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Zuo WF, Pang Q, Zhu X, Yang QQ, Zhao Q, He G, Han B, Huang W. Heat shock proteins as hallmarks of cancer: insights from molecular mechanisms to therapeutic strategies. J Hematol Oncol 2024; 17:81. [PMID: 39232809 PMCID: PMC11375894 DOI: 10.1186/s13045-024-01601-1] [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: 07/04/2024] [Accepted: 08/20/2024] [Indexed: 09/06/2024] Open
Abstract
Heat shock proteins are essential molecular chaperones that play crucial roles in stabilizing protein structures, facilitating the repair or degradation of damaged proteins, and maintaining proteostasis and cellular functions. Extensive research has demonstrated that heat shock proteins are highly expressed in cancers and closely associated with tumorigenesis and progression. The "Hallmarks of Cancer" are the core features of cancer biology that collectively define a series of functional characteristics acquired by cells as they transition from a normal state to a state of tumor growth, including sustained proliferative signaling, evasion of growth suppressors, resistance to cell death, enabled replicative immortality, the induction of angiogenesis, and the activation of invasion and metastasis. The pivotal roles of heat shock proteins in modulating the hallmarks of cancer through the activation or inhibition of various signaling pathways has been well documented. Therefore, this review provides an overview of the roles of heat shock proteins in vital biological processes from the perspective of the hallmarks of cancer and summarizes the small-molecule inhibitors that target heat shock proteins to regulate various cancer hallmarks. Moreover, we further discuss combination therapy strategies involving heat shock proteins and promising dual-target inhibitors to highlight the potential of targeting heat shock proteins for cancer treatment. In summary, this review highlights how targeting heat shock proteins could regulate the hallmarks of cancer, which will provide valuable information to better elucidate and understand the roles of heat shock proteins in oncology and the mechanisms of cancer occurrence and development and aid in the development of more efficacious and less toxic novel anticancer agents.
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Affiliation(s)
- Wei-Fang Zuo
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Qiwen Pang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xinyu Zhu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Qian-Qian Yang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Qian Zhao
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Gu He
- Department of Dermatology and Venereology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Hospital of Chengdu University of Traditional Chinese Medicine, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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2
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Mao JJ, Dai XY, Liu YZ, Ren LJ, Zhang JQZ, Yan L, Li JF, Tian YJ, Zhu JB, Chen JK. DNAJA1 regulates protein ubiquitination and is essential for spermatogenesis in the testes of mice and rats. Reprod Toxicol 2024; 130:108701. [PMID: 39208916 DOI: 10.1016/j.reprotox.2024.108701] [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: 06/07/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
DNAJA1 is a member of type I DnaJ proteins, which is essential for spermatogenesis and male fertility. However, its expression pattern in the testes and its impact on spermatogenesis remains unclear. Our study aimed to elucidate the mechanism of action of DNAJA1. We employed DNAJA1 knockout mice in this study. Western blotting and immunofluorescence analysis were conducted to determine the protein abundance of DNAJA1 in testes at various developmental stages. Our results revealed that DNAJA1 is predominantly expressed in the testes, and its knockout leads to complete infertility in male mice. We observed that DNAJA1 protein levels increased on postnatal days 14, 21, and 28, peaking on postnatal day 35 in mice. Immunofluorescence staining indicated that DNAJA1 expression varies across different stages of the spermatogenesis cycle. Additionally, DNAJA1 was absent in epididymal sperm. In early- and mid-stage tubules, DNAJA1 protein distribution was co-localized with residual bodies in elongating spermatids. Furthermore, we found that DNAJA1 knockout significantly reduced protein polyubiquitination in the testis. Analysis of the GEO database showed that DNAJA1 levels were significantly decreased in semen samples from subjects with teratozoospermia, asthenozoospermia, and impaired spermatogenesis. Our findings suggest that DNAJA1 is an essential protein for spermatogenesis, and its deletion reduces protein polyubiquitination in the testis, ultimately resulting in infertility and spermatogenesis defects.
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Affiliation(s)
- Jing-Jing Mao
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China; Key Laboratory of Biosafety Defense (Naval Medical University), Ministry of Education, Shanghai 200433, China
| | - Xiao-Yu Dai
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Yun-Zi Liu
- Department of Stress Medicine, Faculty of Psychology and Mental Health, Second Military Medical University, Shanghai 200433, China
| | - Li-Jun Ren
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Ji-Qian-Zhu Zhang
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Lang Yan
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China; Key Laboratory of Biosafety Defense (Naval Medical University), Ministry of Education, Shanghai 200433, China
| | - Jin-Feng Li
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Yi-Jun Tian
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China
| | - Jiang-Bo Zhu
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China; Key Laboratory of Biosafety Defense (Naval Medical University), Ministry of Education, Shanghai 200433, China.
| | - Ji-Kuai Chen
- Department of Health Toxicology, Faculty of Naval Medicine, Second Military Medical University, Shanghai 200433, China; Key Laboratory of Biosafety Defense (Naval Medical University), Ministry of Education, Shanghai 200433, China.
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3
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Guarra F, Sciva C, Bonollo G, Pasala C, Chiosis G, Moroni E, Colombo G. Cracking the chaperone code through the computational microscope. Cell Stress Chaperones 2024:S1355-8145(24)00110-X. [PMID: 39142378 DOI: 10.1016/j.cstres.2024.08.001] [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: 07/04/2024] [Accepted: 08/09/2024] [Indexed: 08/16/2024] Open
Abstract
The Hsp90 chaperone machinery plays a crucial role in maintaining cellular homeostasis. Beyond its traditional role in protein folding, Hsp90 is integral to key pathways influencing cellular function in health and disease. Hsp90 operates through the modular assembly of large multiprotein complexes, with their composition, stability, and localization adapting to the cell's needs. Its functional dynamics are finely tuned by ligand binding and post-translational modifications (PTMs). Here, we discuss how to disentangle the intricacies of the complex code that governs the crosstalk between dynamics, binding, PTMs, and the functions of the Hsp90 machinery using computer-based approaches. Specifically, we outline the contributions of computational and theoretical methods to the understanding of Hsp90 functions, ranging from providing atomic-level insights into its dynamics to clarifying the mechanisms of interactions with protein clients, co-chaperones, and ligands. The knowledge generated in this framework can be actionable for the design and development of chemical tools and drugs targeting Hsp90 in specific disease-associated cellular contexts. Finally, we provide our perspective on how computation can be integrated into the study of the fine-tuning of functions in the highly complex Hsp90 landscape, complementing experimental methods for a comprehensive understanding of this important chaperone system.
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Affiliation(s)
| | | | | | - Chiranjeevi Pasala
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gabriela Chiosis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elisabetta Moroni
- Institute of Chemical Sciences and Technologies (SCITEC) - Italian National Research Council (CNR), 20131, Milano, Italy.
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4
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Vogel A, Arnese R, Gudino Carrillo RM, Sehr D, Deszcz L, Bylicki A, Meinhart A, Clausen T. UNC-45 assisted myosin folding depends on a conserved FX 3HY motif implicated in Freeman Sheldon Syndrome. Nat Commun 2024; 15:6272. [PMID: 39054317 PMCID: PMC11272940 DOI: 10.1038/s41467-024-50442-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 07/11/2024] [Indexed: 07/27/2024] Open
Abstract
Myosin motors are critical for diverse motility functions, ranging from cytokinesis and endocytosis to muscle contraction. The UNC-45 chaperone controls myosin function mediating the folding, assembly, and degradation of the muscle protein. Here, we analyze the molecular mechanism of UNC-45 as a hub in myosin quality control. We show that UNC-45 forms discrete complexes with folded and unfolded myosin, forwarding them to downstream chaperones and E3 ligases. Structural analysis of a minimal chaperone:substrate complex reveals that UNC-45 binds to a conserved FX3HY motif in the myosin motor domain. Disrupting the observed interface by mutagenesis prevents myosin maturation leading to protein aggregation in vivo. We also show that a mutation in the FX3HY motif linked to the Freeman Sheldon Syndrome impairs UNC-45 assisted folding, reducing the level of functional myosin. These findings demonstrate that a faulty myosin quality control is a critical yet unexplored cause of human myopathies.
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Affiliation(s)
- Antonia Vogel
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Renato Arnese
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Ricardo M Gudino Carrillo
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Medical University, Vienna, Austria
| | - Daria Sehr
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Luiza Deszcz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Andrzej Bylicki
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Anton Meinhart
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Tim Clausen
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
- Vienna BioCenter Core Facilities, Vienna, Austria.
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5
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Ruger-Herreros C, Svoboda L, Mogk A, Bukau B. Role of J-domain Proteins in Yeast Physiology and Protein Quality Control. J Mol Biol 2024; 436:168484. [PMID: 38331212 DOI: 10.1016/j.jmb.2024.168484] [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: 10/20/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
The Hsp70 chaperone system is a central component of cellular protein quality control (PQC) by acting in a multitude of protein folding processes ranging from the folding of newly synthesized proteins to the disassembly and refolding of protein aggregates. This multifunctionality of Hsp70 is governed by J-domain proteins (JDPs), which act as indispensable co-chaperones that target specific substrates to Hsp70. The number of distinct JDPs present in a species always outnumbers Hsp70, documenting JDP function in functional diversification of Hsp70. In this review, we describe the physiological roles of JDPs in the Saccharomyces cerevisiae PQC system, with a focus on the abundant JDP generalists, Zuo1, Ydj1 and Sis1, which function in fundamental cellular processes. Ribosome-bound Zuo1 cooperates with the Hsp70 chaperones Ssb1/2 in folding and assembly of nascent polypeptides. Ydj1 and Sis1 cooperate with the Hsp70 members Ssa1 to Ssa4 to exert overlapping functions in protein folding and targeting of newly synthesized proteins to organelles including mitochondria and facilitating the degradation of aberrant proteins by E3 ligases. Furthermore, they act in protein disaggregation reactions, though Ydj1 and Sis1 differ in their modes of Hsp70 cooperation and substrate specificities. This results in functional specialization as seen in prion propagation and the underlying dominant role of Sis1 in targeting Hsp70 for shearing of prion amyloid fibrils.
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Affiliation(s)
- Carmen Ruger-Herreros
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n, E-41013 Sevilla, Spain
| | - Lucia Svoboda
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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Roeselová A, Maslen SL, Shivakumaraswamy S, Pellowe GA, Howell S, Joshi D, Redmond J, Kjær S, Skehel JM, Balchin D. Mechanism of chaperone coordination during cotranslational protein folding in bacteria. Mol Cell 2024; 84:2455-2471.e8. [PMID: 38908370 DOI: 10.1016/j.molcel.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/12/2024] [Accepted: 06/01/2024] [Indexed: 06/24/2024]
Abstract
Protein folding is assisted by molecular chaperones that bind nascent polypeptides during mRNA translation. Several structurally distinct classes of chaperones promote de novo folding, suggesting that their activities are coordinated at the ribosome. We used biochemical reconstitution and structural proteomics to explore the molecular basis for cotranslational chaperone action in bacteria. We found that chaperone binding is disfavored close to the ribosome, allowing folding to precede chaperone recruitment. Trigger factor recognizes compact folding intermediates that expose an extensive unfolded surface, and dictates DnaJ access to nascent chains. DnaJ uses a large surface to bind structurally diverse intermediates and recruits DnaK to sequence-diverse solvent-accessible sites. Neither Trigger factor, DnaJ, nor DnaK destabilize cotranslational folding intermediates. Instead, the chaperones collaborate to protect incipient structure in the nascent polypeptide well beyond the ribosome exit tunnel. Our findings show how the chaperone network selects and modulates cotranslational folding intermediates.
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Affiliation(s)
- Alžběta Roeselová
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Sarah L Maslen
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Grant A Pellowe
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Steven Howell
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Dhira Joshi
- Chemical Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Joanna Redmond
- Chemical Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - J Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - David Balchin
- Protein Biogenesis Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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7
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Huang D, Yu Z, Lu H, Jiang P, Qian X, Han Y, Qian P. Adhesion GPCR ADGRE2 Maintains Proteostasis to Promote Progression in Acute Myeloid Leukemia. Cancer Res 2024; 84:2090-2108. [PMID: 39082681 DOI: 10.1158/0008-5472.can-23-2314] [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: 08/01/2023] [Revised: 01/19/2024] [Accepted: 03/28/2024] [Indexed: 08/15/2024]
Abstract
Acute myeloid leukemia (AML) is an aggressive and heterogeneous hematologic malignancy. In elderly patients, AML incidence is high and has a poor prognosis due to a lack of effective therapies. G protein-coupled receptors (GPCR) play integral roles in physiologic processes and human diseases. Particularly, one third of adhesion GPCRs, the second largest group of GPCRs, are highly expressed in hematopoietic stem and progenitor cells or lineage cells. Here, we investigate the role of adhesion GPCRs in AML and whether they could be harnessed as antileukemia targets. Systematic screening of the impact of adhesion GPCRs on AML functionality by bioinformatic and functional analyses revealed high expression of ADGRE2 in AML, particularly in leukemic stem cells, which is associated with poor patient outcomes. Silencing ADGRE2 not only exerts antileukemic effects in AML cell lines and cells derived from patients with AML in vitro, but also delays AML progression in xenograft models in vivo. Mechanistically, ADGRE2 activates phospholipase Cβ/protein kinase C/MEK/ERK signaling to enhance the expression of AP1 and transcriptionally drive the expression of DUSP1, a protein phosphatase. DUSP1 dephosphorylates Ser16 in the J-domain of the co-chaperone DNAJB1, which facilitates the DNAJB1-HSP70 interaction and maintenance of proteostasis in AML. Finally, combined inhibition of MEK, AP1, and DUSP1 exhibits robust therapeutic efficacy in AML xenograft mouse models. Collectively, this study deciphers the roles and mechanisms of ADGRE2 in AML and provides a promising therapeutic strategy for treating AML. Significance: Increased expression of the adhesion GPCR member ADGRE2 in AML supports leukemia stem cell self-renewal and leukemogenesis by modulating proteostasis via an MEK/AP1/DUSP1 axis, which can be targeted to suppress AML progression.
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MESH Headings
- Animals
- Humans
- Mice
- Cell Line, Tumor
- Cell Proliferation
- Disease Progression
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/genetics
- Mice, Inbred NOD
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Proteostasis
- Receptors, G-Protein-Coupled/metabolism
- Receptors, G-Protein-Coupled/genetics
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Deyu Huang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University and Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Zebin Yu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University and Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Huan Lu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University and Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Penglei Jiang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University and Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Xinyue Qian
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University and Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Yingli Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Pengxu Qian
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University and Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
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Chen J, Gao G, Liu X. The characteristics of PtHSP40 gene family in Phaeodactylum tricornutum and its response to environmental stresses. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106625. [PMID: 38959781 DOI: 10.1016/j.marenvres.2024.106625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 06/13/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Diatom has evolved response mechanisms to cope with multiple environmental stresses. Heat shock protein 40 (HSP40) plays a key role in these response mechanisms. HSP40 gene family in higher plants has been well-studied. However, the HSP40 gene family has not been systematically investigated in marine diatom. In this study, the bioinformatic characteristics, phylogenetic relationship, conserved motifs, gene structure, chromosome distribution and the transcriptional response of PtHSP40 to different environmental stresses were analyzed in the diatom Phaeodactylum tricornutum, and quantitative real-time PCR was conducted. Totally, 55 putative PtHSP40 genes are distributed to 21 chromosomes. All PtHSP40 proteins can be divided into four groups based on their evolutionary relationship, and 54 of them contain a conserved HPD (histidine-proline-aspartic acid tripeptide) motif. Additionally, six, eleven, ten and four PtHSP40 genes were significantly upregulated under the treatments of nitrogen starvation, phosphorus deprivation, 2,2',4,4'-tetrabrominated biphenyl ether (BDE-47) and ocean acidification, respectively. More interestingly, the expression level of 9 PtHSP40 genes was obviously upregulated in response to nickel stress, suggesting the sensitive to metal stress. The different expression models of PtHSP40 genes to environmental stresses imply the specificity of PtHSP40 proteins under different stresses. This study provides a systematic understanding of the PtHSP40 gene family in P. tricornutum and a comprehensive cognition in its functions and response mechanisms to environmental stresses.
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Affiliation(s)
- Jichen Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology and Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, College of Sciences, Shantou University, Shantou, 515063, Guangdong, China; State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Guang Gao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
| | - Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology and Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, College of Sciences, Shantou University, Shantou, 515063, Guangdong, China.
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9
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Wickramaratne AC, Wickner S, Kravats AN. Hsp90, a team player in protein quality control and the stress response in bacteria. Microbiol Mol Biol Rev 2024; 88:e0017622. [PMID: 38534118 PMCID: PMC11332350 DOI: 10.1128/mmbr.00176-22] [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: 03/28/2024] Open
Abstract
SUMMARYHeat shock protein 90 (Hsp90) participates in proteostasis by facilitating protein folding, activation, disaggregation, prevention of aggregation, degradation, and protection against degradation of various cellular proteins. It is highly conserved from bacteria to humans. In bacteria, protein remodeling by Hsp90 involves collaboration with the Hsp70 molecular chaperone and Hsp70 cochaperones. In eukaryotes, protein folding by Hsp90 is more complex and involves collaboration with many Hsp90 cochaperones as well as Hsp70 and Hsp70 cochaperones. This review focuses primarily on bacterial Hsp90 and highlights similarities and differences between bacterial and eukaryotic Hsp90. Seminal research findings that elucidate the structure and the mechanisms of protein folding, disaggregation, and reactivation promoted by Hsp90 are discussed. Understanding the mechanisms of bacterial Hsp90 will provide fundamental insight into the more complex eukaryotic chaperone systems.
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Affiliation(s)
- Anushka C. Wickramaratne
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrea N. Kravats
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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10
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Frédérick PM, Jannot G, Banville I, Simard M. Interaction between a J-domain co-chaperone and a specific Argonaute protein contributes to microRNA function in animals. Nucleic Acids Res 2024; 52:6253-6268. [PMID: 38613392 PMCID: PMC11194074 DOI: 10.1093/nar/gkae272] [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: 08/18/2023] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
MicroRNAs (miRNAs) are essential regulators of several biological processes. They are loaded onto Argonaute (AGO) proteins to achieve their repressive function, forming the microRNA-Induced Silencing Complex known as miRISC. While several AGO proteins are expressed in plants and animals, it is still unclear why specific AGOs are strictly binding miRNAs. Here, we identified the co-chaperone DNJ-12 as a new interactor of ALG-1, one of the two major miRNA-specific AGOs in Caenorhabditis elegans. DNJ-12 does not interact with ALG-2, the other major miRNA-specific AGO, and PRG-1 and RDE-1, two AGOs involved in other small RNA pathways, making it a specific actor in ALG-1-dependent miRNA-mediated gene silencing. The loss of DNJ-12 causes developmental defects associated with defective miRNA function. Using the Auxin Inducible Degron system, a powerful tool to acutely degrade proteins in specific tissues, we show that DNJ-12 depletion hampers ALG-1 interaction with HSP70, a chaperone required for miRISC loading in vitro. Moreover, DNJ-12 depletion leads to the decrease of several miRNAs and prevents their loading onto ALG-1. This study uncovers the importance of a co-chaperone for the miRNA function in vivo and provides insights to explain how different small RNAs associate with specific AGO in animals.
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Affiliation(s)
- Pierre-Marc Frédérick
- Oncology Division, CHU de Québec—Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
| | - Guillaume Jannot
- Oncology Division, CHU de Québec—Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
| | - Isabelle Banville
- Oncology Division, CHU de Québec—Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
| | - Martin J Simard
- Oncology Division, CHU de Québec—Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
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11
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Qu X, Zhao S, Wan C, Zhu L, Ji T, Rossi P, Wang J, Kalodimos CG, Wang C, Xu W, Huang C. Structural basis for the dynamic chaperoning of disordered clients by Hsp90. Nat Struct Mol Biol 2024:10.1038/s41594-024-01337-z. [PMID: 38890550 DOI: 10.1038/s41594-024-01337-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/28/2024] [Indexed: 06/20/2024]
Abstract
Molecular chaperone heat shock protein 90 (Hsp90) is a ubiquitous regulator that fine-tunes and remodels diverse client proteins, exerting profound effects on normal biology and diseases. Unraveling the mechanistic details of Hsp90's function requires atomic-level insights into its client interactions throughout the adenosine triphosphate-coupled functional cycle. However, the structural details of the initial encounter complex in the chaperone cycle, wherein Hsp90 adopts an open conformation while engaging with the client, remain elusive. Here, using nuclear magnetic resonance spectroscopy, we determined the solution structure of Hsp90 in its open state, bound to a disordered client. Our findings reveal that Hsp90 uses two distinct binding sites, collaborating synergistically to capture discrete hydrophobic segments within client proteins. This bipartite interaction generates a versatile complex that facilitates rapid conformational sampling. Moreover, our investigations spanning various clients and Hsp90 orthologs demonstrate a pervasive mechanism used by Hsp90 orthologs to accommodate the vast array of client proteins. Collectively, our work contributes to establish a unified conceptual and mechanistic framework, elucidating the intricate interplay between Hsp90 and its clients.
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Affiliation(s)
- Xiaozhan Qu
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, University of Science and Technology of China, Hefei, China
| | - Shuo Zhao
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, University of Science and Technology of China, Hefei, China
| | - Chanjuan Wan
- Division of Life Sciences and Medicine, University of Science and Technology of China, University of Science and Technology of China, Hefei, China
| | - Lei Zhu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Tuo Ji
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, University of Science and Technology of China, Hefei, China
| | - Paolo Rossi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | | | - Chao Wang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, University of Science and Technology of China, Hefei, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Weiya Xu
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei, China.
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Division of Life Sciences and Medicine, University of Science and Technology of China, University of Science and Technology of China, Hefei, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
| | - Chengdong Huang
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei, China.
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Division of Life Sciences and Medicine, University of Science and Technology of China, University of Science and Technology of China, Hefei, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
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12
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Omkar S, Shrader C, Hoskins JR, Kline JT, Mitchem MM, Nitika, Fornelli L, Wickner S, Truman AW. Acetylation of the yeast Hsp40 chaperone protein Ydj1 fine-tunes proteostasis and translational fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598777. [PMID: 38915721 PMCID: PMC11195281 DOI: 10.1101/2024.06.13.598777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Proteostasis, the maintenance of cellular protein balance, is essential for cell viability and is highly conserved across all organisms. Newly synthesized proteins, or "clients," undergo sequential processing by Hsp40, Hsp70, and Hsp90 chaperones to achieve proper folding and functionality. Despite extensive characterization of post-translational modifications (PTMs) on Hsp70 and Hsp90, the modifications on Hsp40 remain less understood. This study aims to elucidate the role of lysine acetylation on the yeast Hsp40, Ydj1. By mutating acetylation sites on Ydj1's J-domain to either abolish or mimic constitutive acetylation, we observed that preventing acetylation had no noticeable phenotypic impact, whereas acetyl-mimic mutants exhibited various defects indicative of impaired Ydj1 function. Proteomic analysis revealed several Ydj1 interactions affected by J-domain acetylation, notably with proteins involved in translation. Further investigation uncovered a novel role for Ydj1 acetylation in stabilizing ribosomal subunits and ensuring translational fidelity. Our data suggest that acetylation may facilitate the transfer of Ydj1 between Ssa1 and Hsp82. Collectively, this work highlights the critical role of Ydj1 acetylation in proteostasis and translational fidelity.
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Affiliation(s)
- Siddhi Omkar
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223 USA
| | - Courtney Shrader
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223 USA
| | - Joel R. Hoskins
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jake T. Kline
- School of Biological Sciences, University of Oklahoma, Norman, OK 73019 USA
| | - Megan M. Mitchem
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223 USA
| | - Nitika
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223 USA
| | - Luca Fornelli
- School of Biological Sciences, University of Oklahoma, Norman, OK 73019 USA
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew W. Truman
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223 USA
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13
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Marszalek J, Craig EA, Pitek M, Dutkiewicz R. Chaperone function in Fe-S protein biogenesis: Three possible scenarios. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119717. [PMID: 38574821 DOI: 10.1016/j.bbamcr.2024.119717] [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: 01/19/2024] [Revised: 02/22/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Among the six known iron‑sulfur (FeS) cluster biogenesis machineries that function across all domains of life only one involves a molecular chaperone system. This machinery, called ISC for 'iron sulfur cluster', functions in bacteria and in mitochondria of eukaryotes including humans. The chaperone system - a dedicated J-domain protein co-chaperone termed Hsc20 and its Hsp70 partner - is essential for proper ISC machinery function, interacting with the scaffold protein IscU which serves as a platform for cluster assembly and subsequent transfer onto recipient apo-proteins. Despite many years of research, surprisingly little is known about the specific role(s) that the chaperones play in the ISC machinery. Here we review three non-exclusive scenarios that range from involvement of the chaperones in the cluster transfer to regulation of the cellular levels of IscU itself.
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Affiliation(s)
- Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States of America.
| | - Marcin Pitek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Rafal Dutkiewicz
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
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14
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Lin J, Carman PJ, Gambogi CW, Kendsersky NM, Chuang E, Gates SN, Yokom AL, Rizo AN, Southworth DR, Shorter J. Design principles to tailor Hsp104 therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591398. [PMID: 38712168 PMCID: PMC11071516 DOI: 10.1101/2024.04.26.591398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The hexameric AAA+ disaggregase, Hsp104, collaborates with Hsp70 and Hsp40 via its autoregulatory middle domain (MD) to solubilize aggregated protein conformers. However, how ATP- or ADP-specific MD configurations regulate Hsp104 hexamers remains poorly understood. Here, we define an ATP-specific network of interprotomer contacts between nucleotide-binding domain 1 (NBD1) and MD helix L1, which tunes Hsp70 collaboration. Manipulating this network can: (a) reduce Hsp70 collaboration without enhancing activity; (b) generate Hsp104 hypomorphs that collaborate selectively with class B Hsp40s; (c) produce Hsp70-independent potentiated variants; or (d) create species barriers between Hsp104 and Hsp70. Conversely, ADP-specific intraprotomer contacts between MD helix L2 and NBD1 restrict activity, and their perturbation frequently potentiates Hsp104. Importantly, adjusting the NBD1:MD helix L1 rheostat via rational design enables finely tuned collaboration with Hsp70 to safely potentiate Hsp104, minimize off-target toxicity, and counteract FUS proteinopathy in human cells. Thus, we establish important design principles to tailor Hsp104 therapeutics.
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Affiliation(s)
- JiaBei Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Peter J. Carman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Craig W. Gambogi
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Nathan M. Kendsersky
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Edward Chuang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
| | - Stephanie N. Gates
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
- Current address: Department of Biochemistry, University of Missouri, Columbia, MO 65211. U.S.A
| | - Adam L. Yokom
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
- Current address: Department of Biochemistry, University of Missouri, Columbia, MO 65211. U.S.A
| | - Alexandrea N. Rizo
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109. U.S.A
| | - Daniel R. Southworth
- Department of Biochemistry and Biophysics and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158. U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
- Pharmacology Graduate Group Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104. U.S.A
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15
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Zoltsman G, Dang TL, Kuchersky M, Faust O, Silva MS, Ilani T, Wentink AS, Bukau B, Rosenzweig R. A unique chaperoning mechanism in class A JDPs recognizes and stabilizes mutant p53. Mol Cell 2024; 84:1512-1526.e9. [PMID: 38508184 DOI: 10.1016/j.molcel.2024.02.018] [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: 02/22/2023] [Revised: 12/14/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
J-domain proteins (JDPs) constitute a large family of molecular chaperones that bind a broad spectrum of substrates, targeting them to Hsp70, thus determining the specificity of and activating the entire chaperone functional cycle. The malfunction of JDPs is therefore inextricably linked to myriad human disorders. Here, we uncover a unique mechanism by which chaperones recognize misfolded clients, present in human class A JDPs. Through a newly identified β-hairpin site, these chaperones detect changes in protein dynamics at the initial stages of misfolding, prior to exposure of hydrophobic regions or large structural rearrangements. The JDPs then sequester misfolding-prone proteins into large oligomeric assemblies, protecting them from aggregation. Through this mechanism, class A JDPs bind destabilized p53 mutants, preventing clearance of these oncoproteins by Hsp70-mediated degradation, thus promoting cancer progression. Removal of the β-hairpin abrogates this protective activity while minimally affecting other chaperoning functions. This suggests the class A JDP β-hairpin as a highly specific target for cancer therapeutics.
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Affiliation(s)
- Guy Zoltsman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 761000, Israel
| | - Thi Lieu Dang
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH-Alliance, Im Neuenheimer Feld 282, Heidelberg 69120, Germany
| | - Miriam Kuchersky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 761000, Israel
| | - Ofrah Faust
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 761000, Israel
| | - Micael S Silva
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 761000, Israel
| | - Tal Ilani
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 761000, Israel
| | - Anne S Wentink
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH-Alliance, Im Neuenheimer Feld 282, Heidelberg 69120, Germany; Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, the Netherlands
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH-Alliance, Im Neuenheimer Feld 282, Heidelberg 69120, Germany.
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 761000, Israel.
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16
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Rebeaud ME, Tiwari S, Fauvet B, Mohr A, Goloubinoff P, De Los Rios P. Autorepression of yeast Hsp70 cochaperones by intramolecular interactions involving their J-domains. Cell Stress Chaperones 2024; 29:338-348. [PMID: 38521349 PMCID: PMC10999819 DOI: 10.1016/j.cstres.2024.03.008] [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: 02/09/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024] Open
Abstract
The 70 kDa heat shock protein (Hsp70) chaperones control protein homeostasis in all ATP-containing cellular compartments. J-domain proteins (JDPs) coevolved with Hsp70s to trigger ATP hydrolysis and catalytically upload various substrate polypeptides in need to be structurally modified by the chaperone. Here, we measured the protein disaggregation and refolding activities of the main yeast cytosolic Hsp70, Ssa1, in the presence of its most abundant JDPs, Sis1 and Ydj1, and two swap mutants, in which the J-domains have been interchanged. The observed differences by which the four constructs differently cooperate with Ssa1 and cooperate with each other, as well as their observed intrinsic ability to bind misfolded substrates and trigger Ssa1's ATPase, indicate the presence of yet uncharacterized intramolecular dynamic interactions between the J-domains and the remaining C-terminal segments of these proteins. Taken together, the data suggest an autoregulatory role to these intramolecular interactions within both type A and B JDPs, which might have evolved to reduce energy-costly ATPase cycles by the Ssa1-4 chaperones that are the most abundant Hsp70s in the yeast cytosol.
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Affiliation(s)
- Mathieu E Rebeaud
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Vaud, Switzerland; Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Satyam Tiwari
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Bruno Fauvet
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Adelaïde Mohr
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Vaud, Switzerland.
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland; Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne - EPFL, 1015 Lausanne, Vaud, Switzerland.
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17
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Amankwah YS, Fleifil Y, Unruh E, Collins P, Wang Y, Vitou K, Bates A, Obaseki I, Sugoor M, Alao JP, McCarrick RM, Gewirth DT, Sahu ID, Li Z, Lorigan GA, Kravats AN. Structural transitions modulate the chaperone activities of Grp94. Proc Natl Acad Sci U S A 2024; 121:e2309326121. [PMID: 38483986 PMCID: PMC10962938 DOI: 10.1073/pnas.2309326121] [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: 06/02/2023] [Accepted: 01/30/2024] [Indexed: 03/17/2024] Open
Abstract
Hsp90s are ATP-dependent chaperones that collaborate with co-chaperones and Hsp70s to remodel client proteins. Grp94 is the ER Hsp90 homolog essential for folding multiple secretory and membrane proteins. Grp94 interacts with the ER Hsp70, BiP, although the collaboration of the ER chaperones in protein remodeling is not well understood. Grp94 undergoes large-scale conformational changes that are coupled to chaperone activity. Within Grp94, a region called the pre-N domain suppresses ATP hydrolysis and conformational transitions to the active chaperone conformation. In this work, we combined in vivo and in vitro functional assays and structural studies to characterize the chaperone mechanism of Grp94. We show that Grp94 directly collaborates with the BiP chaperone system to fold clients. Grp94's pre-N domain is not necessary for Grp94-client interactions. The folding of some Grp94 clients does not require direct interactions between Grp94 and BiP in vivo, suggesting that the canonical collaboration may not be a general chaperone mechanism for Grp94. The BiP co-chaperone DnaJB11 promotes the interaction between Grp94 and BiP, relieving the pre-N domain suppression of Grp94's ATP hydrolysis activity. In structural studies, we find that ATP binding by Grp94 alters the ATP lid conformation, while BiP binding stabilizes a partially closed Grp94 intermediate. Together, BiP and ATP push Grp94 into the active closed conformation for client folding. We also find that nucleotide binding reduces Grp94's affinity for clients, which is important for productive client folding. Alteration of client affinity by nucleotide binding may be a conserved chaperone mechanism for a subset of ER chaperones.
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Affiliation(s)
- Yaa S. Amankwah
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
- Pelotonia Institute for Immuno-Oncology, Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center–Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH43210
| | - Yasmeen Fleifil
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
| | - Erin Unruh
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, OH45056
| | - Preston Collins
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
| | - Yi Wang
- Pelotonia Institute for Immuno-Oncology, Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center–Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH43210
| | - Katherine Vitou
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
| | - Alison Bates
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
| | - Ikponwmosa Obaseki
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
| | - Meghana Sugoor
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
| | - John Paul Alao
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
| | | | | | - Indra D. Sahu
- Natural Sciences Division, Campbellsville University, Campbellsville, KY42718
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center–Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH43210
| | - Gary. A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, OH45056
| | - Andrea N. Kravats
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH45056
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, OH45056
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18
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Kim H, Kim J, Son N, Kuo P, Morgan C, Chambon A, Byun D, Park J, Lee Y, Park YM, Fozard JA, Guérin J, Hurel A, Lambing C, Howard M, Hwang I, Mercier R, Grelon M, Henderson IR, Choi K. Control of meiotic crossover interference by a proteolytic chaperone network. NATURE PLANTS 2024; 10:453-468. [PMID: 38379086 DOI: 10.1038/s41477-024-01633-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
Meiosis is a specialized eukaryotic division that produces genetically diverse gametes for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal exchanges, called crossovers, which recombine genetic variation. Meiotic crossovers are stringently controlled with at least one obligate exchange forming per chromosome pair, while closely spaced crossovers are inhibited by interference. In Arabidopsis, crossover positions can be explained by a diffusion-mediated coarsening model, in which large, approximately evenly spaced foci of the pro-crossover E3 ligase HEI10 grow at the expense of smaller, closely spaced clusters. However, the mechanisms that control HEI10 dynamics during meiosis remain unclear. Here, through a forward genetic screen in Arabidopsis, we identified high crossover rate3 (hcr3), a dominant-negative mutant that reduces crossover interference and increases crossovers genome-wide. HCR3 encodes J3, a co-chaperone related to HSP40, which acts to target protein aggregates and biomolecular condensates to the disassembly chaperone HSP70, thereby promoting proteasomal degradation. Consistently, we show that a network of HCR3 and HSP70 chaperones facilitates proteolysis of HEI10, thereby regulating interference and the recombination landscape. These results reveal a new role for the HSP40/J3-HSP70 chaperones in regulating chromosome-wide dynamics of recombination via control of HEI10 proteolysis.
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Affiliation(s)
- Heejin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jaeil Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Namil Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Pallas Kuo
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Rothamsted Research, Harpenden, UK
| | - Chris Morgan
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Aurélie Chambon
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Dohwan Byun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jihye Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Youngkyung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yeong Mi Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - John A Fozard
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Julie Guérin
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Aurélie Hurel
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Rothamsted Research, Harpenden, UK
| | - Martin Howard
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Ildoo Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, Versailles, France
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
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19
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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20
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Muraoka T, Okumura M, Saio T. Enzymatic and synthetic regulation of polypeptide folding. Chem Sci 2024; 15:2282-2299. [PMID: 38362427 PMCID: PMC10866363 DOI: 10.1039/d3sc05781j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Proper folding is essential for the biological functions of all proteins. The folding process is intrinsically error-prone, and the misfolding of a polypeptide chain can cause the formation of toxic aggregates related to pathological outcomes such as neurodegenerative disease and diabetes. Chaperones and some enzymes are involved in the cellular proteostasis systems that assist polypeptide folding to diminish the risk of aggregation. Elucidating the molecular mechanisms of chaperones and related enzymes is important for understanding proteostasis systems and protein misfolding- and aggregation-related pathophysiology. Furthermore, mechanistic studies of chaperones and related enzymes provide important clues to designing chemical mimics, or chemical chaperones, that are potentially useful for recovering proteostasis activities as therapeutic approaches for treating and preventing protein misfolding-related diseases. In this Perspective, we provide a comprehensive overview of the latest understanding of the folding-promotion mechanisms by chaperones and oxidoreductases and recent progress in the development of chemical mimics that possess activities comparable to enzymes, followed by a discussion of future directions.
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Affiliation(s)
- Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology Koganei Tokyo 184-8588 Japan
- Kanagawa Institute of Industrial Science and Technology (KISTEC) Kanagawa 243-0435 Japan
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University Sendai Miyagi 980-8578 Japan
| | - Tomohide Saio
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University Tokushima 770-8503 Japan
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21
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Ambrose AJ, Zerio CJ, Sivinski J, Zhu X, Godek J, Sanchez JL, Khanna M, Khanna R, Lairson L, Zhang DD, Chapman E. Human Hsp70 Substrate-Binding Domains Recognize Distinct Client Proteins. Biochemistry 2024; 63:251-263. [PMID: 38243804 DOI: 10.1021/acs.biochem.3c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
The 13 Hsp70 proteins in humans act on unique sets of substrates with diversity often being attributed to J-domain-containing protein (Hsp40 or JDP) cofactors. We were therefore surprised to find drastically different binding affinities for Hsp70-peptide substrates, leading us to probe substrate specificity among the 8 canonical Hsp70s from humans. We used peptide arrays to characterize Hsp70 binding and then mined these data using machine learning to develop an algorithm for isoform-specific prediction of Hsp70 binding sequences. The results of this algorithm revealed recognition patterns not predicted based on local sequence alignments. We then showed that none of the human isoforms can complement heat-shocked DnaK knockout Escherichia coli cells. However, chimeric Hsp70s consisting of the human nucleotide-binding domain and the substrate-binding domain of DnaK complement during heat shock, providing further evidence in vivo of the divergent function of the Hsp70 substrate-binding domains. We also demonstrated that the differences in heat shock complementation among the chimeras are not due to loss of DnaJ binding. Although we do not exclude JDPs as additional specificity factors, our data demonstrate substrate specificity among the Hsp70s, which has important implications for inhibitor development in cancer and neurodegeneration.
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Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher J Zerio
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jared Sivinski
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Xiaoyi Zhu
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jack Godek
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jonathan L Sanchez
- Department of Pharmacology, College of Medicine, The University of Arizona Health Sciences, Tucson, Arizona 85424, United States
| | - May Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York 10010, United States
| | - Rajesh Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York 10010, United States
| | - Luke Lairson
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Eli Chapman
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
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22
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Mitchem MM, Shrader C, Abedi E, Truman AW. Novel insights into the post-translational modifications of Ydj1/DNAJA1 co-chaperones. Cell Stress Chaperones 2024; 29:1-9. [PMID: 38309209 PMCID: PMC10939075 DOI: 10.1016/j.cstres.2023.11.001] [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: 09/16/2023] [Revised: 10/18/2023] [Accepted: 11/04/2023] [Indexed: 02/05/2024] Open
Abstract
The activity of the Hsp70 molecular chaperone is regulated by a suite of helper co-chaperones that include J-proteins. Studies on J-proteins have historically focused on their expression, localization, and activation of Hsp70. There is growing evidence that the post-translational modifications (PTMs) of chaperones (the chaperone code) fine-tune chaperone function. This mini-review summarizes the current understanding of the role and regulation of PTMs on the major J-proteins Ydj1 and DNAJA1. Understanding these PTMs may provide novel therapeutic avenues for targeting chaperone activity in cancer and neurodegenerative diseases.
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Affiliation(s)
- Megan M Mitchem
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Courtney Shrader
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Elizabeth Abedi
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Andrew W Truman
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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23
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Apostolidou D, Zhang P, Pandya D, Bock K, Liu Q, Yang W, Marszalek PE. Tandem repeats of highly bioluminescent NanoLuc are refolded noncanonically by the Hsp70 machinery. Protein Sci 2024; 33:e4895. [PMID: 38284490 PMCID: PMC10804678 DOI: 10.1002/pro.4895] [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: 08/17/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
Chaperones are a large family of proteins crucial for maintaining cellular protein homeostasis. One such chaperone is the 70 kDa heat shock protein (Hsp70), which plays a crucial role in protein (re)folding, stability, functionality, and translocation. While the key events in the Hsp70 chaperone cycle are well established, a relatively small number of distinct substrates were repetitively investigated. This is despite Hsp70 engaging with a plethora of cellular proteins of various structural properties and folding pathways. Here we analyzed novel Hsp70 substrates, based on tandem repeats of NanoLuc (Nluc), a small and highly bioluminescent protein with unique structural characteristics. In previous mechanical unfolding and refolding studies, we have identified interesting misfolding propensities of these Nluc-based tandem repeats. In this study, we further investigate these properties through in vitro bulk experiments. Similar to monomeric Nluc, engineered Nluc dyads and triads proved to be highly bioluminescent. Using the bioluminescence signal as the proxy for their structural integrity, we determined that heat-denatured Nluc dyads and triads can be efficiently refolded by the E. coli Hsp70 chaperone system, which comprises DnaK, DnaJ, and GrpE. In contrast to previous studies with other substrates, we observed that Nluc repeats can be efficiently refolded by DnaK and DnaJ, even in the absence of GrpE co-chaperone. Taken together, our study offers a new powerful substrate for chaperone research and raises intriguing questions about the Hsp70 mechanisms, particularly in the context of structurally diverse proteins.
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Affiliation(s)
- Dimitra Apostolidou
- Department of Mechanical Engineering and Materials ScienceDuke UniversityDurhamNorth CarolinaUnited States
| | - Pan Zhang
- Department of ChemistryDuke UniversityDurhamNorth CarolinaUnited States
| | - Devanshi Pandya
- Department of Electrical and Computer EngineeringDuke UniversityDurhamNorth CarolinaUnited States
| | - Kaden Bock
- Department of Biomedical EngineeringDuke UniversityDurhamNorth CarolinaUnited States
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUnited States
| | - Weitao Yang
- Department of ChemistryDuke UniversityDurhamNorth CarolinaUnited States
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials ScienceDuke UniversityDurhamNorth CarolinaUnited States
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24
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Roterman I, Stapor K, Konieczny L. Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone. BMC Bioinformatics 2023; 24:418. [PMID: 37932669 PMCID: PMC10629080 DOI: 10.1186/s12859-023-05545-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/27/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The aqueous environment directs the protein folding process towards the generation of micelle-type structures, which results in the exposure of hydrophilic residues on the surface (polarity) and the concentration of hydrophobic residues in the center (hydrophobic core). Obtaining a structure without a hydrophobic core requires a different type of external force field than those generated by a water. The examples are membrane proteins, where the distribution of hydrophobicity is opposite to that of water-soluble proteins. Apart from these two extreme examples, the process of protein folding can be directed by chaperones, resulting in a structure devoid of a hydrophobic core. RESULTS The current work presents such example: DnaJ Hsp40 in complex with alkaline phosphatase PhoA-U (PDB ID-6PSI)-the client molecule. The availability of WT form of the folding protein-alkaline phosphatase (PDB ID-1EW8) enables a comparative analysis of the structures: at the stage of interaction with the chaperone and the final, folded structure of this biologically active protein. The fuzzy oil drop model in its modified FOD-M version was used in this analysis, taking into account the influence of an external force field, in this case coming from a chaperone. CONCLUSIONS The FOD-M model identifies the external force field introduced by chaperon influencing the folding proces. The identified specific external force field can be applied in Ab Initio protein structure prediction as the environmental conditioning the folding proces.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Medyczna 7, 30-688, Krakow, Poland.
| | - Katarzyna Stapor
- Department of Applied Informatics, Silesian University of Technology, Gliwice, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University - Medical College, Kopernika 7, 31-034, Krakow, Poland
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25
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Abayev-Avraham M, Salzberg Y, Gliksberg D, Oren-Suissa M, Rosenzweig R. DNAJB6 mutants display toxic gain of function through unregulated interaction with Hsp70 chaperones. Nat Commun 2023; 14:7066. [PMID: 37923706 PMCID: PMC10624832 DOI: 10.1038/s41467-023-42735-z] [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: 06/15/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Molecular chaperones are essential cellular components that aid in protein folding and preventing the abnormal aggregation of disease-associated proteins. Mutations in one such chaperone, DNAJB6, were identified in patients with LGMDD1, a dominant autosomal disorder characterized by myofibrillar degeneration and accumulations of aggregated protein within myocytes. The molecular mechanisms through which such mutations cause this dysfunction, however, are not well understood. Here we employ a combination of solution NMR and biochemical assays to investigate the structural and functional changes in LGMDD1 mutants of DNAJB6. Surprisingly, we find that DNAJB6 disease mutants show no reduction in their aggregation-prevention activity in vitro, and instead differ structurally from the WT protein, affecting their interaction with Hsp70 chaperones. While WT DNAJB6 contains a helical element regulating its ability to bind and activate Hsp70, in LGMDD1 disease mutants this regulation is disrupted. These variants can thus recruit and hyperactivate Hsp70 chaperones in an unregulated manner, depleting Hsp70 levels in myocytes, and resulting in the disruption of proteostasis. Interfering with DNAJB6-Hsp70 binding, however, reverses the disease phenotype, suggesting future therapeutic avenues for LGMDD1.
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Affiliation(s)
- Meital Abayev-Avraham
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Yehuda Salzberg
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Dar Gliksberg
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Meital Oren-Suissa
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, 761000, Israel
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 761000, Israel.
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26
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Ciesielski SJ, Young C, Ciesielska EJ, Ciesielski GL. The Hsp70 and JDP proteins: Structure-function perspective on molecular chaperone activity. Enzymes 2023; 54:221-245. [PMID: 37945173 DOI: 10.1016/bs.enz.2023.07.008] [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: 11/12/2023]
Abstract
Proteins are the most structurally diverse cellular biomolecules that act as molecular machines driving essential activities of all living organisms. To be functional, most of the proteins need to fold into a specific three-dimensional structure, which on one hand should be stable enough to oppose disruptive conditions and on the other hand flexible enough to allow conformational dynamics necessary for their biological functions. This compromise between stability and dynamics makes proteins susceptible to stress-induced misfolding and aggregation. Moreover, the folding process itself is intrinsically prone to conformational errors. Molecular chaperones are proteins that mitigate folding defects and maintain the structural integrity of the cellular proteome. Promiscuous Hsp70 chaperones are central to these processes and their activity depends on the interaction with obligatory J-domain protein (JDP) partners. In this review, we discuss structural aspects of Hsp70s, JDPs, and their interaction in the context of biological activities.
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Affiliation(s)
- Szymon J Ciesielski
- Department of Chemistry and Biochemistry, University of North Florida, Jacksonville, FL, United States.
| | - Cameron Young
- Department of Chemistry and Biochemistry, University of North Florida, Jacksonville, FL, United States
| | - Elena J Ciesielska
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States; Department of Biology, University of North Florida, Jacksonville, FL, United States
| | - Grzegorz L Ciesielski
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States; Department of Biology, University of North Florida, Jacksonville, FL, United States
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27
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Shirokikh NE, Jensen KB, Thakor N. Editorial: RNA machines. Front Genet 2023; 14:1290420. [PMID: 37829284 PMCID: PMC10565666 DOI: 10.3389/fgene.2023.1290420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023] Open
Affiliation(s)
- Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kirk Blomquist Jensen
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
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28
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Velasco-Carneros L, Cuéllar J, Dublang L, Santiago C, Maréchal JD, Martín-Benito J, Maestro M, Fernández-Higuero JÁ, Orozco N, Moro F, Valpuesta JM, Muga A. The self-association equilibrium of DNAJA2 regulates its interaction with unfolded substrate proteins and with Hsc70. Nat Commun 2023; 14:5436. [PMID: 37670029 PMCID: PMC10480186 DOI: 10.1038/s41467-023-41150-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/24/2023] [Indexed: 09/07/2023] Open
Abstract
J-domain proteins tune the specificity of Hsp70s, engaging them in precise functions. Despite their essential role, the structure and function of many J-domain proteins remain largely unknown. We explore human DNAJA2, finding that it reversibly forms highly-ordered, tubular structures that can be dissociated by Hsc70, the constitutively expressed Hsp70 isoform. Cryoelectron microscopy and mutational studies reveal that different domains are involved in self-association. Oligomer dissociation into dimers potentiates its interaction with unfolded client proteins. The J-domains are accessible to Hsc70 within the tubular structure. They allow binding of closely spaced Hsc70 molecules that could be transferred to the unfolded substrate for its cooperative remodelling, explaining the efficient recovery of DNAJA2-bound clients. The disordered C-terminal domain, comprising the last 52 residues, regulates its holding activity and productive interaction with Hsc70. These in vitro findings suggest that the association equilibrium of DNAJA2 could regulate its interaction with client proteins and Hsc70.
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Affiliation(s)
- Lorea Velasco-Carneros
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Jorge Cuéllar
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - Leire Dublang
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - César Santiago
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, (UAB), 08193, Bellaterra (Barcelona), Spain
| | - Jaime Martín-Benito
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - Moisés Maestro
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain
| | - José Ángel Fernández-Higuero
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Natalia Orozco
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
| | - Fernando Moro
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - José María Valpuesta
- Department of Macromolecular Structure, National Centre for Biotechnology (CNB-CSIC), 28049, Madrid, Spain.
| | - Arturo Muga
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, 48940, Leioa, Spain.
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940, Leioa, Spain.
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29
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Malinverni D, Zamuner S, Rebeaud ME, Barducci A, Nillegoda NB, De Los Rios P. Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins. Proc Natl Acad Sci U S A 2023; 120:e2218217120. [PMID: 37523524 PMCID: PMC10410713 DOI: 10.1073/pnas.2218217120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/23/2023] [Indexed: 08/02/2023] Open
Abstract
The 70-kD heat shock protein (Hsp70) chaperone system is a central hub of the proteostasis network that helps maintain protein homeostasis in all organisms. The recruitment of Hsp70 to perform different and specific cellular functions is regulated by the J-domain protein (JDP) co-chaperone family carrying the small namesake J-domain, required to interact and drive the ATPase cycle of Hsp70s. Besides the J-domain, prokaryotic and eukaryotic JDPs display a staggering diversity in domain architecture, function, and cellular localization. Very little is known about the overall JDP family, despite their essential role in cellular proteostasis, development, and its link to a broad range of human diseases. In this work, we leverage the exponentially increasing number of JDP gene sequences identified across all kingdoms owing to the advancements in sequencing technology and provide a broad overview of the JDP repertoire. Using an automated classification scheme based on artificial neural networks (ANNs), we demonstrate that the sequences of J-domains carry sufficient discriminatory information to reliably recover the phylogeny, localization, and domain composition of the corresponding full-length JDP. By harnessing the interpretability of the ANNs, we find that many of the discriminatory sequence positions match residues that form the interaction interface between the J-domain and Hsp70. This reveals that key residues within the J-domains have coevolved with their obligatory Hsp70 partners to build chaperone circuits for specific functions in cells.
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Affiliation(s)
- Duccio Malinverni
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN38105
| | - Stefano Zamuner
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Mathieu E. Rebeaud
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Alessandro Barducci
- Centre de Biologie Structurale, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Nadinath B. Nillegoda
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC3800, Australia
- Centre for Dementia and Brain Repair at the Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC3800, Australia
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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30
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Kotler JLM, Street TO. Mechanisms of Protein Quality Control in the Endoplasmic Reticulum by a Coordinated Hsp40-Hsp70-Hsp90 System. Annu Rev Biophys 2023; 52:509-524. [PMID: 37159299 DOI: 10.1146/annurev-biophys-111622-091309] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The Hsp40, Hsp70, and Hsp90 chaperone families are ancient, highly conserved, and critical to cellular protein homeostasis. Hsp40 chaperones can transfer their protein clients to Hsp70, and Hsp70 can transfer clients to Hsp90, but the functional benefits of these transfers are unclear. Recent structural and mechanistic work has opened up the possibility of uncovering how Hsp40, Hsp70, and Hsp90 work together as unified system. In this review, we compile mechanistic data on the ER J-domain protein 3 (ERdj3) (an Hsp40), BiP (an Hsp70), and Grp94 (an Hsp90) chaperones within the endoplasmic reticulum; what is known about how these chaperones work together; and gaps in this understanding. Using calculations, we examine how client transfer could impact the solubilization of aggregates, the folding of soluble proteins, and the triage decisions by which proteins are targeted for degradation. The proposed roles of client transfer among Hsp40-Hsp70-Hsp90 chaperones are new hypotheses, and we discuss potential experimental tests of these ideas.
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Affiliation(s)
- Judy L M Kotler
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA;
| | - Timothy O Street
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA;
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31
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Marszalek J, Craig EA, Tomiczek B. J-Domain Proteins Orchestrate the Multifunctionality of Hsp70s in Mitochondria: Insights from Mechanistic and Evolutionary Analyses. Subcell Biochem 2023; 101:293-318. [PMID: 36520311 DOI: 10.1007/978-3-031-14740-1_10] [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] [Indexed: 06/17/2023]
Abstract
Mitochondrial J-domain protein (JDP) co-chaperones orchestrate the function of their Hsp70 chaperone partner(s) in critical organellar processes that are essential for cell function. These include folding, refolding, and import of mitochondrial proteins, maintenance of mitochondrial DNA, and biogenesis of iron-sulfur cluster(s) (FeS), prosthetic groups needed for function of mitochondrial and cytosolic proteins. Consistent with the organelle's endosymbiotic origin, mitochondrial Hsp70 and the JDPs' functioning in protein folding and FeS biogenesis clearly descended from bacteria, while the origin of the JDP involved in protein import is less evident. Regardless of their origin, all mitochondrial JDP/Hsp70 systems evolved unique features that allowed them to perform mitochondria-specific functions. Their modes of functional diversification and specialization illustrate the versatility of JDP/Hsp70 systems and inform our understanding of system functioning in other cellular compartments.
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Affiliation(s)
- Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Bartlomiej Tomiczek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
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32
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Abstract
Cellular homeostasis and stress survival requires maintenance of the proteome and suppression of proteotoxicity. Molecular chaperones promote cell survival through repair of misfolded proteins and cooperation with protein degradation machines to discard terminally damaged proteins. Hsp70 family members play an essential role in cellular protein metabolism by binding and releasing non-native proteins to facilitate protein folding, refolding, and degradation. Hsp40 (DnaJ-like proteins) family members are Hsp70 co-chaperones that determine the fate of Hsp70 clients by facilitating protein folding, assembly, and degradation. Hsp40s select substrates for Hsp70 via use of an intrinsic chaperone activity to bind non-native regions of proteins. During delivery of bound cargo Hsp40s employ a conserved J-domain to stimulate Hsp70 ATPase activity and thereby stabilize complexes between Hsp70 and non-native proteins. This review describes the mechanisms by which different Hsp40s use specialized sub-domains to direct clients of Hsp70 for triage between folding versus degradation.
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Affiliation(s)
- Douglas M Cyr
- Department of Cell Biology and Physiology, School of Medicine University of North Carolina, Chapel Hill, NC, USA.
| | - Carlos H Ramos
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil.
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33
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Zhang H, Hu H, Wu S, Perrett S. Effect of evolution of the C-terminal region on chaperone activity of Hsp70. Protein Sci 2023; 32:e4549. [PMID: 36533311 PMCID: PMC9798248 DOI: 10.1002/pro.4549] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Dynamic interdomain interactions within the Hsp70 protein is the basis for the allosteric and functional properties of Hsp70s. While Hsp70s are generally conserved in terms of structure, allosteric behavior, and some overlapping functions, Hsp70s also contain variable sequence regions which are related to distinct functions. In the Hsp70 sequence, the part with the greatest sequence variation is the C-terminal α-helical lid subdomain of substrate-binding domain (SBDα) together with the intrinsically disordered region. Dynamic interactions between the SBDα and β-sandwich substrate-binding subdomain (SBDβ) contribute to the chaperone functions of Hsp70s by tuning kinetics of substrate binding. To investigate how the C-terminal region of Hsp70 has evolved from prokaryotic to eukaryotic organisms, we tested whether this region can be exchanged among different Hsp70 members to support basic chaperone functions. We found that this region from eukaryotic Hsp70 members cannot substitute for the same region in Escherichia coli DnaK to facilitate normal chaperone activity of DnaK. In contrast, this region from E. coli DnaK and Saccharomyces cerevisiae Hsp70 (Ssa1 and Ssa4) can partially support some roles of human stress inducible Hsp70 (hHsp70) and human cognate Hsp70 (hHsc70). Our results indicate that the C-terminal region from eukaryotic Hsp70 members cannot properly support SBDα-SBDβ interactions in DnaK, but this region from DnaK/Ssa1/Ssa4 can still form some SBDα-SBDβ interactions in hHsp70 or hHsc70, which suggests that the mode for SBDα-SBDβ interactions is different in prokaryotic and eukaryotic Hsp70 members. This study provides new insight in the divergency among different Hsp70 homologs and the evolution of Hsp70s.
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Affiliation(s)
- Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
- State Key Laboratory of Medical Molecular Biology, School of Basic MedicineInstitute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Huimin Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of the Chinese Academy of SciencesBeijingChina
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34
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Zhang R, Malinverni D, Cyr DM, Rios PDL, Nillegoda NB. J-domain protein chaperone circuits in proteostasis and disease. Trends Cell Biol 2023; 33:30-47. [PMID: 35729039 PMCID: PMC9759622 DOI: 10.1016/j.tcb.2022.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 12/27/2022]
Abstract
The J-domain proteins (JDP) form the largest protein family among cellular chaperones. In cooperation with the Hsp70 chaperone system, these co-chaperones orchestrate a plethora of distinct functions, including those that help maintain cellular proteostasis and development. JDPs evolved largely through the fusion of a J-domain with other protein subdomains. The highly conserved J-domain facilitates the binding and activation of Hsp70s. How JDPs (re)wire Hsp70 chaperone circuits and promote functional diversity remains insufficiently explained. Here, we discuss recent advances in our understanding of the JDP family with a focus on the regulation built around J-domains to ensure correct pairing and assembly of JDP-Hsp70 machineries that operate on different clientele under various cellular growth conditions.
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Affiliation(s)
- Ruobing Zhang
- Australian Regenerative Medicine Institute (ARMI), Monash University, Melbourne, Victoria, Australia
| | - Duccio Malinverni
- MRC Laboratory of Molecular Biology, Cambridge, UK; Department of Structural Biology and Center for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Douglas M Cyr
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences and Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nadinath B Nillegoda
- Australian Regenerative Medicine Institute (ARMI), Monash University, Melbourne, Victoria, Australia.
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35
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Marzano NR, Paudel BP, van Oijen AM, Ecroyd H. Real-time single-molecule observation of chaperone-assisted protein folding. SCIENCE ADVANCES 2022; 8:eadd0922. [PMID: 36516244 PMCID: PMC9750156 DOI: 10.1126/sciadv.add0922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The ability of heat shock protein 70 (Hsp70) molecular chaperones to remodel the conformation of their clients is central to their biological function; however, questions remain regarding the precise molecular mechanisms by which Hsp70 machinery interacts with the client and how this contributes toward efficient protein folding. Here, we used total internal reflection fluorescence (TIRF) microscopy and single-molecule fluorescence resonance energy transfer (smFRET) to temporally observe the conformational changes that occur to individual firefly luciferase proteins as they are folded by the bacterial Hsp70 system. We observed multiple cycles of chaperone binding and release to an individual client during refolding and determined that high rates of chaperone cycling improves refolding yield. Furthermore, we demonstrate that DnaJ remodels misfolded proteins via a conformational selection mechanism, whereas DnaK resolves misfolded states via mechanical unfolding. This study illustrates that the temporal observation of chaperone-assisted folding enables the elucidation of key mechanistic details inaccessible using other approaches.
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Affiliation(s)
- Nicholas R. Marzano
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Bishnu P. Paudel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Antoine M. van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
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36
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Gaur D, Kumar N, Ghosh A, Singh P, Kumar P, Guleria J, Kaur S, Malik N, Saha S, Nystrom T, Sharma D. Ydj1 interaction at nucleotide-binding-domain of yeast Ssa1 impacts Hsp90 collaboration and client maturation. PLoS Genet 2022; 18:e1010442. [PMID: 36350833 PMCID: PMC9645627 DOI: 10.1371/journal.pgen.1010442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/24/2022] [Indexed: 11/11/2022] Open
Abstract
Hsp90 constitutes one of the major chaperone machinery in the cell. The Hsp70 assists Hsp90 in its client maturation though the underlying basis of the Hsp70 role remains to be explored. In the present study, using S. cerevisiae strain expressing Ssa1 as sole Ssa Hsp70, we identified novel mutations in the nucleotide-binding domain of yeast Ssa1 Hsp70 (Ssa1-T175N and Ssa1-D158N) that adversely affect the maturation of Hsp90 clients v-Src and Ste11. The identified Ssa1 amino acids critical for Hsp90 function were also found to be conserved across species such as in E.coli DnaK and the constitutive Hsp70 isoform (HspA8) in humans. These mutations are distal to the C-terminus of Hsp70, that primarily mediates Hsp90 interaction through the bridge protein Sti1, and proximal to Ydj1 (Hsp40 co-chaperone of Hsp70 family) binding region. Intriguingly, we found that the bridge protein Sti1 is critical for cellular viability in cells expressing Ssa1-T175N (A1-T175N) or Ssa1-D158N (A1-D158N) as sole Ssa Hsp70. The growth defect was specific for sti1Δ, as deletion of none of the other Hsp90 co-chaperones showed lethality in A1-T175N or A1-D158N. Mass-spectrometry based whole proteome analysis of A1-T175N cells lacking Sti1 showed an altered abundance of various kinases and transcription factors suggesting compromised Hsp90 activity. Further proteomic analysis showed that pathways involved in signaling, signal transduction, and protein phosphorylation are markedly downregulated in the A1-T175N upon repressing Sti1 expression using doxycycline regulatable promoter. In contrast to Ssa1, the homologous mutations in Ssa4 (Ssa4-T175N/D158N), the stress inducible Hsp70 isoform, supported cell growth even in the absence of Sti1. Overall, our data suggest that Ydj1 competes with Hsp90 for binding to Hsp70, and thus regulates Hsp90 interaction with the nucleotide-binding domain of Hsp70. The study thus provides new insight into the Hsp70-mediated regulation of Hsp90 and broadens our understanding of the intricate complexities of the Hsp70-Hsp90 network. Hsp70-Hsp90 constitutes major cellular chaperone machinery in cells. The Hsp70 plays critical role in Hsp90 chaperoning pathway. We have now identified novel mutations in the nucleotide-binding domain of yeast Ssa1 Hsp70 (Ssa1-T175N and Ssa1-D158N) that adversely affect Hsp90 client maturation. As compared to wt Ssa1, the identified Ssa1 mutants bind relatively better with Ydj1, and poorly support growth in the absence of Sti1, when present as the sole source of Ssa Hsp70 in S. cerevisiae. The cells expressing Ssa1-T175N as sole Ssa Hsp70 show downregulation of pathways involved in signaling, signal transduction, and protein phosphorylation upon repressing Sti1. The study shows that Ydj1 interaction at the nucleotide-binding domain of Ssa1 Hsp70 influences Hsp90 function.
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Affiliation(s)
- Deepika Gaur
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Navinder Kumar
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-Age Cap, University of Gothenburg, Gothenburg, Sweden
| | - Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Prashant Singh
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Pradeep Kumar
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Jyoti Guleria
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Satinderdeep Kaur
- Pharmacology Department, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Nikhil Malik
- Department of Biochemistry, School of Interdisciplinary and Applied Life Sciences, Central University of Haryana, Mahendergarh, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Thomas Nystrom
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health-Age Cap, University of Gothenburg, Gothenburg, Sweden
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific & Innovative Research, Ghaziabad, India
- * E-mail:
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37
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Harari A, Zoltsman G, Levin T, Rosenzweig R. Hsp104 N-terminal domain interaction with substrates plays a regulatory role in protein disaggregation. FEBS J 2022; 289:5359-5377. [PMID: 35305079 PMCID: PMC9541529 DOI: 10.1111/febs.16441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/01/2022] [Accepted: 03/17/2022] [Indexed: 01/19/2023]
Abstract
Heat shock protein 104 (Hsp104) protein disaggregases are powerful molecular machines that harness the energy derived from ATP binding and hydrolysis to disaggregate a wide range of protein aggregates and amyloids, as well as to assist in yeast prion propagation. Little is known, however, about how Hsp104 chaperones recognize such a diversity of substrates, or indeed the contribution of the substrate‐binding N‐terminal domain (NTD) to Hsp104 function. Herein, we present a NMR spectroscopy study, which structurally characterizes the Hsp104 NTD‐substrate interaction. We show that the NTD includes a substrate‐binding groove that specifically recognizes exposed hydrophobic stretches in unfolded, misfolded, amyloid and prion substrates of Hsp104. In addition, we find that the NTD itself has chaperoning activities which help to protect the exposed hydrophobic regions of its substrates from further misfolding and aggregation, thereby priming them for threading through the Hsp104 central channel. We further demonstrate that mutations to this substrate‐binding groove abolish Hsp104 activation by client proteins and keep the chaperone in a partially inhibited state. The Hsp104 variant with these mutations also exhibited significantly reduced disaggregation activity and cell survival at extreme temperatures. Together, our findings provide both a detailed characterization of the NTD‐substrate complex and insight into the functional regulatory role of the NTD in protein disaggregation and yeast thermotolerance.
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Affiliation(s)
- Anna Harari
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Zoltsman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Levin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rina Rosenzweig
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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38
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Ruff KM, Choi YH, Cox D, Ormsby AR, Myung Y, Ascher DB, Radford SE, Pappu RV, Hatters DM. Sequence grammar underlying the unfolding and phase separation of globular proteins. Mol Cell 2022; 82:3193-3208.e8. [PMID: 35853451 PMCID: PMC10846692 DOI: 10.1016/j.molcel.2022.06.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 05/05/2022] [Accepted: 06/15/2022] [Indexed: 12/23/2022]
Abstract
Aberrant phase separation of globular proteins is associated with many diseases. Here, we use a model protein system to understand how the unfolded states of globular proteins drive phase separation and the formation of unfolded protein deposits (UPODs). We find that for UPODs to form, the concentrations of unfolded molecules must be above a threshold value. Additionally, unfolded molecules must possess appropriate sequence grammars to drive phase separation. While UPODs recruit molecular chaperones, their compositional profiles are also influenced by synergistic physicochemical interactions governed by the sequence grammars of unfolded proteins and cellular proteins. Overall, the driving forces for phase separation and the compositional profiles of UPODs are governed by the sequence grammars of unfolded proteins. Our studies highlight the need for uncovering the sequence grammars of unfolded proteins that drive UPOD formation and cause gain-of-function interactions whereby proteins are aberrantly recruited into UPODs.
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Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering, Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yoon Hee Choi
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Dezerae Cox
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Angelique R Ormsby
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Yoochan Myung
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Systems and Computational Biology, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Systems and Computational Biology, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sheena E Radford
- Astbury Centre for Structural and Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Danny M Hatters
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.
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39
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Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT. Nat Commun 2022; 13:4692. [PMID: 35948542 PMCID: PMC9365803 DOI: 10.1038/s41467-022-32370-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
Huntington’s disease is a neurodegenerative disease caused by an expanded polyQ stretch within Huntingtin (HTT) that renders the protein aggregation-prone, ultimately resulting in the formation of amyloid fibrils. A trimeric chaperone complex composed of Hsc70, DNAJB1 and Apg2 can suppress and reverse the aggregation of HTTExon1Q48. DNAJB1 is the rate-limiting chaperone and we have here identified and characterized the binding interface between DNAJB1 and HTTExon1Q48. DNAJB1 exhibits a HTT binding motif (HBM) in the hinge region between C-terminal domains (CTD) I and II and binds to the polyQ-adjacent proline rich domain (PRD) of soluble as well as aggregated HTT. The PRD of HTT represents an additional binding site for chaperones. Mutation of the highly conserved H244 of the HBM of DNAJB1 completely abrogates the suppression and disaggregation of HTT fibrils by the trimeric chaperone complex. Notably, this mutation does not affect the binding and remodeling of any other protein substrate, suggesting that the HBM of DNAJB1 is a specific interaction site for HTT. Overexpression of wt DNAJB1, but not of DNAJB1H244A can prevent the accumulation of HTTExon1Q97 aggregates in HEK293 cells, thus validating the biological significance of the HBM within DNAJB1. Ayala Mariscal et al have identified and characterized the interface of pathogenic Huntingtin and the molecular chaperone DNAJB1. Histidine-244 of the C-terminal domain of DNAJB1 is a key residues for binding to the poly-proline region of HTT. This binding site is specific for the interaction with Huntingtin.
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40
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ThhspA1 is involved in lacA transcriptional regulation of Trametes hirsuta AH28-2 exposed to o-toluidine. Fungal Genet Biol 2022; 161:103716. [PMID: 35691497 DOI: 10.1016/j.fgb.2022.103716] [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: 11/03/2021] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/20/2022]
Abstract
White rot fungi, especially Trametes spp., respond to a wide range of aromatic compounds and dramatically enhance laccase activity, while the activation mechanisms remain to be elucidated. Here, we show that an Hsp70 homolog named ThhspA1 regulates the transcription of laccase LacA in Trametes hirsuta AH28-2 when confronted with o-toluidine. ThhspA1 is pulled down by lacA promoter sequence from the nuclear mixture extracted from T. hirsuta AH28-2 induced by 2 mM o-toluidine. Silencing of ThhspA1 results in a sharp decrease in lacA transcripts and laccase activity in vivo. By comparison, ThhspA1 overexpression does not affect lacA transcription, and laccase activity shows slight enhancement or remains unchanged upon induction with o-toluidine. Electrophoretic mobility shift assays suggest a direct interaction between ThhspA1 and the lacA promoter region. Further investigation shows that the integrity of ThhspA1 is critical since its substrate binding domain (SBD) and nucleotide-binding domain (NBD) are both necessary for DNA binding, with a higher affinity of SBD than NBD based on fluorescence polarization assay. Our results demonstrate that ThhspA1 functions as an aromatic-stress-related DNA binding transcriptional factor required for LacA expression.
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41
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Tamadaddi C, Verma AK, Zambare V, Vairagkar A, Diwan D, Sahi C. J-like protein family of Arabidopsis thaliana: the enigmatic cousins of J-domain proteins. PLANT CELL REPORTS 2022; 41:1343-1355. [PMID: 35290497 DOI: 10.1007/s00299-022-02857-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
J-like proteins (JLPs) are emerging as ancillaries to the cellular chaperone network. They modulate functions of Hsp70:J-domain protein (JDP) systems in novel ways thereby having key roles in diverse plant processes. J-domain proteins (JDPs) form an obligate co-chaperone partnership with Hsp70s with their highly conserved J-domain to steer protein quality control processes in the cell. The HPD motif between helix II and helix III of the J-domain is crucial for JDP's interaction with Hsp70s. According to the most recent classification, J-like proteins (JLPs) form an extended class of the JDP family possessing a degenerate J-domain with the HPD motif non-conservatively replaced by other amino acid residues and hence are not able to interact with Hsp70s. Considering this most updated and acceptable JLP classification, we identified 21 JLPs in Arabidopsis thaliana that share a structurally conserved J-like domain (JLD), but lack the HPD motif. Analysis of publicly available gene expression data as well as real-time quantitative PCR performed for a few selected JLPs implicated some of these proteins in growth, development and stress response. Here, we summarize the current state of knowledge on plant JLPs and their involvement in vital plant cellular/metabolic processes, including chloroplast division, mitochondrial protein import and flowering. Finally, we propose possible modes of action for these highly elusive proteins and other DnaJ-related proteins (DNAJRs) in regulating the Hsp70 chaperone network.
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Affiliation(s)
- Chetana Tamadaddi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
- Department of Biology, Eberly College of Science, The Pennsylvania State University, University Park, PA, USA
| | - Amit K Verma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Vyankatesh Zambare
- School of Biotechnology and Bioinformatics, D Y Patil Deemed to be University, Navi Mumbai, India
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Avanti Vairagkar
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Danish Diwan
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
- Department of Biology, University of Alabama, Birmingham, AL, USA
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India.
- IISER Bhopal, Room Number 117, AB3, Bhopal Bypass Road, Bhopal, 462066, MP, India.
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42
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Rizzo D, Cerofolini L, Giuntini S, Iozzino L, Pergola C, Sacco F, Palmese A, Ravera E, Luchinat C, Baroni F, Fragai M. Epitope Mapping and Binding Assessment by Solid-State NMR Provide a Way for the Development of Biologics under the Quality by Design Paradigm. J Am Chem Soc 2022; 144:10006-10016. [PMID: 35617699 PMCID: PMC9185746 DOI: 10.1021/jacs.2c03232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Multispecific biologics
are an emerging class of drugs, in which
antibodies and/or proteins designed to bind pharmacological targets
are covalently linked or expressed as fusion proteins to increase
both therapeutic efficacy and safety. Epitope mapping on the target
proteins provides key information to improve the affinity and also
to monitor the manufacturing process and drug stability. Solid-state
NMR has been here used to identify the pattern of the residues of
the programmed cell death ligand 1 (PD-L1) ectodomain that are involved
in the interaction with a new multispecific biological drug. This
is possible because the large size and the intrinsic flexibility of
the complexes are not limiting factors for solid-state NMR.
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Affiliation(s)
- Domenico Rizzo
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Luisa Iozzino
- Analytical Development Biotech Department, Merck Serono S.p.a, Via Luigi Einaudi, 11, 00012 Guidonia, RM, Italy
| | - Carlo Pergola
- Analytical Development Biotech Department, Merck Serono S.p.a, Via Luigi Einaudi, 11, 00012 Guidonia, RM, Italy
| | - Francesca Sacco
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Analytical Development Biotech Department, Merck Serono S.p.a, Via Luigi Einaudi, 11, 00012 Guidonia, RM, Italy
| | - Angelo Palmese
- Analytical Development Biotech Department, Merck Serono S.p.a, Via Luigi Einaudi, 11, 00012 Guidonia, RM, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Fabio Baroni
- Analytical Development Biotech Department, Merck Serono S.p.a, Via Luigi Einaudi, 11, 00012 Guidonia, RM, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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43
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Asgharzadeh F, Moradi-Marjaneh R, Marjaneh MM. The role of heat shock protein 40 in carcinogenesis and biology of colorectal cancer. Curr Pharm Des 2022; 28:1457-1465. [PMID: 35570564 DOI: 10.2174/1381612828666220513124603] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/31/2022] [Indexed: 11/22/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. Despite the enormous amount of effort in the diagnosis and treatment of CRC, the overall survival rate of patients remains low. The precise molecular and cellular basis underlying CRC has not been completely understood yet. Over time, new genes and molecular pathways involved in the pathogenesis of the disease are being identified. Accurate discovery of these genes and signaling pathways are important and urgent missions for the next generation of anticancer therapy research. Chaperone DnaJ, also known as Hsp40 (heat shock protein 40), has been of particular interest in CRC pathogenesis, as it is involved in the fundamental cell activities for maintaining cellular homeostasis. Evidence show that protein family members of DnaJ/Hsp40 play both roles; enhancing and reducing the growth of CRC cells. In the present review, we focus on the current knowledge on the molecular mechanisms responsible for the role of DnaJ/Hsp40 in CRC carcinogenesis and biology.
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Affiliation(s)
- Fereshteh Asgharzadeh
- Department of Physiology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reyhaneh Moradi-Marjaneh
- Department of Physiology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Mahdi Moradi Marjaneh
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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44
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Abstract
The folding of proteins into their native structure is crucial for the functioning of all biological processes. Molecular chaperones are guardians of the proteome that assist in protein folding and prevent the accumulation of aberrant protein conformations that can lead to proteotoxicity. ATP-independent chaperones do not require ATP to regulate their functional cycle. Although these chaperones have been traditionally regarded as passive holdases that merely prevent aggregation, recent work has shown that they can directly affect the folding energy landscape by tuning their affinity to various folding states of the client. This review focuses on emerging paradigms in the mechanism of action of ATP-independent chaperones and on the various modes of regulating client binding and release.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kevin Wu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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45
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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46
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Johnson OT, Nadel CM, Carroll EC, Arhar T, Gestwicki JE. Two distinct classes of cochaperones compete for the EEVD motif in heat shock protein 70 to tune its chaperone activities. J Biol Chem 2022; 298:101697. [PMID: 35148989 PMCID: PMC8913300 DOI: 10.1016/j.jbc.2022.101697] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/30/2022] Open
Abstract
Chaperones of the heat shock protein 70 (Hsp70) family engage in protein-protein interactions with many cochaperones. One "hotspot" for cochaperone binding is the EEVD motif, found at the extreme C terminus of cytoplasmic Hsp70s. This motif is known to bind tetratricopeptide repeat domain cochaperones, such as the E3 ubiquitin ligase CHIP. In addition, the EEVD motif also interacts with a structurally distinct domain that is present in class B J-domain proteins, such as DnaJB4. These observations suggest that CHIP and DnaJB4 might compete for binding to Hsp70's EEVD motif; however, the molecular determinants of such competition are not clear. Using a collection of EEVD-derived peptides, including mutations and truncations, we explored which residues are critical for binding to both CHIP and DnaJB4. These results revealed that some features, such as the C-terminal carboxylate, are important for both interactions. However, CHIP and DnaJB4 also had unique preferences, especially at the isoleucine position immediately adjacent to the EEVD. Finally, we show that competition between these cochaperones is important in vitro, as DnaJB4 limits the ubiquitination activity of the Hsp70-CHIP complex, whereas CHIP suppresses the client refolding activity of the Hsp70-DnaJB4 complex. Together, these data suggest that the EEVD motif has evolved to support diverse protein-protein interactions, such that competition between cochaperones may help guide whether Hsp70-bound proteins are folded or degraded.
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Affiliation(s)
- Oleta T Johnson
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA
| | - Cory M Nadel
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA
| | - Emma C Carroll
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA
| | - Taylor Arhar
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA; Department of Chemistry, Beloit College, Beloit, Wisconsin, USA.
| | - Jason E Gestwicki
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA.
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47
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Abstract
Cellular redox homeostasis is precisely balanced by generation and elimination of reactive oxygen species (ROS). ROS are not only capable of causing oxidation of proteins, lipids and DNA to damage cells but can also act as signaling molecules to modulate transcription factors and epigenetic pathways that determine cell survival and death. Hsp70 proteins are central hubs for proteostasis and are important factors to ameliorate damage from different kinds of stress including oxidative stress. Hsp70 members often participate in different cellular signaling pathways via their clients and cochaperones. ROS can directly cause oxidative cysteine modifications of Hsp70 members to alter their structure and chaperone activity, resulting in changes in the interactions between Hsp70 and their clients or cochaperones, which can then transfer redox signals to Hsp70-related signaling pathways. On the other hand, ROS also activate some redox-related signaling pathways to indirectly modulate Hsp70 activity and expression. Post-translational modifications including phosphorylation together with elevated Hsp70 expression can expand the capacity of Hsp70 to deal with ROS-damaged proteins and support antioxidant enzymes. Knowledge about the response and role of Hsp70 in redox homeostasis will facilitate our understanding of the cellular knock-on effects of inhibitors targeting Hsp70 and the mechanisms of redox-related diseases and aging.
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48
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Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding. Int J Mol Sci 2022; 23:ijms23052485. [PMID: 35269628 PMCID: PMC8910466 DOI: 10.3390/ijms23052485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/10/2022] Open
Abstract
Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires the assistance of molecular chaperones. Molecular chaperones promote or delay the folding of the client protein, but the detailed mechanisms are still unclear. This review summarizes the findings of biophysical and structural studies on the mechanism of multidomain protein folding mediated by molecular chaperones and explains how molecular chaperones recognize the client proteins and alter their folding properties. Furthermore, we introduce several recent studies that describe the concept of kinetics-activity relationships to explain the mechanism of functional diversity of molecular chaperones.
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Yoo H, Bard JA, Pilipenko E, Drummond DA. Chaperones directly and efficiently disperse stress-triggered biomolecular condensates. Mol Cell 2022; 82:741-755.e11. [PMID: 35148816 PMCID: PMC8857057 DOI: 10.1016/j.molcel.2022.01.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/30/2021] [Accepted: 01/06/2022] [Indexed: 12/28/2022]
Abstract
Stresses such as heat shock trigger the formation of protein aggregates and the induction of a disaggregation system composed of molecular chaperones. Recent work reveals that several cases of apparent heat-induced aggregation, long thought to be the result of toxic misfolding, instead reflect evolved, adaptive biomolecular condensation, with chaperone activity contributing to condensate regulation. Here we show that the yeast disaggregation system directly disperses heat-induced biomolecular condensates of endogenous poly(A)-binding protein (Pab1) orders of magnitude more rapidly than aggregates of the most commonly used misfolded model substrate, firefly luciferase. Beyond its efficiency, heat-induced condensate dispersal differs from heat-induced aggregate dispersal in its molecular requirements and mechanistic behavior. Our work establishes a bona fide endogenous heat-induced substrate for long-studied heat shock proteins, isolates a specific example of chaperone regulation of condensates, and underscores needed expansion of the proteotoxic interpretation of the heat shock response to encompass adaptive, chaperone-mediated regulation.
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Affiliation(s)
- Haneul Yoo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jared A.M. Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Evgeny Pilipenko
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - D. Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA,Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA,Lead Contact,Correspondence: (D.A.D.)
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50
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Xie T, Saleh T, Rossi P, Miller D, Kalodimos CG. Imatinib can act as an Allosteric Activator of Abl Kinase. J Mol Biol 2022; 434:167349. [PMID: 34774565 PMCID: PMC8752476 DOI: 10.1016/j.jmb.2021.167349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/15/2021] [Accepted: 11/05/2021] [Indexed: 02/01/2023]
Abstract
Imatinib is an ATP-competitive inhibitor of Bcr-Abl kinase and the first drug approved for chronic myelogenous leukemia (CML) treatment. Here we show that imatinib binds to a secondary, allosteric site located in the myristoyl pocket of Abl to function as an activator of the kinase activity. Abl transitions between an assembled, inhibited state and an extended, activated state. The equilibrium is regulated by the conformation of the αΙ helix, which is located nearby the allosteric pocket. Imatinib binding to the allosteric pocket elicits an αΙ helix conformation that is not compatible with the assembled state, thereby promoting the extended state and stimulating the kinase activity. Although in wild-type Abl the catalytic pocket has a much higher affinity for imatinib than the allosteric pocket does, the two binding affinities are comparable in Abl variants carrying imatinib-resistant mutations in the catalytic site. A previously isolated imatinib-resistant mutation in patients appears to be mediating its function by increasing the affinity of imatinib for the allosteric pocket, providing a hitherto unknown mechanism of drug resistance. Our results highlight the benefit of combining imatinib with allosteric inhibitors to maximize their inhibitory effect on Bcr-Abl.
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Affiliation(s)
- Tao Xie
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Tamjeed Saleh
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Paolo Rossi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Darcie Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Charalampos G Kalodimos
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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