1
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Iljina M, Mazal H, Goloubinoff P, Riven I, Haran G. Entropic Inhibition: How the Activity of a AAA+ Machine Is Modulated by Its Substrate-Binding Domain. ACS Chem Biol 2021; 16:775-785. [PMID: 33739813 PMCID: PMC8056383 DOI: 10.1021/acschembio.1c00156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
ClpB is a tightly regulated AAA+ disaggregation machine. Each ClpB molecule is composed of a flexibly attached N-terminal domain (NTD), an essential middle domain (MD) that activates the machine by tilting, and two nucleotide-binding domains. The NTD is not well-characterized structurally and is commonly considered to serve as a dispensable substrate-binding domain. Here, we use single-molecule FRET spectroscopy to directly monitor the real-time dynamics of ClpB's NTD and reveal its unexpected autoinhibitory function. We find that the NTD fluctuates on the microsecond time scale, and these dynamics result in steric hindrance that limits the conformational space of the MD to restrict its tilting. This leads to significantly inhibited ATPase and disaggregation activities of ClpB, an effect that is alleviated upon binding of a substrate protein or the cochaperone DnaK. This entropic inhibition mechanism, which is mediated by ultrafast motions of the NTD and is not dependent on any strong interactions, might be common in related ATP-dependent proteases and other multidomain proteins to ensure their fast and reversible activation.
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Affiliation(s)
- Marija Iljina
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
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2
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Shorter J, Southworth DR. Spiraling in Control: Structures and Mechanisms of the Hsp104 Disaggregase. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a034033. [PMID: 30745294 DOI: 10.1101/cshperspect.a034033] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hsp104 is a hexameric AAA+ ATPase and protein disaggregase found in yeast, which couples ATP hydrolysis to the dissolution of diverse polypeptides trapped in toxic preamyloid oligomers, phase-transitioned gels, disordered aggregates, amyloids, and prions. Hsp104 shows plasticity in disaggregating diverse substrates, but how its hexameric architecture operates as a molecular machine has remained unclear. Here, we highlight structural advances made via cryoelectron microscopy (cryo-EM) that enhance our mechanistic understanding of Hsp104 and other related AAA+ translocases. Hsp104 hexamers are dynamic and adopt open "lock-washer" spiral states and closed ring structures that envelope polypeptide substrate inside the axial channel. ATP hydrolysis-driven conformational changes at the spiral seam ratchet substrate deeper into the channel. Remarkably, this mode of polypeptide translocation is reminiscent of models for how hexameric helicases unwind DNA and RNA duplexes. Thus, Hsp104 likely adapts elements of a deeply rooted, ring-translocase mechanism to the specialized task of protein disaggregation.
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Affiliation(s)
- James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics; and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California 94158
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3
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Chamera T, Kłosowska A, Janta A, Wyszkowski H, Obuchowski I, Gumowski K, Liberek K. Selective Hsp70-Dependent Docking of Hsp104 to Protein Aggregates Protects the Cell from the Toxicity of the Disaggregase. J Mol Biol 2019; 431:2180-2196. [PMID: 31026451 DOI: 10.1016/j.jmb.2019.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/11/2019] [Accepted: 04/13/2019] [Indexed: 02/01/2023]
Abstract
Hsp104 is a yeast chaperone that rescues misfolded proteins from aggregates associated with proteotoxic stress and aging. Hsp104 consists of N-terminal domain, regulatory M-domain and two ATPase domains, assembled into a spiral-shaped hexamer. Protein disaggregation involves polypeptide extraction from an aggregate and its translocation through the central channel. This process relies on Hsp104 cooperation with the Hsp70 chaperone, which also plays important role in regulation of the disaggregase. Although Hsp104 protein-unfolding activity enables cells to survive stress, when uncontrolled, it becomes toxic to the cell. In this work, we investigated the significance of the interaction between Hsp70 and the M-domain of Hsp104 for functioning of the disaggregation system. We identified phenylalanine at position 508 in Hsp104 to be the key site of interaction with Hsp70. Disruption of this site makes Hsp104 unable to bind protein aggregates and to confer tolerance in yeast cells. The use of this Hsp104 variant demonstrates that Hsp70 allows successful initiation of disaggregation only as long as it is able to interact with the disaggregase. As reported previously, this interaction causes release of the M-domain-driven repression of Hsp104. Now we reveal that, apart from this allosteric effect, the interaction between the chaperone partners itself contributes to effective initiation of disaggregation and plays important role in cell protection against Hsp104-induced toxicity. Interaction with Hsp70 shifts Hsp104 substrate specificity from non-aggregated, disordered substrates toward protein aggregates. Accordingly, Hsp70-mediated sequestering of the Hsp104 unfoldase in aggregates makes it less toxic and more productive.
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Affiliation(s)
- Tomasz Chamera
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Agnieszka Kłosowska
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland.
| | - Anna Janta
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Hubert Wyszkowski
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Igor Obuchowski
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Krzysztof Gumowski
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland
| | - Krzysztof Liberek
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland.
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4
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de Marco A, Ferrer-Miralles N, Garcia-Fruitós E, Mitraki A, Peternel S, Rinas U, Trujillo-Roldán MA, Valdez-Cruz NA, Vázquez E, Villaverde A. Bacterial inclusion bodies are industrially exploitable amyloids. FEMS Microbiol Rev 2019; 43:53-72. [PMID: 30357330 DOI: 10.1093/femsre/fuy038] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022] Open
Abstract
Understanding the structure, functionalities and biology of functional amyloids is an issue of emerging interest. Inclusion bodies, namely protein clusters formed in recombinant bacteria during protein production processes, have emerged as unanticipated, highly tunable models for the scrutiny of the physiology and architecture of functional amyloids. Based on an amyloidal skeleton combined with varying amounts of native or native-like protein forms, bacterial inclusion bodies exhibit an unusual arrangement that confers mechanical stability, biological activity and conditional protein release, being thus exploitable as versatile biomaterials. The applicability of inclusion bodies in biotechnology as enriched sources of protein and reusable catalysts, and in biomedicine as biocompatible topographies, nanopills or mimetics of endocrine secretory granules has been largely validated. Beyond these uses, the dissection of how recombinant bacteria manage the aggregation of functional protein species into structures of highly variable complexity offers insights about unsuspected connections between protein quality (conformational status compatible with functionality) and cell physiology.
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Affiliation(s)
- Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000 Nova Gorica, Slovenia
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Vassilika Vouton, 70013 Heraklion, Crete, Greece.,Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology Hellas (FORTH), N. Plastira 100, Vassilika Vouton, 70013 Heraklion, Crete, Greece
| | | | - Ursula Rinas
- Leibniz University of Hannover, Technical Chemistry and Life Science, 30167 Hannover, Germany.,Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Unidad de Bioprocesos, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, México
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina (IBB), Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,Departament de Genètica i de Microbiologia, Carrer de la Vall Moronta s/n, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Carrer de la Vall Moronta s/n, 08193 Cerdanyola del Vallès, Spain
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5
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Tripathi P, Parijat P, Patel VK, Batra JK. The amino-terminal domain of Mycobacterium tuberculosis ClpB protein plays a crucial role in its substrate disaggregation activity. FEBS Open Bio 2018; 8:1669-1690. [PMID: 30338218 PMCID: PMC6168691 DOI: 10.1002/2211-5463.12509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/03/2018] [Accepted: 08/08/2018] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is known to persist in extremely hostile environments within host macrophages. The ability to withstand such proteotoxic stress comes from its highly conserved molecular chaperone machinery. ClpB, a unique member of the AAA+ family of chaperones, is responsible for resolving aggregates in Mtb and many other bacterial pathogens. Mtb produces two isoforms of ClpB, a full length and an N-terminally truncated form (ClpB∆N), with the latter arising from an internal translation initiation site. It is not clear why this internal start site is conserved and what role the N-terminal domain (NTD) of Mtb ClpB plays in its function. In the current study, we functionally characterized and compared the two isoforms of Mtb ClpB. We found the NTD to be dispensable for oligomerization, ATPase activity and prevention of aggregation activity of ClpB. Both ClpB and ClpB∆N were found to be capable of resolubilizing protein aggregates. However, the efficiency of ClpB∆N at resolubilizing higher order aggregates was significantly lower than that of ClpB. Further, ClpB∆N exhibited reduced affinity for substrates as compared to ClpB. We also demonstrated that the surface of the NTD of Mtb ClpB has a hydrophobic groove that contains four hydrophobic residues: L97, L101, F140 and V141. These residues act as initial contacts for the substrate and are crucial for stable interaction between ClpB and highly aggregated substrates.
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Affiliation(s)
| | - Priyanka Parijat
- National Institute of ImmunologyNew DelhiIndia
- Present address:
Randall Division of Cell and Molecular BiophysicsKing's College LondonUK
| | | | - Janendra K. Batra
- National Institute of ImmunologyNew DelhiIndia
- Department of BiochemistrySchool of Chemical and Life SciencesJamia HamdardNew DelhiIndia
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6
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Durie CL, Duran EC, Lucius AL. Escherichia coli DnaK Allosterically Modulates ClpB between High- and Low-Peptide Affinity States. Biochemistry 2018; 57:3665-3675. [PMID: 29812913 DOI: 10.1021/acs.biochem.8b00045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
ClpB and DnaKJE provide protection to Escherichia coli cells during extreme environmental stress. Together, this co-chaperone system can resolve protein aggregates, restoring misfolded proteins to their native form and function in solubilizing damaged proteins for removal by the cell's proteolytic systems. DnaK is the component of the KJE system that directly interacts with ClpB. There are many hypotheses for how DnaK affects ClpB-catalyzed disaggregation, each with some experimental support. Here, we build on our recent work characterizing the molecular mechanism of ClpB-catalyzed polypeptide translocation by developing a stopped-flow FRET assay that allows us to detect ClpB's movement on model polypeptide substrates in the absence or presence of DnaK. We find that DnaK induces ClpB to dissociate from the polypeptide substrate. We propose that DnaK acts as a peptide release factor, binding ClpB and causing the ClpB conformation to change to a low-peptide affinity state. Such a role for DnaK would allow ClpB to rebind to another portion of an aggregate and continue nonprocessive translocation to disrupt the aggregate.
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Affiliation(s)
- Clarissa L Durie
- Department of Chemistry , University of Alabama at Birmingham , Birmingham , Alabama 35294-1240 , United States
| | - Elizabeth C Duran
- Department of Chemistry , University of Alabama at Birmingham , Birmingham , Alabama 35294-1240 , United States
| | - Aaron L Lucius
- Department of Chemistry , University of Alabama at Birmingham , Birmingham , Alabama 35294-1240 , United States
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7
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Johnston CL, Marzano NR, van Oijen AM, Ecroyd H. Using Single-Molecule Approaches to Understand the Molecular Mechanisms of Heat-Shock Protein Chaperone Function. J Mol Biol 2018; 430:4525-4546. [PMID: 29787765 DOI: 10.1016/j.jmb.2018.05.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/11/2018] [Accepted: 05/13/2018] [Indexed: 02/01/2023]
Abstract
The heat-shock proteins (Hsp) are a family of molecular chaperones, which collectively form a network that is critical for the maintenance of protein homeostasis. Traditional ensemble-based measurements have provided a wealth of knowledge on the function of individual Hsps and the Hsp network; however, such techniques are limited in their ability to resolve the heterogeneous, dynamic and transient interactions that molecular chaperones make with their client proteins. Single-molecule techniques have emerged as a powerful tool to study dynamic biological systems, as they enable rare and transient populations to be identified that would usually be masked in ensemble measurements. Thus, single-molecule techniques are particularly amenable for the study of Hsps and have begun to be used to reveal novel mechanistic details of their function. In this review, we discuss the current understanding of the chaperone action of Hsps and how gaps in the field can be addressed using single-molecule methods. Specifically, this review focuses on the ATP-independent small Hsps and the broader Hsp network and describes how these dynamic systems are amenable to single-molecule techniques.
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Affiliation(s)
- Caitlin L Johnston
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Nicholas R Marzano
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Antoine M van Oijen
- School of Chemistry, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| | - Heath Ecroyd
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
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8
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Activation of the DnaK-ClpB Complex is Regulated by the Properties of the Bound Substrate. Sci Rep 2018; 8:5796. [PMID: 29643454 PMCID: PMC5895705 DOI: 10.1038/s41598-018-24140-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 03/28/2018] [Indexed: 12/20/2022] Open
Abstract
The chaperone ClpB in bacteria is responsible for the reactivation of aggregated proteins in collaboration with the DnaK system. Association of these chaperones at the aggregate surface stimulates ATP hydrolysis, which mediates substrate remodeling. However, a question that remains unanswered is whether the bichaperone complex can be selectively activated by substrates that require remodeling. We find that large aggregates or bulky, native-like substrates activates the complex, whereas a smaller, permanently unfolded protein or extended, short peptides fail to stimulate it. Our data also indicate that ClpB interacts differently with DnaK in the presence of aggregates or small peptides, displaying a higher affinity for aggregate-bound DnaK, and that DnaK-ClpB collaboration requires the coupled ATPase-dependent remodeling activities of both chaperones. Complex stimulation is mediated by residues at the β subdomain of DnaK substrate binding domain, which become accessible to the disaggregase when the lid is allosterically detached from the β subdomain. Complex activation also requires an active NBD2 and the integrity of the M domain-ring of ClpB. Disruption of the M-domain ring allows the unproductive stimulation of the DnaK-ClpB complex in solution. The ability of the DnaK-ClpB complex to discrimínate different substrate proteins might allow its activation when client proteins require remodeling.
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9
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Fusion protein analysis reveals the precise regulation between Hsp70 and Hsp100 during protein disaggregation. Sci Rep 2017; 7:8648. [PMID: 28819163 PMCID: PMC5561102 DOI: 10.1038/s41598-017-08917-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/13/2017] [Indexed: 12/19/2022] Open
Abstract
ClpB, a bacterial Hsp100, is a ring-shaped AAA+ chaperone that can reactivate aggregated proteins in cooperation with DnaK, a bacterial Hsp70, and its co-factors. ClpB subunits comprise two AAA+ modules with an interstitial rod-shaped M-domain. The M-domain regulates ClpB ATPase activity and interacts directly with the DnaK nucleotide-binding domain (NBD). Here, to clarify how these functions contribute to the disaggregation process, we constructed ClpB, DnaK, and aggregated YFP fusion proteins in various combinations. Notably, i) DnaK activates ClpB only when the DnaK substrate-binding domain (SBD) is in the closed conformation, affording high DnaK-peptide affinity; ii) although NBD alone can activate ClpB, SBD is required for disaggregation; and iii) tethering aggregated proteins to the activated ClpB obviates SBD requirements. These results indicate that DnaK activates ClpB only when the SBD tightly holds aggregated proteins adjacent to ClpB for effective disaggregation.
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10
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Duran EC, Weaver CL, Lucius AL. Comparative Analysis of the Structure and Function of AAA+ Motors ClpA, ClpB, and Hsp104: Common Threads and Disparate Functions. Front Mol Biosci 2017; 4:54. [PMID: 28824920 PMCID: PMC5540906 DOI: 10.3389/fmolb.2017.00054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/13/2017] [Indexed: 11/25/2022] Open
Abstract
Cellular proteostasis involves not only the expression of proteins in response to environmental needs, but also the timely repair or removal of damaged or unneeded proteins. AAA+ motor proteins are critically involved in these pathways. Here, we review the structure and function of AAA+ proteins ClpA, ClpB, and Hsp104. ClpB and Hsp104 rescue damaged proteins from toxic aggregates and do not partner with any protease. ClpA functions as the regulatory component of the ATP dependent protease complex ClpAP, and also remodels inactive RepA dimers into active monomers in the absence of the protease. Because ClpA functions both with and without a proteolytic component, it is an ideal system for developing strategies that address one of the major challenges in the study of protein remodeling machines: how do we observe a reaction in which the substrate protein does not undergo covalent modification? Here, we review experimental designs developed for the examination of polypeptide translocation catalyzed by the AAA+ motors in the absence of proteolytic degradation. We propose that transient state kinetic methods are essential for the examination of elementary kinetic mechanisms of these motor proteins. Furthermore, rigorous kinetic analysis must also account for the thermodynamic properties of these complicated systems that reside in a dynamic equilibrium of oligomeric states, including the biologically active hexamer.
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Affiliation(s)
- Elizabeth C Duran
- Department of Chemistry, University of Alabama at BirminghamBirmingham, AL, United States
| | - Clarissa L Weaver
- Department of Chemistry, University of Alabama at BirminghamBirmingham, AL, United States
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at BirminghamBirmingham, AL, United States
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11
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Coordinated Hsp110 and Hsp104 Activities Power Protein Disaggregation in Saccharomyces cerevisiae. Mol Cell Biol 2017; 37:MCB.00027-17. [PMID: 28289075 PMCID: PMC5440654 DOI: 10.1128/mcb.00027-17] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/06/2017] [Indexed: 01/16/2023] Open
Abstract
Protein aggregation is intimately associated with cellular stress and is accelerated during aging, disease, and cellular dysfunction. Yeast cells rely on the ATP-consuming chaperone Hsp104 to disaggregate proteins together with Hsp70. Hsp110s are ancient and abundant chaperones that form complexes with Hsp70. Here we provide in vivo data showing that the Saccharomyces cerevisiae Hsp110s Sse1 and Sse2 are essential for Hsp104-dependent protein disaggregation. Following heat shock, complexes of Hsp110 and Hsp70 are recruited to protein aggregates and function together with Hsp104 in the disaggregation process. In the absence of Hsp110, targeting of Hsp70 and Hsp104 to the aggregates is impaired, and the residual Hsp104 that still reaches the aggregates fails to disaggregate. Thus, coordinated activities of both Hsp104 and Hsp110 are required to reactivate aggregated proteins. These findings have important implications for the understanding of how eukaryotic cells manage misfolded and amyloid proteins.
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12
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Franke KB, Bukau B, Mogk A. Mutant Analysis Reveals Allosteric Regulation of ClpB Disaggregase. Front Mol Biosci 2017; 4:6. [PMID: 28275610 PMCID: PMC5319980 DOI: 10.3389/fmolb.2017.00006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
The members of the hexameric AAA+ disaggregase of E. coli and S. cerevisiae, ClpB, and Hsp104, cooperate with the Hsp70 chaperone system in the solubilization of aggregated proteins. Aggregate solubilization relies on a substrate threading activity of ClpB/Hsp104 fueled by ATP hydrolysis in both ATPase rings (AAA-1, AAA-2). ClpB/Hsp104 ATPase activity is controlled by the M-domains, which associate to the AAA-1 ring to downregulate ATP hydrolysis. Keeping M-domains displaced from the AAA-1 ring by association with Hsp70 increases ATPase activity due to enhanced communication between protomers. This communication involves conserved arginine fingers. The control of ClpB/Hsp104 activity is crucial, as hyperactive mutants with permanently dissociated M-domains exhibit cellular toxicity. Here, we analyzed AAA-1 inter-ring communication in relation to the M-domain mediated ATPase regulation, by subjecting a conserved residue of the AAA-1 domain subunit interface of ClpB (A328) to mutational analysis. While all A328X mutants have reduced disaggregation activities, their ATPase activities strongly differed. ClpB-A328I/L mutants have reduced ATPase activity and when combined with the hyperactive ClpB-K476C M-domain mutation, suppress cellular toxicity. This underlines that ClpB ATPase activation by M-domain dissociation relies on increased subunit communication. The ClpB-A328V mutant in contrast has very high ATPase activity and exhibits cellular toxicity on its own, qualifying it as novel hyperactive ClpB mutant. ClpB-A328V hyperactivity is however, different from that of M-domain mutants as M-domains stay associated with the AAA-1 ring. The high ATPase activity of ClpB-A328V primarily relies on the AAA-2 ring and correlates with distinct conformational changes in the AAA-2 catalytic site. These findings characterize the subunit interface residue A328 as crucial regulatory element to control ATP hydrolysis in both AAA rings.
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Affiliation(s)
- Kamila B Franke
- Center for Molecular Biology of the Heidelberg University, German Cancer Research Center Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of the Heidelberg University, German Cancer Research Center Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of the Heidelberg University, German Cancer Research Center Heidelberg, Germany
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13
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Spiral architecture of the Hsp104 disaggregase reveals the basis for polypeptide translocation. Nat Struct Mol Biol 2016; 23:830-7. [PMID: 27478928 DOI: 10.1038/nsmb.3277] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/11/2016] [Indexed: 12/28/2022]
Abstract
Hsp104, a conserved AAA+ protein disaggregase, promotes survival during cellular stress. Hsp104 remodels amyloids, thereby supporting prion propagation, and disassembles toxic oligomers associated with neurodegenerative diseases. However, a definitive structural mechanism for its disaggregase activity has remained elusive. We determined the cryo-EM structure of wild-type Saccharomyces cerevisiae Hsp104 in the ATP state, revealing a near-helical hexamer architecture that coordinates the mechanical power of the 12 AAA+ domains for disaggregation. An unprecedented heteromeric AAA+ interaction defines an asymmetric seam in an apparent catalytic arrangement that aligns the domains in a two-turn spiral. N-terminal domains form a broad channel entrance for substrate engagement and Hsp70 interaction. Middle-domain helices bridge adjacent protomers across the nucleotide pocket, thus explaining roles in ATP hydrolysis and protein disaggregation. Remarkably, substrate-binding pore loops line the channel in a spiral arrangement optimized for substrate transfer across the AAA+ domains, thereby establishing a continuous path for polypeptide translocation.
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14
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Comparative Proteomic Analysis of Streptomyces aureochromogenes Under Different Carbon Sources and Insights into Polyoxin Production. Appl Biochem Biotechnol 2016; 180:491-503. [DOI: 10.1007/s12010-016-2112-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
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15
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Lin J, Lucius AL. Examination of ClpB Quaternary Structure and Linkage to Nucleotide Binding. Biochemistry 2016; 55:1758-71. [PMID: 26891079 DOI: 10.1021/acs.biochem.6b00122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Escherichia coli caseinolytic peptidase B (ClpB) is a molecular chaperone with the unique ability to catalyze protein disaggregation in collaboration with the KJE system of chaperones. Like many AAA+ molecular motors, ClpB assembles into hexameric rings, and this reaction is thermodynamically linked to nucleotide binding. Here we show that ClpB exists in a dynamic equilibrium of monomers, dimers, tetramers, and hexamers in the presence of both limiting and excess ATPγS. We find that ClpB monomer is only able to bind one nucleotide, whereas all 12 sites in the hexameric ring are bound by nucleotide at saturating concentrations. Interestingly, dimers and tetramers exhibit stoichiometries of ∼3 and 7, respectively, which is one fewer than the maximum number of binding sites in the formed oligomer. This observation suggests an open conformation for the intermediates based on the need for an adjacent monomer to fully form the binding pocket. We also report the protein-protein interaction constants for dimers, tetramers, and hexamers and their dependencies on nucleotide. These interaction constants make it possible to predict the concentration of hexamers present and able to bind to cochaperones and polypeptide substrates. Such information is essential for the interpretation of many in vitro studies. Finally, the strategies presented here are broadly applicable to a large number of AAA+ molecular motors that assemble upon nucleotide binding and interact with partner proteins.
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Affiliation(s)
- JiaBei Lin
- Department of Chemistry, The University of Alabama at Birmingham , 1530 Third Avenue S, Birmingham, Alabama 35294-1240, United States
| | - Aaron L Lucius
- Department of Chemistry, The University of Alabama at Birmingham , 1530 Third Avenue S, Birmingham, Alabama 35294-1240, United States
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Chaperone-assisted protein aggregate reactivation: Different solutions for the same problem. Arch Biochem Biophys 2015; 580:121-34. [PMID: 26159839 DOI: 10.1016/j.abb.2015.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 12/15/2022]
Abstract
The oligomeric AAA+ chaperones Hsp104 in yeast and ClpB in bacteria are responsible for the reactivation of aggregated proteins, an activity essential for cell survival during severe stress. The protein disaggregase activity of these members of the Hsp100 family is linked to the activity of chaperones from the Hsp70 and Hsp40 families. The precise mechanism by which these proteins untangle protein aggregates remains unclear. Strikingly, Hsp100 proteins are not present in metazoans. This does not mean that animal cells do not have a disaggregase activity, but that this activity is performed by the Hsp70 system and a representative of the Hsp110 family instead of a Hsp100 protein. This review describes the actual view of Hsp100-mediated aggregate reactivation, including the ATP-induced conformational changes associated with their disaggregase activity, the dynamics of the oligomeric assembly that is regulated by its ATPase cycle and the DnaK system, and the tight allosteric coupling between the ATPase domains within the hexameric ring complexes. The lack of homologs of these disaggregases in metazoans has suggested that they might be used as potential targets to develop antimicrobials. The current knowledge of the human disaggregase machinery and the role of Hsp110 are also discussed.
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Alfonso C, del Castillo U, Martín I, Muga A, Rivas G. Sedimentation Equilibrium Analysis of ClpB Self-Association in Diluted and Crowded Solutions. Methods Enzymol 2015; 562:135-60. [PMID: 26412650 DOI: 10.1016/bs.mie.2015.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
ClpB belongs to the Hsp100 family of ring-forming heat-shock proteins involved in degradation of unfolded/misfolded proteins and in reactivation of protein aggregates. ClpB monomers reversibly associate to form the hexameric molecular chaperone that, together with the DnaK system, has the ability to disaggregate stress-denatured proteins. Here, we summarize the use of sedimentation equilibrium approaches, complemented with sedimentation velocity and composition-gradient static light scattering measurements, to study the self-association properties of ClpB in dilute and crowded solutions. As the functional unit of ClpB is the hexamer, we study the effect of environmental factors, i.e., ionic strength and natural ligands, in the association equilibrium of ClpB as well as the role of the flexible N-terminal and M domains of the protein in the self-association process. The application of the nonideal sedimentation equilibrium technique to measure the effects of volume exclusion, reproducing in part the natural crowded conditions inside a cell, on the self-association and on the stability of the oligomeric species of the disaggregase will be described. Finally, the biochemical and physiological implications of these studies and future experimental challenges to eventually reconstitute minimal disaggregating machineries will be discussed.
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Affiliation(s)
- Carlos Alfonso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Urko del Castillo
- Unidad de Biofísica (CSIC/UPV-EHU), Departamento de Bioquímica y Biología Molecular, Universidad de País Vasco-Euskal Herriko Unibertsitatea (UPV-EHU), Bilbao, Biscay, Spain
| | - Ianire Martín
- Unidad de Biofísica (CSIC/UPV-EHU), Departamento de Bioquímica y Biología Molecular, Universidad de País Vasco-Euskal Herriko Unibertsitatea (UPV-EHU), Bilbao, Biscay, Spain
| | - Arturo Muga
- Unidad de Biofísica (CSIC/UPV-EHU), Departamento de Bioquímica y Biología Molecular, Universidad de País Vasco-Euskal Herriko Unibertsitatea (UPV-EHU), Bilbao, Biscay, Spain.
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
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Mogk A, Kummer E, Bukau B. Cooperation of Hsp70 and Hsp100 chaperone machines in protein disaggregation. Front Mol Biosci 2015; 2:22. [PMID: 26042222 PMCID: PMC4436881 DOI: 10.3389/fmolb.2015.00022] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/04/2015] [Indexed: 11/13/2022] Open
Abstract
Unicellular and sessile organisms are particularly exposed to environmental stress such as heat shock causing accumulation and aggregation of misfolded protein species. To counteract protein aggregation, bacteria, fungi, and plants encode a bi-chaperone system composed of ATP-dependent Hsp70 and hexameric Hsp100 (ClpB/Hsp104) chaperones, which rescue aggregated proteins and provide thermotolerance to cells. The partners act in a hierarchic manner with Hsp70 chaperones coating first the surface of protein aggregates and next recruiting Hsp100 through direct physical interaction. Hsp100 proteins bind to the ATPase domain of Hsp70 via their unique M-domain. This extra domain functions as a molecular toggle allosterically controlling ATPase and threading activities of Hsp100. Interactions between neighboring M-domains and the ATPase ring keep Hsp100 in a repressed state exhibiting low ATP turnover. Breakage of intermolecular M-domain interactions and dissociation of M-domains from the ATPase ring relieves repression and allows for Hsp70 interaction. Hsp70 binding in turn stabilizes Hsp100 in the activated state and primes Hsp100 ATPase domains for high activity upon substrate interaction. Hsp70 thereby couples Hsp100 substrate binding and motor activation. Hsp100 activation presumably relies on increased subunit cooperation leading to high ATP turnover and threading power. This Hsp70-mediated activity control of Hsp100 is crucial for cell viability as permanently activated Hsp100 variants are toxic. Hsp100 activation requires simultaneous binding of multiple Hsp70 partners, restricting high Hsp100 activity to the surface of protein aggregates and ensuring Hsp100 substrate specificity.
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Affiliation(s)
- Axel Mogk
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance Heidelberg, Germany
| | - Eva Kummer
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance Heidelberg, Germany
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