1
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Hur JI, Kim J, Ryu S, Jeon B. ClpB enhances thermotolerance in Campylobacter jejuni through protein disaggregation independent of DnaK. Microbiol Spectr 2025:e0229324. [PMID: 40304467 DOI: 10.1128/spectrum.02293-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 04/04/2025] [Indexed: 05/02/2025] Open
Abstract
Campylobacter jejuni is a leading cause of foodborne infections worldwide and primarily transmitted to humans through the consumption of contaminated poultry meat. To enhance Campylobacter-associated food safety, it is critical to understand how C. jejuni survives during the thermal processing of poultry products. In this study, we monitored the survival of 86 C. jejuni strains during heat treatment and observed that some strains exhibited elevated heat tolerance. Notably, multilocus sequence typing clonal complex (CC)-443 and CC-607 were dominant among heat-tolerant strains, while the CC-21 strains were mostly heat-sensitive, indicating phylogenetic association with thermotolerance. We also investigated the function of heat shock chaperones in the thermotolerance of C. jejuni. Among several knockout mutants of heat shock chaperones, a mutant lacking clpB exhibited significantly lower survival than the wild type under heat treatment. Moreover, we observed a significantly higher accumulation of protein aggregates in the absence of ClpB, demonstrating that ClpB functions as a disaggregase during heat exposure. Additionally, ClpB from the heat-tolerant CC-443 group possessed distinct amino acid substitutions in the functional nucleotide-binding domain compared to ClpB in other CC groups. Interestingly, despite the well-known interaction of these proteins in many other bacteria, a two-hybrid assay demonstrated that ClpB of C. jejuni does not bind to DnaK, suggesting that C. jejuni may have a distinct mechanism for protein disaggregation and stress tolerance. Our findings demonstrate that ClpB plays a crucial role in the thermotolerance of C. jejuni through unique protein disaggregation mechanisms during poultry processing.IMPORTANCEThis study unveils a distinctive mechanism of thermotolerance involving protein disaggregation in Campylobacter jejuni, a major foodborne pathogen. Understanding C. jejuni's ability to withstand heat stress is crucial for comprehending the occurrence of Campylobacter infections resulting from the consumption of contaminated poultry meat. Our research elucidates the roles of heat shock proteins, particularly ClpB, in the thermotolerance of C. jejuni. These findings significantly contribute to our fundamental understanding of bacterial physiology related to stress tolerance, which has important implications for public health and food safety.
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Affiliation(s)
- Jeong In Hur
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Gwanak-gu, Seoul, South Korea
| | - Jinshil Kim
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Gwanak-gu, Seoul, South Korea
- Center for Food and Bioconvergence, Seoul National University, Gwanak-gu, Seoul, South Korea
- Department of Food Science and Biotechnology, and Carbohydrate Bioproduct Research Center, Sejong University, Gwangjin-gu, Seoul, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Gwanak-gu, Seoul, South Korea
- Center for Food and Bioconvergence, Seoul National University, Gwanak-gu, Seoul, South Korea
| | - Byeonghwa Jeon
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
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2
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Singh D, Tripathi P, Sharma R, Grover S, Batra JK. Role of a substrate binding pocket in the amino terminal domain of Mycobacterium tuberculosis caseinolytic protease B (ClpB) in its function. J Biomol Struct Dyn 2024; 42:6189-6199. [PMID: 37418201 DOI: 10.1080/07391102.2023.2232032] [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: 12/28/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis when infects the host encounters several stresses within the host, resulting in aggregation of its proteins. To resolve this problem Mtb uses chaperones to either repair the damage or degrade the aggregated proteins. Mtb caseinolytic protein B (ClpB) helps in the prevention of aggregation and also resolubilization of aggregated proteins in bacteria, which is important for the survival of Mtb in the host. To function optimally, ClpB associates with its co-partners DnaK, DnaJ, and GrpE. The role of N-terminal domain (NTD) of Mtb ClpB in its function is not well understood. In this context, we investigated the interaction of three substrate mimicking peptides with the NTD of Mtb ClpB in silico. A substrate binding pocket, within the NTD of ClpB comprising of residues L136, R137, E138, K142, R144, R148, V149, Y158, and Y162 forming an ɑ-helix was thus identified. The residues L136 and R137 of the ɑ-helix were found to be important for the interaction of DnaK to ClpB. Further, nine single alanine recombinant variants of the identified residues were generated. As compared to the wild-type Mtb ClpB all the Mtb ClpB variants generated in this study were found to have reduced ATPase and protein refolding activity indicating the importance of the substrate binding pocket in ClpB function. The study demonstrates that the NTD of Mtb ClpB is important for its substrate interaction activity, and the substrate binding pocket identified in this study plays a crucial role in this interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Digvijay Singh
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | | | - Rahul Sharma
- Department of Molecular Medicine, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Sonam Grover
- Department of Molecular Medicine, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Janendra K Batra
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
- ICMR-National Institute of Pathology, Safdarjung Hospital Complex, New Delhi, India
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3
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Iljina M, Mazal H, Dayananda A, Zhang Z, Stan G, Riven I, Haran G. Single-molecule FRET probes allosteric effects on protein-translocating pore loops of a AAA+ machine. Biophys J 2024; 123:374-388. [PMID: 38196191 PMCID: PMC10870172 DOI: 10.1016/j.bpj.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
AAA+ proteins (ATPases associated with various cellular activities) comprise a family of powerful ring-shaped ATP-dependent translocases that carry out numerous vital substrate-remodeling functions. ClpB is a AAA+ protein disaggregation machine that forms a two-tiered hexameric ring, with flexible pore loops protruding into its center and binding to substrate proteins. It remains unknown whether these pore loops contribute only passively to substrate-protein threading or have a more active role. Recently, we have applied single-molecule FRET spectroscopy to directly measure the dynamics of substrate-binding pore loops in ClpB. We have reported that the three pore loops of ClpB (PL1-3) undergo large-scale fluctuations on the microsecond timescale that are likely to be mechanistically important for disaggregation. Here, using single-molecule FRET, we study the allosteric coupling between the pore loops and the two nucleotide-binding domains of ClpB (NBD1-2). By mutating the conserved Walker B motifs within the NBDs to abolish ATP hydrolysis, we demonstrate how the nucleotide state of each NBD tunes pore-loop dynamics. This effect is surprisingly long-ranged; in particular, PL2 and PL3 respond differentially to a Walker B mutation in either NBD1 or NBD2, as well as to mutations in both. We characterize the conformational dynamics of pore loops and the allosteric paths connecting NBDs to pore loops by molecular dynamics simulations and find that both principal motions and allosteric paths can be altered by changing the ATPase state of ClpB. Remarkably, PL3, which is highly conserved in AAA+ machines, is found to favor an upward conformation when only NBD1 undergoes ATP hydrolysis but a downward conformation when NBD2 is active. These results explicitly demonstrate a significant long-range allosteric effect of ATP hydrolysis sites on pore-loop dynamics. Pore loops are therefore established as active participants that undergo ATP-dependent conformational changes to translocate substrate proteins through the central pores of AAA+ machines.
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Affiliation(s)
- Marija Iljina
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Ashan Dayananda
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio
| | - Zhaocheng Zhang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio.
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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4
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Lao S, Xiong S, Fang Q, Ye G. Identification and functional analysis of αB-crystallins in Pteromalus puparum. Front Physiol 2023; 14:1214835. [PMID: 37520833 PMCID: PMC10382227 DOI: 10.3389/fphys.2023.1214835] [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: 04/30/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Heat shock proteins, including αB-crystallins (CRYAB), are pivotal in cellular defense mechanisms and stress response. This study presents a comprehensive investigation of heat shock proteins (HSPs), with a specific focus on the CRYAB family, within the genome of Pteromalus puparum. The analysis encompasses the identification of these proteins, exploration of their phylogenetic relationships, examination of conserved domains, and evaluation of their response to high temperature conditions. A total of 46 HSPs were identified in the P. puparum genome, and the differential expression of mRNA at 35°C and 25°C drew attention to five genes belonging to the CRYAB family, namely, PpCRYAB-1 to PpCRYAB-5. The conservation level of CRYAB family genes across different species was observed to be relatively modest. Through genome-wide screening of 22 species representing six insect orders, a total of 235 CRYAB proteins were identified, with P. puparum harboring eight CRYAB proteins, indicative of a moderate abundance compared to other species. Intriguingly, evolutionary analysis highlighted PpCRYAB-4 with potentially intricate differentiation in comparison to other members of the CRYAB family. Furthermore, RNA interference (RNAi) results demonstrated significant regulatory effects on adult lifespan under heat stress at 35°C for PpCRYAB-4 and PpCRYAB-5. These findings lay a groundwork for future investigations into stress resistance mechanisms in parasitic wasps, providing fresh insights for the study of insect resilience amidst the backdrop of global climate change.
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Kim H, Moon S, Ham S, Lee K, Römling U, Lee C. Cytoplasmic molecular chaperones in Pseudomonas species. J Microbiol 2022; 60:1049-1060. [PMID: 36318358 DOI: 10.1007/s12275-022-2425-0] [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: 09/21/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Pseudomonas is widespread in various environmental and host niches. To promote rejuvenation, cellular protein homeostasis must be finely tuned in response to diverse stresses, such as extremely high and low temperatures, oxidative stress, and desiccation, which can result in protein homeostasis imbalance. Molecular chaperones function as key components that aid protein folding and prevent protein denaturation. Pseudomonas, an ecologically important bacterial genus, includes human and plant pathogens as well as growth-promoting symbionts and species useful for bioremediation. In this review, we focus on protein quality control systems, particularly molecular chaperones, in ecologically diverse species of Pseudomonas, including the opportunistic human pathogen Pseudomonas aeruginosa, the plant pathogen Pseudomonas syringae, the soil species Pseudomonas putida, and the psychrophilic Pseudomonas antarctica.
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Affiliation(s)
- Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Seongjoon Moon
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Soojeong Ham
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Kihyun Lee
- CJ Bioscience, Seoul, 04527, Republic of Korea
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea.
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6
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Riven I, Mazal H, Iljina M, Haran G. Fast dynamics shape the function of the
AAA
+ machine
ClpB
: lessons from single‐molecule
FRET
spectroscopy. FEBS J 2022. [DOI: 10.1111/febs.16539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/04/2022] [Accepted: 05/30/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Inbal Riven
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
| | - Hisham Mazal
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
| | - Marija Iljina
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics Weizmann Institute of Science Rehovot Israel
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7
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Katikaridis P, Bohl V, Mogk A. Resisting the Heat: Bacterial Disaggregases Rescue Cells From Devastating Protein Aggregation. Front Mol Biosci 2021; 8:681439. [PMID: 34017857 PMCID: PMC8129007 DOI: 10.3389/fmolb.2021.681439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/12/2021] [Indexed: 11/23/2022] Open
Abstract
Bacteria as unicellular organisms are most directly exposed to changes in environmental growth conditions like temperature increase. Severe heat stress causes massive protein misfolding and aggregation resulting in loss of essential proteins. To ensure survival and rapid growth resume during recovery periods bacteria are equipped with cellular disaggregases, which solubilize and reactivate aggregated proteins. These disaggregases are members of the Hsp100/AAA+ protein family, utilizing the energy derived from ATP hydrolysis to extract misfolded proteins from aggregates via a threading activity. Here, we describe the two best characterized bacterial Hsp100/AAA+ disaggregases, ClpB and ClpG, and compare their mechanisms and regulatory modes. The widespread ClpB disaggregase requires cooperation with an Hsp70 partner chaperone, which targets ClpB to protein aggregates. Furthermore, Hsp70 activates ClpB by shifting positions of regulatory ClpB M-domains from a repressed to a derepressed state. ClpB activity remains tightly controlled during the disaggregation process and high ClpB activity states are likely restricted to initial substrate engagement. The recently identified ClpG (ClpK) disaggregase functions autonomously and its activity is primarily controlled by substrate interaction. ClpG provides enhanced heat resistance to selected bacteria including pathogens by acting as a more powerful disaggregase. This disaggregase expansion reflects an adaption of bacteria to extreme temperatures experienced during thermal based sterilization procedures applied in food industry and medicine. Genes encoding for ClpG are transmissible by horizontal transfer, allowing for rapid spreading of extreme bacterial heat resistance and posing a threat to modern food production.
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Affiliation(s)
- Panagiotis Katikaridis
- Center for Molecular Biology of the Heidelberg University and German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Valentin Bohl
- Center for Molecular Biology of the Heidelberg University and German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of the Heidelberg University and German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
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8
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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: 10] [Impact Index Per Article: 2.5] [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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9
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PV1 Protein from Plasmodium falciparum Exhibits Chaperone-Like Functions and Cooperates with Hsp100s. Int J Mol Sci 2020; 21:ijms21228616. [PMID: 33207549 PMCID: PMC7697860 DOI: 10.3390/ijms21228616] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/17/2023] Open
Abstract
Plasmodium falciparum parasitophorous vacuolar protein 1 (PfPV1), a protein unique to malaria parasites, is localized in the parasitophorous vacuolar (PV) and is essential for parasite growth. Previous studies suggested that PfPV1 cooperates with the Plasmodium translocon of exported proteins (PTEX) complex to export various proteins from the PV. However, the structure and function of PfPV1 have not been determined in detail. In this study, we undertook the expression, purification, and characterization of PfPV1. The tetramer appears to be the structural unit of PfPV1. The activity of PfPV1 appears to be similar to that of molecular chaperones, and it may interact with various proteins. PfPV1 could substitute CtHsp40 in the CtHsp104, CtHsp70, and CtHsp40 protein disaggregation systems. Based on these results, we propose a model in which PfPV1 captures various PV proteins and delivers them to PTEX through a specific interaction with HSP101.
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10
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Rydzek S, Shein M, Bielytskyi P, Schütz AK. Observation of a Transient Reaction Intermediate Illuminates the Mechanochemical Cycle of the AAA-ATPase p97. J Am Chem Soc 2020; 142:14472-14480. [DOI: 10.1021/jacs.0c03180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Simon Rydzek
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Mikhail Shein
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Pavlo Bielytskyi
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Anne K. Schütz
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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11
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Deville C, Franke K, Mogk A, Bukau B, Saibil HR. Two-Step Activation Mechanism of the ClpB Disaggregase for Sequential Substrate Threading by the Main ATPase Motor. Cell Rep 2019; 27:3433-3446.e4. [PMID: 31216466 PMCID: PMC6593972 DOI: 10.1016/j.celrep.2019.05.075] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/26/2019] [Accepted: 05/20/2019] [Indexed: 11/20/2022] Open
Abstract
AAA+ proteins form asymmetric hexameric rings that hydrolyze ATP and thread substrate proteins through a central channel via mobile substrate-binding pore loops. Understanding how ATPase and threading activities are regulated and intertwined is key to understanding the AAA+ protein mechanism. We studied the disaggregase ClpB, which contains tandem ATPase domains (AAA1, AAA2) and shifts between low and high ATPase and threading activities. Coiled-coil M-domains repress ClpB activity by encircling the AAA1 ring. Here, we determine the mechanism of ClpB activation by comparing ATPase mechanisms and cryo-EM structures of ClpB wild-type and a constitutively active ClpB M-domain mutant. We show that ClpB activation reduces ATPase cooperativity and induces a sequential mode of ATP hydrolysis in the AAA2 ring, the main ATPase motor. AAA1 and AAA2 rings do not work synchronously but in alternating cycles. This ensures high grip, enabling substrate threading via a processive, rope-climbing mechanism.
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Affiliation(s)
- Célia Deville
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Kamila Franke
- Center for Molecular Biology of University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Bernd Bukau
- Center for Molecular Biology of University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Helen R Saibil
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK.
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12
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Cavalazzi B, Barbieri R, Gómez F, Capaccioni B, Olsson-Francis K, Pondrelli M, Rossi A, Hickman-Lewis K, Agangi A, Gasparotto G, Glamoclija M, Ori G, Rodriguez N, Hagos M. The Dallol Geothermal Area, Northern Afar (Ethiopia)-An Exceptional Planetary Field Analog on Earth. ASTROBIOLOGY 2019; 19:553-578. [PMID: 30653331 PMCID: PMC6459281 DOI: 10.1089/ast.2018.1926] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The Dallol volcano and its associated hydrothermal field are located in a remote area of the northern Danakil Depression in Ethiopia, a region only recently appraised after decades of inaccessibility due to severe political instability and the absence of infrastructure. The region is notable for hosting environments at the very edge of natural physical-chemical extremities. It is surrounded by a wide, hyperarid salt plain and is one of the hottest (average annual temperatureDallol: 36-38°C) and most acidic natural systems (pHDallol ≈0) on Earth. Spectacular geomorphologies and mineral deposits produced by supersaturated hydrothermal waters and brines are the result of complex interactions between active and inactive hydrothermal alteration of the bedrock, sulfuric hot springs and pools, fumaroles and geysers, and recrystallization processes driven by hydrothermal waters, degassing, and rapid evaporation. The study of planetary field analog environments plays a crucial role in characterizing the physical and chemical boundaries within which life can exist on Earth and other planets. It is essential for the definition and assessment of the conditions of habitability on other planets, including the possibility for biosignature preservation and in situ testing of technologies for life detection. The Dallol area represents an excellent Mars analog environment given that the active volcanic environment, the associated diffuse hydrothermalism and hydrothermal alteration, and the vast acidic sulfate deposits are reminiscent of past hydrothermal activity on Mars. The work presented in this paper is an overview of the Dallol volcanic area and its hydrothermal field that integrates previous literature with observations and results obtained from field surveys and monitoring coupled with sample characterization. In so doing, we highlight its exceptional potential as a planetary field analog as well as a site for future astrobiological and exploration programs.
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Affiliation(s)
- B. Cavalazzi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
- Address correspondence to: Barbara Cavalazzi, Dipartimento di Scienze Biologiche, Geologiche e Ambientali - BiGeA, Università di Bologna, Via Zamboni 67, I-40126 Bologna, Italy
| | - R. Barbieri
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - F. Gómez
- Centro de Astrobiologia and Instituto Nacional de Técnica Aeroespacial, Madrid, Spain
| | - B. Capaccioni
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - K. Olsson-Francis
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, United Kingdom
| | - M. Pondrelli
- Int'l Research School of Planetary Sciences, Università d'Annunzio, Chieti Scalo, Italy
| | | | - K. Hickman-Lewis
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- CNRS Centre de Biophysique Moléculaire, Orléans, France
| | - A. Agangi
- Department of Geology, University of Johannesburg, Johannesburg, South Africa
| | - G. Gasparotto
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - M. Glamoclija
- Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, USA
| | - G.G. Ori
- Int'l Research School of Planetary Sciences, Università d'Annunzio, Chieti Scalo, Italy
| | - N. Rodriguez
- Centro de Astrobiologia and Instituto Nacional de Técnica Aeroespacial, Madrid, Spain
| | - M. Hagos
- Department of Earth Sciences, Mekelle University, Mekelle, Ethiopia
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13
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Tunable microsecond dynamics of an allosteric switch regulate the activity of a AAA+ disaggregation machine. Nat Commun 2019; 10:1438. [PMID: 30926805 PMCID: PMC6440998 DOI: 10.1038/s41467-019-09474-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/14/2019] [Indexed: 12/13/2022] Open
Abstract
Large protein machines are tightly regulated through allosteric communication channels. Here we demonstrate the involvement of ultrafast conformational dynamics in allosteric regulation of ClpB, a hexameric AAA+ machine that rescues aggregated proteins. Each subunit of ClpB contains a unique coiled-coil structure, the middle domain (M domain), proposed as a control element that binds the co-chaperone DnaK. Using single-molecule FRET spectroscopy, we probe the M domain during the chaperone cycle and find it to jump on the microsecond time scale between two states, whose structures are determined. The M-domain jumps are much faster than the overall activity of ClpB, making it an effectively continuous, tunable switch. Indeed, a series of allosteric interactions are found to modulate the dynamics, including binding of nucleotides, DnaK and protein substrates. This mode of dynamic control enables fast cellular adaptation and may be a general mechanism for the regulation of cellular machineries. Large protein machines are tightly regulated through allosteric communication channels. Here authors use single-molecule FRET and demonstrate the involvement of ultrafast conformational dynamics in the allosteric regulation of ClpB, a hexameric AAA+ machine that rescues aggregated proteins.
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14
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Uchihashi T, Watanabe YH, Nakazaki Y, Yamasaki T, Watanabe H, Maruno T, Ishii K, Uchiyama S, Song C, Murata K, Iino R, Ando T. Dynamic structural states of ClpB involved in its disaggregation function. Nat Commun 2018; 9:2147. [PMID: 29858573 PMCID: PMC5984625 DOI: 10.1038/s41467-018-04587-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/09/2018] [Indexed: 11/09/2022] Open
Abstract
The ATP-dependent bacterial protein disaggregation machine, ClpB belonging to the AAA+ superfamily, refolds toxic protein aggregates into the native state in cooperation with the cognate Hsp70 partner. The ring-shaped hexamers of ClpB unfold and thread its protein substrate through the central pore. However, their function-related structural dynamics has remained elusive. Here we directly visualize ClpB using high-speed atomic force microscopy (HS-AFM) to gain a mechanistic insight into its disaggregation function. The HS-AFM movies demonstrate massive conformational changes of the hexameric ring during ATP hydrolysis, from a round ring to a spiral and even to a pair of twisted half-spirals. HS-AFM observations of Walker-motif mutants unveil crucial roles of ATP binding and hydrolysis in the oligomer formation and structural dynamics. Furthermore, repressed and hyperactive mutations result in significantly different oligomeric forms. These results provide a comprehensive view for the ATP-driven oligomeric-state transitions that enable ClpB to disentangle protein aggregates. The bacterial protein disaggregation machine ClpB uses ATP to generate mechanical force to unfold and thread its protein substrates. Here authors visualize the ClpB ring using high-speed atomic force microscopy and capture conformational changes of the hexameric ring during the ATPase reaction.
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Affiliation(s)
- Takayuki Uchihashi
- Department of Physics and Structural Biology Research Center, Nagoya University, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yo-Hei Watanabe
- Department of Biology, Faculty of Science and Engineering, Konan University, Okamoto 8-9-1, Kobe, 658-8501, Japan. .,Institute for Integrative Neurobiology, Konan University, Okamoto 8-9-1, Kobe, 658-8501, Japan.
| | - Yosuke Nakazaki
- Department of Biology, Faculty of Science and Engineering, Konan University, Okamoto 8-9-1, Kobe, 658-8501, Japan.,Institute for Integrative Neurobiology, Konan University, Okamoto 8-9-1, Kobe, 658-8501, Japan
| | - Takashi Yamasaki
- Department of Biology, Faculty of Science and Engineering, Konan University, Okamoto 8-9-1, Kobe, 658-8501, Japan.,Institute for Integrative Neurobiology, Konan University, Okamoto 8-9-1, Kobe, 658-8501, Japan
| | - Hiroki Watanabe
- Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Takahiro Maruno
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan
| | - Kentaro Ishii
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Chihong Song
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan
| | - Ryota Iino
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8787, Japan. .,Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Kanagawa, 240-0193, Japan.
| | - Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, 920-1192, Japan.
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15
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Ziemski M, Jomaa A, Mayer D, Rutz S, Giese C, Veprintsev D, Weber-Ban E. Cdc48-like protein of actinobacteria (Cpa) is a novel proteasome interactor in mycobacteria and related organisms. eLife 2018; 7:34055. [PMID: 29809155 PMCID: PMC6017811 DOI: 10.7554/elife.34055] [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: 12/03/2017] [Accepted: 05/21/2018] [Indexed: 01/18/2023] Open
Abstract
Cdc48 is a AAA+ ATPase that plays an essential role for many cellular processes in eukaryotic cells. An archaeal homologue of this highly conserved enzyme was shown to directly interact with the 20S proteasome. Here, we analyze the occurrence and phylogeny of a Cdc48 homologue in Actinobacteria and assess its cellular function and possible interaction with the bacterial proteasome. Our data demonstrate that Cdc48-like protein of actinobacteria (Cpa) forms hexameric rings and that the oligomeric state correlates directly with the ATPase activity. Furthermore, we show that the assembled Cpa rings can physically interact with the 20S core particle. Comparison of the Mycobacterium smegmatis wild-type with a cpa knockout strain under carbon starvation uncovers significant changes in the levels of around 500 proteins. Pathway mapping of the observed pattern of changes identifies ribosomal proteins as a particular hotspot, pointing amongst others toward a role of Cpa in ribosome adaptation during starvation. Cells use proteins to carry out the biological processes necessary for life. If a protein becomes damaged or is no longer needed, cells must dispose of it, just as we might take out the trash. The cell’s main ‘garbage disposal unit’ is the proteasome, a barrel-shaped molecular machine that breaks down unwanted proteins. The proteasome binds to other molecules called regulators, which select the proteins to be dismantled. The proteasomes of mycobacteria – a group that includes the bacteria that cause tuberculosis – help them to survive hostile or rapidly changing environments. Mycobacteria contain a molecule called Cpa whose structure is like a regulator that is found in many non-bacterial cells. Ziemski et al. therefore set out to investigate whether Cpa performs a similar role in bacteria. The results of biochemical experiments performed in test tubes revealed that Cpa forms rings made up of six copies of itself. These rings can bind to proteasomes. Ziemski et al. also created genetically modified mycobacteria that could not produce Cpa and studied how they coped with starvation. These modified bacteria stopped growing sooner than their similarly starved genetically normal counterparts. The two groups of bacteria also produced different amounts of some proteins. Ziemski et al. used a technique that pulled Cpa out of the starving genetically normal cells to analyse the proteins that Cpa physically interacts with. These proteins included building blocks of the ribosome, the cellular machinery that produces new proteins. It therefore appears that Cpa helps mycobacteria to cope with starvation by reducing the amount of protein made by the cell. Cpa may also help mycobacteria to survive in other stressful conditions, such as those that the bacteria experience when they infect the human body. Developing drugs that prevent Cpa from working could therefore potentially lead to new treatments for a number of diseases caused by mycobacteria, such as tuberculosis.
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Affiliation(s)
- Michal Ziemski
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Ahmad Jomaa
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Daniel Mayer
- Laboratory of Biomolecular Research, Paul Scherrer Institute, ETH Zurich, Villigen, Switzerland
| | - Sonja Rutz
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Christoph Giese
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Dmitry Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institute, ETH Zurich, Villigen, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
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16
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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: 1.4] [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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17
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Schwerter DP, Grimm I, Platta HW, Erdmann R. ATP-driven processes of peroxisomal matrix protein import. Biol Chem 2017; 398:607-624. [PMID: 27977397 DOI: 10.1515/hsz-2016-0293] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/11/2016] [Indexed: 12/13/2022]
Abstract
In peroxisomal matrix protein import two processes directly depend on the binding and hydrolysis of ATP, both taking place at the late steps of the peroxisomal import cycle. First, ATP hydrolysis is required to initiate a ubiquitin-transfer cascade to modify the import (co-)receptors. These receptors display a dual localization in the cytosol and at the peroxisomal membrane, whereas only the membrane bound fraction receives the ubiquitin modification. The second ATP-dependent process of the import cycle is carried out by the two AAA+-proteins Pex1p and Pex6p. These ATPases form a heterohexameric complex, which is recruited to the peroxisomal import machinery by the membrane anchor protein Pex15p. The Pex1p/Pex6p complex recognizes the ubiquitinated import receptors, pulls them out of the membrane and releases them into the cytosol. There the deubiquitinated receptors are provided for further rounds of import. ATP binding and hydrolysis are required for Pex1p/Pex6p complex formation and receptor export. In this review, we summarize the current knowledge on the peroxisomal import cascade. In particular, we will focus on the ATP-dependent processes, which are so far best understood in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Daniel P Schwerter
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
| | - Immanuel Grimm
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
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18
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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: 0.9] [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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19
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Kummer E, Szlachcic A, Franke KB, Ungelenk S, Bukau B, Mogk A. Bacterial and Yeast AAA + Disaggregases ClpB and Hsp104 Operate through Conserved Mechanism Involving Cooperation with Hsp70. J Mol Biol 2016; 428:4378-4391. [DOI: 10.1016/j.jmb.2016.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/10/2016] [Accepted: 09/06/2016] [Indexed: 11/28/2022]
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20
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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: 1.1] [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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21
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Lin J, Lucius AL. Examination of the dynamic assembly equilibrium for E. coli ClpB. Proteins 2015; 83:2008-24. [PMID: 26313457 DOI: 10.1002/prot.24914] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/03/2015] [Accepted: 08/18/2015] [Indexed: 12/17/2022]
Abstract
Escherichia coli ClpB is a heat shock protein that belongs to the AAA+ protein superfamily. Studies have shown that ClpB and its homologue in yeast, Hsp104, can disrupt protein aggregates in vivo. It is thought that ClpB requires binding of nucleoside triphosphate to assemble into hexameric rings with protein binding activity. In addition, it is widely assumed that ClpB is uniformly hexameric in the presence of nucleotides. Here we report, in the absence of nucleotide, that increasing ClpB concentration leads to ClpB hexamer formation, decreasing NaCl concentration stabilizes ClpB hexamers, and the ClpB assembly reaction is best described by a monomer, dimer, tetramer, hexamer equilibrium under the three salt concentrations examined. Further, we found that ClpB oligomers exhibit relatively fast dissociation on the time scale of sedimentation. We anticipate our studies on ClpB assembly to be a starting point to understand how ClpB assembly is linked to the binding and disaggregation of denatured proteins.
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Affiliation(s)
- JiaBei Lin
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
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22
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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: 2.5] [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: 0.5] [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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24
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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: 129] [Impact Index Per Article: 12.9] [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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25
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Yamasaki T, Oohata Y, Nakamura T, Watanabe YH. Analysis of the cooperative ATPase cycle of the AAA+ chaperone ClpB from Thermus thermophilus by using ordered heterohexamers with an alternating subunit arrangement. J Biol Chem 2015; 290:9789-800. [PMID: 25713084 DOI: 10.1074/jbc.m114.617696] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 01/17/2023] Open
Abstract
The ClpB/Hsp104 chaperone solubilizes and reactivates protein aggregates in cooperation with DnaK/Hsp70 and its cofactors. The ClpB/Hsp104 protomer has two AAA+ modules, AAA-1 and AAA-2, and forms a homohexamer. In the hexamer, these modules form a two-tiered ring in which each tier consists of homotypic AAA+ modules. By ATP binding and its hydrolysis at these AAA+ modules, ClpB/Hsp104 exerts the mechanical power required for protein disaggregation. Although ATPase cycle of this chaperone has been studied by several groups, an integrated understanding of this cycle has not been obtained because of the complexity of the mechanism and differences between species. To improve our understanding of the ATPase cycle, we prepared many ordered heterohexamers of ClpB from Thermus thermophilus, in which two subunits having different mutations were cross-linked to each other and arranged alternately and measured their nucleotide binding, ATP hydrolysis, and disaggregation abilities. The results indicated that the ATPase cycle of ClpB proceeded as follows: (i) the 12 AAA+ modules randomly bound ATP, (ii) the binding of four or more ATP to one AAA+ ring was sensed by a conserved Arg residue and converted another AAA+ ring into the ATPase-active form, and (iii) ATP hydrolysis occurred cooperatively in each ring. We also found that cooperative ATP hydrolysis in at least one ring was needed for the disaggregation activity of ClpB.
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Affiliation(s)
- Takashi Yamasaki
- From the Department of Biology, Faculty of Science and Engineering and the Institute for Integrative Neurobiology, Konan University, Okamoto 8-9-1, Kobe 658-8501, Japan
| | - Yukiko Oohata
- From the Department of Biology, Faculty of Science and Engineering and
| | - Toshiki Nakamura
- From the Department of Biology, Faculty of Science and Engineering and
| | - Yo-hei Watanabe
- From the Department of Biology, Faculty of Science and Engineering and the Institute for Integrative Neurobiology, Konan University, Okamoto 8-9-1, Kobe 658-8501, Japan
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26
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Kellner JN, Reinstein J, Meinhart A. Synergistic effects of ATP and RNA binding to human DEAD-box protein DDX1. Nucleic Acids Res 2015; 43:2813-28. [PMID: 25690890 PMCID: PMC4357711 DOI: 10.1093/nar/gkv106] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RNA helicases of the DEAD-box protein family form the largest group of helicases. The human DEAD-box protein 1 (DDX1) plays an important role in tRNA and mRNA processing, is involved in tumor progression and is also hijacked by several virus families such as HIV-1 for replication and nuclear export. Although important in many cellular processes, the mechanism of DDX1′s enzymatic function is unknown. We have performed equilibrium titrations and transient kinetics to determine affinities for nucleotides and RNA. We find an exceptional tight binding of DDX1 to adenosine diphosphate (ADP), one of the strongest affinities observed for DEAD-box helicases. ADP binds tighter by three orders of magnitude when compared to adenosine triphosphate (ATP), arresting the enzyme in a potential dead-end ADP conformation under physiological conditions. We thus suggest that a nucleotide exchange factor leads to DDX1 recycling. Furthermore, we find a strong cooperativity in binding of RNA and ATP to DDX1 that is also reflected in ATP hydrolysis. We present a model in which either ATP or RNA binding alone can partially shift the equilibrium from an ‘open’ to a ‘closed’-state; this shift appears to be not further pronounced substantially even in the presence of both RNA and ATP as the low rate of ATP hydrolysis does not change.
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Affiliation(s)
- Julian N Kellner
- Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jochen Reinstein
- Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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Nakazaki Y, Watanabe YH. ClpB chaperone passively threads soluble denatured proteins through its central pore. Genes Cells 2014; 19:891-900. [PMID: 25288401 DOI: 10.1111/gtc.12188] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/08/2014] [Indexed: 11/27/2022]
Abstract
ClpB disaggregase forms a ring-shaped hexamer that threads substrate proteins through the central pore using energy from ATP. The ClpB protomer consists of an N-terminal domain, a middle domain, and two AAA+ modules. These two AAA+ modules bind and hydrolyze ATP and construct the core of the hexameric ring. Here, we investigated the roles of the two AAA+ modules in substrate threading. BAP is an engineered ClpB that can bind ClpP proteolytic chamber; substrates threaded by BAP are degraded by ClpP. We combined BAP with conserved motif mutations in two AAA+ modules and measured the steady-state rates of threading of soluble denatured proteins by these mutants over a range of substrate concentrations. By fitting the data to the Michaelis-Menten equation, k(cat) and K(m) values were determined. We found that the kinetic parameters of the substrate threading correlate with the type of mutation introduced rather than the ATPase activity of the mutant. Moreover, some mutants having no or marginal ATPase activity could thread denatured proteins significantly. These results indicate that ClpB can passively thread soluble denatured proteins.
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Affiliation(s)
- Yosuke Nakazaki
- Department of Biology, Faculty of Science and Engineering, Konan University, Okamoto 8-9-1, Kobe, 658-8501, Japan; Institute for Integrative Neurobiology, Konan University, Okamoto 8-9-1, Kobe, 658-8501, Japan
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28
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Zeymer C, Fischer S, Reinstein J. trans-Acting arginine residues in the AAA+ chaperone ClpB allosterically regulate the activity through inter- and intradomain communication. J Biol Chem 2014; 289:32965-76. [PMID: 25253689 PMCID: PMC4239642 DOI: 10.1074/jbc.m114.608828] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The molecular chaperone ClpB/Hsp104, a member of the AAA+ superfamily (ATPases associated with various cellular activities), rescues proteins from the aggregated state in collaboration with the DnaK/Hsp70 chaperone system. ClpB/Hsp104 forms a hexameric, ring-shaped complex that functions as a tightly regulated, ATP-powered molecular disaggregation machine. Highly conserved and essential arginine residues, often called arginine fingers, are located at the subunit interfaces of the complex, which also harbor the catalytic sites. Several AAA+ proteins, including ClpB/Hsp104, possess a pair of such trans-acting arginines in the N-terminal nucleotide binding domain (NBD1), both of which were shown to be crucial for oligomerization and ATPase activity. Here, we present a mechanistic study elucidating the role of this conserved arginine pair. First, we found that the arginines couple nucleotide binding to oligomerization of NBD1, which is essential for the activity. Next, we designed a set of covalently linked, dimeric ClpB NBD1 variants, carrying single subunits deficient in either ATP binding or hydrolysis, to study allosteric regulation and intersubunit communication. Using this well defined environment of site-specifically modified, cross-linked AAA+ domains, we found that the conserved arginine pair mediates the cooperativity of ATP binding and hydrolysis in an allosteric fashion.
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Affiliation(s)
- Cathleen Zeymer
- From the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Sebastian Fischer
- From the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Jochen Reinstein
- From the Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
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29
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Zeymer C, Barends TRM, Werbeck ND, Schlichting I, Reinstein J. Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor. ACTA ACUST UNITED AC 2014; 70:582-95. [PMID: 24531492 PMCID: PMC3940203 DOI: 10.1107/s1399004713030629] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 11/07/2013] [Indexed: 12/12/2022]
Abstract
ATPases of the AAA+ superfamily are large oligomeric molecular machines that remodel their substrates by converting the energy from ATP hydrolysis into mechanical force. This study focuses on the molecular chaperone ClpB, the bacterial homologue of Hsp104, which reactivates aggregated proteins under cellular stress conditions. Based on high-resolution crystal structures in different nucleotide states, mutational analysis and nucleotide-binding kinetics experiments, the ATPase cycle of the C-terminal nucleotide-binding domain (NBD2), one of the motor subunits of this AAA+ disaggregation machine, is dissected mechanistically. The results provide insights into nucleotide sensing, explaining how the conserved sensor 2 motif contributes to the discrimination between ADP and ATP binding. Furthermore, the role of a conserved active-site arginine (Arg621), which controls binding of the essential Mg2+ ion, is described. Finally, a hypothesis is presented as to how the ATPase activity is regulated by a conformational switch that involves the essential Walker A lysine. In the proposed model, an unusual side-chain conformation of this highly conserved residue stabilizes a catalytically inactive state, thereby avoiding unnecessary ATP hydrolysis.
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Affiliation(s)
- Cathleen Zeymer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Thomas R M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Nicolas D Werbeck
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jochen Reinstein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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30
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Liu J, Mei Z, Li N, Qi Y, Xu Y, Shi Y, Wang F, Lei J, Gao N. Structural dynamics of the MecA-ClpC complex: a type II AAA+ protein unfolding machine. J Biol Chem 2013; 288:17597-608. [PMID: 23595989 DOI: 10.1074/jbc.m113.458752] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The MecA-ClpC complex is a bacterial type II AAA(+) molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA(+) proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA(+) rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA(+) rings and suggest that concerted actions of the two AAA(+) rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA(+) hexamers.
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Affiliation(s)
- Jing Liu
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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31
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Zeymer C, Werbeck ND, Schlichting I, Reinstein J. The molecular mechanism of Hsp100 chaperone inhibition by the prion curing agent guanidinium chloride. J Biol Chem 2013; 288:7065-76. [PMID: 23341453 DOI: 10.1074/jbc.m112.432583] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Hsp100 chaperones ClpB and Hsp104 utilize the energy from ATP hydrolysis to reactivate aggregated proteins in concert with the DnaK/Hsp70 chaperone system, thereby playing an important role in protein quality control. They belong to the family of AAA+ proteins (ATPases associated with various cellular activities), possess two nucleotide binding domains per monomer (NBD1 and NBD2), and oligomerize into hexameric ring complexes. Furthermore, Hsp104 is involved in yeast prion propagation and inheritance. It is well established that low concentrations of guanidinium chloride (GdmCl) inhibit the ATPase activity of Hsp104, leading to so called "prion curing," the loss of prion-related phenotypes. Here, we present mechanistic details about the Hsp100 chaperone inhibition by GdmCl using the Hsp104 homolog ClpB from Thermus thermophilus. Initially, we demonstrate that NBD1 of ClpB, which was previously considered inactive as a separately expressed construct, is a fully active ATPase on its own. Next, we show that only NBD1, but not NBD2, is affected by GdmCl. We present a crystal structure of ClpB NBD1 in complex with GdmCl and ADP, showing that the Gdm(+) ion binds specifically to the active site of NBD1. A conserved essential glutamate residue is involved in this interaction. Additionally, Gdm(+) interacts directly with the nucleotide, thereby increasing the nucleotide binding affinity of NBD1. We propose that both the interference with the essential glutamate and the modulation of nucleotide binding properties in NBD1 is responsible for the GdmCl-specific inhibition of Hsp100 chaperones.
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Affiliation(s)
- Cathleen Zeymer
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
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32
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Oguchi Y, Kummer E, Seyffer F, Berynskyy M, Anstett B, Zahn R, Wade RC, Mogk A, Bukau B. A tightly regulated molecular toggle controls AAA+ disaggregase. Nat Struct Mol Biol 2012; 19:1338-46. [PMID: 23160353 DOI: 10.1038/nsmb.2441] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 10/15/2012] [Indexed: 01/22/2023]
Abstract
The ring-forming AAA+ protein ClpB cooperates with the DnaK chaperone system to refold aggregated proteins in Escherichia coli. The M domain, a ClpB-specific coiled-coil structure with two wings, motif 1 and motif 2, is essential to disaggregation, but the positioning and mechanistic role of M domains in ClpB hexamers remain unresolved. We show that M domains nestle at the ClpB ring surface, with both M-domain motifs contacting the first ATPase domain (AAA-1). Both wings contribute to maintaining a repressed ClpB activity state. Motif 2 docks intramolecularly to AAA-1 to regulate ClpB unfolding power, and motif 1 contacts a neighboring AAA-1 domain. Mutations that stabilize motif 2 docking repress ClpB, whereas destabilization leads to derepressed ClpB activity with greater unfolding power that is toxic in vivo. Our results underline the vital nature of tight ClpB activity control and elucidate a regulated M-domain toggle control mechanism.
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Affiliation(s)
- Yuki Oguchi
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
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33
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Hodson S, Marshall JJT, Burston SG. Mapping the road to recovery: the ClpB/Hsp104 molecular chaperone. J Struct Biol 2012; 179:161-71. [PMID: 22659404 DOI: 10.1016/j.jsb.2012.05.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 05/09/2012] [Accepted: 05/12/2012] [Indexed: 11/26/2022]
Abstract
The AAA(+)-ATPases are a family of molecular motors which have been seconded into a plethora of cellular tasks. One subset, the Hsp100 molecular chaperones, are general protein remodellers that help to maintain the integrity of the cellular proteome by means of protein destruction or resurrection. In this review we focus on one family of Hsp100s, the homologous ClpB and Hsp104 molecular chaperones that convey thermotolerance by resolubilising and rescuing proteins from aggregates. We explore how the nucleotide binding and hydrolysis properties at the twelve nucleotide-binding domains of these hexameric rings are coupled to protein disaggregation, highlighting similarities and differences between ClpB and Hsp104.
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Affiliation(s)
- Skye Hodson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
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34
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Mizuno S, Nakazaki Y, Yoshida M, Watanabe YH. Orientation of the amino-terminal domain of ClpB affects the disaggregation of the protein. FEBS J 2012; 279:1474-84. [PMID: 22348341 DOI: 10.1111/j.1742-4658.2012.08540.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ClpB/Hsp104 efficiently reactivates protein aggregates in cooperation with the DnaK/Hsp70 system. As a member of the AAA+ protein family (i.e. an expanded superfamily of ATPases associated with diverse cellular activities), ClpB forms a ring-shaped hexamer in an ATP-dependent manner. A protomer of ClpB consists of an N-terminal domain (NTD), an AAA+ module, a middle domain and another AAA+ module. In the crystal structures, the NTDs point to two different directions relative to other domains and are not visible in the single-particle cryo-electron microscopy reconstruction, suggesting that the NTD is highly mobile. In the present study, we generated mutants in which the NTD was anchored to other domain by disulfide cross-linking and compared several aspects of ClpB function between the reduced and oxidized mutants, using the wild-type and NTD-truncated ClpB (ClpBΔN) as references. In their oxidized form, the mutants and wild-type bind casein with a similar affinity, although the affinity of ClpBΔN for casein was significantly low. However, the extent of casein-induced stimulation of ATPase, the rate of substrate threading and the efficiency of protein disaggregation of these mutants were all lower than those of the wild-type but similar to those of ClpBΔN. These results indicate that the NTD supports the substrate binding of ClpB and that its conformational shift assists the threading and disaggregation of substrate proteins.
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Affiliation(s)
- Sayaka Mizuno
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
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35
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Naik S, Zhang N, Gao P, Fisher MT. On the design of broad based screening assays to identify potential pharmacological chaperones of protein misfolding diseases. Curr Top Med Chem 2012; 12:2504-22. [PMID: 23339304 PMCID: PMC3751797 DOI: 10.2174/1568026611212220006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/18/2012] [Accepted: 09/21/2012] [Indexed: 01/11/2023]
Abstract
Correcting aberrant folds that develop during protein folding disease states is now an active research endeavor that is attracting increasing attention from both academic and industrial circles. One particular approach focuses on developing or identifying small molecule correctors or pharmacological chaperones that specifically stabilize the native fold. Unfortunately, the limited screening platforms available to rapidly identify or validate potential drug candidates are usually inadequate or slow because the folding disease proteins in question are often transiently folded and/or aggregation-prone, complicating and/or interfering with the assay outcomes. In this review, we outline and discuss the numerous platform options currently being employed to identify small molecule therapeutics for folding diseases. Finally, we describe a new stability screening approach that is broad based and is easily applicable toward a very large number of both common and rare protein folding diseases. The label free screening method described herein couples the promiscuity of the GroEL binding to transient aggregation-prone hydrophobic folds with surface plasmon resonance enabling one to rapidly identify potential small molecule pharmacological chaperones.
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Affiliation(s)
- Subhashchandra Naik
- University of Kansas Medical Center, Department of Biochemistry, Kansas City KS, USA
| | - Na Zhang
- University of Kansas, Protein Production Facility, Lawrence KS, USA
| | - Phillip Gao
- University of Kansas, Protein Production Facility, Lawrence KS, USA
| | - Mark T. Fisher
- University of Kansas Medical Center, Department of Biochemistry, Kansas City KS, USA
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36
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Wendler P, Ciniawsky S, Kock M, Kube S. Structure and function of the AAA+ nucleotide binding pocket. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:2-14. [PMID: 21839118 DOI: 10.1016/j.bbamcr.2011.06.014] [Citation(s) in RCA: 214] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 06/17/2011] [Accepted: 06/27/2011] [Indexed: 10/17/2022]
Abstract
Members of the diverse superfamily of AAA+ proteins are molecular machines responsible for a wide range of essential cellular processes. In this review we summarise structural and functional data surrounding the nucleotide binding pocket of these versatile complexes. Protein Data Bank (PDB) structures of closely related AAA+ ATPase are overlaid and biologically relevant motifs are displayed. Interactions between protomers are illustrated on the basis of oligomeric structures of each AAA+ subgroup. The possible role of conserved motifs in the nucleotide binding pocket is assessed with regard to ATP binding and hydrolysis, oligomerisation and inter-subunit communication. Our comparison indicates that in particular the roles of the arginine finger and sensor 2 residues differ subtly between AAA+ subgroups, potentially providing a means for functional diversification.
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Affiliation(s)
- Petra Wendler
- Gene Center, Ludwig-Maximilians-Universität München, München, Germany.
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37
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Fernández-Higuero JÁ, Acebrón SP, Taneva SG, Del Castillo U, Moro F, Muga A. Allosteric communication between the nucleotide binding domains of caseinolytic peptidase B. J Biol Chem 2011; 286:25547-55. [PMID: 21642426 DOI: 10.1074/jbc.m111.231365] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ClpB is a hexameric chaperone that solubilizes and reactivates protein aggregates in cooperation with the Hsp70/DnaK chaperone system. Each of the identical protein monomers contains two nucleotide binding domains (NBD), whose ATPase activity must be coupled to exert on the substrate the mechanical work required for its reactivation. However, how communication between these sites occurs is at present poorly understood. We have studied herein the affinity of each of the NBDs for nucleotides in WT ClpB and protein variants in which one or both sites are mutated to selectively impair nucleotide binding or hydrolysis. Our data show that the affinity of NBD2 for nucleotides (K(d) = 3-7 μm) is significantly higher than that of NBD1. Interestingly, the affinity of NBD1 depends on nucleotide binding to NBD2. Binding of ATP, but not ADP, to NBD2 increases the affinity of NBD1 (the K(d) decreases from ≈160-300 to 50-60 μm) for the corresponding nucleotide. Moreover, filling of the NBD2 ring with ATP allows the cooperative binding of this nucleotide and substrates to the NBD1 ring. Data also suggest that a minimum of four subunits cooperate to bind and reactivate two different aggregated protein substrates.
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Affiliation(s)
- José Ángel Fernández-Higuero
- Biophysics Unit (Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (Universidad del País Vasco/Euskal Herriko Unibertsitatea), Bilbao, Spain
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38
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Yamasaki T, Nakazaki Y, Yoshida M, Watanabe YH. Roles of conserved arginines in ATP-binding domains of AAA+ chaperone ClpB from Thermus thermophilus. FEBS J 2011; 278:2395-403. [PMID: 21554542 DOI: 10.1111/j.1742-4658.2011.08167.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ClpB, a member of the expanded superfamily of ATPases associated with diverse cellular activities (AAA+), forms a ring-shaped hexamer and cooperates with the DnaK chaperone system to reactivate aggregated proteins in an ATP-dependent manner. The ClpB protomer consists of an N-terminal domain, an AAA+ module (AAA-1), a middle domain, and a second AAA+ module (AAA-2). Each AAA+ module contains highly conserved WalkerA and WalkerB motifs, and two arginines (AAA-1) or one arginine (AAA-2). Here, we investigated the roles of these arginines (Arg322, Arg323, and Arg747) of ClpB from Thermus thermophilus in the ATPase cycle and chaperone function by alanine substitution. These mutations did not affect nucleotide binding, but did inhibit the hydrolysis of the bound ATP and slow the threading of the denatured protein through the central pore of the T. thermophilus ClpB ring, which severely impaired the chaperone functions. Previously, it was demonstrated that ATP binding to the AAA-1 module induced motion of the middle domain and stabilized the ClpB hexamer. However, the arginine mutations of the AAA-1 module destabilized the ClpB hexamer, even though ATP-induced motion of the middle domain was not affected. These results indicated that the three arginines are crucial for ATP hydrolysis and chaperone activity, but not for ATP binding. In addition, the two arginines in AAA-1 and the ATP-induced motion of the middle domain independently contribute to the stabilization of the hexamer.
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Affiliation(s)
- Takashi Yamasaki
- Department of Biology, Faculty of Science and Engineering, Konan University, Okamoto, Kobe, Japan
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39
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del Castillo U, Alfonso C, Acebrón SP, Martos A, Moro F, Rivas G, Muga A. A quantitative analysis of the effect of nucleotides and the M domain on the association equilibrium of ClpB. Biochemistry 2011; 50:1991-2003. [PMID: 21309513 DOI: 10.1021/bi101670s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ClpB is a hexameric molecular chaperone that, together with the DnaK system, has the ability to disaggregate stress-denatured proteins. The hexamer is a highly dynamic complex, able to reshuffle subunits. To further characterize the biological implications of the ClpB oligomerization state, the association equilibrium of the wild-type (wt) protein and of two deletion mutants, which lack part or the whole M domain, was quantitatively analyzed under different experimental conditions, using several biophysical [analytical ultracentrifugation, composition-gradient (CG) static light scattering, and circular dichroism] and biochemical (ATPase and chaperone activity) methods. We have found that (i) ClpB self-associates from monomers to form hexamers and higher-order oligomers that have been tentatively assigned to dodecamers, (ii) oligomer dissociation is not accompanied by modifications of the protein secondary structure, (iii) the M domain is engaged in intersubunit interactions that stabilize the protein hexamer, and (iv) the nucleotide-induced rearrangement of ClpB affects the protein oligomeric core, in addition to the proposed radial extension of the M domain. The difference in the stability of the ATP- and ADP-bound states [ΔΔG(ATP-ADP) = -10 kJ/mol] might explain how nucleotide exchange promotes the conformational change of the protein particle that drives its functional cycle.
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Affiliation(s)
- Urko del Castillo
- Unidad de Biofísica (Consejo Superior de Investigaciones Científicas/Universidad del País Vasco-Euskal Herriko Unibertsitatea) and Departamento de Bioquímica y Biología Molecular, Universidad del País Vasco, Bilbao 48080, Spain
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40
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Werbeck ND, Zeymer C, Kellner JN, Reinstein J. Coupling of oligomerization and nucleotide binding in the AAA+ chaperone ClpB. Biochemistry 2011; 50:899-909. [PMID: 21182296 DOI: 10.1021/bi1018286] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Members of the family of ATPases associated with various cellular activities (AAA+) typically form homohexameric ring complexes and are able to remodel their substrates, such as misfolded proteins or protein-protein complexes, in an ATP-driven process. The molecular mechanism by which ATP hydrolysis is coordinated within the multimeric complex and the energy is converted into molecular motions, however, is poorly understood. This is partly due to the fact that the oligomers formed by AAA+ proteins represent a highly complex system and analysis depends on simplification and prior knowledge. Here, we present nucleotide binding and oligomer assembly kinetics of the AAA+ protein ClpB, a molecular chaperone that is able to disaggregate protein aggregates in concert with the DnaK chaperone system. ClpB bears two AAA+ domains (NBD1 and NBD2) on one subunit and forms homohexameric ring complexes. In order to dissect individual mechanistic steps, we made use of a reconstituted system based on two individual constructs bearing either the N-terminal (NBD1) or the C-terminal AAA+ domain (NBD2). In contrast to the C-terminal construct, the N-terminal construct does not bind the fluorescent nucleotide MANT-dADP in isolation. However, sequential mixing experiments suggest that NBD1 obtains nucleotide binding competence when incorporated into an oligomeric complex. These findings support a model in which nucleotide binding to NBD1 is dependent on and regulated by trans-acting elements from neighboring subunits, either by direct interaction with the nucleotide or by stabilization of a nucleotide binding-competent state. In this way, they provide a basis for intersubunit communication within the functional ClpB complex.
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Affiliation(s)
- Nicolas D Werbeck
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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41
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Wendler P, Saibil HR. Cryo electron microscopy structures of Hsp100 proteins: crowbars in or out? Biochem Cell Biol 2010; 88:89-96. [PMID: 20130682 DOI: 10.1139/o09-164] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Independent cryo electron microscopy (cryo-EM) studies of the closely related protein disaggregases ClpB and Hsp104 have resulted in two different models of subunit arrangement in the active hexamer. We compare the EM maps and resulting atomic structure fits, discuss their differences, and relate them to published experimental information in an attempt to discriminate between models. In addition, we present some general assessment criteria for low-resolution cryo-EM maps to offer non-structural biologists tools to evaluate these structures.
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Affiliation(s)
- Petra Wendler
- Department of Crystallography, Birkbeck College, Malet St., London WC1E 7HX, UK
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Grimminger-Marquardt V, Lashuel HA. Structure and function of the molecular chaperone Hsp104 from yeast. Biopolymers 2010; 93:252-76. [PMID: 19768774 DOI: 10.1002/bip.21301] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The molecular chaperone Hsp104 plays a central role in the clearance of aggregates after heat shock and the propagation of yeast prions. Hsp104's disaggregation activity and prion propagation have been linked to its ability to resolubilize or remodel protein aggregates. However, Hsp104 has also the capacity to catalyze protein aggregation of some substrates at specific conditions. Hence, it is a molecular chaperone with two opposing activities with respect to protein aggregation. In yeast models of Huntington's disease, Hsp104 is required for the aggregation and toxicity of polyglutamine (polyQ), but the expression of Hsp104 in cellular and animal models of Huntington's and Parkinson's disease protects against polyQ and alpha-synuclein toxicity. Therefore, elucidating the molecular determinants and mechanisms underlying the ability of Hsp104 to switch between these two activities is of critical importance for understanding its function and could provide insight into novel strategies aimed at preventing or reversing the formation of toxic protein aggregation in systemic and neurodegenerative protein misfolding diseases. Here, we present an overview of the current molecular models and hypotheses that have been proposed to explain the role of Hsp104 in modulating protein aggregation and prion propagation. The experimental approaches and the evidences presented so far in relation to these models are examined. Our primary objective is to offer a critical review that will inspire the use of novel techniques and the design of new experiments to proceed towards a qualitative and quantitative understanding of the molecular mechanisms underlying the multifunctional properties of Hsp104 in vivo.
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Affiliation(s)
- Valerie Grimminger-Marquardt
- Laboratory of Molecular Neurobiology and Neuroproteomics, Swiss Federal Institute of Technology Lausanne (EPFL), FSV-BMI AI 2137.1, Station 15, CH-1015 Lausanne, Switzerland
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43
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Mizutani T, Nemoto S, Yoshida M, Watanabe YH. Temperature-dependent regulation of Thermus thermophilus DnaK/DnaJ chaperones by DafA protein. Genes Cells 2009; 14:1405-13. [PMID: 19930469 DOI: 10.1111/j.1365-2443.2009.01357.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
DafA, a unique 8-kDa protein found in Thermus thermophilus, assembles the chaperones DnaK and DnaJ to produce a DnaK(3)-DnaJ(3)-DafA(3) complex (KJA complex). Although, it is known that DafA is denatured irreversibly at nonphysiological 89 degrees C and the KJA complex dissociates into fully active DnaK and DnaJ, the function of the KJA complex is not fully understood. In this article, we report that the reversible dissociation of the KJA complex occurs in a temperature-dependent manner even below physiological 75 degrees C and that excess DafA completely inhibits the chaperone activities of the DnaK system. The inhibited activities are not rescued by supplementing DnaK or DnaJ. The results indicate that DafA inhibits the chaperone activities of both DnaK and DnaJ by forming the KJA complex and can act as a thermosensor under both heat stress and optimal growth conditions.
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Affiliation(s)
- Tadashi Mizutani
- Department of Biology, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Kobe 658-8501, Japan
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Stability of the two wings of the coiled-coil domain of ClpB chaperone is critical for its disaggregation activity. Biochem J 2009; 421:71-7. [DOI: 10.1042/bj20082238] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ClpB chaperone forms a hexamer ring and rescues aggregated proteins in co-operation with the DnaK system. Each subunit of ClpB has two nucleotide-binding modules, AAA (ATPase associated with various cellular activities)-1 and AAA-2, and an 85-Å (1 Å=0.1 nm)-long coiled-coil. The coiled-coil consists of two halves: wing-1, leaning toward AAA-1, and wing-2, leaning away from all the domains. The coiled-coil is stabilized by leucine zipper-like interactions between leucine and isoleucine residues of two amphipathic α-helices that twist around each other to form each wing. To destabilize the two wings, we developed a series of mutants by replacing these residues with alanine. As the number of replaced residues increased, the chaperone activity was lost and the hexamer became unstable. The mutants, which had a stable hexameric structure but lost the chaperone activities, were able to exert the threading of soluble denatured proteins through their central pore. The destabilization of wing-1, but not wing-2, resulted in a several-fold stimulation of ATPase activity. These results indicate that stability of both wings of the coiled-coil is critical for full functioning of ClpB, but not for the central-pore threading of substrate proteins, and that wing-1 is involved in the communication between AAA-1 and AAA-2.
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45
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Zhang X, Wigley DB. The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins. Nat Struct Mol Biol 2008; 15:1223-7. [PMID: 18849995 PMCID: PMC2806578 DOI: 10.1038/nsmb.1501] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 09/23/2008] [Indexed: 11/25/2022]
Abstract
AAA+ proteins carry out diverse functions in cells. In most cases, their ATPase activity is tightly regulated by protein partners and target ligands, but the mechanism for this control has remained unclear. We have identified a conserved link between the ligand binding and ATPase sites in AAA+ proteins. This link, which we call the 'glutamate switch', regulates ATPase activity directly in response to the binding of target ligands by controlling the orientation of the conserved glutamate residue in the DExx motif, switching it between active and inactive conformations. The reasons for this level of control of the ATPase activity are discussed in the context of the biological processes catalyzed by AAA+ proteins.
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Affiliation(s)
- Xiaodong Zhang
- Division of Molecular Biosciences, Centre for Structural Biology, Dept. of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Dale B. Wigley
- Cancer Research UK Clare Hall Laboratories, The London Research Institute, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3LD,U.K
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46
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Leskovar A, Reinstein J. Photophysical properties of popular fluorescent adenosine nucleotide analogs used in enzyme mechanism probing. Arch Biochem Biophys 2008; 473:16-24. [PMID: 18342617 DOI: 10.1016/j.abb.2008.02.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 02/26/2008] [Accepted: 02/26/2008] [Indexed: 11/24/2022]
Abstract
Fluorescent nucleotide analogs are widely used in mechanistic studies of nucleotide binding and utilizing proteins. We describe here an overview of the photophysical parameters of the most popular nucleotide analogs that have a fluorescent N-methylanthraniloyl-group attached at various positions of the nucleotide. Steady state absorption and fluorescence spectra of free chromophores depend on the type of modification (ribose, base or phosphate moiety) and the addition of proteins suggests that the labeled nucleotides also vary in sensitivity depending upon their local protein environment. Fluorescence lifetime measurements imply two to three lifetimes for each nucleotide with complex changes in dependence on solvent but more importantly also on the protein. The measured quantum yields quantify the increase in fluorescence for (C8)-MABA-ADP, MANT-ATP and (Pgamma)-MABA-ATP as 153%, 93% and 14% when bound to DnaK, ClpB and Trap1, respectively, compared to free in buffer solution.
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Affiliation(s)
- Adriane Leskovar
- Max-Planck-Institute for Medical Research, Department of Biomolecular Mechanisms, Jahnstrasse 29, D-69120 Heidelberg, Germany
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Werbeck ND, Schlee S, Reinstein J. Coupling and dynamics of subunits in the hexameric AAA+ chaperone ClpB. J Mol Biol 2008; 378:178-90. [PMID: 18343405 DOI: 10.1016/j.jmb.2008.02.026] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 02/13/2008] [Accepted: 02/14/2008] [Indexed: 10/22/2022]
Abstract
The bacterial AAA+ protein ClpB and its eukaryotic homologue Hsp104 ensure thermotolerance of their respective organisms by reactivating aggregated proteins in cooperation with the Hsp70/Hsp40 chaperone system. Like many members of the AAA+ superfamily, the ClpB protomers form ringlike homohexameric complexes. The mechanical energy necessary to disentangle protein aggregates is provided by ATP hydrolysis at the two nucleotide-binding domains of each monomer. Previous studies on ClpB and Hsp104 show a complex interplay of domains and subunits resulting in homotypic and heterotypic cooperativity. Using mutations in the Walker A and Walker B nucleotide-binding motifs in combination with mixing experiments we investigated the degree of inter-subunit coupling with respect to different aspects of the ClpB working cycle. We find that subunits are tightly coupled with regard to ATPase and chaperone activity, but no coupling can be observed for ADP binding. Comparison of the data with statistical calculations suggests that for double Walker mutants, approximately two in six subunits are sufficient to abolish chaperone and ATPase activity completely. In further experiments, we determined the dynamics of subunit reshuffling. Our results show that ClpB forms a very dynamic complex, reshuffling subunits on a timescale comparable to steady-state ATP hydrolysis. We propose that this could be a protection mechanism to prevent very stable aggregates from becoming suicide inhibitors for ClpB.
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Affiliation(s)
- Nicolas D Werbeck
- Max-Planck-Institute for Medical Research, Department of Biomolecular Mechanisms, Jahnstrasse 29 D-69120 Heidelberg, Germany
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48
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Larsen J, Kuhnert P, Frey J, Christensen H, Bisgaard M, Olsen JE. Analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus Mannheimia. BMC Evol Biol 2007; 7:184. [PMID: 17915007 PMCID: PMC2228313 DOI: 10.1186/1471-2148-7-184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Accepted: 10/03/2007] [Indexed: 12/30/2022] Open
Abstract
Background The Mannheimia subclades belong to the same bacterial genus, but have taken divergent paths toward their distinct lifestyles. For example, M. haemolytica + M. glucosida are potential pathogens of the respiratory tract in the mammalian suborder Ruminantia, whereas M. ruminalis, the supposed sister group, lives as a commensal in the ovine rumen. We have tested the hypothesis that vertical inheritance of the leukotoxin (lktCABD) operon has occurred from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades by exploring gene order data. Results We examined the gene order in the 5' flanking region of the leukotoxin operon and found that the 5' flanking gene strings, hslVU-lapB-artJ-lktC and xylAB-lktC, are peculiar to M. haemolytica + M. glucosida and M. granulomatis, respectively, whereas the gene string hslVU-lapB-lktC is present in M. ruminalis, the supposed sister group of M. haemolytica + M. glucosida, and in the most ancient subclade M. varigena. In M. granulomatis, we found remnants of the gene string hslVU-lapB-lktC in the xylB-lktC intergenic region. Conclusion These observations indicate that the gene string hslVU-lapB-lktC is more ancient than the hslVU-lapB-artJ-lktC and xylAB-lktC gene strings. The presence of (remnants of) the ancient gene string hslVU-lapB-lktC among any subclades within genus Mannheimia supports that it has been vertically inherited from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades, thus reaffirming the hypothesis of vertical inheritance of the leukotoxin operon. The presence of individual 5' flanking regions in M. haemolytica + M. glucosida and M. granulomatis reflects later genome rearrangements within each subclade. The evolution of the novel 5' flanking region in M. haemolytica + M. glucosida resulted in transcriptional coupling between the divergently arranged artJ and lkt promoters. We propose that the chimeric promoter have led to high level expression of the leukotoxin operon which could explain the increased potential of certain M. haemolytica + M. glucosida strains to cause a particular type of infection.
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Affiliation(s)
- Jesper Larsen
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, University of Berne, Länggass-Strasse 122, CH-3012 Berne, Switzerland
| | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Berne, Länggass-Strasse 122, CH-3012 Berne, Switzerland
| | - Henrik Christensen
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Magne Bisgaard
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - John E Olsen
- Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
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Schaupp A, Marcinowski M, Grimminger V, Bösl B, Walter S. Processing of proteins by the molecular chaperone Hsp104. J Mol Biol 2007; 370:674-86. [PMID: 17543332 DOI: 10.1016/j.jmb.2007.04.070] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 04/26/2007] [Accepted: 04/27/2007] [Indexed: 11/21/2022]
Abstract
The molecular chaperone Hsp104 is an AAA+ ATPase (ATPase associated with a variety of cellular activities) from yeast that catalyzes protein disaggregation. Using mutagenesis, we impaired nucleotide binding or hydrolysis in the two nucleotide-binding domains (NBD) of Hsp104 and analyzed the consequences for chaperone function by monitoring ATP hydrolysis, polypeptide binding, polypeptide processing, and disaggregation. Our results reveal that ATP binding to NBD1 serves as a central regulatory switch for the chaperone; it triggers binding of polypeptides, and stimulates ATP hydrolysis in the C-terminal NBD2 by more than two orders of magnitude, implying that ATP hydrolysis in this domain is important for disaggregation. Moreover, we show that Hsp104 actively unfolds its polypeptide substrates during processing, demonstrating that AAA+ proteins involved in disaggregation share a common threading mechanism with AAA+ proteins mediating protein unfolding/degradation.
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Affiliation(s)
- Andreas Schaupp
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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50
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Haslberger T, Weibezahn J, Zahn R, Lee S, Tsai FTF, Bukau B, Mogk A. M domains couple the ClpB threading motor with the DnaK chaperone activity. Mol Cell 2007; 25:247-60. [PMID: 17244532 DOI: 10.1016/j.molcel.2006.11.008] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Revised: 10/10/2006] [Accepted: 11/08/2006] [Indexed: 11/17/2022]
Abstract
The AAA(+) chaperone ClpB mediates the reactivation of aggregated proteins in cooperation with the DnaK chaperone system. ClpB consists of two AAA domains that drive the ATP-dependent threading of substrates through a central translocation channel. Its unique middle (M) domain forms a coiled-coil structure that laterally protrudes from the ClpB ring and is essential for aggregate solubilization. Here, we demonstrate that the conserved helix 3 of the M domain is specifically required for the DnaK-dependent shuffling of aggregated proteins, but not of soluble denatured substrates, to the pore entrance of the ClpB translocation channel. Helix 3 exhibits nucleotide-driven conformational changes possibly involving a transition between folded and unfolded states. This molecular switch controls the ClpB ATPase cycle by contacting the first ATPase domain and establishes the M domain as a regulatory device that acts in the disaggregation process by coupling the threading motor of ClpB with the DnaK chaperone activity.
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Affiliation(s)
- Tobias Haslberger
- ZMBH, Universität Heidelberg, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
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