1
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Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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2
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Xu X, Zhang L, Yang T, Qiu Z, Bai L, Luo Y. Targeting caseinolytic protease P and its AAA1 chaperone for tuberculosis treatment. Drug Discov Today 2023; 28:103508. [PMID: 36706830 DOI: 10.1016/j.drudis.2023.103508] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
Caseinolytic protease P with its AAA1 chaperone, known as Mycobacterium tuberculosis (Mtb)ClpP1P2 proteolytic machinery, maintains protein homeostasis in Mtb cells and is essential for bacterial survival. It is regarded as an important biological target with the potential to address the increasingly serious issue of multidrug-resistant (MDR) TB. Over the past 10 years, many MtbClpP1P2-targeted modulators have been identified and characterized, some of which have shown potent anti-TB activity. In this review, we describe current understanding of the substrates, structure and function of MtbClpP1P2, classify the modulators of this important protein machine into several categories based on their binding subunits or pockets, and discuss their binding details; Such information provides insights for use in candidate drug research and development of TB treatments by targeting MtbClpP1P2 proteolytic machinery.
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Affiliation(s)
- Xin Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhiqiang Qiu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Lang Bai
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
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3
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Schwarz M, Hübner I, Sieber SA. Tailored phenyl esters inhibit ClpXP and attenuate Staphylococcus aureus α-hemolysin secretion. Chembiochem 2022; 23:e202200253. [PMID: 35713329 PMCID: PMC9544270 DOI: 10.1002/cbic.202200253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/15/2022] [Indexed: 11/14/2022]
Abstract
Novel strategies against multidrug‐resistant bacteria are urgently needed in order to overcome the current silent pandemic. Manipulation of toxin production in pathogenic species serves as a promising approach to attenuate virulence and prevent infections. In many bacteria such as Staphylococcus aureus or Listeria monocyotgenes, serine protease ClpXP is a key contributor to virulence and thus represents a prime target for antimicrobial drug discovery. The limited stability of previous electrophilic warheads has prevented a sustained effect of virulence attenuation in bacterial culture. Here, we systematically tailor the stability and inhibitory potency of phenyl ester ClpXP inhibitors by steric shielding of the ester bond and fine‐tuning the phenol leaving group. Out of 17 derivatives, two (MAS‐19 and MAS‐30) inhibited S. aureus ClpP peptidase and ClpXP protease activities by >60 % at 1 μM. Furthermore, the novel inhibitors did not exhibit pronounced cytotoxicity against human and bacterial cells. Unlike the first generation phenylester AV170, these molecules attenuated S. aureus virulence markedly and displayed increased stability in aqueous buffer compared to the previous benchmark AV170.
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Affiliation(s)
- Markus Schwarz
- Technical University Munich: Technische Universitat Munchen, Chemistry, Ernst-Otto-Fischer-Straße 8, 85748, Garching bei München, GERMANY
| | - Ines Hübner
- Technical University of Munich: Technische Universitat Munchen, Chemistry, GERMANY
| | - Stephan Axel Sieber
- Technische Universitat Munchen, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, GERMANY
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4
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Soni IV, Hardy JA. Caspase-9 Activation of Procaspase-3 but Not Procaspase-6 Is Based on the Local Context of Cleavage Site Motifs and on Sequence. Biochemistry 2021; 60:2824-2835. [PMID: 34472839 DOI: 10.1021/acs.biochem.1c00459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Studying the interactions between a protease and its protein substrates at a molecular level is crucial for identifying the factors facilitating selection of particular proteolytic substrates and not others. These selection criteria include both the sequence and the local context of the substrate cleavage site where the active site of the protease initially binds and then performs proteolytic cleavage. Caspase-9, an initiator of the intrinsic apoptotic pathway, mediates activation of executioner procaspase-3 by cleavage of the intersubunit linker (ISL) at site 172IETD↓S. Although procaspase-6, another executioner, possesses two ISL cleavage sites (site 1, 176DVVD↓N; site 2, 190TEVD↓A), neither is directly cut by caspase-9. Thus, caspase-9 directly activates procaspase-3 but not procaspase-6. To elucidate this selectivity of caspase-9, we engineered constructs of procaspase-3 (e.g., swapping the ISL site, 172IETD↓S, with DVVDN and TEVDA) and procaspase-6 (e.g., swapping site 1, 176DVVD↓N, and site 2, 190TEVD↓A, with IETDS). Using the substrate digestion data of these constructs, we show here that the P4-P1' sequence of procaspase-6 ISL site 1 (DVVDN) can be accessed but not cleaved by caspase-9. We also found that caspase-9 can recognize the P4-P1' sequence of procaspase-6 ISL site 2 (TEVDA); however, the local context of this cleavage site is the critical factor that prevents proteolytic cleavage. Overall, our data have demonstrated that both the sequence and the local context of the ISL cleavage sites play a vital role in preventing the activation of procaspase-6 directly by caspase-9.
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Affiliation(s)
- Ishankumar V Soni
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States.,Models to Medicine Center, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
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5
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Mawla GD, Hall BM, Cárcamo-Oyarce G, Grant RA, Zhang JJ, Kardon JR, Ribbeck K, Sauer RT, Baker TA. ClpP1P2 peptidase activity promotes biofilm formation in Pseudomonas aeruginosa. Mol Microbiol 2021; 115:1094-1109. [PMID: 33231899 PMCID: PMC8141546 DOI: 10.1111/mmi.14649] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/07/2023]
Abstract
Caseinolytic proteases (Clp) are central to bacterial proteolysis and control cellular physiology and stress responses. They are composed of a double-ring compartmentalized peptidase (ClpP) and a AAA+ unfoldase (ClpX or ClpA/ClpC). Unlike many bacteria, the opportunistic pathogen Pseudomonas aeruginosa contains two ClpP homologs: ClpP1 and ClpP2. The specific functions of these homologs, however, are largely elusive. Here, we report that the active form of PaClpP2 is a part of a heteromeric PaClpP17 P27 tetradecamer that is required for proper biofilm development. PaClpP114 and PaClpP17 P27 complexes exhibit distinct peptide cleavage specificities and interact differentially with P. aeruginosa ClpX and ClpA. Crystal structures reveal that PaClpP2 has non-canonical features in its N- and C-terminal regions that explain its poor interaction with unfoldases. However, experiments in vivo indicate that the PaClpP2 peptidase active site uniquely contributes to biofilm development. These data strongly suggest that the specificity of different classes of ClpP peptidase subunits contributes to the biological outcome of proteolysis. This specialized role of PaClpP2 highlights it as an attractive target for developing antimicrobial agents that interfere specifically with late-stage P. aeruginosa development.
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Affiliation(s)
- Gina D. Mawla
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Branwen M. Hall
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Gerardo Cárcamo-Oyarce
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Robert A. Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jia Jia Zhang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Julia R. Kardon
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Tania A. Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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6
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Small molecule inhibitors of the mitochondrial ClpXP protease possess cytostatic potential and re-sensitize chemo-resistant cancers. Sci Rep 2021; 11:11185. [PMID: 34045646 PMCID: PMC8160014 DOI: 10.1038/s41598-021-90801-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/17/2021] [Indexed: 12/18/2022] Open
Abstract
The human mitochondrial ClpXP protease complex (HsClpXP) has recently attracted major attention as a target for novel anti-cancer therapies. Despite its important role in disease progression, the cellular role of HsClpXP is poorly characterized and only few small molecule inhibitors have been reported. Herein, we screened previously established S. aureus ClpXP inhibitors against the related human protease complex and identified potent small molecules against human ClpXP. The hit compounds showed anti-cancer activity in a panoply of leukemia, liver and breast cancer cell lines. We found that the bacterial ClpXP inhibitor 334 impairs the electron transport chain (ETC), enhances the production of mitochondrial reactive oxygen species (mtROS) and thereby promotes protein carbonylation, aberrant proteostasis and apoptosis. In addition, 334 induces cell death in re-isolated patient-derived xenograft (PDX) leukemia cells, potentiates the effect of DNA-damaging cytostatics and re-sensitizes resistant cancers to chemotherapy in non-apoptotic doses.
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7
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Luo B, Ma Y, Zhou Y, Zhang N, Luo Y. Human ClpP protease, a promising therapy target for diseases of mitochondrial dysfunction. Drug Discov Today 2021; 26:968-981. [PMID: 33460621 DOI: 10.1016/j.drudis.2021.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/02/2020] [Accepted: 01/08/2021] [Indexed: 02/05/2023]
Abstract
Human caseinolytic protease P (HsClpP), an ATP-dependent unfolding peptidase protein in the mitochondrial matrix, controls protein quality, regulates mitochondrial metabolism, and maintains the integrity and enzyme activity of the mitochondrial respiratory chain (RC). Studies show that abnormalities in HsClpP lead to mitochondrial dysfunction and various human diseases. In this review, we provide a comprehensive overview of the structure and biological function of HsClpP, and the involvement of its dysexpression or mutation in mitochondria for a panel of important human diseases. We also summarize the structural types and binding modes of known HsClpP modulators. Finally, we discuss the challenges and future directions of HsClpP targeting as promising approach for the treatment of human diseases of mitochondrial origin.
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Affiliation(s)
- Baozhu Luo
- National Center for Birth Defect Monitoring, West China Second University Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yu Ma
- Radiation therapy and chemotherapy for gynecological cancer, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, Sichuan, China
| | - YuanZheng Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Nannan Zhang
- National Center for Birth Defect Monitoring, West China Second University Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China.
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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8
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Choudhury M, Dhara A, Kumar M. Trigger Factor in Association with the ClpP1P2 Heterocomplex of Leptospira Promotes Protease/Peptidase Activity. ACS OMEGA 2021; 6:1400-1409. [PMID: 33490799 PMCID: PMC7818586 DOI: 10.1021/acsomega.0c05057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/28/2020] [Indexed: 05/07/2023]
Abstract
The genomic analysis of Leptospira reveals a trigger factor (TF) encoding gene (tig) to be colocalized along with the clpP1 and clpX. The TF is a crouching dragon-like protein known to be a ribosome-associated chaperone that is involved in cotranslational protein folding in bacteria in an ATP-independent mode. In Leptospira, tig is localized upstream of the clpP1 with a short (4 bp) overlap. In the present study, we document the distinctive role of Leptospira TF (LinTF) in the caseinolytic protease (ClpP) system. The recombinant LinTF (rLinTF) was found to improve the peptidase or protease activity of the ClpP1P2 heterocomplex and ClpXP1P2 complex, respectively, on model substrates. In addition, on supplementation of rLinTF to rClpP1P2 bound to its physiological ATPase chaperone ClpX or the antibiotic analogue acyldepsipeptide (ADEP), an augmentation in the activity of ClpP1P2 was observed. These studies underscore the novel role of LinTF in aiding the caseinolytic protease activity of Leptospira. Supplementation of rLinTF to a peptidase assay of rClpP1P2 conditionally in the presence of a salt (sodium citrate) with high Hofmeister strength led us to speculate that rLinTF may have a role in the assembly of multimeric proteins. The deletion of one of the arms (arm-2) of the LinTF structure from the carboxy terminal domain indicated a reduction in its capacity to stimulate rClpP1P2 activity. Thus, the C-terminal domain of LinTF may have a role in the assembly of multimeric ClpP protein, leading to enhancement of ClpP activity.
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Affiliation(s)
| | | | - Manish Kumar
- . Phone: +91-361-258-2230. Fax: +91-361-258-2249
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9
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Tremblay CY, Vass RH, Vachet RW, Chien P. The Cleavage Profile of Protein Substrates by ClpXP Reveals Deliberate Starts and Pauses. Biochemistry 2020; 59:4294-4301. [PMID: 33135889 DOI: 10.1021/acs.biochem.0c00553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cells rely on protein degradation by AAA+ proteases. A well-known example is the hexameric ClpX unfoldase, which captures ATP hydrolysis to feed substrates into the oligomeric ClpP peptidase. Recent studies show that an asymmetric ClpX spiral cycles protein translocation upon ATP hydrolysis. However, how this cycle affects peptide products is less explored in part because ClpP cleavage is thought to be solely defined by sequence constraints. Here, we comprehensively characterize peptides from Caulobacter crescentus ClpXP degradation of three different substrates using high-resolution mass spectrometry and find that cleavage of translocated substrates is driven by factors other than sequence. We report that defined locations in a translocated protein are especially sensitive to cleavage spaced on average every 10-13 residues. These sites are not exclusively controlled by sequence and are independent of bulk changes in catalytic peptidase sites, ATP hydrolysis, or the efficiency of initial recognition. These results fit a model in which processive translocation through ClpX starts at a specific location in a polypeptide and pauses during reset of the ClpX hexamer after a cycle of translocation. Our work suggests that defined peptides, which could be used as signaling molecules, can be generated from a given substrate by a nonspecific peptidase.
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Affiliation(s)
- Catherine Y Tremblay
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Robert H Vass
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, United States
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10
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Chen S, Yim JJ, Bogyo M. Synthetic and biological approaches to map substrate specificities of proteases. Biol Chem 2020; 401:165-182. [PMID: 31639098 DOI: 10.1515/hsz-2019-0332] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023]
Abstract
Proteases are regulators of diverse biological pathways including protein catabolism, antigen processing and inflammation, as well as various disease conditions, such as malignant metastasis, viral infection and parasite invasion. The identification of substrates of a given protease is essential to understand its function and this information can also aid in the design of specific inhibitors and active site probes. However, the diversity of putative protein and peptide substrates makes connecting a protease to its downstream substrates technically difficult and time-consuming. To address this challenge in protease research, a range of methods have been developed to identify natural protein substrates as well as map the overall substrate specificity patterns of proteases. In this review, we highlight recent examples of both synthetic and biological methods that are being used to define the substrate specificity of protease so that new protease-specific tools and therapeutic agents can be developed.
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Affiliation(s)
- Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua J Yim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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11
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Hofsetz E, Demir F, Szczepanowska K, Kukat A, Kizhakkedathu JN, Trifunovic A, Huesgen PF. The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis. Mol Cell Proteomics 2020; 19:1330-1345. [PMID: 32467259 PMCID: PMC8014998 DOI: 10.1074/mcp.ra120.002082] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/24/2020] [Indexed: 12/29/2022] Open
Abstract
The mammalian mitochondrial proteome consists of more than 1100 annotated proteins and their proteostasis is regulated by only a few ATP-dependent protease complexes. Technical advances in protein mass spectrometry allowed for detailed description of the mitoproteome from different species and tissues and their changes under specific conditions. However, protease-substrate relations within mitochondria are still poorly understood. Here, we combined Terminal Amine Isotope Labeling of Substrates (TAILS) N termini profiling of heart mitochondria proteomes isolated from wild type and Clpp-/- mice with a classical substrate-trapping screen using FLAG-tagged proteolytically active and inactive CLPP variants to identify new ClpXP substrates in mammalian mitochondria. Using TAILS, we identified N termini of more than 200 mitochondrial proteins. Expected N termini confirmed sequence determinants for mitochondrial targeting signal (MTS) cleavage and subsequent N-terminal processing after import, but the majority were protease-generated neo-N termini mapping to positions within the proteins. Quantitative comparison revealed widespread changes in protein processing patterns, including both strong increases or decreases in the abundance of specific neo-N termini, as well as an overall increase in the abundance of protease-generated neo-N termini in CLPP-deficient mitochondria that indicated altered mitochondrial proteostasis. Based on the combination of altered processing patterns, protein accumulation and stabilization in CLPP-deficient mice and interaction with CLPP, we identified OAT, HSPA9 and POLDIP2 and as novel bona fide ClpXP substrates. Finally, we propose that ClpXP participates in the cooperative degradation of UQCRC1. Together, our data provide the first landscape of the heart mitochondria N terminome and give further insights into regulatory and assisted proteolysis mediated by ClpXP.
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Affiliation(s)
- Eduard Hofsetz
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Karolina Szczepanowska
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Alexandra Kukat
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, School of Biomedical Engineering, Department of Pathology & Laboratory Medicine, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aleksandra Trifunovic
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
| | - Pitter F Huesgen
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany; Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany; Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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12
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Dhara A, Hussain MS, Datta D, Kumar M. Insights to the Assembly of a Functionally Active Leptospiral ClpP1P2 Protease Complex along with Its ATPase Chaperone ClpX. ACS OMEGA 2019; 4:12880-12895. [PMID: 31460415 PMCID: PMC6682002 DOI: 10.1021/acsomega.9b00399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/11/2019] [Indexed: 05/05/2023]
Abstract
Leptospira interrogans genome is predicted to encode multiple isoforms of caseinolytic proteases (ClpP1 and ClpP2). The ClpP proteins with the aid of its ATPase chaperone are known to be involved in establishing cellular proteostasis and have emerged as a target for developing new antibiotics. We report the molecular characterization of recombinant ClpP1 (rClpP1) and rClpP2 of Leptospira along with its ATPase chaperone rClpX. The two isoforms of rClpPs when coupled together in an equivalent concentration exhibit optimum activity on small fluorogenic peptide substrates, whereas the pure rClpP isoforms are enzymatically inactive. Isothermal titration calorimetry analysis suggests that the two rClpP isoforms bind each other moderately in a 1:1 stoichiometry with a dissociation constant of 2.02 ± 0.1 μM at 37 °C and is thermodynamically favored. Size exclusion chromatography fractionates the majority of pure rClpP1 at ≥308 kDa (14-21-mer) and the pure rClpP2 at 308 kDa (tetradecamer), whereas the functionally active rClpP isoform mixture fractionates as a tetradecamer. The distinct and unprecedented oligomeric form of rClpP1 was also evident through native-gel and dynamic light scattering. Moreover, the rClpP isoform mixture formed after the site-directed mutation of either or both the isoforms at one of the catalytic triad residues (Ser 98/97 to Ala 98/97) resulted in the complete loss of protease activity. The rClpP isoform mixture gets stimulated to degrade the casein substrate in the presence of rClpX and in an energy-dependent manner. On the contrary, pure rClpP1 or the rClpP2 isoform in association with rClpX are incapable of forming operative protease. The reported finding suggests that in Leptospira, the enzymatic activity of the rClpP protease complex in the presence or absence of cochaperone is performed solely by the tetradecamer structure which is hypothesized to be composed of 2-stacked ClpP heptameric rings, wherein each ring is a homo-oligomer of ClpP1 and ClpP2 subunits. Understanding the activities and regulation principle of multi-isoforms of ClpP in pathogenic bacteria may aid in intervening disease outcomes particularly to the co-evolving antibiotic resistance strains.
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Affiliation(s)
| | | | | | - Manish Kumar
- E-mail: . Phone: +91-361-258-2230. Fax: +91-361-258-2249
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13
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Tan J, Grouleff JJ, Jitkova Y, Diaz DB, Griffith EC, Shao W, Bogdanchikova AF, Poda G, Schimmer AD, Lee RE, Yudin AK. De Novo Design of Boron-Based Peptidomimetics as Potent Inhibitors of Human ClpP in the Presence of Human ClpX. J Med Chem 2019; 62:6377-6390. [PMID: 31187989 DOI: 10.1021/acs.jmedchem.9b00878] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Boronic acids have attracted the attention of synthetic and medicinal chemists due to boron's ability to modulate enzyme function. Recently, we demonstrated that boron-containing amphoteric building blocks facilitate the discovery of bioactive aminoboronic acids. Herein, we have augmented this capability with a de novo library design and a virtual screening platform modified for covalent ligands. This technique has allowed us to rapidly design and identify a series of α-aminoboronic acids as the first inhibitors of human ClpXP, which is responsible for the degradation of misfolded proteins.
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Affiliation(s)
- Joanne Tan
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Julie J Grouleff
- Drug Discovery Program , Ontario Institute for Cancer Research, MaRS Centre , 661 University Avenue , Suite 510 , Toronto , Ontario M5G 0A3 , Canada
| | - Yulia Jitkova
- Princess Margaret Cancer Centre , University Health Network , 610 University Avenue , Toronto , Ontario M5G 2M9 , Canada
| | - Diego B Diaz
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Elizabeth C Griffith
- Department of Chemical Biology and Therapeutics , St. Jude Children's Research Hospital , 262 Danny Thomas Place , Memphis , Tennessee 38105-3678 , United States
| | - Wenjie Shao
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Anastasia F Bogdanchikova
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Gennady Poda
- Drug Discovery Program , Ontario Institute for Cancer Research, MaRS Centre , 661 University Avenue , Suite 510 , Toronto , Ontario M5G 0A3 , Canada.,Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre , University Health Network , 610 University Avenue , Toronto , Ontario M5G 2M9 , Canada
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics , St. Jude Children's Research Hospital , 262 Danny Thomas Place , Memphis , Tennessee 38105-3678 , United States
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
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14
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Lakemeyer M, Bertosin E, Möller F, Balogh D, Strasser R, Dietz H, Sieber SA. Tailored Peptide Phenyl Esters Block ClpXP Proteolysis by an Unusual Breakdown into a Heptamer–Hexamer Assembly. Angew Chem Int Ed Engl 2019; 58:7127-7132. [DOI: 10.1002/anie.201901056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Markus Lakemeyer
- Center for Integrated Protein Science (CIPSM) at theDepartment of ChemistryTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Eva Bertosin
- Physics Department and Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
| | | | - Dóra Balogh
- Center for Integrated Protein Science (CIPSM) at theDepartment of ChemistryTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Ralf Strasser
- Dynamic Biosensors GmbH Lochhamerstr. 15 82152 Planegg Germany
| | - Hendrik Dietz
- Physics Department and Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
| | - Stephan A. Sieber
- Center for Integrated Protein Science (CIPSM) at theDepartment of ChemistryTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
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15
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Lakemeyer M, Bertosin E, Möller F, Balogh D, Strasser R, Dietz H, Sieber SA. Blockade der ClpXP‐vermittelten Proteolyse mit maßgeschneiderten Peptid‐Phenylestern durch den ungewöhnlichen Zerfall in eine Heptamer‐Hexamer‐Anordnung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Markus Lakemeyer
- Center for Integrated Protein Science (CIPSM) amDepartment ChemieTechnische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Eva Bertosin
- Physik Department und Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Deutschland
| | - Friederike Möller
- Dynamic Biosensors GmbH Lochhamerstraße 15 82152 Planegg Deutschland
| | - Dóra Balogh
- Center for Integrated Protein Science (CIPSM) amDepartment ChemieTechnische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Ralf Strasser
- Dynamic Biosensors GmbH Lochhamerstraße 15 82152 Planegg Deutschland
| | - Hendrik Dietz
- Physik Department und Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Deutschland
| | - Stephan A. Sieber
- Center for Integrated Protein Science (CIPSM) amDepartment ChemieTechnische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
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16
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Ishizawa J, Zarabi SF, Davis RE, Halgas O, Nii T, Jitkova Y, Zhao R, St-Germain J, Heese LE, Egan G, Ruvolo VR, Barghout SH, Nishida Y, Hurren R, Ma W, Gronda M, Link T, Wong K, Mabanglo M, Kojima K, Borthakur G, MacLean N, Ma MCJ, Leber AB, Minden MD, Houry W, Kantarjian H, Stogniew M, Raught B, Pai EF, Schimmer AD, Andreeff M. Mitochondrial ClpP-Mediated Proteolysis Induces Selective Cancer Cell Lethality. Cancer Cell 2019; 35:721-737.e9. [PMID: 31056398 PMCID: PMC6620028 DOI: 10.1016/j.ccell.2019.03.014] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/13/2018] [Accepted: 03/29/2019] [Indexed: 12/20/2022]
Abstract
The mitochondrial caseinolytic protease P (ClpP) plays a central role in mitochondrial protein quality control by degrading misfolded proteins. Using genetic and chemical approaches, we showed that hyperactivation of the protease selectively kills cancer cells, independently of p53 status, by selective degradation of its respiratory chain protein substrates and disrupts mitochondrial structure and function, while it does not affect non-malignant cells. We identified imipridones as potent activators of ClpP. Through biochemical studies and crystallography, we show that imipridones bind ClpP non-covalently and induce proteolysis by diverse structural changes. Imipridones are presently in clinical trials. Our findings suggest a general concept of inducing cancer cell lethality through activation of mitochondrial proteolysis.
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MESH Headings
- Animals
- Cell Line, Tumor
- Cell Survival/drug effects
- Crystallography, X-Ray
- Drug Screening Assays, Antitumor
- Endopeptidase Clp/chemistry
- Endopeptidase Clp/genetics
- Endopeptidase Clp/metabolism
- Female
- HCT116 Cells
- HEK293 Cells
- Heterocyclic Compounds, 4 or More Rings/administration & dosage
- Heterocyclic Compounds, 4 or More Rings/chemistry
- Heterocyclic Compounds, 4 or More Rings/pharmacology
- Humans
- Imidazoles
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Mice
- Mitochondria/metabolism
- Models, Molecular
- Point Mutation
- Protein Conformation/drug effects
- Proteolysis
- Pyridines
- Pyrimidines
- Tumor Suppressor Protein p53/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Jo Ishizawa
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Sarah F Zarabi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - R Eric Davis
- The University of Texas MD Anderson Cancer Center; Department of Lymphoma and Myeloma, Houston, TX 77030, USA
| | - Ondrej Halgas
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Takenobu Nii
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Yulia Jitkova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ran Zhao
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Lauren E Heese
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Grace Egan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Vivian R Ruvolo
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Samir H Barghout
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Yuki Nishida
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Rose Hurren
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Wencai Ma
- The University of Texas MD Anderson Cancer Center, Bioinformatics and Comp Biology, Houston, TX 77030, USA
| | - Marcela Gronda
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Todd Link
- The University of Texas MD Anderson Cancer Center, Genomic Medicine, Houston, TX 77030, USA
| | - Keith Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mark Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kensuke Kojima
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA; Saga University, Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Saga 849-8501, Japan
| | - Gautam Borthakur
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA
| | - Neil MacLean
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Man Chun John Ma
- The University of Texas MD Anderson Cancer Center; Department of Lymphoma and Myeloma, Houston, TX 77030, USA
| | - Andrew B Leber
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Walid Houry
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Hagop Kantarjian
- The University of Texas MD Anderson Cancer Center; Department of Leukemia, Houston, TX 77030, USA
| | | | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Emil F Pai
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Michael Andreeff
- The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center; Department of Leukemia, Houston, TX 77030, USA.
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17
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da Silva RR. Controlling proteolysis of Clp peptidase: a possible target for combating mitochondrial diseases. Int J Biochem Cell Biol 2019; 110:140-142. [PMID: 30885675 DOI: 10.1016/j.biocel.2019.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 01/09/2023]
Abstract
Some mechanisms of cellular stress, aging, and apoptosis are related to proteolysis. With respect to ClpP, little is known about the mechanical manner in which the substrate is hydrolyzed in and released from the degradation chamber. Furthermore, what would be the real influence of ClpP in mammalian UPRmt?
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Affiliation(s)
- Ronivaldo Rodrigues da Silva
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto, São Paulo, Brazil.
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18
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Fux A, Korotkov VS, Schneider M, Antes I, Sieber SA. Chemical Cross-Linking Enables Drafting ClpXP Proximity Maps and Taking Snapshots of In Situ Interaction Networks. Cell Chem Biol 2019; 26:48-59.e7. [DOI: 10.1016/j.chembiol.2018.10.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/12/2018] [Accepted: 10/05/2018] [Indexed: 12/21/2022]
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19
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Initial Characterization of the Two ClpP Paralogs of Chlamydia trachomatis Suggests Unique Functionality for Each. J Bacteriol 2018; 201:JB.00635-18. [PMID: 30396899 DOI: 10.1128/jb.00635-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/24/2018] [Indexed: 12/28/2022] Open
Abstract
Members of Chlamydia are obligate intracellular bacteria that differentiate between two distinct functional and morphological forms during their developmental cycle, elementary bodies (EBs) and reticulate bodies (RBs). EBs are nondividing small electron-dense forms that infect host cells. RBs are larger noninfectious replicative forms that develop within a membrane-bound vesicle, termed an inclusion. Given the unique properties of each developmental form of this bacterium, we hypothesized that the Clp protease system plays an integral role in proteomic turnover by degrading specific proteins from one developmental form or the other. Chlamydia spp. have five uncharacterized clp genes, clpX, clpC, two clpP paralogs, and clpB In other bacteria, ClpC and ClpX are ATPases that unfold and feed proteins into the ClpP protease to be degraded, and ClpB is a deaggregase. Here, we focused on characterizing the ClpP paralogs. Transcriptional analyses and immunoblotting determined that these genes are expressed midcycle. Bioinformatic analyses of these proteins identified key residues important for activity. Overexpression of inactive clpP mutants in Chlamydia spp. suggested independent function of each ClpP paralog. To further probe these differences, we determined interactions between the ClpP proteins using bacterial two-hybrid assays and native gel analysis of recombinant proteins. Homotypic interactions of the ClpP proteins, but not heterotypic interactions between the ClpP paralogs, were detected. Interestingly, protease activity of ClpP2, but not ClpP1, was detected in vitro This activity was stimulated by antibiotics known to activate ClpP, which also blocked chlamydial growth. Our data suggest the chlamydial ClpP paralogs likely serve distinct and critical roles in this important pathogen.IMPORTANCE Chlamydia trachomatis is the leading cause of preventable infectious blindness and of bacterial sexually transmitted infections worldwide. Chlamydiae are developmentally regulated obligate intracellular pathogens that alternate between two functional and morphologic forms, with distinct repertoires of proteins. We hypothesize that protein degradation is a critical aspect to the developmental cycle. A key system involved in protein turnover in bacteria is the Clp protease system. Here, we characterized the two chlamydial ClpP paralogs by examining their expression in Chlamydia spp., their ability to oligomerize, and their proteolytic activity. This work will help understand the evolutionarily diverse Clp proteases in the context of intracellular organisms, which may aid in the study of other clinically relevant intracellular bacteria.
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20
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Stahl M, Korotkov VS, Balogh D, Kick LM, Gersch M, Pahl A, Kielkowski P, Richter K, Schneider S, Sieber SA. Selektive Aktivierung der humanen caseinolytischen Protease P (ClpP). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Matthias Stahl
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; Tomtebodavägen 23A 171 65 Solna Schweden
| | - Vadim S. Korotkov
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Dóra Balogh
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Leonhard M. Kick
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Malte Gersch
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Medical Research Council Laboratory of, Molecular Biology; Francis Crick Avenue CB2 0QH Cambridge Großbritannien
| | - Axel Pahl
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Max-Planck-Institut für Molekulare Physiologie; Compound Management and Screening Center (COMAS); Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Pavel Kielkowski
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Klaus Richter
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Sabine Schneider
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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21
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Stahl M, Korotkov VS, Balogh D, Kick LM, Gersch M, Pahl A, Kielkowski P, Richter K, Schneider S, Sieber SA. Selective Activation of Human Caseinolytic Protease P (ClpP). Angew Chem Int Ed Engl 2018; 57:14602-14607. [DOI: 10.1002/anie.201808189] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/15/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Matthias Stahl
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address: Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; Tomtebodavägen 23A 171 65 Solna Sweden
| | - Vadim S. Korotkov
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Dóra Balogh
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Leonhard M. Kick
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Malte Gersch
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address; Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue CB2 0QH Cambridge UK
| | - Axel Pahl
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address: Max-Planck-Institut für Molekulare Physiologie; Compound Management and Screening Center (COMAS); Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Pavel Kielkowski
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Klaus Richter
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Sabine Schneider
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Stephan A. Sieber
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
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22
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Perrault syndrome type 3 caused by diverse molecular defects in CLPP. Sci Rep 2018; 8:12862. [PMID: 30150665 PMCID: PMC6110781 DOI: 10.1038/s41598-018-30311-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/25/2018] [Indexed: 02/02/2023] Open
Abstract
The maintenance of mitochondrial protein homeostasis (proteostasis) is crucial for correct cellular function. Recently, several mutations in the mitochondrial protease CLPP have been identified in patients with Perrault syndrome 3 (PRLTS3). These mutations can be arranged into two groups, those that cluster near the docking site (hydrophobic pocket, Hp) for the cognate unfoldase CLPX (i.e. T145P and C147S) and those that are adjacent to the active site of the peptidase (i.e. Y229D). Here we report the biochemical consequence of mutations in both regions. The Y229D mutant not only inhibited CLPP-peptidase activity, but unexpectedly also prevented CLPX-docking, thereby blocking the turnover of both peptide and protein substrates. In contrast, Hp mutations cause a range of biochemical defects in CLPP, from no observable change to CLPP activity for the C147S mutant, to dramatic disruption of most activities for the “gain-of-function” mutant T145P - including loss of oligomeric assembly and enhanced peptidase activity.
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23
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Ding B, Martin DW, Rampello AJ, Glynn SE. Dissecting Substrate Specificities of the Mitochondrial AFG3L2 Protease. Biochemistry 2018; 57:4225-4235. [PMID: 29932645 DOI: 10.1021/acs.biochem.8b00565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. Identifying how AFG3L2 selects substrates from the diverse complement of matrix-localized proteins is essential for understanding mitochondrial protein biogenesis and quality control. Here, we create solubilized forms of AFG3L2 to examine the enzyme's substrate specificity mechanisms. We show that conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form. Moreover, these residues can act as a degron, delivering diverse model proteins to AFG3L2 for degradation. By determining the sequence of degradation products from multiple substrates using mass spectrometry, we construct a peptidase specificity profile that displays constrained product lengths and is dominated by the identity of the residue at the P1' position, with a strong preference for hydrophobic and small polar residues. This specificity profile is validated by examining the cleavage of both fluorogenic reporter peptides and full polypeptide substrates bearing different P1' residues. Together, these results demonstrate that AFG3L2 contains multiple modes of specificity, discriminating between potential substrates by recognizing accessible degron sequences and performing peptide bond cleavage at preferred patterns of residues within the compartmental chamber.
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24
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Fuchs ACD, Maldoner L, Hipp K, Hartmann MD, Martin J. Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double-ring complex with unique inner cavity properties. J Biol Chem 2017; 293:920-930. [PMID: 29183996 PMCID: PMC5777263 DOI: 10.1074/jbc.m117.815258] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/10/2017] [Indexed: 01/24/2023] Open
Abstract
Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ HslU; the ClpP protease with its partner AAA+ ClpX; and Anbu, a recently characterized ancestral proteasome variant. Previous bioinformatic analysis has revealed a novel bacterial member of the proteasome family Betaproteobacteria proteasome homolog (BPH). Using cluster analysis, we here affirmed that BPH evolutionarily descends from HslV. Crystal structures of the Thiobacillus denitrificans and Cupriavidus metallidurans BPHs disclosed a homo-oligomeric double-ring architecture in which the active sites face the interior of the cylinder. Using small-angle X-ray scattering (SAXS) and electron microscopy averaging, we found that BPH forms tetradecamers in solution, unlike the dodecamers seen in HslV. Although the highly acidic inner surface of BPH was in striking contrast to the cavity characteristics of the proteasome and HslV, a classical proteasomal reaction mechanism could be inferred from the covalent binding of the proteasome-specific inhibitor epoxomicin to BPH. A ligand-bound structure implied that the elongated BPH inner pore loop may be involved in substrate recognition. The apparent lack of a partner unfoldase and other unique features, such as Ser replacing Thr as the catalytic residue in certain BPH subfamilies, suggest a proteolytic function for BPH distinct from those of known bacterial self-compartmentalizing proteases.
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Affiliation(s)
| | | | - Katharina Hipp
- Electron Microscopy Facility, Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076 Tübingen, Germany
| | | | - Jörg Martin
- From the Department of Protein Evolution and
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25
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Synthesis of a HyCoSuL peptide substrate library to dissect protease substrate specificity. Nat Protoc 2017; 12:2189-2214. [PMID: 28933778 DOI: 10.1038/nprot.2017.091] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Many biologically and chemically based approaches have been developed to design highly active and selective protease substrates and probes. It is, however, difficult to find substrate sequences that are truly selective for any given protease, as different proteases can demonstrate a great deal of overlap in substrate specificities. In some cases, better enzyme selectivity can be achieved using peptide libraries containing unnatural amino acids such as the hybrid combinatorial substrate library (HyCoSuL), which uses both natural and unnatural amino acids. HyCoSuL is a combinatorial library of tetrapeptides containing amino acid mixtures at the P4-P2 positions, a fixed amino acid at the P1 position, and an ACC (7-amino-4-carbamoylmethylcoumarin) fluorescent tag occupying the P1' position. Once the peptide is recognized and cleaved by a protease, the ACC is released and produces a readable fluorescence signal. Here, we describe the synthesis and screening of HyCoSuL for human caspases and legumain. We also discuss possible modifications and adaptations of this approach that make it a useful tool for developing highly active and selective reagents for a wide variety of proteolytic enzymes. The protocol can be divided into three major parts: (i) solid-phase synthesis of the fluorescence-labeled HyCoSuL, (ii) screening of protease P4-P2 preferences, and (iii) synthesis of the optimized activity probes equipped with an AOMK (acyloxymethyl ketone) reactive group and a biotin label for easy detection. Beginning with the library design, the entire protocol can be completed in 4-8 weeks (HyCoSuL synthesis: 3-5 weeks; HyCoSuL screening per enzyme: 4-8 d; and activity-based probe synthesis: 1-2 weeks).
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26
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An amino acid domino effect orchestrates ClpP's conformational states. Curr Opin Chem Biol 2017; 40:102-110. [PMID: 28910721 DOI: 10.1016/j.cbpa.2017.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/26/2017] [Accepted: 08/22/2017] [Indexed: 01/08/2023]
Abstract
Maintaining the cellular protein homeostasis means managing life on the brink of death. This balance is largely based on precise fine-tuning of enzyme activities. For instance, the ClpP protease possesses several conformational switches which are fundamental to regulating its activity. Efforts have focused on revealing the structural basis of ClpP's conformational control. In the last decade, several amino acid clusters have been identified and functionally linked to specific activation states. Researchers have now begun to couple these hotspots to one another, uncovering a global network of residues that switch in response to internal and external stimuli. For these studies, they used small molecules to mimic intermolecular interactions and point-mutational studies to shortcut regulating amino acid circuits.
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27
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Mutation in human CLPX elevates levels of δ-aminolevulinate synthase and protoporphyrin IX to promote erythropoietic protoporphyria. Proc Natl Acad Sci U S A 2017; 114:E8045-E8052. [PMID: 28874591 DOI: 10.1073/pnas.1700632114] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Loss-of-function mutations in genes for heme biosynthetic enzymes can give rise to congenital porphyrias, eight forms of which have been described. The genetic penetrance of the porphyrias is clinically variable, underscoring the role of additional causative, contributing, and modifier genes. We previously discovered that the mitochondrial AAA+ unfoldase ClpX promotes heme biosynthesis by activation of δ-aminolevulinate synthase (ALAS), which catalyzes the first step of heme synthesis. CLPX has also been reported to mediate heme-induced turnover of ALAS. Here we report a dominant mutation in the ATPase active site of human CLPX, p.Gly298Asp, that results in pathological accumulation of the heme biosynthesis intermediate protoporphyrin IX (PPIX). Amassing of PPIX in erythroid cells promotes erythropoietic protoporphyria (EPP) in the affected family. The mutation in CLPX inactivates its ATPase activity, resulting in coassembly of mutant and WT protomers to form an enzyme with reduced activity. The presence of low-activity CLPX increases the posttranslational stability of ALAS, causing increased ALAS protein and ALA levels, leading to abnormal accumulation of PPIX. Our results thus identify an additional molecular mechanism underlying the development of EPP and further our understanding of the multiple mechanisms by which CLPX controls heme metabolism.
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28
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Ye F, Li J, Yang CG. The development of small-molecule modulators for ClpP protease activity. MOLECULAR BIOSYSTEMS 2017; 13:23-31. [PMID: 27831584 DOI: 10.1039/c6mb00644b] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The global spread of antibiotic resistance among important human pathogens emphasizes the need to find new antibacterial drugs with a novel mode of action. The ClpP protease has been shown to demonstrate its pivotal importance to both the survival and the virulence of pathogenic bacteria during host infection. Deregulating ClpP activity either through overactivation or inhibition could lead to antibacterial activity, declaiming the dual molecular mechanism for small-molecule modulation. Recently, natural products acyldepsipeptides (ADEPs) have been identified as a new class of antibiotics that activate ClpP to a dysfunctional state in the absence of cognate ATPases. ADEPs in combination with rifampicin eradicate deep-seated mouse biofilm infections. In addition, several non-ADEP compounds have been identified as activators of the ClpP proteolytic core without the involvement of ATPases. These findings indicate a general principle for killing dormant cells, the activation and corruption of the ClpP protease, rather than through conventional inhibition. Deletion of the clpP gene reduced the virulence of Staphylococcus aureus, thus making it an ideal antivirulence target. Multiple inhibitors have been developed in order to attenuate the production of extracellular virulence factors of bacteria through covalent modifications on serine in the active site or disruption of oligomerization of ClpP. Interestingly, due to the unusual composition and activation mechanism of ClpP in Mycobacterium tuberculosis, mycobacteria are killed by ADEPs through inhibition of ClpP activity rather than overactivation. In this short review, we will summarize recent progress in the development of small molecules modulating ClpP protease activity for both antibiotics and antivirulence.
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Affiliation(s)
- Fei Ye
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jiahui Li
- Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Cai-Guang Yang
- Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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29
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Two Isoforms of Clp Peptidase in Pseudomonas aeruginosa Control Distinct Aspects of Cellular Physiology. J Bacteriol 2017; 199:JB.00568-16. [PMID: 27849175 DOI: 10.1128/jb.00568-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/20/2016] [Indexed: 02/07/2023] Open
Abstract
Caseinolytic peptidases (ClpPs) regulate diverse aspects of cellular physiology in bacteria. Some species have multiple ClpPs, including the opportunistic pathogen Pseudomonas aeruginosa, in which there is an archetypical isoform, ClpP1, and a second isoform, ClpP2, about which little is known. Here, we use phenotypic assays to investigate the biological roles of ClpP1 and ClpP2 and biochemical assays to characterize purified ClpP1, ClpP2, ClpX, and ClpA. Interestingly, ClpP1 and ClpP2 have distinct intracellular roles for motility, pigment production, iron scavenging, and biofilm formation. Of particular interest, ClpP2, but not ClpP1, is required for microcolony organization, where multicellular organized structures first form on the pathway to biofilm production. We found that purified ClpP1 with ClpX or ClpA was enzymatically active, yet to our surprise, ClpP2 was inactive and not fully assembled in vitro; attempts to assist ClpP2 assembly and activation by mixing with the other Clp components failed to turn on ClpP2, as did solution conditions that have helped activate other ClpPs in vitro We postulate that the active form of ClpP2 has yet to be discovered, and we present several potential models to explain its activation as well as the unique role ClpP2 plays in the development of the clinically important biofilms in P. aeruginosaIMPORTANCEPseudomonas aeruginosa is responsible for severe infections of immunocompromised patients. Our work demonstrates that two different isoforms of the Clp peptidase, ClpP1 and ClpP2, control distinct aspects of cellular physiology for this organism. In particular, we identify ClpP2 as being necessary for microcolony organization. Pure active forms of ClpP1 and either ClpX or ClpA were characterized as assembled and active, and ClpP2 was incompletely assembled and inactive. By establishing both the unique biological roles of ClpP1 and ClpP2 and their initial biochemical assemblies, we have set the stage for important future work on the structure, function, and biological targets of Clp proteolytic enzymes in this important opportunistic pathogen.
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30
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Balogh D, Dahmen M, Stahl M, Poreba M, Gersch M, Drag M, Sieber SA. Insights into ClpXP proteolysis: heterooligomerization and partial deactivation enhance chaperone affinity and substrate turnover in Listeria monocytogenes. Chem Sci 2016; 8:1592-1600. [PMID: 28451288 PMCID: PMC5361862 DOI: 10.1039/c6sc03438a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/26/2016] [Indexed: 01/04/2023] Open
Abstract
Caseinolytic proteases (ClpP) are important for recognition and controlled degradation of damaged proteins. While the majority of bacterial organisms utilize only a single ClpP, Listeria monocytogenes expresses two isoforms (LmClpP1 and LmClpP2). LmClpPs assemble into either a LmClpP2 homocomplex or a LmClpP1/2 heterooligomeric complex. The heterocomplex in association with the chaperone ClpX, exhibits a boost in proteolytic activity for unknown reasons. Here, we use a combined chemical and biochemical strategy to unravel two activation principles of LmClpPs. First, determination of apparent affinity constants revealed a 7-fold elevated binding affinity between the LmClpP1/2 heterocomplex and ClpX, compared to homooligomeric LmClpP2. This tighter interaction favors the formation of the proteolytically active complex between LmClpX and LmClpP1/2 and thereby accelerating the overall turnover. Second, screening a diverse library of fluorescent labeled peptides and proteins with various ClpP mutants allowed the individual analysis of substrate preferences for both isoforms within the heterocomplex. In addition to Leu and Met, LmClpP2 preferred a long aliphatic chain (2-Aoc) in the P1 position for cleavage. Strikingly, design and synthesis of a corresponding 2-Aoc chloromethyl ketone inhibitor resulted in stimulation of proteolysis by 160% when LmClpP2 was partially alkylated on 20% of the active sites. Determination of apparent affinity constants also revealed an elevated complex stability between partially modified LmClpP2 and the cognate chaperone LmClpX. Thus, the stimulation of proteolysis through enhanced binding to the chaperone seems to be a characteristic feature of LmClpPs.
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Affiliation(s)
- Dóra Balogh
- Center for Integrated Protein Science at the Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , Garching bei München , D-85747 , Germany .
| | - Maria Dahmen
- Center for Integrated Protein Science at the Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , Garching bei München , D-85747 , Germany .
| | - Matthias Stahl
- Center for Integrated Protein Science at the Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , Garching bei München , D-85747 , Germany .
| | - Marcin Poreba
- Department of Bioorganic Chemistry , Faculty of Chemistry , Wrocław University of Technology , Wybrzeże Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Malte Gersch
- Center for Integrated Protein Science at the Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , Garching bei München , D-85747 , Germany .
| | - Marcin Drag
- Department of Bioorganic Chemistry , Faculty of Chemistry , Wrocław University of Technology , Wybrzeże Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Stephan A Sieber
- Center for Integrated Protein Science at the Department of Chemistry , Technische Universität München , Lichtenbergstraße 4 , Garching bei München , D-85747 , Germany .
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31
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Ni T, Ye F, Liu X, Zhang J, Liu H, Li J, Zhang Y, Sun Y, Wang M, Luo C, Jiang H, Lan L, Gan J, Zhang A, Zhou H, Yang CG. Characterization of Gain-of-Function Mutant Provides New Insights into ClpP Structure. ACS Chem Biol 2016; 11:1964-72. [PMID: 27171654 DOI: 10.1021/acschembio.6b00390] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
ATP-dependent Clp protease (ClpP), a highly conserved serine protease in vast bacteria, could be converted into a noncontrollable enzyme capable of degrading mature proteins in the presence of acyldepsipeptides (ADEPs). Here, we design such a gain-of-function mutant of Staphylococcus aureus ClpP (SaClpP) capable of triggering the same level of dysfunctional activity that occurs upon ADEPs treatment. The SaClpPY63A mutant degrades FtsZ in vivo and inhibits staphylococcal growth. The crystal structure of SaClpPY63A indicates that Asn42 would be an important domino to fall for further activation of ClpP. Indeed, the SaClpPN42AY63A mutant demonstrates promoted self-activated proteolysis, which is a result of an enlarged entrance pore as observed in cryo-electron microscopy images. In addition, the expression of the engineered clpP allele phenocopies treatment with ADEPs; inhibition of cell division occurs as does showing sterilizing with rifampicin antibiotics. Collectively, we show that the gain-of-function SaClpPN42AY63A mutant becomes a fairly nonspecific protease and kills persisters by degrading over 500 proteins, thus providing new insights into the structure of the ClpP protease.
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Affiliation(s)
- Tengfeng Ni
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Ye
- College
of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Drug
Design and Discovery Center, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xing Liu
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jie Zhang
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongchuan Liu
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiahui Li
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingyi Zhang
- National
Center for Protein Science Shanghai, Institute of Biochemistry and
Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yinqiang Sun
- Experiment
Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Meining Wang
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- Drug
Design and Discovery Center, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Drug
Design and Discovery Center, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lefu Lan
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Gan
- School
of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ao Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hu Zhou
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cai-Guang Yang
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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