1
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Ulfig A, Jakob U. Cellular oxidants and the proteostasis network: balance between activation and destruction. Trends Biochem Sci 2024; 49:761-774. [PMID: 39168791 DOI: 10.1016/j.tibs.2024.07.001] [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: 04/05/2024] [Revised: 06/27/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024]
Abstract
Loss of protein homeostasis (proteostasis) is a common hallmark of aging and age-associated diseases. Considered as the guardian of proteostasis, the proteostasis network (PN) acts to preserve the functionality of proteins during their lifetime. However, its activity declines with age, leading to disease manifestation. While reactive oxygen species (ROS) were traditionally considered culprits in this process, recent research challenges this view. While harmful at high concentrations, moderate ROS levels protect the cell against age-mediated onset of proteotoxicity by activating molecular chaperones, stress response pathways, and autophagy. This review explores the nuanced roles of ROS in proteostasis and discusses the most recent findings regarding the redox regulation of the PN and its potential in extending healthspan and delaying age-related pathologies.
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Affiliation(s)
- Agnes Ulfig
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Biological Chemistry Department, University of Michigan Medical School, Ann Arbor, MI, USA.
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2
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Erdős G, Dosztányi Z. AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder. Nucleic Acids Res 2024; 52:W176-W181. [PMID: 38747347 PMCID: PMC11223784 DOI: 10.1093/nar/gkae385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 07/06/2024] Open
Abstract
Intrinsically disordered proteins and protein regions (IDPs/IDRs) carry out important biological functions without relying on a single well-defined conformation. As these proteins are a challenge to study experimentally, computational methods play important roles in their characterization. One of the commonly used tools is the IUPred web server which provides prediction of disordered regions and their binding sites. IUPred is rooted in a simple biophysical model and uses a limited number of parameters largely derived on globular protein structures only. This enabled an incredibly fast and robust prediction method, however, its limitations have also become apparent in light of recent breakthrough methods using deep learning techniques. Here, we present AIUPred, a novel version of IUPred which incorporates deep learning techniques into the energy estimation framework. It achieves improved performance while keeping the robustness of the original method. Based on the evaluation of recent benchmark datasets, AIUPred scored amongst the top three single sequence based methods. With a new web server we offer fast and reliable visual analysis for users as well as options to analyze whole genomes in mere seconds with the downloadable package. AIUPred is available at https://aiupred.elte.hu.
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Affiliation(s)
- Gábor Erdős
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter stny 1/c, Budapest H-1117, Hungary
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter stny 1/c, Budapest H-1117, Hungary
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3
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Gupta MN, Uversky VN. Reexamining the diverse functions of arginine in biochemistry. Biochem Biophys Res Commun 2024; 705:149731. [PMID: 38432110 DOI: 10.1016/j.bbrc.2024.149731] [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: 12/24/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Arginine in a free-state and as part of peptides and proteins shows distinct tendency to form clusters. In free-form, it has been found useful in cryoprotection, as a drug excipient for both solid and liquid formulations, as an aggregation suppressor, and an eluent in protein chromatography. In many cases, the mechanisms by which arginine acts in all these applications is either debatable or at least continues to attract interest. It is quite possible that arginine clusters may be involved in many such applications. Furthermore, it is possible that such clusters are likely to behave as intrinsically disordered polypeptides. These considerations may help in understanding the roles of arginine in diverse applications and may even lead to better strategies for using arginine in different situations.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India.
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya Str., 7, Pushchino, Moscow Region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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4
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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [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: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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5
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Choudhary D, Mediani L, Avellaneda MJ, Bjarnason S, Alberti S, Boczek EE, Heidarsson PO, Mossa A, Carra S, Tans SJ, Cecconi C. Human Small Heat Shock Protein B8 Inhibits Protein Aggregation without Affecting the Native Folding Process. J Am Chem Soc 2023. [PMID: 37411010 PMCID: PMC10360156 DOI: 10.1021/jacs.3c02022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Small Heat Shock Proteins (sHSPs) are key components of our Protein Quality Control system and are thought to act as reservoirs that neutralize irreversible protein aggregation. Yet, sHSPs can also act as sequestrases, promoting protein sequestration into aggregates, thus challenging our understanding of their exact mechanisms of action. Here, we employ optical tweezers to explore the mechanisms of action of the human small heat shock protein HSPB8 and its pathogenic mutant K141E, which is associated with neuromuscular disease. Through single-molecule manipulation experiments, we studied how HSPB8 and its K141E mutant affect the refolding and aggregation processes of the maltose binding protein. Our data show that HSPB8 selectively suppresses protein aggregation without affecting the native folding process. This anti-aggregation mechanism is distinct from previous models that rely on the stabilization of unfolded polypeptide chains or partially folded structures, as has been reported for other chaperones. Rather, it appears that HSPB8 selectively recognizes and binds to aggregated species formed at the early stages of aggregation, preventing them from growing into larger aggregated structures. Consistently, the K141E mutation specifically targets the affinity for aggregated structures without impacting native folding, and hence impairs its anti-aggregation activity.
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Affiliation(s)
- Dhawal Choudhary
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, and Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Mario J Avellaneda
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Edgar E Boczek
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, D-01307 Dresden, Germany
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102 Reykjavík, Iceland
| | - Alessandro Mossa
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
- INFN Firenze, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, and Centre for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Via G. Campi 287, 41125 Modena, Italy
| | - Sander J Tans
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Ciro Cecconi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125 Modena, Italy
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6
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Chen G, Leppert A, Poska H, Nilsson HE, Alvira CP, Zhong X, Koeck P, Jegerschöld C, Abelein A, Hebert H, Johansson J. Short hydrophobic loop motifs in BRICHOS domains determine chaperone activity against amorphous protein aggregation but not against amyloid formation. Commun Biol 2023; 6:497. [PMID: 37156997 PMCID: PMC10167226 DOI: 10.1038/s42003-023-04883-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
ATP-independent molecular chaperones are important for maintaining cellular fitness but the molecular determinants for preventing aggregation of partly unfolded protein substrates remain unclear, particularly regarding assembly state and basis for substrate recognition. The BRICHOS domain can perform small heat shock (sHSP)-like chaperone functions to widely different degrees depending on its assembly state and sequence. Here, we observed three hydrophobic sequence motifs in chaperone-active domains, and found that they get surface-exposed when the BRICHOS domain assembles into larger oligomers. Studies of loop-swap variants and site-specific mutants further revealed that the biological hydrophobicities of the three short motifs linearly correlate with the efficiency to prevent amorphous protein aggregation. At the same time, they do not at all correlate with the ability to prevent ordered amyloid fibril formation. The linear correlations also accurately predict activities of chimeras containing short hydrophobic sequence motifs from a sHSP that is unrelated to BRICHOS. Our data indicate that short, exposed hydrophobic motifs brought together by oligomerisation are sufficient and necessary for efficient chaperone activity against amorphous protein aggregation.
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Affiliation(s)
- Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden.
| | - Axel Leppert
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, 171 65, Solna, Sweden
| | - Helen Poska
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
- School of Natural Sciences and Health, Tallinn University, Tallinn, Estonia
| | - Harriet E Nilsson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, 141 52, Huddinge, Sweden
| | | | - Xueying Zhong
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, 141 52, Huddinge, Sweden
| | - Philip Koeck
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, 141 52, Huddinge, Sweden
| | - Caroline Jegerschöld
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, 141 52, Huddinge, Sweden
| | - Axel Abelein
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Hans Hebert
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, 141 52, Huddinge, Sweden
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden.
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7
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Ulrich K. Redox-regulated chaperones in cell stress responses. Biochem Soc Trans 2023:233014. [PMID: 37140269 DOI: 10.1042/bst20221304] [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: 01/30/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023]
Abstract
Proteostasis and redox homeostasis are tightly interconnected and most protein quality control pathways are under direct redox regulation which allow cells to immediately respond to oxidative stress conditions. The activation of ATP-independent chaperones serves as a first line of defense to counteract oxidative unfolding and aggregation of proteins. Conserved cysteine residues evolved as redox-sensitive switches which upon reversible oxidation induce substantial conformational rearrangements and the formation of chaperone-active complexes. In addition to harnessing unfolding proteins, these chaperone holdases interact with ATP-dependent chaperone systems to facilitate client refolding and restoring proteostasis during stress recovery. This minireview gives an insight into highly orchestrated mechanisms regulating the stress-specific activation and inactivation of redox-regulated chaperones and their role in cell stress responses.
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Affiliation(s)
- Kathrin Ulrich
- Institute of Biochemistry, Cellular Biochemistry, University of Cologne, Zuelpicher Str. 47a, 50674 Cologne, Germany
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8
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HslO ameliorates arrested ΔrecA polA cell growth and reduces DNA damage and oxidative stress responses. Sci Rep 2022; 12:22182. [PMID: 36564489 PMCID: PMC9789031 DOI: 10.1038/s41598-022-26703-z] [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: 07/04/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Chromosome damage combined with defective recombinase activity has been widely considered to render cells inviable, owing to deficient double-strand break repair. However, temperature-sensitive recAts polA cells grow well upon induction of DNA damage and supplementation with catalase at restrictive temperatures. These treatments reduce intracellular reactive oxygen species (ROS) levels, which suggests that recAts polA cells are susceptible to ROS, but not chronic chromosome damage. Therefore, we investigated whether polA cells can tolerate a complete lack of recombinase function. We introduced a ΔrecA allele in polA cells in the presence or absence of the hslO-encoding redox molecular chaperon Hsp33 expression plasmid. Induction of the hslO gene with IPTG resulted in increased cell viability in ΔrecA polA cells with the hslO expression plasmid. ΔrecA polA cells in the absence of the hslO expression plasmid showed rich medium sensitivity with increasing ROS levels. Adding catalase to the culture medium considerably rescued growth arrest and decreased ROS. These results suggest that hslO expression manages oxidative stress to an acceptable level in cells with oxidative damage and rescues cell growth. Overall, ROS may regulate several processes, from damage response to cell division, via ROS-sensitive cell metabolism.
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9
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Gestaut D, Zhao Y, Park J, Ma B, Leitner A, Collier M, Pintilie G, Roh SH, Chiu W, Frydman J. Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT. Cell 2022; 185:4770-4787.e20. [PMID: 36493755 PMCID: PMC9735246 DOI: 10.1016/j.cell.2022.11.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022]
Abstract
The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human prefoldin and TRiC. We find unstructured β-tubulin is delivered by prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure. Cryo-EM resolves four near-atomic-resolution structures containing progressively folded β-tubulin intermediates within the closed TRiC chamber, culminating in native tubulin. This substrate folding pathway appears closely guided by site-specific interactions with conserved regions in the TRiC chamber. Initial electrostatic interactions between the TRiC interior wall and both the folded tubulin N domain and its C-terminal E-hook tail establish the native substrate topology, thus enabling C-domain folding. Intrinsically disordered CCT C termini within the chamber promote subsequent folding of tubulin's core and middle domains and GTP-binding. Thus, TRiC's chamber provides chemical and topological directives that shape the folding landscape of its obligate substrates.
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Affiliation(s)
- Daniel Gestaut
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Yanyan Zhao
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Junsun Park
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Boxue Ma
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Dept of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Miranda Collier
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Grigore Pintilie
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Soung-Hun Roh
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea,Co-Corresponding authors: (lead contact), ,
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA,Co-Corresponding authors: (lead contact), ,
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA,Department of Genetics, Stanford University, Stanford, CA 94305, USA,Co-Corresponding authors: (lead contact), ,
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10
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Kaidow A, Ishii N, Suzuki S, Shiina T, Kasahara H. Vitamin C Maintenance against Cell Growth Arrest and Reactive Oxygen Species Accumulation in the Presence of Redox Molecular Chaperone hslO Gene. Int J Mol Sci 2022; 23:12786. [PMID: 36361576 PMCID: PMC9659236 DOI: 10.3390/ijms232112786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 12/03/2022] Open
Abstract
Chromosome damage combined with defective recombinase activity renders cells inviable, owing to deficient double-strand break repair. Despite this, recA polA cells grow well under either DNA damage response (SOS) conditions or catalase medium supplementation. Catalase treatments reduce intracellular reactive oxygen species (ROS) levels, suggesting that recA polA cells are susceptible to not only chronic chromosome damage but also ROS. In this study, we used a reducing agent, vitamin C, to confirm whether cell growth could be improved. Vitamin C reduced ROS levels and rescued colony formation in recAts polA cells under restrictive temperatures in the presence of hslO, the gene encoding a redox molecular chaperone. Subsequently, we investigated the role of hslO in the cell growth failure of recAts polA cells. The effects of vitamin C were observed in hslO+ cells; simultaneously, cells converged along several ploidies likely through a completion of replication, with the addition of vitamin C at restrictive temperatures. These results suggest that HslO could manage oxidative stress to an acceptable level, allowing for cell division as well as rescuing cell growth. Overall, ROS may regulate several processes, from damage response to cell division. Our results provide a basis for understanding the unsolved regulatory interplay of cellular processes.
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Affiliation(s)
- Akihiro Kaidow
- Department of Biology, School of Biological Sciences, Tokai University, Sapporo 005-8601, Japan
- Hokkaido Regional Research Center, Tokai University, Sapporo 005-8601, Japan
| | - Noriko Ishii
- Department of Biology, School of Biological Sciences, Tokai University, Sapporo 005-8601, Japan
| | - Shingo Suzuki
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara 259-1193, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara 259-1193, Japan
| | - Hirokazu Kasahara
- Department of Biology, School of Biological Sciences, Tokai University, Sapporo 005-8601, Japan
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11
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Kaidow A, Ishii N, Suzuki S, Shiina T, Kasahara H. Reactive oxygen species accumulation is synchronised with growth inhibition of temperature-sensitive recAts polA Escherichia coli. Arch Microbiol 2022; 204:396. [PMID: 35705748 PMCID: PMC9200703 DOI: 10.1007/s00203-022-02957-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 11/30/2022]
Abstract
When combined with recombinase defects, chromosome breakage and double-strand break repair deficiencies render cells inviable. However, cells are viable when an SOS response occurs in recAts polA cells in Escherichia coli. Here, we aimed to elucidate the underlying mechanisms of this process. Transposon mutagenesis revealed that the hslO gene, a redox chaperone Hsp33 involved in reactive oxidative species (ROS) metabolism, was required for the suppression of recAts polA lethality at a restricted temperature. Recently, it has been reported that lethal treatments trigger ROS accumulation. We also found that recAts polA cells accumulated ROS at the restricted temperature. A catalase addition to the medium alleviates the temperature sensitivity of recAts polA cells and decreases ROS accumulation. These results suggest that the SOS response and hslO manage oxidative insult to an acceptable level in cells with oxidative damage and rescue cell growth. Overall, ROS might regulate several cellular processes.
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Affiliation(s)
- Akihiro Kaidow
- Department of Biology, School of Biology, Tokai University, Sapporo, 005-8601, Japan.
| | - Noriko Ishii
- Department of Bioscience and Technology, School of Biology, Tokai University, Sapporo, 005-8601, Japan
| | - Sinngo Suzuki
- Department of Molecular Medicine, School of Medicine, Tokai University, Isehara, 259-1193, Japan
| | - Takashi Shiina
- Department of Molecular Medicine, School of Medicine, Tokai University, Isehara, 259-1193, Japan
| | - Hirokazu Kasahara
- Department of Bioscience and Technology, School of Biology, Tokai University, Sapporo, 005-8601, Japan
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12
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Predicting protein intrinsically disordered regions by applying natural language processing practices. Soft comput 2022. [DOI: 10.1007/s00500-022-07085-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Ren C, Zheng Y, Liu C, Mencius J, Wu Z, Quan S. Molecular Characterization of an Intrinsically Disordered Chaperone Reveals Net-Charge Regulation in Chaperone Action. J Mol Biol 2021; 434:167405. [PMID: 34914967 DOI: 10.1016/j.jmb.2021.167405] [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: 08/13/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/18/2022]
Abstract
Molecular chaperones are diverse biomacromolecules involved in the maintenance of cellular protein homeostasis (proteostasis). Here we demonstrate that in contrast to most chaperones with defined three-dimensional structures, the acid-inducible protein Asr in Escherichia coli is intrinsically disordered and exhibits varied aggregation-preventing or aggregation-promoting activities, acting as a "conditionally active chaperone". Bioinformatics and experimental analyses of Asr showed that it is devoid of hydrophobic patches but rich in positive charges and local polyproline II backbone structures. Asr contributes to the integrity of the bacterial outer membrane under mildly acidic conditions in vivo and possesses chaperone activities toward model clients in vitro. Notably, its chaperone activity is dependent on the net charges of clients: on the one hand, it inhibits the aggregation of clients with similar net charges; on the other hand, it stimulates the aggregation of clients with opposite net charges. Mutational analysis confirmed that positively charged residues in Asr are essential for the varied effects on protein aggregation, suggesting that electrostatic interactions are the major driving forces underlying Asr's proteostasis-related activity. These findings present a unique example of an intrinsically disordered molecular chaperone with distinctive dual functions-as an aggregase or as a chaperone-depending on the net charges of clients.
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Affiliation(s)
- Chang Ren
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China
| | - Yongxin Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China
| | - Chunlan Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China
| | - Jun Mencius
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China
| | - Zhili Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai 200237, China.
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14
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Molecular Effects of Elongation Factor Ts and Trigger Factor on the Unfolding and Aggregation of Elongation Factor Tu Induced by the Prokaryotic Molecular Chaperone Hsp33. BIOLOGY 2021; 10:biology10111171. [PMID: 34827164 PMCID: PMC8614738 DOI: 10.3390/biology10111171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/13/2022]
Abstract
Simple Summary Proteins are versatile biological macromolecules involved in most biological processes. However, because of the highly labile nature of protein structures, protein quality control (PQC) to ensure proteostasis (i.e., protein homeostasis)is difficult. Therefore, proteins of a specialized class (i.e., molecular chaperones) are required that assist in proper folding and prevent aberrant folding of other proteins. Hsp33 was originally discovered as a holding chaperone that is overexpressed upon heat shock and activated by oxidation to prevent the misfolding of client proteins. Recently, an unfoldase/aggregase activity of Hsp33 was identified in its reduced state against a specific substrate, EF-Tu, which plays a key role in protein biosynthesis in cells. The present study demonstrates that EF-Tu unfolding/aggregation by Hsp33 can be accelerated by another molecular chaperone trigger factor. Given that the unfolded/aggregated EF-Tu is finally degraded by another chaperone, Lon protease, it is likely that a chaperone network dysregulating EF-Tu operates in heat shock to attenuate protein biosynthesis, which is harmful to cell survival under stressed conditions. Therefore, the apparently contradictory chaperone function (i.e., promotion of client misfolding) of Hsp33 can also be associated with the PQC processes to ensure proteostasis in cells. Abstract Hsp33, a prokaryotic redox-regulated holding chaperone, has been recently identified to be able to exhibit an unfoldase and aggregase activity against elongation factor Tu (EF-Tu) in its reduced state. In this study, we investigated the effect of elongation factor Ts (EF-Ts) and trigger factor (TF) on Hsp33-mediated EF-Tu unfolding and aggregation using gel filtration, light scattering, circular dichroism, and isothermal titration calorimetry. We found that EF-Tu unfolding and subsequent aggregation induced by Hsp33 were evident even in its complex state with EF-Ts, which enhanced EF-Tu stability. In addition, although TF alone had no substantial effect on the stability of EF-Tu, it markedly amplified the Hsp33-mediated EF-Tu unfolding and aggregation. Collectively, the present results constitute the first example of synergistic unfoldase/aggregase activity of molecular chaperones and suggest that the stability of EF-Tu is modulated by a sophisticated network of molecular chaperones to regulate protein biosynthesis in cells under stress conditions.
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Nomura K, Kitagawa Y, Aihara M, Ohki Y, Furuyama K, Hirokawa T. Heme-dependent recognition of 5-aminolevulinate synthase by the human mitochondrial molecular chaperone ClpX. FEBS Lett 2021; 595:3019-3029. [PMID: 34704252 DOI: 10.1002/1873-3468.14214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/21/2021] [Accepted: 10/15/2021] [Indexed: 11/08/2022]
Abstract
The caseinolytic mitochondrial matrix peptidase chaperone subunit (ClpX) plays an important role in the heme-dependent regulation of 5-aminolevulinate synthase (ALAS1), a key enzyme in heme biosynthesis. However, the mechanisms underlying the role of ClpX in this process remain unclear. In this in vitro study, we confirmed the direct binding between ALAS1 and ClpX in a heme-dependent manner. The substitution of C108 P109 [CP motif 3 (CP3)] with A108 A109 in ALAS1 resulted in a loss of ability to bind ClpX. Computational disorder analyses revealed that CP3 was located in a potential intrinsically disordered protein region (IDPR). Thus, we propose that conditional disorder-to-order transitions in the IDPRs of ALAS1 may represent key mechanisms underlying the heme-dependent recognition of ALAS1 by ClpX.
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Affiliation(s)
- Kazumi Nomura
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | - Yu Kitagawa
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | - Marina Aihara
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | - Yusuke Ohki
- Department of Molecular Biochemistry, Iwate Medical University, Japan
| | | | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Japan.,Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Japan.,Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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16
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The binding of the small heat-shock protein αB-crystallin to fibrils of α-synuclein is driven by entropic forces. Proc Natl Acad Sci U S A 2021; 118:2108790118. [PMID: 34518228 PMCID: PMC8463877 DOI: 10.1073/pnas.2108790118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2021] [Indexed: 11/18/2022] Open
Abstract
Molecular chaperones are key components of the cellular proteostasis network whose role includes the suppression of the formation and proliferation of pathogenic aggregates associated with neurodegenerative diseases. The molecular principles that allow chaperones to recognize misfolded and aggregated proteins remain, however, incompletely understood. To address this challenge, here we probe the thermodynamics and kinetics of the interactions between chaperones and protein aggregates under native solution conditions using a microfluidic platform. We focus on the binding between amyloid fibrils of α-synuclein, associated with Parkinson's disease, to the small heat-shock protein αB-crystallin, a chaperone widely involved in the cellular stress response. We find that αB-crystallin binds to α-synuclein fibrils with high nanomolar affinity and that the binding is driven by entropy rather than enthalpy. Measurements of the change in heat capacity indicate significant entropic gain originates from the disassembly of the oligomeric chaperones that function as an entropic buffer system. These results shed light on the functional roles of chaperone oligomerization and show that chaperones are stored as inactive complexes which are capable of releasing active subunits to target aberrant misfolded species.
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17
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Fassler R, Zuily L, Lahrach N, Ilbert M, Reichmann D. The Central Role of Redox-Regulated Switch Proteins in Bacteria. Front Mol Biosci 2021; 8:706039. [PMID: 34277710 PMCID: PMC8282892 DOI: 10.3389/fmolb.2021.706039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/18/2021] [Indexed: 01/11/2023] Open
Abstract
Bacteria possess the ability to adapt to changing environments. To enable this, cells use reversible post-translational modifications on key proteins to modulate their behavior, metabolism, defense mechanisms and adaptation of bacteria to stress. In this review, we focus on bacterial protein switches that are activated during exposure to oxidative stress. Such protein switches are triggered by either exogenous reactive oxygen species (ROS) or endogenous ROS generated as by-products of the aerobic lifestyle. Both thiol switches and metal centers have been shown to be the primary targets of ROS. Cells take advantage of such reactivity to use these reactive sites as redox sensors to detect and combat oxidative stress conditions. This in turn may induce expression of genes involved in antioxidant strategies and thus protect the proteome against stress conditions. We further describe the well-characterized mechanism of selected proteins that are regulated by redox switches. We highlight the diversity of mechanisms and functions (as well as common features) across different switches, while also presenting integrative methodologies used in discovering new members of this family. Finally, we point to future challenges in this field, both in uncovering new types of switches, as well as defining novel additional functions.
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Affiliation(s)
- Rosi Fassler
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lisa Zuily
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Nora Lahrach
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Marianne Ilbert
- Aix-Marseille University, CNRS, BIP, UMR 7281, IMM, Marseille, France
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
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Macošek J, Mas G, Hiller S. Redefining Molecular Chaperones as Chaotropes. Front Mol Biosci 2021; 8:683132. [PMID: 34195228 PMCID: PMC8237284 DOI: 10.3389/fmolb.2021.683132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/20/2021] [Indexed: 01/27/2023] Open
Abstract
Molecular chaperones are the key instruments of bacterial protein homeostasis. Chaperones not only facilitate folding of client proteins, but also transport them, prevent their aggregation, dissolve aggregates and resolve misfolded states. Despite this seemingly large variety, single chaperones can perform several of these functions even on multiple different clients, thus suggesting a single biophysical mechanism underlying. Numerous recently elucidated structures of bacterial chaperone–client complexes show that dynamic interactions between chaperones and their client proteins stabilize conformationally flexible non-native client states, which results in client protein denaturation. Based on these findings, we propose chaotropicity as a suitable biophysical concept to rationalize the generic activity of chaperones. We discuss the consequences of applying this concept in the context of ATP-dependent and -independent chaperones and their functional regulation.
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19
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Activation of Nm23-H1 to suppress breast cancer metastasis via redox regulation. Exp Mol Med 2021; 53:346-357. [PMID: 33753879 PMCID: PMC8080780 DOI: 10.1038/s12276-021-00575-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/21/2020] [Accepted: 01/12/2021] [Indexed: 02/05/2023] Open
Abstract
Non-metastatic protein 23 H1 (Nm23-H1), a housekeeping enzyme, is a nucleoside diphosphate kinase-A (NDPK-A). It was the first identified metastasis suppressor protein. Nm23-H1 prolongs disease-free survival and is associated with a good prognosis in breast cancer patients. However, the molecular mechanisms underlying the role of Nm23-H1 in biological processes are still not well understood. This is a review of recent studies focusing on controlling NDPK activity based on the redox regulation of Nm23-H1, structural, and functional changes associated with the oxidation of cysteine residues, and the relationship between NDPK activity and cancer metastasis. Further understanding of the redox regulation of the NDPK function will likely provide a new perspective for developing new strategies for the activation of NDPK-A in suppressing cancer metastasis.
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20
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Radzinski M, Oppenheim T, Metanis N, Reichmann D. The Cys Sense: Thiol Redox Switches Mediate Life Cycles of Cellular Proteins. Biomolecules 2021; 11:469. [PMID: 33809923 PMCID: PMC8004198 DOI: 10.3390/biom11030469] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/14/2022] Open
Abstract
Protein homeostasis is an essential component of proper cellular function; however, sustaining protein health is a challenging task, especially during the aerobic lifestyle. Natural cellular oxidants may be involved in cell signaling and antibacterial defense; however, imbalanced levels can lead to protein misfolding, cell damage, and death. This merges together the processes of protein homeostasis and redox regulation. At the heart of this process are redox-regulated proteins or thiol-based switches, which carefully mediate various steps of protein homeostasis across folding, localization, quality control, and degradation pathways. In this review, we discuss the "redox code" of the proteostasis network, which shapes protein health during cell growth and aging. We describe the sources and types of thiol modifications and elaborate on diverse strategies of evolving antioxidant proteins in proteostasis networks during oxidative stress conditions. We also highlight the involvement of cysteines in protein degradation across varying levels, showcasing the importance of cysteine thiols in proteostasis at large. The individual examples and mechanisms raised open the door for extensive future research exploring the interplay between the redox and protein homeostasis systems. Understanding this interplay will enable us to re-write the redox code of cells and use it for biotechnological and therapeutic purposes.
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Affiliation(s)
- Meytal Radzinski
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; (M.R.); (T.O.)
| | - Tal Oppenheim
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; (M.R.); (T.O.)
| | - Norman Metanis
- Institute of Chemistry, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; (M.R.); (T.O.)
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21
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Ba M, Paillat M, Tronche N, Vigneron-Bouquet A, Latifi A. [Role of chaperons in bacterial adaptive mechanisms]. Med Sci (Paris) 2021; 37:293-297. [PMID: 33739279 DOI: 10.1051/medsci/2021020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Moly Ba
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille Université, Marseille, France
| | - Maëlle Paillat
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille Université, Marseille, France
| | - Nolan Tronche
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille Université, Marseille, France
| | - Amélie Vigneron-Bouquet
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille Université, Marseille, France
| | - Amel Latifi
- Master 2 Microbiologie intégrative et fondamentale, Aix Marseille Université, Marseille, France
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Varatnitskaya M, Degrossoli A, Leichert LI. Redox regulation in host-pathogen interactions: thiol switches and beyond. Biol Chem 2020; 402:299-316. [PMID: 33021957 DOI: 10.1515/hsz-2020-0264] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/29/2020] [Indexed: 12/23/2022]
Abstract
Our organism is exposed to pathogens on a daily basis. Owing to this age-old interaction, both pathogen and host evolved strategies to cope with these encounters. Here, we focus on the consequences of the direct encounter of cells of the innate immune system with bacteria. First, we will discuss the bacterial strategies to counteract powerful reactive species. Our emphasis lies on the effects of hypochlorous acid (HOCl), arguably the most powerful oxidant produced inside the phagolysosome of professional phagocytes. We will highlight individual examples of proteins in gram-negative bacteria activated by HOCl via thiol-disulfide switches, methionine sulfoxidation, and N-chlorination of basic amino acid side chains. Second, we will discuss the effects of HOCl on proteins of the host. Recent studies have shown that both host and bacteria address failing protein homeostasis by activation of chaperone-like holdases through N-chlorination. After discussing the role of individual proteins in the HOCl-defense, we will turn our attention to the examination of effects on host and pathogen on a systemic level. Recent studies using genetically encoded redox probes and redox proteomics highlight differences in redox homeostasis in host and pathogen and give first hints at potential cellular HOCl signaling beyond thiol-disulfide switch mechanisms.
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Affiliation(s)
- Marharyta Varatnitskaya
- Institute for Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Adriana Degrossoli
- Faculty of Health Science - Health Science Department, Federal University of Lavras, Lavras, Brazil
| | - Lars I Leichert
- Institute for Biochemistry and Pathobiochemistry - Microbial Biochemistry, Ruhr University Bochum, Bochum, Germany
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23
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Ulrich K, Schwappach B, Jakob U. Thiol-based switching mechanisms of stress-sensing chaperones. Biol Chem 2020; 402:239-252. [PMID: 32990643 DOI: 10.1515/hsz-2020-0262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/11/2020] [Indexed: 12/13/2022]
Abstract
Thiol-based redox switches evolved as efficient post-translational regulatory mechanisms that enable individual proteins to rapidly respond to sudden environmental changes. While some protein functions need to be switched off to save resources and avoid potentially error-prone processes, protective functions become essential and need to be switched on. In this review, we focus on thiol-based activation mechanisms of stress-sensing chaperones. Upon stress exposure, these chaperones convert into high affinity binding platforms for unfolding proteins and protect cells against the accumulation of potentially toxic protein aggregates. Their chaperone activity is independent of ATP, a feature that becomes especially important under oxidative stress conditions, where cellular ATP levels drop and canonical ATP-dependent chaperones no longer operate. Vice versa, reductive inactivation and substrate release require the restoration of ATP levels, which ensures refolding of client proteins by ATP-dependent foldases. We will give an overview over the different strategies that cells evolved to rapidly increase the pool of ATP-independent chaperones upon oxidative stress and provide mechanistic insights into how stress conditions are used to convert abundant cellular proteins into ATP-independent holding chaperones.
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Affiliation(s)
- Kathrin Ulrich
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI48109, USA
| | - Blanche Schwappach
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 1105 N. University Ave., Ann Arbor, MI48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI48109, USA
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Mas G, Burmann BM, Sharpe T, Claudi B, Bumann D, Hiller S. Regulation of chaperone function by coupled folding and oligomerization. SCIENCE ADVANCES 2020; 6:6/43/eabc5822. [PMID: 33087350 PMCID: PMC7577714 DOI: 10.1126/sciadv.abc5822] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/03/2020] [Indexed: 05/03/2023]
Abstract
The homotrimeric molecular chaperone Skp of Gram-negative bacteria facilitates the transport of outer membrane proteins across the periplasm. It has been unclear how its activity is modulated during its functional cycle. Here, we report an atomic-resolution characterization of the Escherichia coli Skp monomer-trimer transition. We find that the monomeric state of Skp is intrinsically disordered and that formation of the oligomerization interface initiates folding of the α-helical coiled-coil arms via a unique "stapling" mechanism, resulting in the formation of active trimeric Skp. Native client proteins contact all three Skp subunits simultaneously, and accordingly, their binding shifts the Skp population toward the active trimer. This activation mechanism is shown to be essential for Salmonella fitness in a mouse infection model. The coupled mechanism is a unique example of how an ATP-independent chaperone can modulate its activity as a function of the presence of client proteins.
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Affiliation(s)
- Guillaume Mas
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Björn M Burmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Timothy Sharpe
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Beatrice Claudi
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Dirk Bumann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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25
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Abstract
M. tuberculosis infections are responsible for more than 1 million deaths per year. Developing effective strategies to combat this disease requires a greater understanding of M. tuberculosis biology. As in all cells, protein quality control is essential for the viability of M. tuberculosis, which likely faces proteotoxic stress within a host. Here, we identify an M. tuberculosis protein, Ruc, that gains chaperone activity upon oxidation. Ruc represents a previously unrecognized family of redox-regulated chaperones found throughout the bacterial superkingdom. Additionally, we found that oxidized Ruc promotes the protein-folding activity of the essential M. tuberculosis Hsp70 chaperone system. This work contributes to a growing body of evidence that oxidative stress provides a particular strain on cellular protein stability. The bacterial pathogen Mycobacterium tuberculosis is the leading cause of death by an infectious disease among humans. Here, we describe a previously uncharacterized M. tuberculosis protein, Rv0991c, as a molecular chaperone that is activated by oxidation. Rv0991c has homologs in most bacterial lineages and appears to function analogously to the well-characterized Escherichia coli redox-regulated chaperone Hsp33, despite a dissimilar protein sequence. Rv0991c is transcriptionally coregulated with hsp60 and hsp70 chaperone genes in M. tuberculosis, suggesting that Rv0991c functions with these chaperones in maintaining protein quality control. Supporting this hypothesis, we found that, like oxidized Hsp33, oxidized Rv0991c prevents the aggregation of a model unfolded protein in vitro and promotes its refolding by the M. tuberculosis Hsp70 chaperone system. Furthermore, Rv0991c interacts with DnaK and can associate with many other M. tuberculosis proteins. We therefore propose that Rv0991c, which we named “Ruc” (redox-regulated protein with unstructured C terminus), represents a founding member of a new chaperone family that protects M. tuberculosis and other species from proteotoxicity during oxidative stress.
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Zavaliev R, Mohan R, Chen T, Dong X. Formation of NPR1 Condensates Promotes Cell Survival during the Plant Immune Response. Cell 2020; 182:1093-1108.e18. [PMID: 32810437 DOI: 10.1016/j.cell.2020.07.016] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 04/20/2020] [Accepted: 07/13/2020] [Indexed: 01/07/2023]
Abstract
In plants, pathogen effector-triggered immunity (ETI) often leads to programmed cell death, which is restricted by NPR1, an activator of systemic acquired resistance. However, the biochemical activities of NPR1 enabling it to promote defense and restrict cell death remain unclear. Here we show that NPR1 promotes cell survival by targeting substrates for ubiquitination and degradation through formation of salicylic acid-induced NPR1 condensates (SINCs). SINCs are enriched with stress response proteins, including nucleotide-binding leucine-rich repeat immune receptors, oxidative and DNA damage response proteins, and protein quality control machineries. Transition of NPR1 into condensates is required for formation of the NPR1-Cullin 3 E3 ligase complex to ubiquitinate SINC-localized substrates, such as EDS1 and specific WRKY transcription factors, and promote cell survival during ETI. Our analysis of SINCs suggests that NPR1 is centrally integrated into the cell death or survival decisions in plant immunity by modulating multiple stress-responsive processes in this quasi-organelle.
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Affiliation(s)
- Raul Zavaliev
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Tianyuan Chen
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | - Xinnian Dong
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA.
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Murvai N, Kalmar L, Szalaine Agoston B, Szabo B, Tantos A, Csikos G, Micsonai A, Kardos J, Vertommen D, Nguyen PN, Hristozova N, Lang A, Kovacs D, Buday L, Han KH, Perczel A, Tompa P. Interplay of Structural Disorder and Short Binding Elements in the Cellular Chaperone Function of Plant Dehydrin ERD14. Cells 2020; 9:E1856. [PMID: 32784707 PMCID: PMC7465474 DOI: 10.3390/cells9081856] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 12/23/2022] Open
Abstract
Details of the functional mechanisms of intrinsically disordered proteins (IDPs) in living cells is an area not frequently investigated. Here, we dissect the molecular mechanism of action of an IDP in cells by detailed structural analyses based on an in-cell nuclear magnetic resonance experiment. We show that the ID stress protein (IDSP) A. thaliana Early Response to Dehydration (ERD14) is capable of protecting E. coli cells under heat stress. The overexpression of ERD14 increases the viability of E. coli cells from 38.9% to 73.9% following heat stress (50 °C × 15 min). We also provide evidence that the protection is mainly achieved by protecting the proteome of the cells. In-cell NMR experiments performed in E. coli cells show that the protective activity is associated with a largely disordered structural state with conserved, short sequence motifs (K- and H-segments), which transiently sample helical conformations in vitro and engage in partner binding in vivo. Other regions of the protein, such as its S segment and its regions linking and flanking the binding motifs, remain unbound and disordered in the cell. Our data suggest that the cellular function of ERD14 is compatible with its residual structural disorder in vivo.
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Affiliation(s)
- Nikoletta Murvai
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Bianka Szalaine Agoston
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
- MTA-ELTE Protein Modelling Research Group and Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös L. University, 1117 Budapest, Hungary; (A.L.); (A.P.)
| | - Beata Szabo
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
| | - Gyorgy Csikos
- Department of General Zoology, Eötvös Loránd University, 1117 Budapest, Hungary;
| | - András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.M.); (J.K.)
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.M.); (J.K.)
| | - Didier Vertommen
- Faculty of Medicine and de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Phuong N. Nguyen
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; (P.N.N.); (N.H.); (D.K.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
| | - Nevena Hristozova
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; (P.N.N.); (N.H.); (D.K.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
| | - Andras Lang
- MTA-ELTE Protein Modelling Research Group and Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös L. University, 1117 Budapest, Hungary; (A.L.); (A.P.)
| | - Denes Kovacs
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; (P.N.N.); (N.H.); (D.K.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
| | - Laszlo Buday
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
| | - Kyou-Hoon Han
- Gene Editing Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
- Biomedical Translational Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Andras Perczel
- MTA-ELTE Protein Modelling Research Group and Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös L. University, 1117 Budapest, Hungary; (A.L.); (A.P.)
| | - Peter Tompa
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.A.); (B.S.); (A.T.); (L.B.)
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium; (P.N.N.); (N.H.); (D.K.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
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Aramin S, Fassler R, Chikne V, Goldenberg M, Arian T, Kolet Eliaz L, Rimon O, Ram O, Michaeli S, Reichmann D. TrypOx, a Novel Eukaryotic Homolog of the Redox-Regulated Chaperone Hsp33 in Trypanosoma brucei. Front Microbiol 2020; 11:1844. [PMID: 32849441 PMCID: PMC7423844 DOI: 10.3389/fmicb.2020.01844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/14/2020] [Indexed: 01/28/2023] Open
Abstract
ATP-independent chaperones are widespread across all domains of life and serve as the first line of defense during protein unfolding stresses. One of the known crucial chaperones for bacterial survival in a hostile environment (e.g., heat and oxidative stress) is the highly conserved, redox-regulated ATP-independent bacterial chaperone Hsp33. Using a bioinformatic analysis, we describe novel eukaryotic homologs of Hsp33 identified in eukaryotic pathogens belonging to the kinetoplastids, a family responsible for lethal human diseases such as Chagas disease as caused by Trypanosoma cruzi, African sleeping sickness caused by Trypanosoma brucei spp., and leishmaniasis pathologies delivered by various Leishmania species. During their pathogenic life cycle, kinetoplastids need to cope with elevated temperatures and oxidative stress, the same conditions which convert Hsp33 into a powerful chaperone in bacteria, thus preventing aggregation of a wide range of misfolded proteins. Here, we focused on a functional characterization of the Hsp33 homolog in one of the members of the kinetoplastid family, T. brucei, (Tb927.6.2630), which we have named TrypOx. RNAi silencing of TrypOx led to a significant decrease in the survival of T. brucei under mild oxidative stress conditions, implying a protective role of TrypOx during the Trypanosomes growth. We then adopted a proteomics-driven approach to investigate the role of TrypOx in defining the oxidative stress response. Depletion of TrypOx significantly altered the abundance of proteins mediating redox homeostasis, linking TrypOx with the antioxidant system. Using biochemical approaches, we identified the redox-switch domain of TrypOx, showing its modularity and oxidation-dependent structural plasticity. Kinetoplastid parasites such as T. brucei need to cope with high levels of oxidants produced by the innate immune system, such that parasite-specific antioxidant proteins like TrypOx - which are depleted in mammals - are highly promising candidates for drug targeting.
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Affiliation(s)
- Samar Aramin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rosi Fassler
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vaibhav Chikne
- The Mina and Everard Goodman Faculty of Life Sciences, Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat Gan, Israel
| | - Mor Goldenberg
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tal Arian
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Liat Kolet Eliaz
- The Mina and Everard Goodman Faculty of Life Sciences, Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat Gan, Israel
| | - Oded Rimon
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oren Ram
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences, Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat Gan, Israel
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, Israel
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29
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Nava Ramírez T, Hansberg W. Características comunes de las chaperonas pequeñas y diméricas. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2020. [DOI: 10.22201/fesz.23958723e.2020.0.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Las chaperonas moleculares constituyen un mecanismo importante para evitar la muerte celular provocada por la agregación de proteínas. Las chaperonas independientes del ATP son un grupo de proteínas de bajo peso molecular que pueden proteger y ayudar a alcanzar la estructura nativa de las proteínas desplegadas o mal plegadas sin necesidad de un gasto energético. Hemos encontrado que el dominio C-terminal de las catalasas de subunidad grande tiene actividad de chaperona. Por ello, en esta revisión analizamos las características más comunes de las chaperonas pequeñas y más estudiadas como: αB-cristalina, Hsp20, Spy, Hsp33 y Hsp31. En particular, se examina la participación de los aminoácidos hidrofóbicos y de los aminoácidos con carga en el reconocimiento de las proteínas sustrato, así como el papel que tiene la forma dimérica y su oligomerización en la actividad de chaperona. En cada una de esas chaperonas revisaremos la estructura de la proteína, su función, localización celular e importancia para la célula.
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30
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Bhopatkar AA, Uversky VN, Rangachari V. Disorder and cysteines in proteins: A design for orchestration of conformational see-saw and modulatory functions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:331-373. [PMID: 32828470 DOI: 10.1016/bs.pmbts.2020.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Being responsible for more than 90% of cellular functions, protein molecules are workhorses in all the life forms. In order to cater for such a high demand, proteins have evolved to adopt diverse structures that allow them to perform myriad of functions. Beginning with the genetically directed amino acid sequence, the classical understanding of protein function involves adoption of hierarchically complex yet ordered structures. However, advances made over the last two decades have revealed that inasmuch as 50% of eukaryotic proteome exists as partially or fully disordered structures. Significance of such intrinsically disordered proteins (IDPs) is further realized from their ability to exhibit multifunctionality, a feature attributable to their conformational plasticity. Among the coded amino acids, cysteines are considered to be "order-promoting" due to their ability to form inter- or intramolecular disulfide bonds, which confer robust thermal stability to the protein structure in oxidizing conditions. The co-existence of order-promoting cysteines with disorder-promoting sequences seems counter-intuitive yet many proteins have evolved to contain such sequences. In this chapter, we review some of the known cysteine-containing protein domains categorized based on the number of cysteines they possess. We show that many protein domains contain disordered sequences interspersed with cysteines. We show that a positive correlation exists between the degree of cysteines and disorder within the sequences that flank them. Furthermore, based on the computational platform, IUPred2A, we show that cysteine-rich sequences display significant disorder in the reduced but not the oxidized form, increasing the potential for such sequences to function in a redox-sensitive manner. Overall, this chapter provides insights into an exquisite evolutionary design wherein disordered sequences with interspersed cysteines enable potential modulatory protein functions under stress and environmental conditions, which thus far remained largely inconspicuous.
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Affiliation(s)
- Anukool A Bhopatkar
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States; Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS, United States; Center of Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, United States.
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31
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Abstract
Neutrophils kill invading microbes and therefore represent the first line of defense of the innate immune response. Activated neutrophils assemble NADPH oxidase to convert substantial amounts of molecular oxygen into superoxide, which, after dismutation into peroxide, serves as the substrate for the generation of the potent antimicrobial hypochlorous acid (HOCl) in the phagosomal space. In this minireview, we explore the most recent insights into physiological consequences of HOCl stress. Not surprisingly, Gram-negative bacteria have evolved diverse posttranslational defense mechanisms to protect their proteins, the main targets of HOCl, from HOCl-mediated damage. We discuss the idea that oxidation of conserved cysteine residues and partial unfolding of its structure convert the heat shock protein Hsp33 into a highly active chaperone holdase that binds unfolded proteins and prevents their aggregation. We examine two novel members of the Escherichia coli chaperone holdase family, RidA and CnoX, whose thiol-independent activation mechanism differs from that of Hsp33 and requires N-chlorination of positively charged amino acids during HOCl exposure. Furthermore, we summarize the latest findings with respect to another bacterial defense strategy employed in response to HOCl stress, which involves the accumulation of the universally conserved biopolymer inorganic polyphosphate. We then discuss sophisticated adaptive strategies that bacteria have developed to enhance their survival during HOCl stress. Understanding bacterial defense and survival strategies against one of the most powerful neutrophilic oxidants may provide novel insights into treatment options that potentially compromise the ability of pathogens to resist HOCl stress and therefore may increase the efficacy of the innate immune response.
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32
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Affiliation(s)
- Gábor Erdős
- Department of Biochemistry, MTA‐ELTE Momentum Bioinformatics Research Group ELTE Eötvös Loránd University Budapest Hungary
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, MTA‐ELTE Momentum Bioinformatics Research Group ELTE Eötvös Loránd University Budapest Hungary
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33
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Dissecting the Functional Contributions of the Intrinsically Disordered C-terminal Tail of Bacillus subtilis FtsZ. J Mol Biol 2020; 432:3205-3221. [PMID: 32198113 DOI: 10.1016/j.jmb.2020.03.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/13/2020] [Accepted: 03/07/2020] [Indexed: 01/12/2023]
Abstract
FtsZ is a bacterial GTPase that is central to the spatial and temporal control of cell division. It is a filament-forming enzyme that encompasses a well-folded core domain and a disordered C-terminal tail (CTT). The CTT is essential for ensuring proper assembly of the cytokinetic ring, and its deletion leads to mis-localization of FtsZ, aberrant assembly, and cell death. In this work, we dissect the contributions of modules within the disordered CTT to assembly and enzymatic activity of Bacillus subtilis FtsZ (Bs-FtsZ). The CTT features a hypervariable C-terminal linker (CTL) and a conserved C-terminal peptide (CTP). Our in vitro studies show that the CTL weakens the driving forces for forming single-stranded active polymers and suppresses lateral associations of these polymers, whereas the CTP promotes the formation of alternative assemblies. Accordingly, in full-length Bs-FtsZ, the CTL acts as a spacer that spatially separates the CTP sticker from the core, thus ensuring filament formation through core-driven polymerization and lateral associations through CTP-mediated interactions. We also find that the CTL weakens GTP binding while enhancing the catalytic rate, whereas the CTP has opposite effects. The joint contributions of the CTL and CTP make Bs-FtsZ, an enzyme that is only half as efficient as a truncated version that lacks the CTT. Overall, our data suggest that the CTT acts as an auto-regulator of Bs-FtsZ assembly and as an auto-inhibitor of enzymatic activity. Based on our results, we propose hypotheses regarding the hypervariability of CTLs and compare FtsZs to other bacterial proteins with tethered IDRs.
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34
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Moayed F, Bezrukavnikov S, Naqvi MM, Groitl B, Cremers CM, Kramer G, Ghosh K, Jakob U, Tans SJ. The Anti-Aggregation Holdase Hsp33 Promotes the Formation of Folded Protein Structures. Biophys J 2019; 118:85-95. [PMID: 31757359 DOI: 10.1016/j.bpj.2019.10.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/04/2019] [Accepted: 10/15/2019] [Indexed: 11/26/2022] Open
Abstract
Holdase chaperones are known to be central to suppressing aggregation, but how they affect substrate conformations remains poorly understood. Here, we use optical tweezers to study how the holdase Hsp33 alters folding transitions within single maltose binding proteins and aggregation transitions between maltose binding protein substrates. Surprisingly, we find that Hsp33 not only suppresses aggregation but also guides the folding process. Two modes of action underlie these effects. First, Hsp33 binds unfolded chains, which suppresses aggregation between substrates and folding transitions within substrates. Second, Hsp33 binding promotes substrate states in which most of the chain is folded and modifies their structure, possibly by intercalating its intrinsically disordered regions. A statistical ensemble model shows how Hsp33 function results from the competition between these two contrasting effects. Our findings reveal an unexpectedly comprehensive functional repertoire for Hsp33 that may be more prevalent among holdases and dispels the notion of a strict chaperone hierarchy.
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Affiliation(s)
| | | | | | - Bastian Groitl
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Claudia M Cremers
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Guenter Kramer
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Colorado
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
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35
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Wu K, Stull F, Lee C, Bardwell JCA. Protein folding while chaperone bound is dependent on weak interactions. Nat Commun 2019; 10:4833. [PMID: 31645566 PMCID: PMC6811625 DOI: 10.1038/s41467-019-12774-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/23/2019] [Indexed: 12/31/2022] Open
Abstract
It is generally assumed that protein clients fold following their release from chaperones instead of folding while remaining chaperone-bound, in part because binding is assumed to constrain the mobility of bound clients. Previously, we made the surprising observation that the ATP-independent chaperone Spy allows its client protein Im7 to fold into the native state while continuously bound to the chaperone. Spy apparently permits sufficient client mobility to allow folding to occur while chaperone bound. Here, we show that strengthening the interaction between Spy and a recently discovered client SH3 strongly inhibits the ability of the client to fold while chaperone bound. The more tightly Spy binds to its client, the more it slows the folding rate of the bound client. Efficient chaperone-mediated folding while bound appears to represent an evolutionary balance between interactions of sufficient strength to mediate folding and interactions that are too tight, which tend to inhibit folding. Spy is an ATP independent chaperone that allows folding of its client protein Im7 while continuously bound to Spy. Here the authors employ kinetics measurements to study the folding of another Spy client protein SH3 and find that Spy’s ability to allow a client to fold while bound is inversely related to how strongly it interacts with that client.
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Affiliation(s)
- Kevin Wu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Frederick Stull
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Changhan Lee
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA. .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA.
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36
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Launay H, Receveur-Bréchot V, Carrière F, Gontero B. Orchestration of algal metabolism by protein disorder. Arch Biochem Biophys 2019; 672:108070. [PMID: 31408624 DOI: 10.1016/j.abb.2019.108070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Accepted: 08/08/2019] [Indexed: 01/12/2023]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that provide many functional advantages in a large number of metabolic and signalling pathways. Because of their high flexibility that endows them with pressure-, heat- and acid-resistance, IDPs are valuable metabolic regulators that help algae to cope with extreme conditions of pH, temperature, pressure and light. They have, however, been overlooked in these organisms. In this review, we present some well-known algal IDPs, including the conditionally disordered CP12, a protein involved in the regulation of CO2 assimilation, as probably the best known example, whose disorder content is strongly dependent on the redox conditions, and the essential pyrenoid component 1 that serves as a scaffold for ribulose-1, 5-bisphosphate carboxylase/oxygenase. We also describe how some enzymes are regulated by protein regions, called intrinsically disordered regions (IDRs), such as ribulose-1, 5-bisphosphate carboxylase/oxygenase activase, the A2B2 form of glyceraldehyde-3-phosphate dehydrogenase and the adenylate kinase. Several molecular chaperones, which are crucial for cell proteostasis, also display significant disorder propensities such as the algal heat shock proteins HSP33, HSP70 and HSP90. This review confirms the wide distribution of IDPs in algae but highlights that further studies are needed to uncover their full role in orchestrating algal metabolism.
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Affiliation(s)
- Hélène Launay
- Aix Marseille Univ, CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, Marseille Cedex 20, 13402, France
| | | | - Frédéric Carrière
- Aix Marseille Univ, CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, Marseille Cedex 20, 13402, France
| | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP UMR 7281, 31 Chemin Joseph Aiguier, Marseille Cedex 20, 13402, France.
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37
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Mészáros B, Erdos G, Dosztányi Z. IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res 2019; 46:W329-W337. [PMID: 29860432 PMCID: PMC6030935 DOI: 10.1093/nar/gky384] [Citation(s) in RCA: 877] [Impact Index Per Article: 175.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/11/2018] [Indexed: 01/31/2023] Open
Abstract
The structural states of proteins include ordered globular domains as well as intrinsically disordered protein regions that exist as highly flexible conformational ensembles in isolation. Various computational tools have been developed to discriminate ordered and disordered segments based on the amino acid sequence. However, properties of IDRs can also depend on various conditions, including binding to globular protein partners or environmental factors, such as redox potential. These cases provide further challenges for the computational characterization of disordered segments. In this work we present IUPred2A, a combined web interface that allows to generate energy estimation based predictions for ordered and disordered residues by IUPred2 and for disordered binding regions by ANCHOR2. The updated web server retains the robustness of the original programs but offers several new features. While only minor bug fixes are implemented for IUPred, the next version of ANCHOR is significantly improved through a new architecture and parameters optimized on novel datasets. In addition, redox-sensitive regions can also be highlighted through a novel experimental feature. The web server offers graphical and text outputs, a RESTful interface, access to software download and extensive help, and can be accessed at a new location: http://iupred2a.elte.hu.
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Affiliation(s)
- Bálint Mészáros
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Gábor Erdos
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
| | - Zsuzsanna Dosztányi
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary
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38
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Schramm A, Bignon C, Brocca S, Grandori R, Santambrogio C, Longhi S. An arsenal of methods for the experimental characterization of intrinsically disordered proteins - How to choose and combine them? Arch Biochem Biophys 2019; 676:108055. [PMID: 31356778 DOI: 10.1016/j.abb.2019.07.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
In this review, we detail the most common experimental approaches to assess and characterize protein intrinsic structural disorder, with the notable exception of NMR and EPR spectroscopy, two ideally suited approaches that will be described in depth in two other reviews within this special issue. We discuss the advantages, the limitations, as well as the caveats of the various methods. We also describe less common and more demanding approaches that enable achieving further insights into the conformational properties of IDPs. Finally, we present recent developments that have enabled assessment of structural disorder in living cells, and discuss the currently available methods to model IDPs as conformational ensembles.
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Affiliation(s)
- Antoine Schramm
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
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39
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Abstract
Cells under stress must adjust their physiology, metabolism, and architecture to adapt to the new conditions. Most importantly, they must down-regulate general gene expression, but at the same time induce synthesis of stress-protective factors, such as molecular chaperones. Here, we investigate how the process of phase separation is used by cells to ensure adaptation to stress. We summarize recent findings and propose that the solubility of important translation factors is specifically affected by changes in physical-chemical parameters such temperature or pH and modulated by intrinsically disordered prion-like domains. These stress-triggered changes in protein solubility induce phase separation into condensates that regulate the activity of the translation factors and promote cellular fitness. Prion-like domains play important roles in this process as environmentally regulated stress sensors and modifier sequences that determine protein solubility and phase behavior. We propose that protein phase separation is an evolutionary conserved feature of proteins that cells harness to regulate adaptive stress responses and ensure survival in extreme environmental conditions.
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Affiliation(s)
- Titus M Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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40
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Unique Unfoldase/Aggregase Activity of a Molecular Chaperone Hsp33 in its Holding-Inactive State. J Mol Biol 2019; 431:1468-1480. [DOI: 10.1016/j.jmb.2019.02.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 11/21/2022]
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41
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Carra S, Alberti S, Benesch JLP, Boelens W, Buchner J, Carver JA, Cecconi C, Ecroyd H, Gusev N, Hightower LE, Klevit RE, Lee HO, Liberek K, Lockwood B, Poletti A, Timmerman V, Toth ME, Vierling E, Wu T, Tanguay RM. Small heat shock proteins: multifaceted proteins with important implications for life. Cell Stress Chaperones 2019; 24:295-308. [PMID: 30758704 PMCID: PMC6439001 DOI: 10.1007/s12192-019-00979-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 12/21/2022] Open
Abstract
Small Heat Shock Proteins (sHSPs) evolved early in the history of life; they are present in archaea, bacteria, and eukaryota. sHSPs belong to the superfamily of molecular chaperones: they are components of the cellular protein quality control machinery and are thought to act as the first line of defense against conditions that endanger the cellular proteome. In plants, sHSPs protect cells against abiotic stresses, providing innovative targets for sustainable agricultural production. In humans, sHSPs (also known as HSPBs) are associated with the development of several neurological diseases. Thus, manipulation of sHSP expression may represent an attractive therapeutic strategy for disease treatment. Experimental evidence demonstrates that enhancing the chaperone function of sHSPs protects against age-related protein conformation diseases, which are characterized by protein aggregation. Moreover, sHSPs can promote longevity and healthy aging in vivo. In addition, sHSPs have been implicated in the prognosis of several types of cancer. Here, sHSP upregulation, by enhancing cellular health, could promote cancer development; on the other hand, their downregulation, by sensitizing cells to external stressors and chemotherapeutics, may have beneficial outcomes. The complexity and diversity of sHSP function and properties and the need to identify their specific clients, as well as their implication in human disease, have been discussed by many of the world's experts in the sHSP field during a dedicated workshop in Québec City, Canada, on 26-29 August 2018.
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Affiliation(s)
- Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, and Centre for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia, via G. Campi 287, 41125, Modena, Italy.
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
- Center for Molecular and Cellular Bioengineering (CMCB), Biotechnology Center (BIOTEC), Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany
| | - Justin L P Benesch
- Department of Chemistry, Physical and Theoretical Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Wilbert Boelens
- Department of Biomolecular Chemistry, Institute of Molecules and Materials, Radboud University, NL-6500, Nijmegen, The Netherlands
| | - Johannes Buchner
- Center for Integrated Protein Science Munich (CIPSM) and Department Chemie, Technische Universität München, D-85748, Garching, Germany
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia
| | - Ciro Cecconi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125, Modena, Italy
- Center S3, CNR Institute Nanoscience, Via Campi 213/A, 41125, Modena, Italy
| | - Heath Ecroyd
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Nikolai Gusev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russian Federation, 117234
| | - Lawrence E Hightower
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT, 06269-3125, USA
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Hyun O Lee
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Krzysztof Liberek
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology UG-MUG, University of Gdansk, Abrahama 58, 80-307, Gdansk, Poland
| | - Brent Lockwood
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Angelo Poletti
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Univrsità degli Studi di Milano, Milan, Italy
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium
| | - Melinda E Toth
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Tangchun Wu
- MOE Key Lab of Environment and Health, Tongji School of Public Health, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 430030, Hubei, China
| | - Robert M Tanguay
- Laboratory of Cell and Developmental Genetics, IBIS, and Department of Molecular Biology, Medical Biochemistry and Pathology, Medical School, Université Laval, QC, Québec, G1V 0A6, Canada.
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42
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Erdős G, Mészáros B, Reichmann D, Dosztányi Z. Large-Scale Analysis of Redox-Sensitive Conditionally Disordered Protein Regions Reveals Their Widespread Nature and Key Roles in High-Level Eukaryotic Processes. Proteomics 2019; 19:e1800070. [PMID: 30628183 DOI: 10.1002/pmic.201800070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/13/2018] [Indexed: 12/17/2022]
Abstract
Recently developed quantitative redox proteomic studies enable the direct identification of redox-sensing cysteine residues that regulate the functional behavior of target proteins in response to changing levels of reactive oxygen species. At the molecular level, redox regulation can directly modify the active sites of enzymes, although a growing number of examples indicate the importance of an additional underlying mechanism that involves conditionally disordered proteins. These proteins alter their functional behavior by undergoing a disorder-to-order transition in response to changing redox conditions. However, the extent to which this mechanism is used in various proteomes is currently unknown. Here, a recently developed sequence-based prediction tool incorporated into the IUPred2A web server is used to estimate redox-sensitive conditionally disordered regions at a large scale. It is shown that redox-sensitive conditional disorder is fairly widespread in various proteomes and that its presence strongly correlates with the expansion of specific domains in multicellular organisms that largely rely on extra stability provided by disulfide bonds or zinc ion binding. The analyses of yeast redox proteomes and human disease data further underlie the significance of this phenomenon in the regulation of a wide range of biological processes, as well as its biomedical importance.
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Affiliation(s)
- Gábor Erdős
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Bálint Mészáros
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69117, Germany
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Zsuzsanna Dosztányi
- MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
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43
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Reichmann D, Voth W, Jakob U. Maintaining a Healthy Proteome during Oxidative Stress. Mol Cell 2019; 69:203-213. [PMID: 29351842 DOI: 10.1016/j.molcel.2017.12.021] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/11/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022]
Abstract
Some of the most challenging stress conditions that organisms encounter during their lifetime involve the transient accumulation of reactive oxygen and chlorine species. Extremely reactive to amino acid side chains, these oxidants cause widespread protein unfolding and aggregation. It is therefore not surprising that cells draw on a variety of different strategies to counteract the damage and maintain a healthy proteome. Orchestrated largely by direct changes in the thiol oxidation status of key proteins, the response strategies involve all layers of protein protection. Reprogramming of basic biological functions helps decrease nascent protein synthesis and restore redox homeostasis. Mobilization of oxidative stress-activated chaperones and production of stress-resistant non-proteinaceous chaperones prevent irreversible protein aggregation. Finally, redox-controlled increase in proteasome activity removes any irreversibly damaged proteins. Together, these systems pave the way to restore protein homeostasis and enable organisms to survive stress conditions that are inevitable when living an aerobic lifestyle.
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Affiliation(s)
- Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Wilhelm Voth
- Department of Molecular, Cellular, and Developmental Biology and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-1048, USA.
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44
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Bignon C, Troilo F, Gianni S, Longhi S. Modulation of Measles Virus N TAIL Interactions through Fuzziness and Sequence Features of Disordered Binding Sites. Biomolecules 2018; 9:biom9010008. [PMID: 30591682 PMCID: PMC6359293 DOI: 10.3390/biom9010008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 12/27/2022] Open
Abstract
In this paper we review our recent findings on the different interaction mechanisms of the C-terminal domain of the nucleoprotein (N) of measles virus (MeV) NTAIL, a model viral intrinsically disordered protein (IDP), with two of its known binding partners, i.e., the C-terminal X domain of the phosphoprotein of MeV XD (a globular viral protein) and the heat-shock protein 70 hsp70 (a globular cellular protein). The NTAIL binds both XD and hsp70 via a molecular recognition element (MoRE) that is flanked by two fuzzy regions. The long (85 residues) N-terminal fuzzy region is a natural dampener of the interaction with both XD and hsp70. In the case of binding to XD, the N-terminal fuzzy appendage of NTAIL reduces the rate of α-helical folding of the MoRE. The dampening effect of the fuzzy appendage on XD and hsp70 binding depends on the length and fuzziness of the N-terminal region. Despite this similarity, NTAIL binding to XD and hsp70 appears to rely on completely different requirements. Almost any mutation within the MoRE decreases XD binding, whereas many of them increase the binding to hsp70. In addition, XD binding is very sensitive to the α-helical state of the MoRE, whereas hsp70 is not. Thus, contrary to hsp70, XD binding appears to be strictly dependent on the wild-type primary and secondary structure of the MoRE.
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Affiliation(s)
- Christophe Bignon
- CNRS and Aix-Marseille Univ Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257 Marseille, France.
| | - Francesca Troilo
- CNRS and Aix-Marseille Univ Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257 Marseille, France.
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli' and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli' and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257 Marseille, France.
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45
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Yu XC, Hu Y, Ding J, Li H, Jin C. Structural basis and mechanism of the unfolding-induced activation of HdeA, a bacterial acid response chaperone. J Biol Chem 2018; 294:3192-3206. [PMID: 30573682 DOI: 10.1074/jbc.ra118.006398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/17/2018] [Indexed: 11/06/2022] Open
Abstract
The role of protein structural disorder in biological functions has gained increasing attention in the past decade. The bacterial acid-resistant chaperone HdeA belongs to a group of "conditionally disordered" proteins, because it is inactive in its well-structured state and becomes activated via an order-to-disorder transition under acid stress. However, the mechanism for unfolding-induced activation remains unclear because of a lack of experimental information on the unfolded state conformation and the chaperone-client interactions. Herein, we used advanced solution NMR methods to characterize the activated-state conformation of HdeA under acidic conditions and identify its client-binding sites. We observed that the structure of activated HdeA becomes largely disordered and exposes two hydrophobic patches essential for client interactions. Furthermore, using the pH-dependent chemical exchange saturation transfer (CEST) NMR method, we identified three acid-sensitive regions that act as structural locks in regulating the exposure of the two client-binding sites during the activation process, revealing a multistep activation mechanism of HdeA's chaperone function at the atomic level. Our results highlight the role of intrinsic protein disorder in chaperone function and the self-inhibitory role of ordered structures under nonstress conditions, offering new insights for improving our understanding of protein structure-function paradigms.
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Affiliation(s)
- Xing-Chi Yu
- From the College of Chemistry and Molecular Engineering.,Beijing Nuclear Magnetic Resonance Center
| | - Yunfei Hu
- From the College of Chemistry and Molecular Engineering, .,Beijing Nuclear Magnetic Resonance Center
| | - Jienv Ding
- Beijing Nuclear Magnetic Resonance Center.,College of Life Sciences
| | - Hongwei Li
- From the College of Chemistry and Molecular Engineering.,Beijing Nuclear Magnetic Resonance Center
| | - Changwen Jin
- From the College of Chemistry and Molecular Engineering, .,Beijing Nuclear Magnetic Resonance Center.,College of Life Sciences.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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46
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Bignon C, Troilo F, Gianni S, Longhi S. Partner-Mediated Polymorphism of an Intrinsically Disordered Protein. J Mol Biol 2018; 430:2493-2507. [DOI: 10.1016/j.jmb.2017.11.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/16/2017] [Accepted: 11/19/2017] [Indexed: 10/18/2022]
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47
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Fassler R, Edinger N, Rimon O, Reichmann D. Defining Hsp33's Redox-regulated Chaperone Activity and Mapping Conformational Changes on Hsp33 Using Hydrogen-deuterium Exchange Mass Spectrometry. J Vis Exp 2018. [PMID: 29939186 DOI: 10.3791/57806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Living organisms regularly need to cope with fluctuating environments during their life cycle, including changes in temperature, pH, the accumulation of reactive oxygen species, and more. These fluctuations can lead to a widespread protein unfolding, aggregation, and cell death. Therefore, cells have evolved a dynamic and stress-specific network of molecular chaperones, which maintain a "healthy" proteome during stress conditions. ATP-independent chaperones constitute one major class of molecular chaperones, which serve as first-line defense molecules, protecting against protein aggregation in a stress-dependent manner. One feature these chaperones have in common is their ability to utilize structural plasticity for their stress-specific activation, recognition, and release of the misfolded client. In this paper, we focus on the functional and structural analysis of one such intrinsically disordered chaperone, the bacterial redox-regulated Hsp33, which protects proteins against aggregation during oxidative stress. Here, we present a toolbox of diverse techniques for studying redox-regulated chaperone activity, as well as for mapping conformational changes of the chaperone, underlying its activity. Specifically, we describe a workflow which includes the preparation of fully reduced and fully oxidized proteins, followed by an analysis of the chaperone anti-aggregation activity in vitro using light-scattering, focusing on the degree of the anti-aggregation activity and its kinetics. To overcome frequent outliers accumulated during aggregation assays, we describe the usage of Kfits, a novel graphical tool which allows easy processing of kinetic measurements. This tool can be easily applied to other types of kinetic measurements for removing outliers and fitting kinetic parameters. To correlate the function with the protein structure, we describe the setup and workflow of a structural mass spectrometry technique, hydrogen-deuterium exchange mass spectrometry, that allows the mapping of conformational changes on the chaperone and substrate during different stages of Hsp33 activity. The same methodology can be applied to other protein-protein and protein-ligand interactions.
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Affiliation(s)
- Rosi Fassler
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem
| | - Nufar Edinger
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem
| | - Oded Rimon
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem;
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48
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Zhang Y, Launay H, Schramm A, Lebrun R, Gontero B. Exploring intrinsically disordered proteins in Chlamydomonas reinhardtii. Sci Rep 2018; 8:6805. [PMID: 29717210 PMCID: PMC5931566 DOI: 10.1038/s41598-018-24772-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/26/2018] [Indexed: 11/14/2022] Open
Abstract
The content of intrinsically disordered protein (IDP) is related to organism complexity, evolution, and regulation. In the Plantae, despite their high complexity, experimental investigation of IDP content is lacking. We identified by mass spectrometry 682 heat-resistant proteins from the green alga, Chlamydomonas reinhardtii. Using a phosphoproteome database, we found that 331 of these proteins are targets of phosphorylation. We analyzed the flexibility propensity of the heat-resistant proteins and their specific features as well as those of predicted IDPs from the same organism. Their mean percentage of disorder was about 20%. Most of the IDPs (~70%) were addressed to other compartments than mitochondrion and chloroplast. Their amino acid composition was biased compared to other classic IDPs. Their molecular functions were diverse; the predominant ones were nucleic acid binding and unfolded protein binding and the less abundant one was catalytic activity. The most represented proteins were ribosomal proteins, proteins associated to flagella, chaperones and histones. We also found CP12, the only experimental IDP from C. reinhardtii that is referenced in disordered protein database. This is the first experimental investigation of IDPs in C. reinhardtii that also combines in silico analysis.
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Affiliation(s)
- Yizhi Zhang
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13402, Marseille, Cedex 20, France
| | - Hélène Launay
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13402, Marseille, Cedex 20, France
| | | | - Régine Lebrun
- Plate-forme Protéomique, Marseille Protéomique (MaP), IBiSA labeled, IMM, FR 3479, CNRS, B.P. 71, 13402, Marseille, Cedex 20, France
| | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13402, Marseille, Cedex 20, France.
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49
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Rimon O, Suss O, Goldenberg M, Fassler R, Yogev O, Amartely H, Propper G, Friedler A, Reichmann D. A Role of Metastable Regions and Their Connectivity in the Inactivation of a Redox-Regulated Chaperone and Its Inter-Chaperone Crosstalk. Antioxid Redox Signal 2017; 27:1252-1267. [PMID: 28394178 DOI: 10.1089/ars.2016.6900] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS A recently discovered group of conditionally disordered chaperones share a very unique feature; they need to lose structure to become active as chaperones. This activation mechanism makes these chaperones particularly suited to respond to protein-unfolding stress conditions, such as oxidative unfolding. However, the role of this disorder in stress-related activation, chaperone function, and the crosstalk with other chaperone systems is not yet clear. Here, we focus on one of the members of the conditionally disordered chaperones, a thiol-redox switch of the bacterial proteostasis system, Hsp33. RESULTS By modifying the Hsp33's sequence, we reveal that the metastable region has evolved to abolish redox-dependent chaperone activity, rather than enhance binding affinity for client proteins. The intrinsically disordered region of Hsp33 serves as an anchor for the reduced, inactive state of Hsp33, and it dramatically affects the crosstalk with the synergetic chaperone system, DnaK/J. Using mass spectrometry, we describe the role that the metastable region plays in determining client specificity during normal and oxidative stress conditions in the cell. Innovation and Conclusion: We uncover a new role of protein plasticity in Hsp33's inactivation, client specificity, crosstalk with the synergistic chaperone system DnaK/J, and oxidative stress-specific interactions in bacteria. Our results also suggest that Hsp33 might serve as a member of the house-keeping proteostasis machinery, tasked with maintaining a "healthy" proteome during normal conditions, and that this function does not depend on the metastable linker region. Antioxid. Redox Signal. 27, 1252-1267.
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Affiliation(s)
- Oded Rimon
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Ohad Suss
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Mor Goldenberg
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Rosi Fassler
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Ohad Yogev
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Hadar Amartely
- 2 Institute of Chemistry, The Hebrew University of Jerusalem , Safra Campus Givat Ram, Jerusalem, Israel
| | - Guy Propper
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Assaf Friedler
- 2 Institute of Chemistry, The Hebrew University of Jerusalem , Safra Campus Givat Ram, Jerusalem, Israel
| | - Dana Reichmann
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
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50
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Voth W, Jakob U. Stress-Activated Chaperones: A First Line of Defense. Trends Biochem Sci 2017; 42:899-913. [PMID: 28893460 DOI: 10.1016/j.tibs.2017.08.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 10/18/2022]
Abstract
Proteins are constantly challenged by environmental stress conditions that threaten their structure and function. Especially problematic are oxidative, acid, and severe heat stress which induce very rapid and widespread protein unfolding and generate conditions that make canonical chaperones and/or transcriptional responses inadequate to protect the proteome. We review here recent advances in identifying and characterizing stress-activated chaperones which are inactive under non-stress conditions but become potent chaperones under specific protein-unfolding stress conditions. We discuss the post-translational mechanisms by which these chaperones sense stress, and consider the role that intrinsic disorder plays in their regulation and function. We examine their physiological roles under both non-stress and stress conditions, their integration into the cellular proteostasis network, and their potential as novel therapeutic targets.
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Affiliation(s)
- Wilhelm Voth
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular Biology, Universitätsmedizin Göttingen, 37073 Göttingen, Germany
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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