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Geng Y, Gai Y, Zhang Y, Zhao S, Jiang A, Li X, Deng K, Zhang F, Tan L, Song L. Genome-Wide Identification and Interaction Analysis of Turbot Heat Shock Protein 40 and 70 Families Suggest the Mechanism of Chaperone Proteins Involved in Immune Response after Bacterial Infection. Int J Mol Sci 2024; 25:7963. [PMID: 39063205 PMCID: PMC11277129 DOI: 10.3390/ijms25147963] [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: 07/03/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Hsp40-Hsp70 typically function in concert as molecular chaperones, and their roles in post-infection immune responses are increasingly recognized. However, in the economically important fish species Scophthalmus maximus (turbot), there is still a lack in the systematic identification, interaction models, and binding site analysis of these proteins. Herein, 62 Hsp40 genes and 16 Hsp70 genes were identified in the turbot at a genome-wide level and were unevenly distributed on 22 chromosomes through chromosomal distribution analysis. Phylogenetic and syntenic analysis provided strong evidence in supporting the orthologies and paralogies of these HSPs. Protein-protein interaction and expression analysis was conducted to predict the expression profile after challenging with Aeromonas salmonicida. dnajb1b and hspa1a were found to have a co-expression trend under infection stresses. Molecular docking was performed using Auto-Dock Tool and PyMOL for this pair of chaperone proteins. It was discovered that in addition to the interaction sites in the J domain, the carboxyl-terminal domain of Hsp40 also plays a crucial role in its interaction with Hsp70. This is important for the mechanistic understanding of the Hsp40-Hsp70 chaperone system, providing a theoretical basis for turbot disease resistance breeding, and effective value for the prevention of certain diseases in turbot.
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Affiliation(s)
- Yuanwei Geng
- School of Life Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (Y.G.)
| | - Yuxuan Gai
- School of Life Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (Y.G.)
- Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanping Zhang
- College of Entrepreneurship and Innovation, Qingdao Agricultural University, Qingdao 266109, China
| | - Shengwei Zhao
- School of Life Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (Y.G.)
| | - Anlan Jiang
- School of Life Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (Y.G.)
| | - Xueqing Li
- School of Life Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (Y.G.)
| | - Kaiqing Deng
- School of Life Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (Y.G.)
| | - Fuxuan Zhang
- School of Life Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (Y.G.)
| | - Lingling Tan
- School of Life Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (Y.G.)
| | - Lin Song
- School of Life Science, Qingdao Agricultural University, Qingdao 266109, China; (Y.G.); (Y.G.)
- Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, China
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2
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Jelen M, Grochowina I, Grabinska-Rogala A, Ciesielski SJ, Dabrowska K, Tomiczek B, Nierzwicki L, Delewski W, Schilke B, Czub J, Dadlez M, Dutkiewicz R, Craig EA, Marszalek J. Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein. J Mol Biol 2023; 435:168283. [PMID: 37730084 PMCID: PMC11457148 DOI: 10.1016/j.jmb.2023.168283] [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: 06/19/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
Hsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP interactions, this key step is not well understood. Here we leverage a well characterized Hsp70 system specialized for iron-sulfur cluster biogenesis, which like many systems, has a JDP that binds substrate on its own. Utilizing an ATPase-deficient Hsp70 variant, we isolated a Hsp70-JDP-substrate tripartite complex. Complex formation and stability depended on residues previously identified as essential for bipartite interactions: JDP-substrate, Hsp70-substrate and J-domain-Hsp70. Computational docking based on the established J-domain-Hsp70(ATP) interaction placed the substrate close to its predicted position in the peptide-binding cleft, with the JDP having the same architecture as when in a bipartite complex with substrate. Together, our results indicate that the structurally rigid JDP-substrate complex recruits Hsp70(ATP) via precise positioning of J-domain and substrate at their respective interaction sites - resulting in functionally high affinity (i.e., avidity). The exceptionally high avidity observed for this specialized system may be unusual because of the rigid architecture of its JDP and the additional JDP-Hsp70 interaction site uncovered in this study. However, functionally important avidity driven by JDP-substrate interactions is likely sufficient to explain synergistic ATPase stimulation and efficient substrate trapping in many Hsp70 systems.
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Affiliation(s)
- Marcin Jelen
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Igor Grochowina
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Aneta Grabinska-Rogala
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Szymon J Ciesielski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Katarzyna Dabrowska
- Laboratory of Mass Spectrometry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Bartlomiej Tomiczek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Lukasz Nierzwicki
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Wojciech Delewski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Brenda Schilke
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland; BioTechMed Center, Gdansk University of Technology, Gdansk, Poland
| | - Michal Dadlez
- Laboratory of Mass Spectrometry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Rafal Dutkiewicz
- 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.
| | - Jaroslaw Marszalek
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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3
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Barriot R, Latour J, Castanié-Cornet MP, Fichant G, Genevaux P. J-Domain Proteins in Bacteria and Their Viruses. J Mol Biol 2020; 432:3771-3789. [DOI: 10.1016/j.jmb.2020.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023]
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A History of Molecular Chaperone Structures in the Protein Data Bank. Int J Mol Sci 2019; 20:ijms20246195. [PMID: 31817979 PMCID: PMC6940948 DOI: 10.3390/ijms20246195] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
Thirty years ago a class of proteins was found to prevent the aggregation of Rubisco. These proteins’ ability to prevent unwanted associations led to their being called chaperones. These chaperone proteins also increased in expression as a response to heat shock, hence their label as heat shock proteins (Hsps). However, neither label encompasses the breadth of these proteins’ functional capabilities. The term “unfoldases” has been proposed, as this basic function is shared by most members of this protein family. Onto this is added specializations that allow the different family members to perform various cellular functions. This current article focuses on the resolved structural bases for these functions. It reviews the currently available molecular structures in the Protein Data Bank for several classes of Hsps (Hsp60, Hsp70, Hsp90, and Hsp104). When possible, it discusses the complete structures for these proteins, and the types of molecular machines to which they have been assigned. The structures of domains and the associated functions are discussed in order to illustrate the rationale for the proposed unfoldase function.
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5
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Newton TM, Duce JA, Bayle ED. The proteostasis network provides targets for neurodegeneration. Br J Pharmacol 2019; 176:3508-3514. [PMID: 30820936 DOI: 10.1111/bph.14643] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/03/2018] [Accepted: 02/15/2019] [Indexed: 12/28/2022] Open
Abstract
The production, quality control, and degradation of proteins are a tightly controlled process necessary for cell health. In order to regulate this process, cells rely upon a network of molecular chaperone proteins that bind misfolded proteins and help them fold correctly. In addition, some molecular chaperones can target terminally misfolded proteins for degradation. Neurons are particularly dependent upon this "proteostasis" system, failures in which lead to neurodegenerative disease. In this review, we identify opportunities for modulating molecular chaperone activity with small molecules, which could lower the burden of misfolded protein within neurons, reducing cell death and ameliorating the effects of neurodegeneration. LINKED ARTICLES: This article is part of a themed section on Therapeutics for Dementia and Alzheimer's Disease: New Directions for Precision Medicine. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.18/issuetoc.
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Affiliation(s)
- Timothy Mark Newton
- ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0AH, UK.,Reflection Therapeutics, IdeaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, UK
| | - James Alex Duce
- ALBORADA Drug Discovery Institute, University of Cambridge Island Research Building Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0AH, UK
| | - Elliott David Bayle
- Alzheimer's Research UK UCL Drug Discovery Institute, University College London, London, UK.,The Francis Crick Institute, 1 Midland Road, Kings Cross, London, NW1 1AT, UK
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(-)-Epigallocatechin-3-Gallate Inhibits the Chaperone Activity of Plasmodium falciparum Hsp70 Chaperones and Abrogates Their Association with Functional Partners. Molecules 2017; 22:molecules22122139. [PMID: 29206141 PMCID: PMC6149709 DOI: 10.3390/molecules22122139] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 11/17/2022] Open
Abstract
Heat shock proteins (Hsps), amongst them, Hsp70 and Hsp90 families, serve mainly as facilitators of protein folding (molecular chaperones) of the cell. The Hsp70 family of proteins represents one of the most important molecular chaperones in the cell. Plasmodium falciparum, the main agent of malaria, expresses six Hsp70 isoforms. Two (PfHsp70-1 and PfHsp70-z) of these localize to the parasite cytosol. PHsp70-1 is known to occur in a functional complex with another chaperone, PfHsp90 via a co-chaperone, P. falciparum Hsp70-Hsp90 organising protein (PfHop). (-)-Epigallocatechin-3-gallate (EGCG) is a green tea constituent that is thought to possess antiplasmodial activity. However, the mechanism by which EGCG exhibits antiplasmodial activity is not fully understood. A previous study proposed that EGCG binds to the N-terminal ATPase domain of Hsp70. In the current study, we overexpressed and purified recombinant forms of two P. falciparum cytosol localized Hsp70s (PfHsp70-1 and PfHsp70-z), and PfHop, a co-chaperone of PfHsp70-1. Using the surface plasmon resonance approach, we demonstrated that EGCG directly binds to the two Hsp70s. We further observed that binding of EGCG to the two proteins resulted in secondary and tertiary conformational changes. In addition, EGCG inhibited the ATPase and chaperone function of the two proteins. Furthermore, EGCG abrogated association of the two Hsp70s with their functional partners. Using parasites cultured in vitro at the blood stages, we observed that 2.9 µM EGCG suppressed 50% P. falciparum parasite growth (IC50). Our findings demonstrate that EGCG directly binds to PfHsp70-1 and PfHsp70-z to inhibit both the ATPase and chaperone functions of the proteins. Our study constitutes the first direct evidence suggesting that the antiplasmodial activity of EGCG is at least in part accounted for by its inhibition of Hsp70 function.
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7
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Xue YL, Wang H, Riedy M, Roberts BL, Sun Y, Song YB, Jones GW, Masison DC, Song Y. Molecular dynamics simulations of Hsp40 J-domain mutants identifies disruption of the critical HPD-motif as the key factor for impaired curing in vivo of the yeast prion [URE3]. J Biomol Struct Dyn 2017; 36:1764-1775. [PMID: 28766406 DOI: 10.1080/07391102.2017.1334594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic screens using Saccharomyces cerevisiae have identified an array of Hsp40 (Ydj1p) J-domain mutants that are impaired in the ability to cure the yeast [URE3] prion through disrupting functional interactions with Hsp70. However, biochemical analysis of some of these Hsp40 J-domain mutants has so far failed to provide major insight into the specific functional changes in Hsp40-Hsp70 interactions. To explore the detailed structural and dynamic properties of the Hsp40 J-domain, 20 ns molecular dynamic simulations of 4 mutants (D9A, D36A, A30T, and F45S) and wild-type J-domain were performed, followed by Hsp70 docking simulations. Results demonstrated that although the Hsp70 interaction mechanism of the mutants may vary, the major structural change was targeted to the critical HPD motif of the J-domain. Our computational analysis fits well with previous yeast genetics studies regarding highlighting the importance of J-domain function in prion propagation. During the molecular dynamics simulations several important residues were identified and predicted to play an essential role in J-domain structure. Among these residues, Y26 and F45 were confirmed, using both in silico and in vivo methods, as being critical for Ydj1p function.
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Affiliation(s)
- You-Lin Xue
- a School of Environmental Science, Liaoning University , Shenyang , China.,d Light Industry College, Liaoning University , Shenyang , China
| | - Hao Wang
- a School of Environmental Science, Liaoning University , Shenyang , China
| | - Michael Riedy
- b Laboratory of Biochemistry and Genetics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , MD , USA
| | - Brittany-Lee Roberts
- b Laboratory of Biochemistry and Genetics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , MD , USA
| | - Yuna Sun
- a School of Environmental Science, Liaoning University , Shenyang , China
| | - Yong-Bo Song
- e School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University , Shenyang , China
| | - Gary W Jones
- c National University of Ireland Maynooth , Maynooth , Ireland
| | - Daniel C Masison
- b Laboratory of Biochemistry and Genetics , National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda , MD , USA
| | - Youtao Song
- a School of Environmental Science, Liaoning University , Shenyang , China
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8
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Bascos NAD, Mayer MP, Bukau B, Landry SJ. The Hsp40 J-domain modulates Hsp70 conformation and ATPase activity with a semi-elliptical spring. Protein Sci 2017; 26:1838-1851. [PMID: 28685898 DOI: 10.1002/pro.3223] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/22/2017] [Accepted: 06/29/2017] [Indexed: 11/12/2022]
Abstract
Regulatory protein interactions are commonly attributed to lock-and-key associations that bring interacting domains together. However, studies in some systems suggest that regulation is not achieved by binding interactions alone. We report our investigations on specific physical characteristics required of the Hsp40 J-domain to stimulate ATP hydrolysis in the Hsp40-Hsp70 molecular chaperone machine. Biophysical analysis using isothermal titration calorimetry, and nuclear magnetic resonance spectroscopy reveals the importance of helix rigidity for the maintenance of Hsp40 function. Our results suggest that the functional J-domain acts like a semi-elliptical spring, wherein the resistance to bending upon binding to the Hsp70 ATPase modulates the ATPase domain conformational change and promotes ATP hydrolysis.
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Affiliation(s)
- Neil Andrew D Bascos
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, 70112
| | - Matthias P Mayer
- Center for Molecular Biology of the University of Heidelberg (ZMBH), Im Neuenheimer Feld 282, Heidelberg, 69120, Germany
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH), Im Neuenheimer Feld 282, Heidelberg, 69120, Germany
| | - Samuel J Landry
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, 70112
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9
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Chehab M, Caza T, Skotnicki K, Landas S, Bratslavsky G, Mollapour M, Bourboulia D. Targeting Hsp90 in urothelial carcinoma. Oncotarget 2015; 6:8454-73. [PMID: 25909217 PMCID: PMC4496161 DOI: 10.18632/oncotarget.3502] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/09/2015] [Indexed: 02/06/2023] Open
Abstract
Urothelial carcinoma, or transitional cell carcinoma, is the most common urologic malignancy that carries significant morbidity, mortality, recurrence risk and associated health care costs. Despite use of current chemotherapies and immunotherapies, long-term remission in patients with muscle-invasive or metastatic disease remains low, and disease recurrence is common. The molecular chaperone Heat Shock Protein-90 (Hsp90) may offer an ideal treatment target, as it is a critical signaling hub in urothelial carcinoma pathogenesis and potentiates chemoradiation. Preclinical testing with Hsp90 inhibitors has demonstrated reduced proliferation, enhanced apoptosis and synergism with chemotherapies and radiation. Despite promising preclinical data, clinical trials utilizing Hsp90 inhibitors for other malignancies had modest efficacy. Therefore, we propose that Hsp90 inhibition would best serve as an adjuvant treatment in advanced muscle-invasive or metastatic bladder cancers to potentiate other therapies. An overview of bladder cancer biology, current treatments, molecular targeted therapies, and the role for Hsp90 inhibitors in the treatment of urothelial carcinoma is the focus of this review.
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MESH Headings
- Angiogenesis Inhibitors/therapeutic use
- Antineoplastic Agents/therapeutic use
- Apoptosis
- BCG Vaccine/therapeutic use
- Carcinoma, Transitional Cell/epidemiology
- Carcinoma, Transitional Cell/metabolism
- Carcinoma, Transitional Cell/pathology
- Carcinoma, Transitional Cell/therapy
- Cell Cycle/drug effects
- Cell Division
- Cell Transformation, Neoplastic
- Chemoradiotherapy
- Chemotherapy, Adjuvant
- Clinical Trials as Topic
- Combined Modality Therapy
- Cystectomy
- Drug Resistance, Neoplasm
- Drugs, Investigational/therapeutic use
- HSP90 Heat-Shock Proteins/antagonists & inhibitors
- HSP90 Heat-Shock Proteins/chemistry
- HSP90 Heat-Shock Proteins/physiology
- Histone Code/drug effects
- Humans
- Models, Biological
- Molecular Targeted Therapy
- Muscle, Smooth/pathology
- Neoplasm Invasiveness
- Neoplasm Proteins/antagonists & inhibitors
- Neoplasm Proteins/physiology
- Protein Kinase Inhibitors/therapeutic use
- Signal Transduction/drug effects
- Transcription, Genetic/drug effects
- Urologic Neoplasms/epidemiology
- Urologic Neoplasms/metabolism
- Urologic Neoplasms/pathology
- Urologic Neoplasms/therapy
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Affiliation(s)
- Mahmoud Chehab
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Tiffany Caza
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Kamil Skotnicki
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Steve Landas
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Gennady Bratslavsky
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Research Institute, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Research Institute, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Research Institute, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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10
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Burmann BM, Hiller S. Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:41-64. [PMID: 25919198 DOI: 10.1016/j.pnmrs.2015.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/19/2015] [Accepted: 02/19/2015] [Indexed: 05/20/2023]
Abstract
The majority of proteins depend on a well-defined three-dimensional structure to obtain their functionality. In the cellular environment, the process of protein folding is guided by molecular chaperones to avoid misfolding, aggregation, and the generation of toxic species. To this end, living cells contain complex networks of molecular chaperones, which interact with substrate polypeptides by a multitude of different functionalities: transport them towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver them towards a proteolysis machinery. Despite the availability of high-resolution crystal structures of many important chaperones in their substrate-free apo forms, structural information about how substrates are bound by chaperones and how they are protected from misfolding and aggregation is very sparse. This lack of information arises from the highly dynamic nature of chaperone-substrate complexes, which so far has largely hindered their crystallization. This highly dynamic nature makes chaperone-substrate complexes good targets for NMR spectroscopy. Here, we review the results achieved by NMR spectroscopy to understand chaperone function in general and details of chaperone-substrate interactions in particular. We assess the information content and applicability of different NMR techniques for the characterization of chaperones and chaperone-substrate complexes. Finally, we highlight three recent studies, which have provided structural descriptions of chaperone-substrate complexes at atomic resolution.
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Affiliation(s)
- Björn M Burmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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11
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Wang Y, Lin S, Song Q, Li K, Tao H, Huang J, Chen X, Que S, He H. Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study. BMC Genomics 2014; 15:344. [PMID: 24884676 PMCID: PMC4035072 DOI: 10.1186/1471-2164-15-344] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/28/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Heat shock proteins (Hsps) perform a fundamental role in protecting plants against abiotic stresses. Although researchers have made great efforts on the functional analysis of individual family members, Hsps have not been fully characterized in rice (Oryza sativa L.) and little is known about their interactors. RESULTS In this study, we combined orthology-based approach with expression association data to screen rice Hsps for the expression patterns of which strongly correlated with that of heat responsive probe-sets. Twenty-seven Hsp candidates were identified, including 12 small Hsps, six Hsp70s, three Hsp60s, three Hsp90s, and three clpB/Hsp100s. Then, using a combination of interolog and expression profile-based methods, we inferred 430 interactors of Hsp70s in rice, and validated the interactions by co-localization and function-based methods. Subsequent analysis showed 13 interacting domains and 28 target motifs were over-represented in Hsp70s interactors. Twenty-four GO terms of biological processes and five GO terms of molecular functions were enriched in the positive interactors, whose expression levels were positively associated with Hsp70s. Hsp70s interaction network implied that Hsp70s were involved in macromolecular translocation, carbohydrate metabolism, innate immunity, photosystem II repair and regulation of kinase activities. CONCLUSIONS Twenty-seven Hsps in rice were identified and 430 interactors of Hsp70s were inferred and validated, then the interacting network of Hsp70s was induced and the function of Hsp70s was analyzed. Furthermore, two databases named Rice Heat Shock Proteins (RiceHsps) and Rice Gene Expression Profile (RGEP), and one online tool named Protein-Protein Interaction Predictor (PPIP), were constructed and could be accessed at http://bioinformatics.fafu.edu.cn/.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Huaqin He
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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12
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Stark JL, Mehla K, Chaika N, Acton TB, Xiao R, Singh PK, Montelione GT, Powers R. Structure and function of human DnaJ homologue subfamily a member 1 (DNAJA1) and its relationship to pancreatic cancer. Biochemistry 2014; 53:1360-72. [PMID: 24512202 PMCID: PMC3985919 DOI: 10.1021/bi401329a] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Pancreatic cancer has a dismal 5 year survival rate of 5.5% that has not been improved over the past 25 years despite an enormous amount of effort. Thus, there is an urgent need to identify truly novel yet druggable protein targets for drug discovery. The human protein DnaJ homologue subfamily A member 1 (DNAJA1) was previously shown to be downregulated 5-fold in pancreatic cancer cells and has been targeted as a biomarker for pancreatic cancer, but little is known about the specific biological function for DNAJA1 or the other members of the DnaJ family encoded in the human genome. Our results suggest the overexpression of DNAJA1 suppresses the stress response capabilities of the oncogenic transcription factor, c-Jun, and results in the diminution of cell survival. DNAJA1 likely activates a DnaK protein by forming a complex that suppresses the JNK pathway, the hyperphosphorylation of c-Jun, and the anti-apoptosis state found in pancreatic cancer cells. A high-quality nuclear magnetic resonance solution structure of the J-domain of DNAJA1 combined with a bioinformatics analysis and a ligand affinity screen identifies a potential DnaK binding site, which is also predicted to overlap with an inhibitory binding site, suggesting DNAJA1 activity is highly regulated.
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Affiliation(s)
- Jaime L Stark
- Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
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Ho SW, Tsui YTC, Wong TT, Cheung SKK, Goggins WB, Yi LM, Cheng KK, Baum L. Effects of 17-allylamino-17-demethoxygeldanamycin (17-AAG) in transgenic mouse models of frontotemporal lobar degeneration and Alzheimer's disease. Transl Neurodegener 2013; 2:24. [PMID: 24344631 PMCID: PMC3878847 DOI: 10.1186/2047-9158-2-24] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 12/13/2013] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD), the most common dementia, is characterized by potentially neurotoxic aggregation of Aβ peptide and tau protein, and their deposition as amyloid plaques and neurofibrillary tangles (NFTs). Tau aggregation also occurs in other common neurodegenerative diseases. Frontotemporal dementia (FTD) can be caused by tau mutations that increase the susceptibility of tau to hyperphosphorylation and aggregation, which may cause neuronal dysfunction and deposition of NFTs. 17-allylamino-17-demethoxygeldanamycin (17-AAG) is a potent inhibitor of heat shock protein 90 (Hsp90), a cytosolic chaperone implicated in the proper folding and functions of a repertoire of client proteins. 17-AAG binds to Hsp90 and enhances degradation of Hsp90 client protein. We sought to determine whether 17-AAG can reduce Aβ and tau pathology in the brains of AD and FTD model mice expressing Aβ or P301L mutant tau, respectively. Mice were randomized to receive 25, 5, or 0 mg/kg 17-AAG thrice weekly from age eight to 11 months. Analysis was performed by rotarod test on motor function, on the area occupied by plaques in hippocampus or NFTs in medulla tissue sections, and on mortality. A high dose of 17-AAG tended to decrease NFTs in male mice (p = 0.08). Further studies are required to confirm the effect of 17-AAG in diseases of tau aggregation.
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Affiliation(s)
| | | | | | | | | | | | | | - Larry Baum
- School of Pharmacy, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Rippey C, Walsh T, Gulsuner S, Brodsky M, Nord AS, Gasperini M, Pierce S, Spurrell C, Coe BP, Krumm N, Lee MK, Sebat J, McClellan JM, King MC. Formation of chimeric genes by copy-number variation as a mutational mechanism in schizophrenia. Am J Hum Genet 2013; 93:697-710. [PMID: 24094746 PMCID: PMC3791253 DOI: 10.1016/j.ajhg.2013.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 08/15/2013] [Accepted: 09/10/2013] [Indexed: 12/28/2022] Open
Abstract
Chimeric genes can be caused by structural genomic rearrangements that fuse together portions of two different genes to create a novel gene. We hypothesize that brain-expressed chimeras may contribute to schizophrenia. Individuals with schizophrenia and control individuals were screened genome wide for copy-number variants (CNVs) that disrupted two genes on the same DNA strand. Candidate events were filtered for predicted brain expression and for frequency < 0.001 in an independent series of 20,000 controls. Four of 124 affected individuals and zero of 290 control individuals harbored such events (p = 0.002); a 47 kb duplication disrupted MATK and ZFR2, a 58 kb duplication disrupted PLEKHD1 and SLC39A9, a 121 kb duplication disrupted DNAJA2 and NETO2, and a 150 kb deletion disrupted MAP3K3 and DDX42. Each fusion produced a stable protein when exogenously expressed in cultured cells. We examined whether these chimeras differed from their parent genes in localization, regulation, or function. Subcellular localizations of DNAJA2-NETO2 and MAP3K3-DDX42 differed from their parent genes. On the basis of the expression profile of the MATK promoter, MATK-ZFR2 is likely to be far more highly expressed in the brain during development than the ZFR2 parent gene. MATK-ZFR2 includes a ZFR2-derived isoform that we demonstrate localizes preferentially to neuronal dendritic branch sites. These results suggest that the formation of chimeric genes is a mechanism by which CNVs contribute to schizophrenia and that, by interfering with parent gene function, chimeras may disrupt critical brain processes, including neurogenesis, neuronal differentiation, and dendritic arborization.
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Affiliation(s)
- Caitlin Rippey
- Departments of Medicine and of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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15
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Zuiderweg ERP, Bertelsen EB, Rousaki A, Mayer MP, Gestwicki JE, Ahmad A. Allostery in the Hsp70 chaperone proteins. Top Curr Chem (Cham) 2013; 328:99-153. [PMID: 22576356 PMCID: PMC3623542 DOI: 10.1007/128_2012_323] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Heat shock 70-kDa (Hsp70) chaperones are essential to in vivo protein folding, protein transport, and protein re-folding. They carry out these activities using repeated cycles of binding and release of client proteins. This process is under allosteric control of nucleotide binding and hydrolysis. X-ray crystallography, NMR spectroscopy, and other biophysical techniques have contributed much to the understanding of the allosteric mechanism linking these activities and the effect of co-chaperones on this mechanism. In this chapter these findings are critically reviewed. Studies on the allosteric mechanisms of Hsp70 have gained enhanced urgency, as recent studies have implicated this chaperone as a potential drug target in diseases such as Alzheimer's and cancer. Recent approaches to combat these diseases through interference with the Hsp70 allosteric mechanism are discussed.
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Affiliation(s)
- Erik R P Zuiderweg
- Department of Biological Chemistry, The University of Michigan, Ann Arbor, MI 48109, USA.
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16
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Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex employs an unusual dynamic interface. Proc Natl Acad Sci U S A 2011; 108:18966-71. [PMID: 22065753 DOI: 10.1073/pnas.1111220108] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The heat shock protein 70 kDa (Hsp70)/DnaJ/nucleotide exchange factor system assists in intracellular protein (re)folding. Using solution NMR, we obtained a three-dimensional structure for a 75-kDa Hsp70-DnaJ complex in the ADP state, loaded with substrate peptide. We establish that the J domain (residues 1-70) binds with its positively charged helix II to a negatively charged loop in the Hsp70 nucleotide-binding domain. The complex shows an unusual "tethered" binding mode which is stoichiometric and saturable, but which has a dynamic interface. The complex represents part of a triple complex of Hsp70 and DnaJ both bound to substrate protein. Mutagenesis data indicate that the interface is also of relevance for the interaction of Hsp70 and DnaJ in the ATP state. The solution complex is completely different from a crystal structure of a disulfide-linked complex of homologous proteins [Jiang, et al. (2007) Mol Cell 28:422-433].
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Sterrenberg JN, Blatch GL, Edkins AL. Human DNAJ in cancer and stem cells. Cancer Lett 2011; 312:129-42. [PMID: 21925790 DOI: 10.1016/j.canlet.2011.08.019] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 07/15/2011] [Accepted: 08/17/2011] [Indexed: 12/12/2022]
Abstract
The heat shock protein 40kDa (HSP40/DNAJ) co-chaperones constitute the largest and most diverse sub-group of the heat shock protein (HSP) family. DNAJ are widely accepted as regulators of HSP70 function, but also have roles as co-chaperones for the HSP90 chaperone machine, and a growing number of biological functions that may be independent of either of these chaperones. The DNAJ proteins are differentially expressed in human tissues and demonstrate the capacity to function to both promote and suppress cancer development by acting as chaperones for tumour suppressors or oncoproteins. We review the current literature on the function and expression of DNAJ in cancer, stem cells and cancer stem cells. Combining data from gene expression, proteomics and studies in other systems, we propose that DNAJ will be key regulators of cancer, stem cell and possibly cancer stem cell function. The diversity of DNAJ and their assorted roles in a range of biological functions means that selected DNAJ, provided there is limited redundancy and that a specific link to malignancy can be established, may yet provide an attractive target for specific and selective drug design for the development of anti-cancer treatments.
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Affiliation(s)
- Jason N Sterrenberg
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, Grahamstown South Africa
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