1
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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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2
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Lee S, Lee SB, Sung N, Xu WW, Chang C, Kim HE, Catic A, Tsai FTF. Structural basis of impaired disaggregase function in the oxidation-sensitive SKD3 mutant causing 3-methylglutaconic aciduria. Nat Commun 2023; 14:2028. [PMID: 37041140 PMCID: PMC10090083 DOI: 10.1038/s41467-023-37657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/23/2023] [Indexed: 04/13/2023] Open
Abstract
Mitochondria are critical to cellular and organismal health. To prevent damage, mitochondria have evolved protein quality control machines to survey and maintain the mitochondrial proteome. SKD3, also known as CLPB, is a ring-forming, ATP-fueled protein disaggregase essential for preserving mitochondrial integrity and structure. SKD3 deficiency causes 3-methylglutaconic aciduria type VII (MGCA7) and early death in infants, while mutations in the ATPase domain impair protein disaggregation with the observed loss-of-function correlating with disease severity. How mutations in the non-catalytic N-domain cause disease is unknown. Here, we show that the disease-associated N-domain mutation, Y272C, forms an intramolecular disulfide bond with Cys267 and severely impairs SKD3Y272C function under oxidizing conditions and in living cells. While Cys267 and Tyr272 are found in all SKD3 isoforms, isoform-1 features an additional α-helix that may compete with substrate-binding as suggested by crystal structure analyses and in silico modeling, underscoring the importance of the N-domain to SKD3 function.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sang Bum Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nuri Sung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wendy W Xu
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA
- Louisiana State University Health New Orleans School of Medicine, New Orleans, LA, 70112, USA
| | - Changsoo Chang
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Hyun-Eui Kim
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Andre Catic
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
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3
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Lee G, Kim RS, Lee SB, Lee S, Tsai FT. Deciphering the mechanism and function of Hsp100 unfoldases from protein structure. Biochem Soc Trans 2022; 50:1725-1736. [PMID: 36454589 PMCID: PMC9784670 DOI: 10.1042/bst20220590] [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: 10/10/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022]
Abstract
Hsp100 chaperones, also known as Clp proteins, constitute a family of ring-forming ATPases that differ in 3D structure and cellular function from other stress-inducible molecular chaperones. While the vast majority of ATP-dependent molecular chaperones promote the folding of either the nascent chain or a newly imported polypeptide to reach its native conformation, Hsp100 chaperones harness metabolic energy to perform the reverse and facilitate the unfolding of a misfolded polypeptide or protein aggregate. It is now known that inside cells and organelles, different Hsp100 members are involved in rescuing stress-damaged proteins from a previously aggregated state or in recycling polypeptides marked for degradation. Protein degradation is mediated by a barrel-shaped peptidase that physically associates with the Hsp100 hexamer to form a two-component system. Notable examples include the ClpA:ClpP (ClpAP) and ClpX:ClpP (ClpXP) proteases that resemble the ring-forming FtsH and Lon proteases, which unlike ClpAP and ClpXP, feature the ATP-binding and proteolytic domains in a single polypeptide chain. Recent advances in electron cryomicroscopy (cryoEM) together with single-molecule biophysical studies have now provided new mechanistic insight into the structure and function of this remarkable group of macromolecular machines.
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Affiliation(s)
- Grace Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Rice University, Houston, Texas 77005, USA
| | - Rebecca S. Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sang Bum Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Francis T.F. Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
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4
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Harari A, Zoltsman G, Levin T, Rosenzweig R. Hsp104 N-terminal domain interaction with substrates plays a regulatory role in protein disaggregation. FEBS J 2022; 289:5359-5377. [PMID: 35305079 PMCID: PMC9541529 DOI: 10.1111/febs.16441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/01/2022] [Accepted: 03/17/2022] [Indexed: 01/19/2023]
Abstract
Heat shock protein 104 (Hsp104) protein disaggregases are powerful molecular machines that harness the energy derived from ATP binding and hydrolysis to disaggregate a wide range of protein aggregates and amyloids, as well as to assist in yeast prion propagation. Little is known, however, about how Hsp104 chaperones recognize such a diversity of substrates, or indeed the contribution of the substrate‐binding N‐terminal domain (NTD) to Hsp104 function. Herein, we present a NMR spectroscopy study, which structurally characterizes the Hsp104 NTD‐substrate interaction. We show that the NTD includes a substrate‐binding groove that specifically recognizes exposed hydrophobic stretches in unfolded, misfolded, amyloid and prion substrates of Hsp104. In addition, we find that the NTD itself has chaperoning activities which help to protect the exposed hydrophobic regions of its substrates from further misfolding and aggregation, thereby priming them for threading through the Hsp104 central channel. We further demonstrate that mutations to this substrate‐binding groove abolish Hsp104 activation by client proteins and keep the chaperone in a partially inhibited state. The Hsp104 variant with these mutations also exhibited significantly reduced disaggregation activity and cell survival at extreme temperatures. Together, our findings provide both a detailed characterization of the NTD‐substrate complex and insight into the functional regulatory role of the NTD in protein disaggregation and yeast thermotolerance.
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Affiliation(s)
- Anna Harari
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Zoltsman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Levin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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5
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Mercado JM, Lee S, Chang C, Sung N, Soong L, Catic A, Tsai FTF. Atomic structure of the
Leishmania spp
. Hsp100
N‐domain. Proteins 2022; 90:1242-1246. [DOI: 10.1002/prot.26310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/14/2022] [Accepted: 02/01/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Jonathan M. Mercado
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston Texas USA
| | - Sukyeong Lee
- Advanced Technology Core for Macromolecular X‐ray Crystallography Baylor College of Medicine Houston Texas USA
- Department of Biochemistry and Molecular Biology Baylor College of Medicine Houston Texas USA
| | - Changsoo Chang
- Structural Biology Center, X‐ray Science Division Argonne National Laboratory Argonne Illinois USA
| | - Nuri Sung
- Department of Biochemistry and Molecular Biology Baylor College of Medicine Houston Texas USA
| | - Lynn Soong
- Department of Microbiology and Immunology, Institute of Human Infections and Immunity University of Texas Medical Branch Galveston Texas USA
| | - Andre Catic
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston Texas USA
- Huffington Center on Aging Baylor College of Medicine Houston Texas USA
| | - Francis T. F. Tsai
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston Texas USA
- Department of Biochemistry and Molecular Biology Baylor College of Medicine Houston Texas USA
- Department of Molecular Virology and Microbiology Baylor College of Medicine Houston Texas USA
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6
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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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7
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Split conformation of Chaetomium thermophilum Hsp104 disaggregase. Structure 2021; 29:721-730.e6. [PMID: 33651974 DOI: 10.1016/j.str.2021.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/08/2020] [Accepted: 02/09/2021] [Indexed: 11/24/2022]
Abstract
Hsp104 and its bacterial homolog ClpB form hexameric ring structures and mediate protein disaggregation. The disaggregated polypeptide is thought to thread through the central channel of the ring. However, the dynamic behavior of Hsp104 during disaggregation remains unclear. Here, we reported the stochastic conformational dynamics and a split conformation of Hsp104 disaggregase from Chaetomium thermophilum (CtHsp104) in the presence of ADP by X-ray crystallography, cryo-electron microscopy (EM), and high-speed atomic force microscopy (AFM). ADP-bound CtHsp104 assembles into a 65 left-handed spiral filament in the crystal structure at a resolution of 2.7 Å. The unit of the filament is a hexamer of the split spiral structure. In the cryo-EM images, staggered and split hexameric rings were observed. Further, high-speed AFM observations showed that a substrate addition enhanced the conformational change and increased the split structure's frequency. Our data suggest that split conformation is an off-pathway state of CtHsp104 during disaggregation.
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8
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Katikaridis P, Römling U, Mogk A. Basic mechanism of the autonomous ClpG disaggregase. J Biol Chem 2021; 296:100460. [PMID: 33639171 PMCID: PMC8024975 DOI: 10.1016/j.jbc.2021.100460] [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: 10/20/2020] [Revised: 02/05/2021] [Accepted: 02/23/2021] [Indexed: 01/19/2023] Open
Abstract
Bacterial survival during lethal heat stress relies on the cellular ability to reactivate aggregated proteins. This activity is typically executed by the canonical 70-kDa heat shock protein (Hsp70)–ClpB bichaperone disaggregase, which is most widespread in bacteria. The ClpB disaggregase is a member of the ATPase associated with diverse cellular activities protein family and exhibits an ATP-driven threading activity. Substrate binding and stimulation of ATP hydrolysis depends on the Hsp70 partner, which initiates the disaggregation reaction. Recently elevated heat resistance in gamma-proteobacterial species was shown to be mediated by the ATPase associated with diverse cellular activities protein ClpG as an alternative disaggregase. Pseudomonas aeruginosa ClpG functions autonomously and does not cooperate with Hsp70 for substrate binding, enhanced ATPase activity, and disaggregation. With the underlying molecular basis largely unknown, the fundamental differences in ClpG- and ClpB-dependent disaggregation are reflected by the presence of sequence alterations and additional ClpG-specific domains. By analyzing the effects of mutants lacking ClpG-specific domains and harboring mutations in conserved motifs implicated in ATP hydrolysis and substrate threading, we show that the N-terminal, ClpG-specific N1 domain generally mediates protein aggregate binding as the molecular basis of autonomous disaggregation activity. Peptide substrate binding strongly stimulates ClpG ATPase activity by overriding repression by the N-terminal N1 and N2 domains. High ATPase activity requires two functional nucleotide binding domains and drives substrate threading which ultimately extracts polypeptides from the aggregate. ClpG ATPase and disaggregation activity is thereby directly controlled by substrate availability.
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Affiliation(s)
- Panagiotis Katikaridis
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; German Cancer Research Center (DKFZ), A250 Chaperones and Proteases, Heidelberg, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; German Cancer Research Center (DKFZ), A250 Chaperones and Proteases, Heidelberg, Germany.
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9
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Lee S, Roh SH, Lee J, Sung N, Liu J, Tsai FTF. Cryo-EM Structures of the Hsp104 Protein Disaggregase Captured in the ATP Conformation. Cell Rep 2020; 26:29-36.e3. [PMID: 30605683 PMCID: PMC6347426 DOI: 10.1016/j.celrep.2018.12.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/12/2018] [Accepted: 12/07/2018] [Indexed: 11/24/2022] Open
Abstract
Hsp104 is a ring-forming, ATP-driven molecular machine that recovers functional protein from both stress-denatured and amyloid-forming aggregates. Although Hsp104 shares a common architecture with Clp/Hsp100 protein unfoldases, different and seemingly conflicting 3D structures have been reported. Examining the structure of Hsp104 poses considerable challenges because Hsp104 readily hydrolyzes ATP, whereas ATP analogs can be slowly turned over and are often contaminated with other nucleotide species. Here, we present the single-particle electron cryo-microscopy (cryo-EM) structures of a catalytically inactive Hsp104 variant (Hsp104DWB) in the ATP-bound state determined between 7.7 Å and 9.3 Å resolution. Surprisingly, we observe that the Hsp104DWB hexamer adopts distinct ring conformations (closed, extended, and open) despite being in the same nucleotide state. The latter underscores the structural plasticity of Hsp104 in solution, with different conformations stabilized by nucleotide binding. Our findings suggest that, in addition to ATP hydrolysis-driven conformational changes, Hsp104 uses stochastic motions to translocate unfolded polypeptides. Hsp104 is a ring-forming ATPase that facilitates the disaggregation of amorphous and amyloid-forming protein aggregates. Lee et al. present three distinct cryo-EM structures of a catalytically inactive Hsp104-ATP variant, demonstrating that Hsp104 is a dynamic molecular machine and providing the structural basis for the passive threading of unfolded polypeptides.
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Affiliation(s)
- Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Soung Hun Roh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jungsoon Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nuri Sung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
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10
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Yu CI, King CY. Forms and abundance of chaperone proteins influence yeast prion variant competition. Mol Microbiol 2019; 111:798-810. [PMID: 30582872 DOI: 10.1111/mmi.14192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2018] [Indexed: 02/01/2023]
Abstract
[PSI+ ] variants are different infectious conformations of the same Sup35 protein. We show that when [PSI+ ] variants VK and VL co-infect a dividing host, only one prevails in the end and the host genetic background is involved in winner selection. In the 5V-H19 background, the VK variant dominates over the VL variant. The order of dominance is reversed in the 74-D694 background, where VL can coexists with VK for a short period, but will eventually take over. Differential interaction of chaperone proteins with distinct prion variant conformations can influence the outcome of competition. Expanding the Glycine/Methionine-rich domain of Sis1, an Hsp40 protein, helps the propagation of VL. Over-expression of the Hsp70 protein Ssa2 lowers the number of prion particles (propagons) in the cell. There is more reduction for VK than VL, causing the latter to dominate in some of the 5V-H19 and all of the 74-D694 cells tested. Consistently, depleting Ssa1 in 74-D694 strengthens VK. Swapping chromosomal alleles of SSA1/2 and SIS1 between 5V-H19 and 74-D694, including cognate promoters, is not sufficient to change the native dominance order of each background, suggesting there exist additional polymorphic factors that modulate [PSI+ ] competition.
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Affiliation(s)
- Chang-I Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Chih-Yen King
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
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11
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Cox D, Raeburn C, Sui X, Hatters DM. Protein aggregation in cell biology: An aggregomics perspective of health and disease. Semin Cell Dev Biol 2018; 99:40-54. [PMID: 29753879 DOI: 10.1016/j.semcdb.2018.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/21/2018] [Accepted: 05/04/2018] [Indexed: 01/08/2023]
Abstract
Maintaining protein homeostasis (proteostasis) is essential for cellular health and is governed by a network of quality control machinery comprising over 800 genes. When proteostasis becomes imbalanced, proteins can abnormally aggregate or become mislocalized. Inappropriate protein aggregation and proteostasis imbalance are two of the central pathological features of common neurodegenerative diseases including Alzheimer, Parkinson, Huntington, and motor neuron diseases. How aggregation contributes to the pathogenic mechanisms of disease remains incompletely understood. Here, we integrate some of the key and emerging ideas as to how protein aggregation relates to imbalanced proteostasis with an emphasis on Huntington disease as our area of main expertise. We propose the term "aggregomics" be coined in reference to how aggregation of particular proteins concomitantly influences the spatial organization and protein-protein interactions of the surrounding proteome. Meta-analysis of aggregated interactomes from various published datasets reveals chaperones and RNA-binding proteins are common components across various disease contexts. We conclude with an examination of therapeutic avenues targeting proteostasis mechanisms.
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Affiliation(s)
- Dezerae Cox
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Australia; Bio21 Molecular Science and Biotechnology Institute, Australia
| | - Candice Raeburn
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Australia; Bio21 Molecular Science and Biotechnology Institute, Australia
| | - Xiaojing Sui
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Australia; Bio21 Molecular Science and Biotechnology Institute, Australia
| | - Danny M Hatters
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Australia; Bio21 Molecular Science and Biotechnology Institute, Australia.
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12
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Structural determinants for protein unfolding and translocation by the Hsp104 protein disaggregase. Biosci Rep 2017; 37:BSR20171399. [PMID: 29175998 PMCID: PMC5741831 DOI: 10.1042/bsr20171399] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/17/2017] [Accepted: 11/22/2017] [Indexed: 01/23/2023] Open
Abstract
The ring-forming Hsp104 ATPase cooperates with Hsp70 and Hsp40 molecular chaperones to rescue stress-damaged proteins from both amorphous and amyloid-forming aggregates. The ability to do so relies upon pore loops present in the first ATP-binding domain (AAA-1; loop-1 and loop-2 ) and in the second ATP-binding domain (AAA-2; loop-3) of Hsp104, which face the protein translocating channel and couple ATP-driven changes in pore loop conformation to substrate translocation. A hallmark of loop-1 and loop-3 is an invariable and mutational sensitive aromatic amino acid (Tyr257 and Tyr662) involved in substrate binding. However, the role of conserved aliphatic residues (Lys256, Lys258, and Val663) flanking the pore loop tyrosines, and the function of loop-2 in protein disaggregation has not been investigated. Here we present the crystal structure of an N-terminal fragment of Saccharomyces cerevisiae Hsp104 exhibiting molecular interactions involving both AAA-1 pore loops, which resemble contacts with bound substrate. Corroborated by biochemical experiments and functional studies in yeast, we show that aliphatic residues flanking Tyr257 and Tyr662 are equally important for substrate interaction, and abolish Hsp104 function when mutated to glycine. Unexpectedly, we find that loop-2 is sensitive to aspartate substitutions that impair Hsp104 function and abolish protein disaggregation when loop-2 is replaced by four aspartate residues. Our observations suggest that Hsp104 pore loops have non-overlapping functions in protein disaggregation and together coordinate substrate binding, unfolding, and translocation through the Hsp104 hexamer.
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