1
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Miller AP, Reichow SL. Mechanism of small heat shock protein client sequestration and induced polydispersity. Nat Commun 2025; 16:3635. [PMID: 40240363 PMCID: PMC12003685 DOI: 10.1038/s41467-025-58964-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2025] [Accepted: 04/07/2025] [Indexed: 04/18/2025] Open
Abstract
Small heat shock proteins (sHSPs) act as first responders during cellular stress, sequestering destabilized proteins (clients) to prevent aggregation and facilitate refolding or degradation. This critical function, conserved across all life, is linked to proteostasis and protein misfolding diseases. However, the extreme molecular plasticity of sHSP/client complexes has limited mechanistic understanding. Here, we present high-resolution cryo-EM structures of Methanocaldococcus jannaschii sHSP (mjHSP16.5) in apo and multiple client-bound states. The ensemble reveals molecular mechanisms of client sequestration, highlighting cooperative chaperone-client interactions. Client engagement polarizes scaffold stability, promoting higher-order assembly and enhanced sequestration. Higher-order states suggest multiple sHSP/client assembly pathways, including subunit insertion at destabilized geometrical features. These findings provide critical insights into sHSP chaperone function and the interplay between polydispersity and client handling under stress.
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Affiliation(s)
- Adam P Miller
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
- Vollum Institute, Oregon Health and Science Institute, Portland, OR, 97239, USA
| | - Steve L Reichow
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA.
- Vollum Institute, Oregon Health and Science Institute, Portland, OR, 97239, USA.
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2
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Berkeley RF, Plonski AP, Phan TM, Grohe K, Becker L, Wegner S, Herzik MA, Mittal J, Debelouchina GT. Capturing the Conformational Heterogeneity of HSPB1 Chaperone Oligomers at Atomic Resolution. J Am Chem Soc 2025. [PMID: 40146081 DOI: 10.1021/jacs.4c18668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2025]
Abstract
Small heat shock proteins (sHSPs), including HSPB1, are essential regulators of cellular proteostasis that interact with unfolded and partially folded proteins to prevent aberrant misfolding and aggregation. These proteins fulfill a similar role in biological condensates, where they interact with intrinsically disordered proteins to modulate their liquid-liquid and liquid-to-solid phase transitions. Characterizing the sHSP structure, dynamics, and client interactions is challenging due to their partially disordered nature, their tendency to form polydisperse oligomers, and their diverse range of clients. In this work, we leverage various biophysical methods, including fast 1H-based magic angle spinning (MAS) NMR spectroscopy, molecular dynamics (MD) simulations, and modeling, to shed new light on the structure and dynamics of HSPB1 oligomers. Using split-intein-mediated segmental labeling, we provide unambiguous evidence that in the oligomer context, the N-terminal domain (NTD) of HSPB1 is rigid and adopts an ensemble of heterogeneous conformations, the α-Crystallin domain (ACD) forms dimers and experiences multiple distinct local environments, while the C-terminal domain (CTD) remains highly dynamic. Our computational models suggest that the NTDs participate in extensive NTD-NTD and NTD-ACD interactions and are sequestered within the oligomer interior. We further demonstrate that HSPB1 higher order oligomers disassemble into smaller oligomeric species in the presence of a client protein and that an accessible NTD is essential for HSPB1 partitioning into condensates and interactions with client proteins. Our integrated approach provides a high-resolution view of the complex oligomeric landscape of HSPB1 and sheds light on the elusive network of interactions that underlies the function of HSPB1 in biological condensates.
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Affiliation(s)
- Raymond F Berkeley
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Alexander P Plonski
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Tien M Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Kristof Grohe
- Bruker BioSpin GmbH & Co. KG, Ettlingen 76275, Germany
| | - Lukas Becker
- Bruker BioSpin GmbH & Co. KG, Ettlingen 76275, Germany
| | | | - Mark A Herzik
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843, United States
| | - Galia T Debelouchina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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3
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Peters C, Haslbeck M, Buchner J. Catchers of folding gone awry: a tale of small heat shock proteins. Trends Biochem Sci 2024; 49:1063-1078. [PMID: 39271417 DOI: 10.1016/j.tibs.2024.08.003] [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: 02/07/2024] [Revised: 08/01/2024] [Accepted: 08/14/2024] [Indexed: 09/15/2024]
Abstract
Small heat shock proteins (sHsps) are an important part of the cellular system maintaining protein homeostasis under physiological and stress conditions. As molecular chaperones, they form complexes with different non-native proteins in an ATP-independent manner. Many sHsps populate ensembles of energetically similar but different-sized oligomers. Regulation of chaperone activity occurs by changing the equilibrium of these ensembles. This makes sHsps a versatile and adaptive system for trapping non-native proteins in complexes, allowing recycling with the help of ATP-dependent chaperones. In this review, we discuss progress in our understanding of the structural principles of sHsp oligomers and their functional principles, as well as their roles in aging and eye lens transparency.
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Affiliation(s)
- Carsten Peters
- School of Natural Sciences, and Department Bioscience, Center for Functional Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer Str. 8, 85748 Garching, Germany
| | - Martin Haslbeck
- School of Natural Sciences, and Department Bioscience, Center for Functional Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer Str. 8, 85748 Garching, Germany.
| | - Johannes Buchner
- School of Natural Sciences, and Department Bioscience, Center for Functional Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer Str. 8, 85748 Garching, Germany.
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4
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Zhou J, Tang X, Li J, Dang S, Ma H, Zhang Y. Comparative transcriptomic and metabolomic analyses provide insights into the responses to high temperature stress in Alfalfa (Medicago sativa L.). BMC PLANT BIOLOGY 2024; 24:776. [PMID: 39143536 PMCID: PMC11325607 DOI: 10.1186/s12870-024-05494-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024]
Abstract
High temperature stress is one of the most severe forms of abiotic stress in alfalfa. With the intensification of climate change, the frequency of high temperature stress will further increase in the future, which will bring challenges to the growth and development of alfalfa. Therefore, untargeted metabolomic and RNA-Seq profiling were implemented to unravel the possible alteration in alfalfa seedlings subjected to different temperature stress (25 ℃, 30 ℃, 35 ℃, 40 ℃) in this study. Results revealed that High temperature stress significantly altered some pivotal transcripts and metabolites. The number of differentially expressed genes (DEGs) markedly up and down-regulated was 1876 and 1524 in T30_vs_CK, 2, 815 and 2667 in T35_vs_CK, and 2115 and 2, 226 in T40_vs_CK, respectively. The number for significantly up-regulated and down-regulated differential metabolites was 173 and 73 in T30_vs_CK, 188 and 57 in T35_vs_CK, and 220 and 66 in T40_vs_CK, respectively. It is worth noting that metabolomics and transcriptomics co-analysis characterized enriched in plant hormone signal transduction (ko04705), glyoxylate and dicarboxylate metabolism (ko00630), from which some differentially expressed genes and differential metabolites participated. In particular, the content of hormone changed significantly under T40 stress, suggesting that maintaining normal hormone synthesis and metabolism may be an important way to improve the HTS tolerance of alfalfa. The qRT-PCR further showed that the expression pattern was similar to the expression abundance in the transcriptome. This study provides a practical and in-depth perspective from transcriptomics and metabolomics in investigating the effects conferred by temperature on plant growth and development, which provided the theoretical basis for breeding heat-resistant alfalfa.
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Affiliation(s)
- Juan Zhou
- College of Forestry and Prataculture, Ningxia University, Yinchuan, 750021, China
| | - Xueshen Tang
- College of Enology and Horticulture, Ningxia University, Yinchuan, Ningxia, 750021, China
| | - Jiahao Li
- College of Enology and Horticulture, Ningxia University, Yinchuan, Ningxia, 750021, China
| | - Shizhuo Dang
- College of Enology and Horticulture, Ningxia University, Yinchuan, Ningxia, 750021, China
| | - Haimei Ma
- College of Enology and Horticulture, Ningxia University, Yinchuan, Ningxia, 750021, China
| | - Yahong Zhang
- College of Enology and Horticulture, Ningxia University, Yinchuan, Ningxia, 750021, China.
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5
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Bergman ME, Kortbeek RWJ, Gutensohn M, Dudareva N. Plant terpenoid biosynthetic network and its multiple layers of regulation. Prog Lipid Res 2024; 95:101287. [PMID: 38906423 DOI: 10.1016/j.plipres.2024.101287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Terpenoids constitute one of the largest and most chemically diverse classes of primary and secondary metabolites in nature with an exceptional breadth of functional roles in plants. Biosynthesis of all terpenoids begins with the universal five‑carbon building blocks, isopentenyl diphosphate (IPP) and its allylic isomer dimethylallyl diphosphate (DMAPP), which in plants are derived from two compartmentally separated but metabolically crosstalking routes, the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways. Here, we review the current knowledge on the terpenoid precursor pathways and highlight the critical hidden constraints as well as multiple regulatory mechanisms that coordinate and homeostatically govern carbon flux through the terpenoid biosynthetic network in plants.
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Affiliation(s)
- Matthew E Bergman
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Ruy W J Kortbeek
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Michael Gutensohn
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States.
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6
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Coco L, Toci EM, Chen PYT, Drennan CL, Freel Meyers CL. Potent Inhibition of E. coli DXP Synthase by a gem-Diaryl Bisubstrate Analog. ACS Infect Dis 2024; 10:1312-1326. [PMID: 38513073 PMCID: PMC11019550 DOI: 10.1021/acsinfecdis.3c00734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/23/2024]
Abstract
New antimicrobial strategies are needed to address pathogen resistance to currently used antibiotics. Bacterial central metabolism is a promising target space for the development of agents that selectively target bacterial pathogens. 1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) converts pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) to DXP, which is required for synthesis of essential vitamins and isoprenoids in bacterial pathogens. Thus, DXPS is a promising antimicrobial target. Toward this goal, our lab has demonstrated selective inhibition of Escherichia coli DXPS by alkyl acetylphosphonate (alkylAP)-based bisubstrate analogs that exploit the requirement for ternary complex formation in the DXPS mechanism. Here, we present the first DXPS structure with a bisubstrate analog bound in the active site. Insights gained from this cocrystal structure guided structure-activity relationship studies of the bisubstrate scaffold. A low nanomolar inhibitor (compound 8) bearing a gem-dibenzyl glycine moiety conjugated to the acetylphosphonate pyruvate mimic via a triazole-based linker emerged from this study. Compound 8 was found to exhibit slow, tight-binding inhibition, with contacts to E. coli DXPS residues R99 and R478 demonstrated to be important for this behavior. This work has discovered the most potent DXPS inhibitor to date and highlights a new role of R99 that can be exploited in future inhibitor designs toward the development of a novel class of antimicrobial agents.
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Affiliation(s)
- Lauren
B. Coco
- Department
of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Eucolona M. Toci
- Department
of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Percival Yang-Ting Chen
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
- Howard
Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Caren L. Freel Meyers
- Department
of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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7
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Pei T, Zhang M, Nwanade CF, Meng H, Bai R, Wang Z, Wang R, Zhang T, Liu J, Yu Z. Sequential expression of small heat shock proteins contributing to the cold response of Haemaphysalis longicornis (Acari: Ixodidae). PEST MANAGEMENT SCIENCE 2024; 80:2061-2071. [PMID: 38117216 DOI: 10.1002/ps.7941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Haemaphysalis longicornis is an important livestock pest and a serious threat to public health. Cold is a common form of stress affecting its survival and distribution. However, H. longicornis exhibits different physiological responses to cold stress. In this study, we systematically explored the regulation and functions of small heat shock proteins (sHsps) in H. longicornis during cold stress. RESULTS Seven sHsp genes (HlsHsp14.9, HlsHsp19.9, HlsHsp20.3, HlsHsp21.4, HlsHsp23.7, HlsHsp24.0, and HlsHsp26.1) with open reading frame lengths ranging from 408 bp (HlsHsp14.9) to 673 bp (HlsHsp26.1) were cloned from H. longicornis, and featured the typical α-crystallin domain. Phylogenetic analysis revealed high similarity with the sHsps of arachnid species. Quantitative polymerase chain reaction analysis revealed that the regulation of sHsp genes depended on the severity and duration of cold treatment. Moreover, the relative expression of each gene was largely dependent on the treatment period (P < 0.01; 3, 6, and 9 days of treatment at 8, 4, 0, and -4 °C). Among all genes, HlsHsp14.9, HlsHsp19.9, HlsHsp20.3, and HlsHsp24.0 were most sensitive to rapid cold treatment. After RNA interference, the mortality of H. longicornis was significantly increased at -14 °C (P < 0.05), suggesting that the expression of sHsp genes is closely related to cold tolerance in H. longicornis. CONCLUSION Our results indicate that sHsps play an important role in the cold stress response of H. longicornis, which may enhance our understanding of the cold adaptation mechanisms in ticks. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Tingwei Pei
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Meng Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Chuks F Nwanade
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Hao Meng
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, China
| | - Ruwei Bai
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zihao Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ruotong Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Tianai Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Research Center of the Basic Discipline of Cell Biology, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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8
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Toci EM, Austin SL, Majumdar A, Woodcock HL, Freel Meyers CL. Disruption of an Active Site Network Leads to Activation of C2α-Lactylthiamin Diphosphate on the Antibacterial Target 1-Deoxy-d-xylulose-5-phosphate Synthase. Biochemistry 2024; 63:671-687. [PMID: 38393327 PMCID: PMC11015862 DOI: 10.1021/acs.biochem.3c00735] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The bacterial metabolic enzyme 1-deoxy-d-xylulose-5-phosphate synthase (DXPS) catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde-3-phosphate (d-GAP). DXP is an essential bacteria-specific metabolite that feeds into the biosynthesis of isoprenoids, pyridoxal phosphate (PLP), and ThDP. DXPS catalyzes the activation of pyruvate to give the C2α-lactylThDP (LThDP) adduct that is long-lived on DXPS in a closed state in the absence of the cosubstrate. Binding of d-GAP shifts the DXPS-LThDP complex to an open state which coincides with LThDP decarboxylation. This gated mechanism distinguishes DXPS in ThDP enzymology. How LThDP persists on DXPS in the absence of cosubstrate, while other pyruvate decarboxylases readily activate LThDP for decarboxylation, is a long-standing question in the field. We propose that an active site network functions to prevent LThDP activation on DXPS until the cosubstrate binds. Binding of d-GAP coincides with a conformational shift and disrupts the network causing changes in the active site that promote LThDP activation. Here, we show that the substitution of putative network residues, as well as nearby residues believed to contribute to network charge distribution, predictably affects LThDP reactivity. Substitutions predicted to disrupt the network have the effect to activate LThDP for decarboxylation, resulting in CO2 and acetate production. In contrast, a substitution predicted to strengthen the network fails to activate LThDP and has the effect to shift DXPS toward the closed state. Network-disrupting substitutions near the carboxylate of LThDP also have a pronounced effect to shift DXPS to an open state. These results offer initial insights to explain the long-lived LThDP intermediate and its activation through disruption of an active site network, which is unique to DXPS. These findings have important implications for DXPS function in bacteria and its development as an antibacterial target.
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Affiliation(s)
- Eucolona M Toci
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Steven L Austin
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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9
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Wijaya LS, Gabor A, Pot IE, van de Have L, Saez-Rodriguez J, Stevens JL, Le Dévédec SE, Callegaro G, van de Water B. A network-based transcriptomic landscape of HepG2 cells uncovering causal gene-cytotoxicity interactions underlying drug-induced liver injury. Toxicol Sci 2024; 198:14-30. [PMID: 38015832 PMCID: PMC10901150 DOI: 10.1093/toxsci/kfad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
Drug-induced liver injury (DILI) remains the main reason for drug development attritions largely due to poor mechanistic understanding. Toxicogenomic to interrogate the mechanism of DILI has been broadly performed. Gene coregulation network-based transcriptome analysis is a bioinformatics approach that potentially contributes to improve mechanistic interpretation of toxicogenomic data. Here we performed an extensive concentration time course response-toxicogenomic study in the HepG2 cell line exposed to 20 DILI compounds, 7 reference compounds for stress response pathways, and 10 agonists for cytokines and growth factor receptors. We performed whole transcriptome targeted RNA sequencing to more than 500 conditions and applied weighted gene coregulated network analysis to the transcriptomics data followed by the identification of gene coregulated networks (modules) that were strongly modulated upon the exposure of DILI compounds. Preservation analysis on the module responses of HepG2 and PHH demonstrated highly preserved adaptive stress response gene coregulated networks. We correlated gene coregulated networks with cell death onset and causal relationships of 67 critical target genes of these modules with the onset of cell death was evaluated using RNA interference screening. We identified GTPBP2, HSPA1B, IRF1, SIRT1, and TSC22D3 as essential modulators of DILI compound-induced cell death. These genes were also induced by DILI compounds in PHH. Altogether, we demonstrate the application of large transcriptome datasets combined with network-based analysis and biological validation to uncover the candidate determinants of DILI.
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Affiliation(s)
- Lukas S Wijaya
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Attila Gabor
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, 69120 Heidelberg, Germany
- Heidelberg University Hospital, Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany
| | - Iris E Pot
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Luca van de Have
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, 69120 Heidelberg, Germany
- Heidelberg University Hospital, Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany
| | - James L Stevens
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Sylvia E Le Dévédec
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Giulia Callegaro
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
| | - Bob van de Water
- Leiden Academic Centre for Drug Research (LACDR), Faculty of Science, Leiden University, 2333 Leiden, The Netherlands
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10
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Lee J, Ryu B, Kim T, Kim KK. Cryo-EM structure of a 16.5-kDa small heat-shock protein from Methanocaldococcus jannaschii. Int J Biol Macromol 2024; 258:128763. [PMID: 38103675 DOI: 10.1016/j.ijbiomac.2023.128763] [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: 10/23/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
The small heat-shock protein (sHSP) from the archaea Methanocaldococcus jannaschii, MjsHSP16.5, functions as a broad substrate ATP-independent holding chaperone protecting misfolded proteins from aggregation under stress conditions. This protein is the first sHSP characterized by X-ray crystallography, thereby contributing significantly to our understanding of sHSPs. However, despite numerous studies assessing its functions and structures, the precise arrangement of the N-terminal domains (NTDs) within this sHSP cage remains elusive. Here we present the cryo-electron microscopy (cryo-EM) structure of MjsHSP16.5 at 2.49-Å resolution. The subunits of MjsHSP16.5 in the cryo-EM structure exhibit lesser compaction compared to their counterparts in the crystal structure. This structural feature holds particular significance in relation to the biophysical properties of MjsHSP16.5, suggesting a close resemblance to this sHSP native state. Additionally, our cryo-EM structure unveils the density of residues 24-33 within the NTD of MjsHSP16.5, a feature that typically remains invisible in the majority of its crystal structures. Notably, these residues show a propensity to adopt a β-strand conformation and engage in antiparallel interactions with strand β1, both intra- and inter-subunit modes. These structural insights are corroborated by structural predictions, disulfide bond cross-linking studies of Cys-substitution mutants, and protein disaggregation assays. A comprehensive understanding of the structural features of MjsHSP16.5 expectedly holds the potential to inspire a wide range of interdisciplinary applications, owing to the renowned versatility of this sHSP as a nanoscale protein platform.
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Affiliation(s)
- Joohyun Lee
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Bumhan Ryu
- Research Solution Center, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Truc Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.
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11
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Di X, Rodriguez-Concepcion M. Exploring the Deoxy-D-xylulose-5-phosphate Synthase Gene Family in Tomato ( Solanum lycopersicum). PLANTS (BASEL, SWITZERLAND) 2023; 12:3886. [PMID: 38005784 PMCID: PMC10675008 DOI: 10.3390/plants12223886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
Isoprenoids are a wide family of metabolites including high-value chemicals, flavors, pigments, and drugs. Isoprenoids are particularly abundant and diverse in plants. The methyl-D-erythritol 4-phosphate (MEP) pathway produces the universal isoprenoid precursors isopentenyl diphosphate and dimethylallyl diphosphate in plant plastids for the downstream production of monoterpenes, diterpenes, and photosynthesis-related isoprenoids such as carotenoids, chlorophylls, tocopherols, phylloquinone, and plastoquinone. The enzyme deoxy-D-xylulose 5-phosphate synthase (DXS) is the first and main rate-determining enzyme of the MEP pathway. In tomato (Solanum lycopersicum), a plant with an active isoprenoid metabolism in several tissues, three genes encode DXS-like proteins (SlDXS1 to 3). Here, we show that the expression patterns of the three genes suggest distinct physiological roles without excluding that they might function together in some tissues. We also confirm that SlDXS1 and 2 are true DXS enzymes, whereas SlDXS3 lacks DXS activity. We further show that SlDXS1 and 2 co-localize in plastidial speckles and that they can be immunoprecipitated together, suggesting that they might form heterodimers in vivo in at least some tissues. These results provide novel insights for the biotechnological use of DXS isoforms in metabolic engineering strategies to up-regulate the MEP pathway flux.
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Affiliation(s)
- Xueni Di
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC—Universitat Politècnica de València, 46022 Valencia, Spain
| | - Manuel Rodriguez-Concepcion
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC—Universitat Politècnica de València, 46022 Valencia, Spain
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12
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Ecroyd H, Bartelt-Kirbach B, Ben-Zvi A, Bonavita R, Bushman Y, Casarotto E, Cecconi C, Lau WCY, Hibshman JD, Joosten J, Kimonis V, Klevit R, Liberek K, McMenimen KA, Miwa T, Mogk A, Montepietra D, Peters C, Rocchetti MT, Saman D, Sisto A, Secco V, Strauch A, Taguchi H, Tanguay M, Tedesco B, Toth ME, Wang Z, Benesch JLP, Carra S. The beauty and complexity of the small heat shock proteins: a report on the proceedings of the fourth workshop on small heat shock proteins. Cell Stress Chaperones 2023; 28:621-629. [PMID: 37462824 PMCID: PMC10746627 DOI: 10.1007/s12192-023-01360-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2023] [Indexed: 12/23/2023] Open
Abstract
The Fourth Cell Stress Society International workshop on small heat shock proteins (sHSPs), a follow-up to successful workshops held in 2014, 2016 and 2018, took place as a virtual meeting on the 17-18 November 2022. The meeting was designed to provide an opportunity for those working on sHSPs to reconnect and discuss their latest work. The diversity of research in the sHSP field is reflected in the breadth of topics covered in the talks presented at this meeting. Here we summarise the presentations at this meeting and provide some perspectives on exciting future topics to be addressed in the field.
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Affiliation(s)
- Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia.
| | | | - Anat Ben-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Raffaella Bonavita
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", 80131, Naples, Italy
| | - Yevheniia Bushman
- Center for Protein Assemblies and Department Chemie, Technische Universität München, München, Germany
| | - Elena Casarotto
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti" (DiSFeB), Dipartimento di Eccellenza, Università degli Studi di Milano, Milan, Italy
| | - Ciro Cecconi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena, Italy
- Istituto Nanoscienze-CNR-NANO, Center S3, Modena, Italy
| | - Wilson Chun Yu Lau
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Jonathan D Hibshman
- Biology Department, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joep Joosten
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Virginia Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, University of California - Irvine, Orange, CA, 92868, USA
- Department of Neurology and Department of Pathology, University of California, Irvine, CA, 92697, USA
| | - Rachel Klevit
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Krzysztof Liberek
- Intercollegiate Faculty of Biotechnology, University of Gdansk, Gdansk, Poland
| | - Kathryn A McMenimen
- Program in Biochemistry and Department of Chemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Tsukumi Miwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8503, Japan
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld, 282, Heidelberg, Germany
| | - Daniele Montepietra
- Istituto Nanoscienze-CNR-NANO, Center S3, Modena, Italy
- Department of Department of Chemical, Life and Environmental sustainability sciences, University of Parma, Parma, Italy
| | - Carsten Peters
- Center for Protein Assemblies and Department Chemie, Technische Universität München, München, Germany
| | - Maria Teresa Rocchetti
- Department of Clinical and Experimental Medicine, University of Foggia, 71122, Foggio, Italy
| | - Dominik Saman
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Angela Sisto
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences and Institute Born Bunge, University of Antwerp, Antwerpen, Belgium
| | - Valentina Secco
- Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annika Strauch
- Center for Protein Assemblies and Department Chemie, Technische Universität München, München, Germany
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8503, Japan
| | - Morgan Tanguay
- Program in Biochemistry and Department of Chemistry, Mount Holyoke College, South Hadley, MA, 01075, USA
| | - Barbara Tedesco
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti" (DiSFeB), Dipartimento di Eccellenza, Università degli Studi di Milano, Milan, Italy
| | - Melinda E Toth
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Temesvári krt. 62, Szeged, H-6726, Hungary
| | - Zihao Wang
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Justin L P Benesch
- Department of Chemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Serena Carra
- Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy.
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13
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Wu Y, Weng Z, Yan H, Yao Z, Li Z, Sun Y, Ma K, Hull JJ, Zhang D, Ma W, Hua H, Lin Y. The microRNA-7322-5p/p38/Hsp19 axis modulates Chilo suppressalis cell-defences against Cry1Ca: an effective target for a stacked transgenic rice approach. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1827-1838. [PMID: 37353991 PMCID: PMC10440986 DOI: 10.1111/pbi.14095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/08/2023] [Accepted: 05/16/2023] [Indexed: 06/25/2023]
Abstract
Bacillus thuringiensis (Bt)-secreted crystal (Cry) toxins form oligomeric pores in host cell membranes and are a common element in generating insect-resistant transgenic crops. Although Cry toxin function has been well documented, cellular defences against pore-formation have not been as well developed. Elucidation of the processes underlying this defence, however, could contribute to the development of enhanced Bt crops. Here, we demonstrate that Cry1Ca-mediated downregulation of microRNA-7322-5p (miR-7322-5p), which binds to the 3' untranslated region of p38, negatively regulates the susceptibility of Chilo suppressalis to Cry1Ca. Moreover, Cry1Ca exposure enhanced phosphorylation of Hsp19, and hsp19 downregulation increased susceptibility to Cry1Ca. Further, Hsp19 phosphorylation occurs downstream of p38, and pull-down assays confirmed the interactions between Hsp19 and Cry1Ca, suggesting that activation of Hsp19 by the miR-7322-5p/p38/Hsp19 pathway promotes Cry1Ca sequestration. To assess the efficacy of targeting this pathway in planta, double-stranded RNA (dsRNA) targeting C. suppressalis p38 (dsp38) was introduced into a previously generated cry1Ca-expressing rice line (1CH1-2) to yield a single-copy cry1Ca/dsp38 rice line (p38-rice). Feeding on this rice line triggered a significant reduction in C. suppressalis p38 expression and the line was more resistant to C. suppressalis than 1CH1-2 in both short term (7-day) and continuous feeding bioassays as well as field trials. These findings provide new insights into invertebrate epithelium cellular defences and demonstrate a potential new pyramiding strategy for Bt crops.
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Affiliation(s)
- Yan Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zijin Weng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Haixia Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhuotian Yao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhenzhen Li
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yajie Sun
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Kangsheng Ma
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - J. Joe Hull
- U.S. Arid Land Agricultural Research Center, Department of AgricultureU.S. Agricultural Research ServiceMaricopaArizonaUSA
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hongxia Hua
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
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14
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Zou Y, Shi H, Liu N, Wang H, Song X, Liu B. Mechanistic insights into heat shock protein 27, a potential therapeutic target for cardiovascular diseases. Front Cardiovasc Med 2023; 10:1195464. [PMID: 37252119 PMCID: PMC10219228 DOI: 10.3389/fcvm.2023.1195464] [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: 03/28/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Heat shock protein 27 (HSP27) is a small chaperone protein that is overexpressed in a variety of cellular stress states. It is involved in regulating proteostasis and protecting cells from multiple sources of stress injury by stabilizing protein conformation and promoting the refolding of misfolded proteins. Previous studies have confirmed that HSP27 is involved in the development of cardiovascular diseases and plays an important regulatory role in this process. Herein, we comprehensively and systematically summarize the involvement of HSP27 and its phosphorylated form in pathophysiological processes, including oxidative stress, inflammatory responses, and apoptosis, and further explore the potential mechanisms and possible roles of HSP27 in the diagnosis and treatment of cardiovascular diseases. Targeting HSP27 is a promising future strategy for the treatment of cardiovascular diseases.
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15
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Di X, Ortega-Alarcon D, Kakumanu R, Iglesias-Fernandez J, Diaz L, Baidoo EEK, Velazquez-Campoy A, Rodríguez-Concepción M, Perez-Gil J. MEP pathway products allosterically promote monomerization of deoxy-D-xylulose-5-phosphate synthase to feedback-regulate their supply. PLANT COMMUNICATIONS 2023; 4:100512. [PMID: 36575800 DOI: 10.1016/j.xplc.2022.100512] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/11/2022] [Accepted: 12/22/2022] [Indexed: 05/11/2023]
Abstract
Isoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. It has been reported that IPP and DMAPP feedback-regulate the activity of deoxyxylulose 5-phosphate synthase (DXS), a dimeric enzyme that catalyzes the main flux-controlling step of the MEP pathway. Here we provide experimental insights into the underlying mechanism. Isothermal titration calorimetry and dynamic light scattering approaches showed that IPP and DMAPP can allosterically bind to DXS in vitro, causing a size shift. In silico ligand binding site analysis and docking calculations identified a potential allosteric site in the contact region between the two monomers of the active DXS dimer. Modulation of IPP and DMAPP contents in vivo followed by immunoblot analyses confirmed that high IPP/DMAPP levels resulted in monomerization and eventual aggregation of the enzyme in bacterial and plant cells. Loss of the enzymatically active dimeric conformation allows a fast and reversible reduction of DXS activity in response to a sudden increase or decrease in IPP/DMAPP supply, whereas aggregation and subsequent removal of monomers that would otherwise be available for dimerization appears to be a more drastic response in the case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our results represent an important step toward understanding the regulation of the MEP pathway and rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems.
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Affiliation(s)
- Xueni Di
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, 46022 Valencia, Spain; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain
| | - David Ortega-Alarcon
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ramu Kakumanu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Lucia Diaz
- Nostrum Biodiscovery SL, 08029 Barcelona, Spain
| | - Edward E K Baidoo
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Adrian Velazquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Manuel Rodríguez-Concepción
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, 46022 Valencia, Spain; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain.
| | - Jordi Perez-Gil
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, 08193 Barcelona, Spain.
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16
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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: 1.0] [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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17
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Wu S, Zhao Y, Wang D, Chen Z. Mode of Action of Heat Shock Protein (HSP) Inhibitors against Viruses through Host HSP and Virus Interactions. Genes (Basel) 2023; 14:genes14040792. [PMID: 37107550 PMCID: PMC10138296 DOI: 10.3390/genes14040792] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
Misfolded proteins after stress-induced denaturation can regain their functions through correct re-folding with the aid of molecular chaperones. As a molecular chaperone, heat shock proteins (HSPs) can help client proteins fold correctly. During viral infection, HSPs are involved with replication, movement, assembly, disassembly, subcellular localization, and transport of the virus via the formation of macromolecular protein complexes, such as the viral replicase complex. Recent studies have indicated that HSP inhibitors can inhibit viral replication by interfering with the interaction of the virus with the HSP. In this review, we describe the function and classification of HSPs, the transcriptional mechanism of HSPs promoted by heat shock factors (HSFs), discuss the interaction between HSPs and viruses, and the mode of action of HSP inhibitors at two aspects of inhibiting the expression of HSPs and targeting the HSPs, and elaborate their potential use as antiviral agents.
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18
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Lei T, Xiao Z, Bi W, Cai S, Yang Y, Du H. Targeting small heat shock proteins to degrade aggregates as a potential strategy in neurodegenerative diseases. Ageing Res Rev 2022; 82:101769. [PMID: 36283618 DOI: 10.1016/j.arr.2022.101769] [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: 03/30/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 01/31/2023]
Abstract
Neurodegenerative diseases (NDs) are aging-related diseases that involve the death of neurons in the brain. Dysregulation of protein homeostasis leads to the production of toxic proteins or the formation of aggregates, which is the pathological basis of NDs. Small heat shock proteins (HSPB) is involved in the establishment of a protein quality control (PQC) system to maintain cellular homeostasis. HSPB can be secreted into the extracellular space and delivered by various routes, especially extracellular vehicles (EVs). HSPB plays an important role in influencing the aggregation phase of toxic proteins involved in heat shock transcription factor (HSF) regulation, oxidative stress, autophagy and apoptosis pathways. HSPB conferred neuroprotective effects by resisting toxic protein aggregation, reducing autophagy and reducing neuronal apoptosis. The HSPB treatment strategies, including targeted PQC system therapy and delivery of EVs-HSPB, can improve disease manifestations for NDs. This review aims to provide a comprehensive insight into the impact of HSPB in NDs and the feasibility of new technology to enhance HSPB expression and EVs-HSPB delivery for neurodegenerative disease.
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Affiliation(s)
- Tong Lei
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; Daxing Research Institute, University of Science and Technology Beijing, Beijing 100083, China
| | - Zhuangzhuang Xiao
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; Daxing Research Institute, University of Science and Technology Beijing, Beijing 100083, China
| | - Wangyu Bi
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; Daxing Research Institute, University of Science and Technology Beijing, Beijing 100083, China
| | - Shanglin Cai
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; Daxing Research Institute, University of Science and Technology Beijing, Beijing 100083, China
| | - Yanjie Yang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; Daxing Research Institute, University of Science and Technology Beijing, Beijing 100083, China
| | - Hongwu Du
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; Daxing Research Institute, University of Science and Technology Beijing, Beijing 100083, China.
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19
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Li DY, Liang S, Wen JH, Tang JX, Deng SL, Liu YX. Extracellular HSPs: The Potential Target for Human Disease Therapy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072361. [PMID: 35408755 PMCID: PMC9000741 DOI: 10.3390/molecules27072361] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/22/2022] [Accepted: 03/29/2022] [Indexed: 12/13/2022]
Abstract
Heat shock proteins (HSPs) are highly conserved stress proteins known as molecular chaperones, which are considered to be cytoplasmic proteins with functions restricted to the intracellular compartment, such as the cytoplasm or cellular organelles. However, an increasing number of observations have shown that HSPs can also be released into the extracellular matrix and can play important roles in the modulation of inflammation and immune responses. Recent studies have demonstrated that extracellular HSPs (eHSPs) were involved in many human diseases, such as cancers, neurodegenerative diseases, and kidney diseases, which are all diseases that are closely linked to inflammation and immunity. In this review, we describe the types of eHSPs, discuss the mechanisms of eHSPs secretion, and then highlight their functions in the modulation of inflammation and immune responses. Finally, we take cancer as an example and discuss the possibility of targeting eHSPs for human disease therapy. A broader understanding of the function of eHSPs in development and progression of human disease is essential for developing new strategies to treat many human diseases that are critically related to inflammation and immunity.
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Affiliation(s)
- Dong-Yi Li
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China; (D.-Y.L.); (S.L.); (J.-H.W.)
| | - Shan Liang
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China; (D.-Y.L.); (S.L.); (J.-H.W.)
| | - Jun-Hao Wen
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China; (D.-Y.L.); (S.L.); (J.-H.W.)
| | - Ji-Xin Tang
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, China; (D.-Y.L.); (S.L.); (J.-H.W.)
- Correspondence: (J.-X.T.); (S.-L.D.); (Y.-X.L.)
| | - Shou-Long Deng
- National Health Commission of China (NHC) Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
- Correspondence: (J.-X.T.); (S.-L.D.); (Y.-X.L.)
| | - Yi-Xun Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (J.-X.T.); (S.-L.D.); (Y.-X.L.)
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Multiple nanocages of a cyanophage small heat shock protein with icosahedral and octahedral symmetries. Sci Rep 2021; 11:21023. [PMID: 34697325 PMCID: PMC8546028 DOI: 10.1038/s41598-021-00172-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/28/2021] [Indexed: 11/08/2022] Open
Abstract
The structures of a cyanophage small heat shock protein (sHSP) were determined as octahedrons of 24-mers and 48-mers and as icosahedrons of 60-mers. An N-terminal deletion construct of an 18 kDa sHSP of Synechococcus sp. phage S-ShM2 crystallized as a 24-mer and its structure was determined at a resolution of 7 Å. The negative stain electron microscopy (EM) images showed that the full-length protein is a mixture of a major population of larger and a minor population of smaller cage-like particles. Their structures have been determined by electron cryomicroscopy 3D image reconstruction at a resolution of 8 Å. The larger particles are 60-mers with icosahedral symmetry and the smaller ones are 48-mers with octahedral symmetry. These structures are the first of the viral/phage origin and the 60-mer is the largest and the first icosahedral assembly to be reported for sHSPs.
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21
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Reinle K, Mogk A, Bukau B. The Diverse Functions of Small Heat Shock Proteins in the Proteostasis Network. J Mol Biol 2021; 434:167157. [PMID: 34271010 DOI: 10.1016/j.jmb.2021.167157] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 01/21/2023]
Abstract
The protein quality control (PQC) system maintains protein homeostasis by counteracting the accumulation of misfolded protein conformers. Substrate degradation and refolding activities executed by ATP-dependent proteases and chaperones constitute major strategies of the proteostasis network. Small heat shock proteins represent ATP-independent chaperones that bind to misfolded proteins, preventing their uncontrolled aggregation. sHsps share the conserved α-crystallin domain (ACD) and gain functional specificity through variable and largely disordered N- and C-terminal extensions (NTE, CTE). They form large, polydisperse oligomers through multiple, weak interactions between NTE/CTEs and ACD dimers. Sequence variations of sHsps and the large variability of sHsp oligomers enable sHsps to fulfill diverse tasks in the PQC network. sHsp oligomers represent inactive yet dynamic resting states that are rapidly deoligomerized and activated upon stress conditions, releasing substrate binding sites in NTEs and ACDs Bound substrates are usually isolated in large sHsp/substrate complexes. This sequestration activity of sHsps represents a third strategy of the proteostasis network. Substrate sequestration reduces the burden for other PQC components during immediate and persistent stress conditions. Sequestered substrates can be released and directed towards refolding pathways by ATP-dependent Hsp70/Hsp100 chaperones or sorted for degradation by autophagic pathways. sHsps can also maintain the dynamic state of phase-separated stress granules (SGs), which store mRNA and translation factors, by reducing the accumulation of misfolded proteins inside SGs and preventing unfolding of SG components. This ensures SG disassembly and regain of translational capacity during recovery periods.
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Affiliation(s)
- Kevin Reinle
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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22
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Shatov VM, Sluchanko NN, Gusev NB. Replacement of Arg in the conserved N-terminal RLFDQxFG motif affects physico-chemical properties and chaperone-like activity of human small heat shock protein HspB8 (Hsp22). PLoS One 2021; 16:e0253432. [PMID: 34143841 PMCID: PMC8213154 DOI: 10.1371/journal.pone.0253432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/04/2021] [Indexed: 01/06/2023] Open
Abstract
The small heat shock protein (sHsp) called HspB8 (formerly, Hsp22) is one of the least typical sHsp members, whose oligomerization status remains debatable. Here we analyze the effect of mutations in a highly conservative sequence located in the N-terminal domain of human HspB8 on its physico-chemical properties and chaperone-like activity. According to size-exclusion chromatography coupled to multi-angle light scattering, the wild type (WT) HspB8 is present as dominating monomeric species (~24 kDa) and a small fraction of oligomers (~60 kDa). The R29A amino acid substitution leads to the predominant formation of 60-kDa oligomers, leaving only a small fraction of monomers. Deletion of the 28–32 pentapeptide (Δ mutant) results in the formation of minor quantities of dimers (~49 kDa) and large quantities of the 24-kDa monomers. Both the WT protein and its Δ mutant efficiently bind a hydrophobic probe bis-ANS and are relatively rapidly hydrolyzed by chymotrypsin, whereas the R29A mutant weakly binds bis-ANS and resists chymotrypsinolysis. In contrast to HspB8 WT and its Δ mutant, which are well phosphorylated by cAMP-dependent and ERK1 protein kinases, the R29A mutant is poorly phosphorylated. R29A mutation affects the chaperone-like activity of HspB8 measured in vitro. It is concluded that the irreplaceable Arg residue located in the only highly conservative motif in the N-terminal domain of all sHsp proteins affects the oligomeric structure and key properties of HspB8.
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Affiliation(s)
- Vladislav M. Shatov
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russian Federation
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Nikolai B. Gusev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russian Federation
- * E-mail:
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