which can convert further normal protein and also spread to neighboring cells as observed in vivo. While fragmentation and seed generation were suggested as crucial steps in aggregate formation decades ago, the biological pathways involved remain largely unknown. Here, we show that mechanisms of aggregate clearance—namely the mammalian Hsp70–Hsp40–Hsp110 tri-chaperone system, macro-autophagy, and the proteasome system—may not only be protective, but also play a role in fragmentation. We further review the challenges that exist in determining the precise contribution of these mechanisms to protein misfolding diseases and suggest future directions to resolve these issues.
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41
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Mechanisms for Curing Yeast Prions. Int J Mol Sci 2020; 21:ijms21186536. [PMID: 32906758 PMCID: PMC7555348 DOI: 10.3390/ijms21186536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/24/2022] Open
Abstract
Prions are infectious proteins that self-propagate by changing from their normal folded conformation to a misfolded conformation. The misfolded conformation, which is typically rich in β-sheet, serves as a template to convert the prion protein into its misfolded conformation. In yeast, the misfolded prion proteins are assembled into amyloid fibers or seeds, which are constantly severed and transmitted to daughter cells. To cure prions in yeast, it is necessary to eliminate all the prion seeds. Multiple mechanisms of curing have been found including inhibiting severing of the prion seeds, gradual dissolution of the prion seeds, asymmetric segregation of the prion seeds between mother and daughter cells during cell division, and degradation of the prion seeds. These mechanisms, achieved by using different protein quality control machinery, are not mutually exclusive; depending on conditions, multiple mechanisms may work simultaneously to achieve curing. This review discusses the various methods that have been used to differentiate between these mechanisms of curing.
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42
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Tariq A, Lin J, Jackrel ME, Hesketh CD, Carman PJ, Mack KL, Weitzman R, Gambogi C, Hernandez Murillo OA, Sweeny EA, Gurpinar E, Yokom AL, Gates SN, Yee K, Sudesh S, Stillman J, Rizo AN, Southworth DR, Shorter J. Mining Disaggregase Sequence Space to Safely Counter TDP-43, FUS, and α-Synuclein Proteotoxicity. Cell Rep 2020; 28:2080-2095.e6. [PMID: 31433984 PMCID: PMC6750954 DOI: 10.1016/j.celrep.2019.07.069] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 05/25/2019] [Accepted: 07/19/2019] [Indexed: 10/31/2022] Open
Abstract
Hsp104 is an AAA+ protein disaggregase, which can be potentiated via diverse mutations in its autoregulatory middle domain (MD) to mitigate toxic misfolding of TDP-43, FUS, and α-synuclein implicated in fatal neurodegenerative disorders. Problematically, potentiated MD variants can exhibit off-target toxicity. Here, we mine disaggregase sequence space to safely enhance Hsp104 activity via single mutations in nucleotide-binding domain 1 (NBD1) or NBD2. Like MD variants, NBD variants counter TDP-43, FUS, and α-synuclein toxicity and exhibit elevated ATPase and disaggregase activity. Unlike MD variants, non-toxic NBD1 and NBD2 variants emerge that rescue TDP-43, FUS, and α-synuclein toxicity. Potentiating substitutions alter NBD1 residues that contact ATP, ATP-binding residues, or the MD. Mutating the NBD2 protomer interface can also safely ameliorate Hsp104. Thus, we disambiguate allosteric regulation of Hsp104 by several tunable structural contacts, which can be engineered to spawn enhanced therapeutic disaggregases with minimal off-target toxicity.
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Affiliation(s)
- Amber Tariq
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - JiaBei Lin
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meredith E Jackrel
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christina D Hesketh
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter J Carman
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Korrie L Mack
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel Weitzman
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Craig Gambogi
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Oscar A Hernandez Murillo
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth A Sweeny
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Esin Gurpinar
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adam L Yokom
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephanie N Gates
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Keolamau Yee
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Saurabh Sudesh
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jacob Stillman
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexandra N Rizo
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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43
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Babazadeh R, Ahmadpour D, Jia S, Hao X, Widlund P, Schneider K, Eisele F, Edo LD, Smits GJ, Liu B, Nystrom T. Syntaxin 5 Is Required for the Formation and Clearance of Protein Inclusions during Proteostatic Stress. Cell Rep 2020; 28:2096-2110.e8. [PMID: 31433985 DOI: 10.1016/j.celrep.2019.07.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 06/14/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
Spatial sorting to discrete quality control sites in the cell is a process harnessing the toxicity of aberrant proteins. We show that the yeast t-snare phosphoprotein syntaxin5 (Sed5) acts as a key factor in mitigating proteotoxicity and the spatial deposition and clearance of IPOD (insoluble protein deposit) inclusions associates with the disaggregase Hsp104. Sed5 phosphorylation promotes dynamic movement of COPII-associated Hsp104 and boosts disaggregation by favoring anterograde ER-to-Golgi trafficking. Hsp104-associated aggregates co-localize with Sed5 as well as components of the ER, trans Golgi network, and endocytic vesicles, transiently during proteostatic stress, explaining mechanistically how misfolded and aggregated proteins formed at the vicinity of the ER can hitchhike toward vacuolar IPOD sites. Many inclusions become associated with mitochondria in a HOPS/vCLAMP-dependent manner and co-localize with Vps39 (HOPS/vCLAMP) and Vps13, which are proteins providing contacts between vacuole and mitochondria. Both Vps39 and Vps13 are required also for efficient Sed5-dependent clearance of aggregates.
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Affiliation(s)
- Roja Babazadeh
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Doryaneh Ahmadpour
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Song Jia
- School of Life Science, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin 150030, China
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Per Widlund
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Kara Schneider
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Frederik Eisele
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Laura Dolz Edo
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1090, the Netherlands
| | - Gertien J Smits
- Department of Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1090, the Netherlands
| | - Beidong Liu
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Thomas Nystrom
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Gothenburg 405 30, Sweden.
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44
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Bousset L, Luckgei N, Kabani M, Gardiennet C, Schütz AK, Melki R, Meier BH, Böckmann A. Prion Amyloid Polymorphs - The Tag Might Change It All. Front Mol Biosci 2020; 7:190. [PMID: 32850974 PMCID: PMC7423878 DOI: 10.3389/fmolb.2020.00190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/20/2020] [Indexed: 11/13/2022] Open
Abstract
Sup35p is a protein from Saccharomyces cerevisiae. It can propagate using a prion-like mechanism, which means that it can recruit non-prion soluble Sup35p into insoluble fibrils. Sup35p is a large protein showing three distinct domains, N, M and an extended globular domain. We have previously studied the conformations of the full-length and truncated NM versions carrying poly-histidine tags on the N-terminus. Comparison with structural data from C-terminally poly-histidine tagged NM from the literature surprisingly revealed discrepancies. Here we investigated fibrils from the untagged, as well as a C-terminally poly-histidine tagged NM construct, using solid-state NMR. We find that the conformation of untagged NM is very close to the N-terminally tagged NM and confirms our previous findings. The C-terminal poly-histidine tag, in contrast, drastically changes the NM fibril structure, and yields data consistent with results obtained previously on this construct. We conclude that the C-terminally located Sup35p globular domain influences the structure of the fibrillar core at the N domain, as previously shown. We further conclude, based on the present data, that small tags on NM C-terminus have a substantial, despite different, impact. Modifications at this remote localization thus shows an unexpected influence on the fibril structure, and importantly also its propensity to induce [PSI+].
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Affiliation(s)
- Luc Bousset
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Nina Luckgei
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universite de Lyon, Lyon, France
| | - Mehdi Kabani
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Carole Gardiennet
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universite de Lyon, Lyon, France
| | - Anne K Schütz
- ETH Zürich, Laboratory of Physical Chemistry, Zurich, Switzerland
| | - Ronald Melki
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Beat H Meier
- ETH Zürich, Laboratory of Physical Chemistry, Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universite de Lyon, Lyon, France
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Abstract
Sustaining a healthy proteome is a lifelong challenge for each individual cell of an organism. However, protein homeostasis or proteostasis is constantly jeopardized since damaged proteins accumulate under proteotoxic stress that originates from ever-changing metabolic, environmental, and pathological conditions. Proteostasis is achieved via a conserved network of quality control pathways that orchestrate the biogenesis of correctly folded proteins, prevent proteins from misfolding, and remove potentially harmful proteins by selective degradation. Nevertheless, the proteostasis network has a limited capacity and its collapse deteriorates cellular functionality and organismal viability, causing metabolic, oncological, or neurodegenerative disorders. While cell-autonomous quality control mechanisms have been described intensely, recent work on Caenorhabditis elegans has demonstrated the systemic coordination of proteostasis between distinct tissues of an organism. These findings indicate the existence of intricately balanced proteostasis networks important for integration and maintenance of the organismal proteome, opening a new door to define novel therapeutic targets for protein aggregation diseases. Here, we provide an overview of individual protein quality control pathways and the systemic coordination between central proteostatic nodes. We further provide insights into the dynamic regulation of cellular and organismal proteostasis mechanisms that integrate environmental and metabolic changes. The use of C. elegans as a model has pioneered our understanding of conserved quality control mechanisms important to safeguard the organismal proteome in health and disease.
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Affiliation(s)
- Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany and
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada (IMRIC), the Hebrew University School of Medicine, Jerusalem 91120, Israel
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46
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Cupo RR, Shorter J. Skd3 (human ClpB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations. eLife 2020; 9:e55279. [PMID: 32573439 PMCID: PMC7343390 DOI: 10.7554/elife.55279] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022] Open
Abstract
Cells have evolved specialized protein disaggregases to reverse toxic protein aggregation and restore protein functionality. In nonmetazoan eukaryotes, the AAA+ disaggregase Hsp78 resolubilizes and reactivates proteins in mitochondria. Curiously, metazoa lack Hsp78. Hence, whether metazoan mitochondria reactivate aggregated proteins is unknown. Here, we establish that a mitochondrial AAA+ protein, Skd3 (human ClpB), couples ATP hydrolysis to protein disaggregation and reactivation. The Skd3 ankyrin-repeat domain combines with conserved AAA+ elements to enable stand-alone disaggregase activity. A mitochondrial inner-membrane protease, PARL, removes an autoinhibitory peptide from Skd3 to greatly enhance disaggregase activity. Indeed, PARL-activated Skd3 solubilizes α-synuclein fibrils connected to Parkinson's disease. Human cells lacking Skd3 exhibit reduced solubility of various mitochondrial proteins, including anti-apoptotic Hax1. Importantly, Skd3 variants linked to 3-methylglutaconic aciduria, a severe mitochondrial disorder, display diminished disaggregase activity (but not always reduced ATPase activity), which predicts disease severity. Thus, Skd3 is a potent protein disaggregase critical for human health.
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Affiliation(s)
- Ryan R Cupo
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Pharmacology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
- Pharmacology Graduate Group, Perelman School of Medicine at the University of PennsylvaniaPhiladelphiaUnited States
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47
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Barbitoff YA, Matveenko AG, Bondarev SA, Maksiutenko EM, Kulikova AV, Zhouravleva GA. Quantitative assessment of chaperone binding to amyloid aggregates identifies specificity of Hsp40 interaction with yeast prion fibrils. FEMS Yeast Res 2020; 20:5831717. [PMID: 32379306 DOI: 10.1093/femsyr/foaa025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/05/2020] [Indexed: 12/18/2022] Open
Abstract
Yeast self-perpetuating protein aggregates (yeast prions) provide a framework to investigate the interaction of misfolded proteins with the protein quality control machinery. The major component of this system that facilitates propagation of all known yeast amyloid prions is the Hsp104 chaperone that catalyzes fibril fragmentation. Overproduction of Hsp104 cures some yeast prions via a fragmentation-independent mechanism. Importantly, major cytosolic chaperones of the Hsp40 group, Sis1 and Ydj1, oppositely affect yeast prion propagation, and are capable of stimulating different activities of Hsp104. In this work, we developed a quantitative method to investigate the Hsp40 binding to amyloid aggregates. We demonstrate that Sis1 binds fibrils formed by the Sup35NM protein with higher affinity compared to Ydj1. Moreover, the interaction of Sis1 with the fibrils formed by the other yeast prion protein, Rnq1, is orders of magnitude weaker. We show that the deletion of the dimerization domain of Sis1 (crucial for the curing of [PSI+] by excess Hsp104) decreases its affinity to both Sup35NM and Rnq1 fibrils. Taken together, these results suggest that tight binding of Hsp40 to the amyloid fibrils is likely to enhance aggregate malpartition instead of fibril fragmentation.
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Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Evgeniia M Maksiutenko
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Alexandra V Kulikova
- Peter the Great St. Petersburg Polytechnic University, Politekhnicheskaya ul. 29, St. Petersburg, 195251 Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
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48
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Kao CH, Ryu SW, Kim MJ, Wen X, Wimalarathne O, Paull TT. Growth-Regulated Hsp70 Phosphorylation Regulates Stress Responses and Prion Maintenance. Mol Cell Biol 2020; 40:e00628-19. [PMID: 32205407 PMCID: PMC7261718 DOI: 10.1128/mcb.00628-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/05/2020] [Accepted: 03/18/2020] [Indexed: 11/20/2022] Open
Abstract
Maintenance of protein homeostasis in eukaryotes under normal growth and stress conditions requires the functions of Hsp70 chaperones and associated cochaperones. Here, we investigate an evolutionarily conserved serine phosphorylation that occurs at the site of communication between the nucleotide-binding and substrate-binding domains of Hsp70. Ser151 phosphorylation in yeast Hsp70 (Ssa1) is promoted by cyclin-dependent kinase (Cdk1) during normal growth. Phosphomimetic substitutions at this site (S151D) dramatically downregulate heat shock responses, a result conserved with HSC70 S153 in human cells. Phosphomimetic forms of Ssa1 also fail to relocalize in response to starvation conditions, do not associate in vivo with Hsp40 cochaperones Ydj1 and Sis1, and do not catalyze refolding of denatured proteins in vitro in cooperation with Ydj1 and Hsp104. Despite these negative effects on HSC70/HSP70 function, the S151D phosphomimetic allele promotes survival of heavy metal exposure and suppresses the Sup35-dependent [PSI+ ] prion phenotype, consistent with proposed roles for Ssa1 and Hsp104 in generating self-nucleating seeds of misfolded proteins. Taken together, these results suggest that Cdk1 can downregulate Hsp70 function through phosphorylation of this site, with potential costs to overall chaperone efficiency but also advantages with respect to reduction of metal-induced and prion-dependent protein aggregate production.
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Affiliation(s)
- Chung-Hsuan Kao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Seung W Ryu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Min J Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Oshadi Wimalarathne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
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Dorweiler JE, Oddo MJ, Lyke DR, Reilly JA, Wisniewski BT, Davis EE, Kuborn AM, Merrill SJ, Manogaran AL. The actin cytoskeletal network plays a role in yeast prion transmission and contributes to prion stability. Mol Microbiol 2020; 114:480-494. [PMID: 32426863 DOI: 10.1111/mmi.14528] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 04/21/2020] [Accepted: 05/09/2020] [Indexed: 01/22/2023]
Abstract
Chaperone networks are required for the shearing and generation of transmissible propagons from pre-existing prion aggregates. However, other cellular networks needed for maintaining yeast prions are largely uncharacterized. Here, we establish a novel role for actin networks in prion maintenance. The [PIN+ ] prion, also known as [RNQ+ ], exists as stable variants dependent upon the chaperone machinery for the transmission of propagons to daughter cells during cell division and cytoplasmic transfer. Loss of the Hsp104 molecular chaperone leads to the growth of prion particles until they are too large to be transmitted. Here, we isolated a unique [PIN+ ] variant, which is unstable in actin mutants. This prion loss is observed over many generations, and coincides with the detection of both high molecular weight species of Rnq1 and large visible aggregates that are asymmetrically retained during cell division. Our data suggest that the irregular actin networks found in these mutants may influence propagon number by slowly permitting aggregate growth over time, resulting in the generation of nontransmissible large aggregates. Thus, we show the potential contribution of cytoskeletal networks in the transmission of prion propagons, which parallels models that have been proposed for cell-to-cell transmission of small amyloids in neurodegenerative protein aggregation diseases.
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Affiliation(s)
- Jane E Dorweiler
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Mitchell J Oddo
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Douglas R Lyke
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Jacob A Reilly
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Brett T Wisniewski
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Emily E Davis
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Abigail M Kuborn
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Stephen J Merrill
- Department of Mathematical and Statistical Sciences, Marquette University, Milwaukee, WI, USA
| | - Anita L Manogaran
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
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50
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Ahmadpour D, Babazadeh R, Nystrom T. Hitchhiking on vesicles: a way to harness age-related proteopathies? FEBS J 2020; 287:5068-5079. [PMID: 32336030 DOI: 10.1111/febs.15345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 12/27/2022]
Abstract
Central to proteopathies and leading to most age-related neurodegenerative disorders is a failure in protein quality control (PQC). To harness the toxicity of misfolded and damaged disease proteins, such proteins are either refolded, degraded by temporal PQC, or sequestered by spatial PQC into specific, organelle-associated, compartments within the cell. Here, we discuss the impact of vesicle trafficking pathways in general, and syntaxin 5 in particular, as key players in spatial PQC directing misfolded proteins to the surface of vacuole and mitochondria, which facilitates their clearance and detoxification. Since boosting vesicle trafficking genetically can positively impact on spatial PQC and make cells less sensitive to misfolded disease proteins, we speculate that regulators of such trafficking might serve as therapeutic targets for age-related neurological disorders.
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Affiliation(s)
- Doryaneh Ahmadpour
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Sweden.,Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Sweden
| | - Roja Babazadeh
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Thomas Nystrom
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-AgeCap, University of Gothenburg, Sweden
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