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Paredes F, Williams HC, Liu X, Holden C, Bogan B, Wang Y, Crotty KM, Yeligar SM, Elorza AA, Lin Z, Rezvan A, San Martin A. The mitochondrial protease ClpP is a druggable target that controls VSMC phenotype by a SIRT1-dependent mechanism. Redox Biol 2024; 73:103203. [PMID: 38823208 DOI: 10.1016/j.redox.2024.103203] [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: 02/19/2024] [Revised: 05/12/2024] [Accepted: 05/20/2024] [Indexed: 06/03/2024] Open
Abstract
Vascular smooth muscle cells (VSMCs), known for their remarkable lifelong phenotypic plasticity, play a pivotal role in vascular pathologies through their ability to transition between different phenotypes. Our group discovered that the deficiency of the mitochondrial protein Poldip2 induces VSMC differentiation both in vivo and in vitro. Further comprehensive biochemical investigations revealed Poldip2's specific interaction with the mitochondrial ATPase caseinolytic protease chaperone subunit X (CLPX), which is the regulatory subunit for the caseinolytic protease proteolytic subunit (ClpP) that forms part of the ClpXP complex - a proteasome-like protease evolutionarily conserved from bacteria to humans. This interaction limits the protease's activity, and reduced Poldip2 levels lead to ClpXP complex activation. This finding prompted the hypothesis that ClpXP complex activity within the mitochondria may regulate the VSMC phenotype. Employing gain-of-function and loss-of-function strategies, we demonstrated that ClpXP activity significantly influences the VSMC phenotype. Notably, both genetic and pharmacological activation of ClpXP inhibits VSMC plasticity and fosters a quiescent, differentiated, and anti-inflammatory VSMC phenotype. The pharmacological activation of ClpP using TIC10, currently in phase III clinical trials for cancer, successfully replicates this phenotype both in vitro and in vivo and markedly reduces aneurysm development in a mouse model of elastase-induced aortic aneurysms. Our mechanistic exploration indicates that ClpP activation regulates the VSMC phenotype by modifying the cellular NAD+/NADH ratio and activating Sirtuin 1. Our findings reveal the crucial role of mitochondrial proteostasis in the regulation of the VSMC phenotype and propose the ClpP protease as a novel, actionable target for manipulating the VSMC phenotype.
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Affiliation(s)
- Felipe Paredes
- Department of Medicine, Division of Cardiology, Emory University, Atlanta, GA, United States
| | - Holly C Williams
- Department of Medicine, Division of Cardiology, Emory University, Atlanta, GA, United States
| | - Xuesong Liu
- Department of Medicine, Division of Cardiology, Emory University, Atlanta, GA, United States; Department of Cardiology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Claire Holden
- Department of Medicine, Division of Cardiology, Emory University, Atlanta, GA, United States
| | - Bethany Bogan
- Department of Medicine, Division of Cardiology, Emory University, Atlanta, GA, United States
| | - Yu Wang
- Department of Medicine, Division of Cardiology, Emory University, Atlanta, GA, United States
| | - Kathryn M Crotty
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, United States; Atlanta Veterans Affairs Health Care System, Decatur, GA, United States
| | - Samantha M Yeligar
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, United States; Atlanta Veterans Affairs Health Care System, Decatur, GA, United States
| | - Alvaro A Elorza
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Zhiyong Lin
- Department of Medicine, Division of Cardiology, Emory University, Atlanta, GA, United States
| | - Amir Rezvan
- Department of Medicine, Division of Cardiology, Emory University, Atlanta, GA, United States
| | - Alejandra San Martin
- Department of Medicine, Division of Cardiology, Emory University, Atlanta, GA, United States; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
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Xu X, Wang Y, Huang W, Li D, Deng Z, Long F. Structural insights into the Clp protein degradation machinery. mBio 2024; 15:e0003124. [PMID: 38501868 PMCID: PMC11005422 DOI: 10.1128/mbio.00031-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
The Clp protease system is important for maintaining proteostasis in bacteria. It consists of ClpP serine proteases and an AAA+ Clp-ATPase such as ClpC1. The hexameric ATPase ClpC1 utilizes the energy of ATP binding and hydrolysis to engage, unfold, and translocate substrates into the proteolytic chamber of homo- or hetero-tetradecameric ClpP for degradation. The assembly between the hetero-tetradecameric ClpP1P2 chamber and the Clp-ATPases containing tandem ATPase domains from the same species has not been studied in depth. Here, we present cryo-EM structures of the substrate-bound ClpC1:shClpP1P2 from Streptomyces hawaiiensis, and shClpP1P2 in complex with ADEP1, a natural compound produced by S. hawaiiensis and known to cause over-activation and dysregulation of the ClpP proteolytic core chamber. Our structures provide detailed information on the shClpP1-shClpP2, shClpP2-ClpC1, and ADEP1-shClpP1/P2 interactions, reveal conformational transition of ClpC1 during the substrate translocation, and capture a rotational ATP hydrolysis mechanism likely dominated by the D1 ATPase activity of chaperones.IMPORTANCEThe Clp-dependent proteolysis plays an important role in bacterial homeostasis and pathogenesis. The ClpP protease system is an effective drug target for antibacterial therapy. Streptomyces hawaiiensis can produce a class of potent acyldepsipeptide antibiotics such as ADEP1, which could affect the ClpP protease activity. Although S. hawaiiensis hosts one of the most intricate ClpP systems in nature, very little was known about its Clp protease mechanism and the impact of ADEP molecules on ClpP. The significance of our research is in dissecting the functional mechanism of the assembled Clp degradation machinery, as well as the interaction between ADEP1 and the ClpP proteolytic chamber, by solving high-resolution structures of the substrate-bound Clp system in S. hawaiiensis. The findings shed light on our understanding of the Clp-dependent proteolysis in bacteria, which will enhance the development of antimicrobial drugs targeting the Clp protease system, and help fighting against bacterial multidrug resistance.
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Affiliation(s)
- Xiaolong Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yanhui Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Wei Huang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Danyang Li
- Cryo-EM Center and the Core Facility of Wuhan University, Wuhan, China
| | - Zixin Deng
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Feng Long
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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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:e0017622. [PMID: 38534118 DOI: 10.1128/mmbr.00176-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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Illigmann A, Vielberg MT, Lakemeyer M, Wolf F, Dema T, Stange P, Kuttenlochner W, Liebhart E, Kulik A, Staudt ND, Malik I, Grond S, Sieber SA, Kaysser L, Groll M, Brötz-Oesterhelt H. Structure of Staphylococcus aureus ClpP Bound to the Covalent Active-Site Inhibitor Cystargolide A. Angew Chem Int Ed Engl 2024; 63:e202314028. [PMID: 38029352 DOI: 10.1002/anie.202314028] [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: 09/19/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023]
Abstract
The caseinolytic protease is a highly conserved serine protease, crucial to prokaryotic and eukaryotic protein homeostasis, and a promising antibacterial and anticancer drug target. Herein, we describe the potent cystargolides as the first natural β-lactone inhibitors of the proteolytic core ClpP. Based on the discovery of two clpP genes next to the cystargolide biosynthetic gene cluster in Kitasatospora cystarginea, we explored ClpP as a potential cystargolide target. We show the inhibition of Staphylococcus aureus ClpP by cystargolide A and B by different biochemical methods in vitro. Synthesis of semisynthetic derivatives and probes with improved cell penetration allowed us to confirm ClpP as a specific target in S. aureus cells and to demonstrate the anti-virulence activity of this natural product class. Crystal structures show cystargolide A covalently bound to all 14 active sites of ClpP from S. aureus, Aquifex aeolicus, and Photorhabdus laumondii, and reveal the molecular mechanism of ClpP inhibition by β-lactones, the predominant class of ClpP inhibitors.
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Affiliation(s)
- Astrid Illigmann
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Marie-Theres Vielberg
- Chair of Biochemistry, Centre for Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Strasse 8, 85748, Garching, Germany
| | - Markus Lakemeyer
- Chair of Organic Chemistry II, Technical University Munich, School of Natural Sciences, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Straße 8/I, 85748, Garching b.München, Germany
- Current address: Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany
| | - Felix Wolf
- Synthetic Biology of Anti-infective Agents, Pharmaceutical Institute, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Taulant Dema
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Patrik Stange
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Wolfgang Kuttenlochner
- Chair of Biochemistry, Centre for Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Strasse 8, 85748, Garching, Germany
| | - Elisa Liebhart
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Andreas Kulik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Nicole D Staudt
- Synthetic Biology of Anti-infective Agents, Pharmaceutical Institute, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Imran Malik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Stephan A Sieber
- Chair of Organic Chemistry II, Technical University Munich, School of Natural Sciences, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Straße 8/I, 85748, Garching b.München, Germany
| | - Leonard Kaysser
- Synthetic Biology of Anti-infective Agents, Pharmaceutical Institute, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- Pharmazeutische Biologie, Institut für Wirkstoffentwicklung, Universitätsklinikum Leipzig, Eilenburger Strasse 15a, 04317, Leipzig, Germany
| | - Michael Groll
- Chair of Biochemistry, Centre for Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Strasse 8, 85748, Garching, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- Cluster of Excellence Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
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5
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Bhardwaj S, Roy KK. ClpP Peptidase as a Plausible Target for the Discovery of Novel Antibiotics. Curr Drug Targets 2024; 25:108-120. [PMID: 38151841 DOI: 10.2174/0113894501274958231220053714] [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: 07/31/2023] [Revised: 11/16/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Antimicrobial resistance (AMR) to currently available antibiotics/drugs is a global threat. It is desirable to develop new drugs that work through a novel target(s) to avoid drug resistance. This review discusses the potential of the caseinolytic protease P (ClpP) peptidase complex as a novel target for finding novel antibiotics, emphasising the ClpP's structure and function. ClpP contributes to the survival of bacteria via its ability to destroy misfolded or aggregated proteins. In consequence, its inhibition may lead to microbial death. Drugs inhibiting ClpP activity are currently being tested, but no drug against this target has been approved yet. It was demonstrated that Nblocked dipeptides are essential for activating ClpP's proteolytic activity. Hence, compounds mimicking these dipeptides could act as inhibitors of the formation of an active ClpP complex. Drugs, including Bortezomib, Cisplatin, Cefmetazole, and Ixazomib, inhibit ClpP activation. However, they were not approved as drugs against the target because of their high toxicity, likely due to the presence of strong electrophiles in their warheads. The modifications of these warheads could be a good strategy to reduce the toxicity of these molecules. For instance, a boronate warhead was replaced by a chloromethyl ketone, and this new molecule was shown to exhibit selectivity for prokaryotic ClpP. A better understanding of the structure and function of the ClpP complex would benefit the search for compounds mimicking N-blocked dipeptides that would inhibit ClpP complex activity and cause bacterial death.
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Affiliation(s)
- Smriti Bhardwaj
- School of Health Sciences and Technology, UPES, Dehradun - 248007, Uttarakhand, India
| | - Kuldeep K Roy
- School of Health Sciences and Technology, UPES, Dehradun - 248007, Uttarakhand, India
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6
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Ishikawa F, Homma M, Tanabe G, Uchihashi T. [Protein degradation in bacteria: focus on the ClpP protease]. Nihon Saikingaku Zasshi 2024; 79:1-13. [PMID: 38382970 DOI: 10.3412/jsb.79.1] [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: 02/23/2024]
Abstract
Proteins in the cells are born (synthesized), work, and die (decomposed). In the life of a protein, its birth is obviously important, but how it dies is equally important in living organisms. Proteases secreted into the outside of cells are used to decompose the external proteins and the degradation products are taken as the nutrients. On the other hand, there are also proteases that decompose unnecessary or harmful proteins which are generated in the cells. In eukaryotes, a large enzyme complex called the proteasome is primarily responsible for degradation of such proteins. Bacteria, which are prokaryotes, have a similar system as the proteasome. We would like to explain the bacterial degradation system of proteins or the death of proteins, which is performed by ATP-dependent protease Clp, with a particular focus on the ClpXP complex, and with an aspect as a target for antibiotics against bacteria.
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Affiliation(s)
| | - Michio Homma
- Division of Physics, Graduate School of Science, Nagoya University
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Yang Y, Zhao N, Xu X, Zhou Y, Luo B, Zhang J, Sui J, Huang J, Qiu Z, Zhang X, Zeng J, Bai L, Bao R, Luo Y. Discovery and Mechanistic Study of Novel Mycobacterium tuberculosis ClpP1P2 Inhibitors. J Med Chem 2023; 66:16597-16614. [PMID: 38088921 DOI: 10.1021/acs.jmedchem.3c01054] [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: 12/29/2023]
Abstract
Caseinolytic protease P (ClpP) responsible for the proteolysis of damaged or misfolded proteins plays a critical role in proteome homeostasis. MtbClpP1P2, a ClpP enzyme complex, is required for survival in Mycobacterium tuberculosis, and it is therefore considered as a promising target for the development of antituberculosis drugs. Here, we discovered that cediranib and some of its derivatives are potent MtbClpP1P2 inhibitors and suppress M. tuberculosis growth. Protein pull-down and loss-of-function assays validated the in situ targeting of MtbClpP1P2 by cediranib and its active derivatives. Structural and mutational studies revealed that cediranib binds to MtbClpP1P2 by binding to an allosteric pocket at the equatorial handle domain of the MtbClpP1 subunit, which represents a unique binding mode compared to other known ClpP modulators. These findings provide us insights for rational drug design of antituberculosis therapies and implications for our understanding of the biological activity of MtbClpP1P2.
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Affiliation(s)
- Yang Yang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
- Capital Institute of Pediatrics, Beijing 100020, PR China
| | - Ninglin Zhao
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Xin Xu
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yuanzheng Zhou
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Baozhu Luo
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Jiangnan Zhang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Jing Sui
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Jiasheng Huang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Zhiqiang Qiu
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Xuelian Zhang
- School of Life Science, Fudan University, Shanghai 200438, PR China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Lang Bai
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Rui Bao
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Youfu Luo
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
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8
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Key J, Gispert S, Koepf G, Steinhoff-Wagner J, Reichlmeir M, Auburger G. Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling. Int J Mol Sci 2023; 24:17503. [PMID: 38139332 PMCID: PMC10743472 DOI: 10.3390/ijms242417503] [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: 11/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The mitochondrial matrix peptidase CLPP is crucial during cell stress. Its loss causes Perrault syndrome type 3 (PRLTS3) with infertility, neurodegeneration, and a growth deficit. Its target proteins are disaggregated by CLPX, which also regulates heme biosynthesis via unfolding ALAS enzymes, providing access for pyridoxal-5'-phosphate (PLP). Despite efforts in diverse organisms with multiple techniques, CLPXP substrates remain controversial. Here, avoiding recombinant overexpression, we employed complexomics in mitochondria from three mouse tissues to identify endogenous targets. A CLPP absence caused the accumulation and dispersion of CLPX-VWA8 as AAA+ unfoldases, and of PLPBP. Similar changes and CLPX-VWA8 co-migration were evident for mitoribosomal central protuberance clusters, translation factors like GFM1-HARS2, the RNA granule components LRPPRC-SLIRP, and enzymes OAT-ALDH18A1. Mitochondrially translated proteins in testes showed reductions to <30% for MTCO1-3, the mis-assembly of the complex IV supercomplex, and accumulated metal-binding assembly factors COX15-SFXN4. Indeed, heavy metal levels were increased for iron, molybdenum, cobalt, and manganese. RT-qPCR showed compensatory downregulation only for Clpx mRNA; most accumulated proteins appeared transcriptionally upregulated. Immunoblots validated VWA8, MRPL38, MRPL18, GFM1, and OAT accumulation. Co-immunoprecipitation confirmed CLPX binding to MRPL38, GFM1, and OAT, so excess CLPX and PLP may affect their activity. Our data mechanistically elucidate the mitochondrial translation fidelity deficits which underlie progressive hearing impairment in PRLTS3.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Julia Steinhoff-Wagner
- TUM School of Life Sciences, Animal Nutrition and Metabolism, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising-Weihenstephan, Germany;
| | - Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
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9
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Obaha A, Novinec M. Regulation of Peptidase Activity beyond the Active Site in Human Health and Disease. Int J Mol Sci 2023; 24:17120. [PMID: 38069440 PMCID: PMC10707025 DOI: 10.3390/ijms242317120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
This comprehensive review addresses the intricate and multifaceted regulation of peptidase activity in human health and disease, providing a comprehensive investigation that extends well beyond the boundaries of the active site. Our review focuses on multiple mechanisms and highlights the important role of exosites, allosteric sites, and processes involved in zymogen activation. These mechanisms play a central role in shaping the complex world of peptidase function and are promising potential targets for the development of innovative drugs and therapeutic interventions. The review also briefly discusses the influence of glycosaminoglycans and non-inhibitory binding proteins on enzyme activities. Understanding their role may be a crucial factor in the development of therapeutic strategies. By elucidating the intricate web of regulatory mechanisms that control peptidase activity, this review deepens our understanding in this field and provides a roadmap for various strategies to influence and modulate peptidase activity.
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Affiliation(s)
| | - Marko Novinec
- Faculty of Chemistry and Chemical Technology, Department of Chemistry and Biochemistry, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia;
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10
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Petkov R, Camp AH, Isaacson RL, Torpey JH. Targeting bacterial degradation machinery as an antibacterial strategy. Biochem J 2023; 480:1719-1731. [PMID: 37916895 PMCID: PMC10657178 DOI: 10.1042/bcj20230191] [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: 05/16/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 11/03/2023]
Abstract
The exploitation of a cell's natural degradation machinery for therapeutic purposes is an exciting research area in its infancy with respect to bacteria. Here, we review current strategies targeting the ClpCP system, which is a proteolytic degradation complex essential in the biology of many bacterial species of scientific interest. Strategies include using natural product antibiotics or acyldepsipeptides to initiate the up- or down-regulation of ClpCP activity. We also examine exciting recent forays into BacPROTACs to trigger the degradation of specific proteins of interest through the hijacking of the ClpCP machinery. These strategies represent an important emerging avenue for combatting antimicrobial resistance.
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Affiliation(s)
- Radoslav Petkov
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Amy H. Camp
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, Massachusetts 01075, U.S.A
| | - Rivka L. Isaacson
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - James H. Torpey
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
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11
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Tomaszkiewicz M, Sahlin K, Medvedev P, Makova KD. Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes. Genome Biol Evol 2023; 15:evad205. [PMID: 37967251 PMCID: PMC10673640 DOI: 10.1093/gbe/evad205] [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: 04/14/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023] Open
Abstract
Y chromosomal ampliconic genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been studied in great apes; however, the diversity of splicing variants remains unexplored. Here, we deciphered the sequences of polyadenylated transcripts of all nine YAG families (BPY2, CDY, DAZ, HSFY, PRY, RBMY, TSPY, VCY, and XKRY) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this data set resulted in several findings. First, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for BPY2 and PRY. Second, our results suggest that BPY2 transcripts and proteins originate from separate genomic regions in bonobo versus human, which is possibly facilitated by acquiring new promoters. Third, our analysis indicates that the PRY gene family, having the highest representation of noncoding transcripts, has been undergoing pseudogenization. Fourth, we have not detected signatures of selection in the five YAG families shared among great apes, even though we identified many species-specific protein-coding transcripts. Fifth, we predicted consensus disorder regions across most gene families and species, which could be used for future investigations of male infertility. Overall, our work illuminates the YAG isoform landscape and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.
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Affiliation(s)
- Marta Tomaszkiewicz
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kristoffer Sahlin
- Department of Mathematics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Paul Medvedev
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Computational Biology and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kateryna D Makova
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Computational Biology and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
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12
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Walther R, Westermann LM, Carmali S, Jackson SE, Brötz-Oesterhelt H, Spring DR. Identification of macrocyclic peptides which activate bacterial cylindrical proteases. RSC Med Chem 2023; 14:1186-1191. [PMID: 37360394 PMCID: PMC10285738 DOI: 10.1039/d3md00136a] [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: 03/22/2023] [Accepted: 05/15/2023] [Indexed: 06/28/2023] Open
Abstract
The caseinolytic protease complex ClpXP is an important house-keeping enzyme in prokaryotes charged with the removal and degradation of misfolded and aggregated proteins and performing regulatory proteolysis. Dysregulation of its function, particularly by inhibition or allosteric activation of the proteolytic core ClpP, has proven to be a promising strategy to reduce virulence and eradicate persistent bacterial infections. Here, we report a rational drug-design approach to identify macrocyclic peptides which increase proteolysis by ClpP. This work expands the understanding of ClpP dynamics and sheds light on the conformational control exerted by its binding partner, the chaperone ClpX, by means of a chemical approach. The identified macrocyclic peptide ligands may, in the future, serve as a starting point for the development of ClpP activators for antibacterial applications.
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Affiliation(s)
- Raoul Walther
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Linda M Westermann
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Bioactive Compounds, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Sheiliza Carmali
- School of Pharmacy, Queen's University Belfast BT9 7BL Belfast UK
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Bioactive Compounds, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence Controlling Microbes to Fight Infections Germany
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
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13
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Daglish SCD, Fennell EMJ, Graves LM. Targeting Mitochondrial DNA Transcription by POLRMT Inhibition or Depletion as a Potential Strategy for Cancer Treatment. Biomedicines 2023; 11:1598. [PMID: 37371693 DOI: 10.3390/biomedicines11061598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Transcription of the mitochondrial genome is essential for the maintenance of oxidative phosphorylation (OXPHOS) and other functions directly related to this unique genome. Considerable evidence suggests that mitochondrial transcription is dysregulated in cancer and cancer metastasis and contributes significantly to cancer cell metabolism. Recently, inhibitors of the mitochondrial DNA-dependent RNA polymerase (POLRMT) were identified as potentially attractive new anti-cancer compounds. These molecules (IMT1, IMT1B) inactivate cancer cell metabolism through reduced transcription of mitochondrially-encoded OXPHOS subunits such as ND1-5 (Complex I) and COI-IV (Complex IV). Studies from our lab have discovered small molecule regulators of the mitochondrial matrix caseinolytic protease (ClpP) as probable inhibitors of mitochondrial transcription. These compounds activate ClpP proteolysis and lead to the rapid depletion of POLRMT and other matrix proteins, resulting in inhibition of mitochondrial transcription and growth arrest. Herein we present a comparison of POLRMT inhibition and ClpP activation, both conceptually and experimentally, and evaluate the results of these treatments on mitochondrial transcription, inhibition of OXPHOS, and ultimately cancer cell growth. We discuss the potential for targeting mitochondrial transcription as a cancer cell vulnerability.
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Affiliation(s)
- Sabrina C D Daglish
- Department of Pharmacology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emily M J Fennell
- Department of Pharmacology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lee M Graves
- Department of Pharmacology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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14
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Lee JW. Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms' Complex Regulation. J Microbiol 2023; 61:273-276. [PMID: 37010794 DOI: 10.1007/s12275-023-00036-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2023] [Indexed: 04/04/2023]
Affiliation(s)
- Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
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15
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Fennell EMJ, Aponte-Collazo LJ, Pathmasiri W, Rushing BR, Barker NK, Partridge MC, Li YY, White CA, Greer YE, Herring LE, Lipkowitz S, Sumner SCJ, Iwanowicz EJ, Graves LM. Multi-omics analyses reveal ClpP activators disrupt essential mitochondrial pathways in triple-negative breast cancer. Front Pharmacol 2023; 14:1136317. [PMID: 37063293 PMCID: PMC10103842 DOI: 10.3389/fphar.2023.1136317] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/27/2023] [Indexed: 04/03/2023] Open
Abstract
ClpP activators ONC201 and related small molecules (TR compounds, Madera Therapeutics), have demonstrated significant anti-cancer potential in vitro and in vivo studies, including clinical trials for refractory solid tumors. Though progress has been made in identifying specific phenotypic outcomes following ClpP activation, the exact mechanism by which ClpP activation leads to broad anti-cancer activity has yet to be fully elucidated. In this study, we utilized a multi-omics approach to identify the ClpP-dependent proteomic, transcriptomic, and metabolomic changes resulting from ONC201 or the TR compound TR-57 in triple-negative breast cancer cells. Applying mass spectrometry-based methods of proteomics and metabolomics, we identified ∼8,000 proteins and 588 metabolites, respectively. From proteomics data, 113 (ONC201) and 191 (TR-57) proteins significantly increased and 572 (ONC201) and 686 (TR-57) proteins significantly decreased in this study. Gene ontological (GO) analysis revealed strong similarities between proteins up- or downregulated by ONC201 or TR-57 treatment. Notably, this included the downregulation of many mitochondrial processes and proteins, including mitochondrial translation and mitochondrial matrix proteins. We performed a large-scale transcriptomic analysis of WT SUM159 cells, identifying ∼7,700 transcripts (746 and 1,100 significantly increasing, 795 and 1,013 significantly decreasing in ONC201 and TR-57 treated cells, respectively). Less than 21% of these genes were affected by these compounds in ClpP null cells. GO analysis of these data demonstrated additional similarity of response to ONC201 and TR-57, including a decrease in transcripts related to the mitochondrial inner membrane and matrix, cell cycle, and nucleus, and increases in other nuclear transcripts and transcripts related to metal-ion binding. Comparison of response between both compounds demonstrated a highly similar response in all -omics datasets. Analysis of metabolites also revealed significant similarities between ONC201 and TR-57 with increases in α-ketoglutarate and 2-hydroxyglutaric acid and decreased ureidosuccinic acid, L-ascorbic acid, L-serine, and cytidine observed following ClpP activation in TNBC cells. Further analysis identified multiple pathways that were specifically impacted by ClpP activation, including ATF4 activation, heme biosynthesis, and the citrulline/urea cycle. In summary the results of our studies demonstrate that ONC201 and TR-57 induce highly similar and broad effects against multiple mitochondrial processes required for cell proliferation.
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Affiliation(s)
- Emily M. J. Fennell
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lucas J. Aponte-Collazo
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Wimal Pathmasiri
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
| | - Blake R. Rushing
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
| | - Natalie K. Barker
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Michael Hooker Proteomics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Megan C. Partridge
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yuan-Yuan Li
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
| | - Cody A. White
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yoshimi E. Greer
- Women’s Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Laura E. Herring
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Michael Hooker Proteomics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stanley Lipkowitz
- Women’s Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Susan C. J. Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
| | | | - Lee M. Graves
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Lee M. Graves,
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16
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Wedam R, Greer YE, Wisniewski DJ, Weltz S, Kundu M, Voeller D, Lipkowitz S. Targeting Mitochondria with ClpP Agonists as a Novel Therapeutic Opportunity in Breast Cancer. Cancers (Basel) 2023; 15:cancers15071936. [PMID: 37046596 PMCID: PMC10093243 DOI: 10.3390/cancers15071936] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Breast cancer is the most frequently diagnosed malignancy worldwide and the leading cause of cancer mortality in women. Despite the recent development of new therapeutics including targeted therapies and immunotherapy, triple-negative breast cancer remains an aggressive form of breast cancer, and thus improved treatments are needed. In recent decades, it has become increasingly clear that breast cancers harbor metabolic plasticity that is controlled by mitochondria. A myriad of studies provide evidence that mitochondria are essential to breast cancer progression. Mitochondria in breast cancers are widely reprogrammed to enhance energy production and biosynthesis of macromolecules required for tumor growth. In this review, we will discuss the current understanding of mitochondrial roles in breast cancers and elucidate why mitochondria are a rational therapeutic target. We will then outline the status of the use of mitochondria-targeting drugs in breast cancers, and highlight ClpP agonists as emerging mitochondria-targeting drugs with a unique mechanism of action. We also illustrate possible drug combination strategies and challenges in the future breast cancer clinic.
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Affiliation(s)
- Rohan Wedam
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yoshimi Endo Greer
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Wisniewski
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah Weltz
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Manjari Kundu
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Donna Voeller
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stanley Lipkowitz
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Mabanglo MF, Wong KS, Barghash MM, Leung E, Chuang SHW, Ardalan A, Majaesic EM, Wong CJ, Zhang S, Lang H, Karanewsky DS, Iwanowicz AA, Graves LM, Iwanowicz EJ, Gingras AC, Houry WA. Potent ClpP agonists with anticancer properties bind with improved structural complementarity and alter the mitochondrial N-terminome. Structure 2023; 31:185-200.e10. [PMID: 36586405 PMCID: PMC9898158 DOI: 10.1016/j.str.2022.12.002] [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: 08/02/2022] [Revised: 11/01/2022] [Accepted: 11/29/2022] [Indexed: 12/31/2022]
Abstract
The mitochondrial ClpP protease is responsible for mitochondrial protein quality control through specific degradation of proteins involved in several metabolic processes. ClpP overexpression is also required in many cancer cells to eliminate reactive oxygen species (ROS)-damaged proteins and to sustain oncogenesis. Targeting ClpP to dysregulate its function using small-molecule agonists is a recent strategy in cancer therapy. Here, we synthesized imipridone-derived compounds and related chemicals, which we characterized using biochemical, biophysical, and cellular studies. Using X-ray crystallography, we found that these compounds have enhanced binding affinities due to their greater shape and charge complementarity with the surface hydrophobic pockets of ClpP. N-terminome profiling of cancer cells upon treatment with one of these compounds revealed the global proteomic changes that arise and identified the structural motifs preferred for protein cleavage by compound-activated ClpP. Together, our studies provide the structural and molecular basis by which dysregulated ClpP affects cancer cell viability and proliferation.
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Affiliation(s)
- Mark F Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Keith S Wong
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Marim M Barghash
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | | | - Afshan Ardalan
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Emily M Majaesic
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Shen Zhang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan 410008, China
| | - Henk Lang
- Madera Therapeutics LLC, Cary, NC 27513, USA
| | | | | | - Lee M Graves
- Department of Pharmacology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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18
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Azadmanesh J, Seleem MA, Struble L, Wood NA, Fisher DJ, Lovelace JJ, Artigues A, Fenton AW, Borgstahl GEO, Ouellette SP, Conda-Sheridan M. The structure of caseinolytic protease subunit ClpP2 reveals a functional model of the caseinolytic protease system from Chlamydia trachomatis. J Biol Chem 2023; 299:102762. [PMID: 36463962 PMCID: PMC9823225 DOI: 10.1016/j.jbc.2022.102762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
Chlamydia trachomatis (ct) is the most reported bacterial sexually transmitted infection worldwide and the leading cause of preventable blindness. Caseinolytic proteases (ClpP) from pathogenic bacteria are attractive antibiotic targets, particularly for bacterial species that form persister colonies with phenotypic resistance against common antibiotics. ClpP functions as a multisubunit proteolytic complex, and bacteria are eradicated when ClpP is disrupted. Although crucial for chlamydial development and the design of agents to treat chlamydia, the structures of ctClpP1 and ctClpP2 have yet to be solved. Here, we report the first crystal structure of full-length ClpP2 as an inactive homotetradecamer in a complex with a candidate antibiotic at 2.66 Å resolution. The structure details the functional domains of the ClpP2 protein subunit and includes the handle domain, which is integral to proteolytic activation. In addition, hydrogen-deuterium exchange mass spectroscopy probed the dynamics of ClpP2, and molecular modeling of ClpP1 predicted an assembly with ClpP2. By leveraging previous enzymatic experiments, we constructed a model of ClpP2 activation and its interaction with the protease subunits ClpP1 and ClpX. The structural information presented will be relevant for future rational drug design against these targets and will lead to a better understanding of ClpP complex formation and activation within this important human pathogen.
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Affiliation(s)
- Jahaun Azadmanesh
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Mohamed A Seleem
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska, USA
| | - Lucas Struble
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nicholas A Wood
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, Nebraska, USA
| | - Derek J Fisher
- School of Biological Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Jeffrey J Lovelace
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Antonio Artigues
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Scot P Ouellette
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, Nebraska, USA
| | - Martin Conda-Sheridan
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska, USA.
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19
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Aljghami ME, Barghash MM, Majaesic E, Bhandari V, Houry WA. Cellular functions of the ClpP protease impacting bacterial virulence. Front Mol Biosci 2022; 9:1054408. [PMID: 36533084 PMCID: PMC9753991 DOI: 10.3389/fmolb.2022.1054408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/15/2022] [Indexed: 09/28/2023] Open
Abstract
Proteostasis mechanisms significantly contribute to the sculpting of the proteomes of all living organisms. ClpXP is a central AAA+ chaperone-protease complex present in both prokaryotes and eukaryotes that facilitates the unfolding and subsequent degradation of target substrates. ClpX is a hexameric unfoldase ATPase, while ClpP is a tetradecameric serine protease. Substrates of ClpXP belong to many cellular pathways such as DNA damage response, metabolism, and transcriptional regulation. Crucially, disruption of this proteolytic complex in microbes has been shown to impact the virulence and infectivity of various human pathogenic bacteria. Loss of ClpXP impacts stress responses, biofilm formation, and virulence effector protein production, leading to decreased pathogenicity in cell and animal infection models. Here, we provide an overview of the multiple critical functions of ClpXP and its substrates that modulate bacterial virulence with examples from several important human pathogens.
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Affiliation(s)
- Mazen E. Aljghami
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Marim M. Barghash
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Emily Majaesic
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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20
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Rowland E, Kim J, Friso G, Poliakov A, Ponnala L, Sun Q, van Wijk KJ. The CLP and PREP protease systems coordinate maturation and degradation of the chloroplast proteome in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 236:1339-1357. [PMID: 35946374 DOI: 10.1111/nph.18426] [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: 05/16/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
A network of peptidases governs proteostasis in plant chloroplasts and mitochondria. This study reveals strong genetic and functional interactions in Arabidopsis between the chloroplast stromal CLP chaperone-protease system and the PREP1,2 peptidases, which are dually localized to chloroplast stroma and the mitochondrial matrix. Higher order mutants defective in CLP or PREP proteins were generated and analyzed by quantitative proteomics and N-terminal proteomics (terminal amine isotopic labeling of substrates (TAILS)). Strong synergistic interactions were observed between the CLP protease system (clpr1-2, clpr2-1, clpc1-1, clpt1, clpt2) and both PREP homologs (prep1, prep2) resulting in embryo lethality or growth and developmental phenotypes. Synergistic interactions were observed even when only one of the PREP proteins was lacking, suggesting that PREP1 and PREP2 have divergent substrates. Proteome phenotypes were driven by the loss of CLP protease capacity, with little impact from the PREP peptidases. Chloroplast N-terminal proteomes showed that many nuclear encoded chloroplast proteins have alternatively processed N-termini in prep1prep2, clpt1clpt2 and prep1prep2clpt1clpt2. Loss of chloroplast protease capacity interferes with stromal processing peptidase (SPP) activity due to folding stress and low levels of accumulated cleaved cTP fragments. PREP1,2 proteolysis of cleaved cTPs is complemented by unknown proteases. A model for CLP and PREP activity within a hierarchical chloroplast proteolysis network is proposed.
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Affiliation(s)
- Elden Rowland
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| | - Jitae Kim
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
- S-Korea Bioenergy Research Center, Chonnam National University, Gwangju, 61186, South Korea
| | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| | - Anton Poliakov
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
| | | | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, NY, 14853, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY, 14853, USA
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