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Benedetti F, Silvestri G, Denaro F, Finesso G, Contreras-Galindo R, Munawwar A, Williams S, Davis H, Bryant J, Wang Y, Radaelli E, Rathinam CV, Gallo RC, Zella D. Mycoplasma DnaK expression increases cancer development in vivo upon DNA damage. Proc Natl Acad Sci U S A 2024; 121:e2320859121. [PMID: 38412130 PMCID: PMC10927570 DOI: 10.1073/pnas.2320859121] [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: 11/27/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024] Open
Abstract
Well-controlled repair mechanisms are involved in the maintenance of genomic stability, and their failure can precipitate DNA abnormalities and elevate tumor risk. In addition, the tumor microenvironment, enriched with factors inducing oxidative stress and affecting cell cycle checkpoints, intensifies DNA damage when repair pathways falter. Recent research has unveiled associations between certain bacteria, including Mycoplasmas, and various cancers, and the causative mechanism(s) are under active investigation. We previously showed that Mycoplasma fermentans DnaK, an HSP70 family chaperone protein, hampers the activity of proteins like PARP1 and p53, crucial for genomic integrity. Moreover, our analysis of its interactome in human cancer cell lines revealed DnaK's engagement with several components of DNA-repair machinery. Finally, in vivo experiments performed in our laboratory using a DnaK knock-in mouse model generated by our group demonstrated that DnaK exposure led to increased DNA copy number variants, indicative of genomic instability. We present here evidence that expression of DnaK is linked to increased i) incidence of tumors in vivo upon exposure to urethane, a DNA damaging agent; ii) spontaneous DNA damage ex vivo; and iii) expression of proinflammatory cytokines ex vivo, variations in reactive oxygen species levels, and increased β-galactosidase activity across tissues. Moreover, DnaK was associated with increased centromeric instability. Overall, these findings highlight the significance of Mycoplasma DnaK in the etiology of cancer and other genetic disorders providing a promising target for prevention, diagnostics, and therapeutics.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD21201
| | - Giovannino Silvestri
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Frank Denaro
- Department of Biology, Morgan State University, Baltimore, MD21251
| | - Giovanni Finesso
- Comparative Pathology Core, Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA19104
| | | | - Arshi Munawwar
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Sumiko Williams
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Biology, Morgan State University, Baltimore, MD21251
| | - Harry Davis
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Joseph Bryant
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Yin Wang
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Surgery, School of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Enrico Radaelli
- Comparative Pathology Core, Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Chozha V. Rathinam
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Robert C. Gallo
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Davide Zella
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD21201
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2
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Xiao X, Fay A, Molina PS, Kovach A, Glickman MS, Li H. Structure of the M. tuberculosis DnaK-GrpE complex reveals how key DnaK roles are controlled. Nat Commun 2024; 15:660. [PMID: 38253530 PMCID: PMC10803776 DOI: 10.1038/s41467-024-44933-9] [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: 03/01/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The molecular chaperone DnaK is essential for viability of Mycobacterium tuberculosis (Mtb). DnaK hydrolyzes ATP to fold substrates, and the resulting ADP is exchanged for ATP by the nucleotide exchange factor GrpE. It has been unclear how GrpE couples DnaK's nucleotide exchange with substrate release. Here we report a cryo-EM analysis of GrpE bound to an intact Mtb DnaK, revealing an asymmetric 1:2 DnaK-GrpE complex. The GrpE dimer ratchets to modulate both DnaK nucleotide-binding domain and the substrate-binding domain. We further show that the disordered GrpE N-terminus is critical for substrate release, and that the DnaK-GrpE interface is essential for protein folding activity both in vitro and in vivo. Therefore, the Mtb GrpE dimer allosterically regulates DnaK to concomitantly release ADP in the nucleotide-binding domain and substrate peptide in the substrate-binding domain.
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Affiliation(s)
- Xiansha Xiao
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Amanda Kovach
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | | | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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Nelson B, Soper N, Lupoli TJ. Bacterial J-Domains with C-Terminal Tags Contact the Substrate Binding Domain of DnaK and Sequester Chaperone Activity. Chembiochem 2023; 24:e202300261. [PMID: 37556312 DOI: 10.1002/cbic.202300261] [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: 03/31/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/11/2023]
Abstract
Functional interactions between the molecular chaperone DnaK and cofactor J-proteins (DnaJs), as well as their homologs, are crucial to the maintenance of proteostasis across cell types. In the bacterial pathogen Mycobacterium tuberculosis, DnaK-DnaJ interactions are essential for cell growth and represent potential targets for antibiotic or adjuvant development. While the N-terminal J-domains of J-proteins are known to form important contacts with DnaK, C-terminal domains have varied roles. Here, we have studied the effect of adding C-terminal tags to N-terminal J-domain truncations of mycobacterial DnaJ1 and DnaJ2 to promote additional interactions with DnaK. We found that His6 tags uniquely promote binding to additional sites in the substrate binding domain at the C-terminus of DnaK. Other C-terminal tags attached to J-domains, even peptides known to interact with DnaK, do not produce the same effects. Expression of C-terminally modified DnaJ1 or DnaJ2 J-domains in mycobacterial cells suppresses chaperone activity following proteotoxic stress, which is exaggerated in the presence of a small-molecule DnaK inhibitor. Hence, this work uncovers genetically encodable J-protein variants that may be used to study chaperone-cofactor interactions in other organisms.
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Affiliation(s)
- Brock Nelson
- Department of Chemistry, New York University, New York, 10003, USA
| | - Nathan Soper
- Department of Chemistry, New York University, New York, 10003, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, 10003, USA
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4
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Richards A, Lupoli TJ. Peptide-based molecules for the disruption of bacterial Hsp70 chaperones. Curr Opin Chem Biol 2023; 76:102373. [PMID: 37516006 PMCID: PMC11217992 DOI: 10.1016/j.cbpa.2023.102373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/31/2023]
Abstract
DnaK is a chaperone that aids in nascent protein folding and the maintenance of proteome stability across bacteria. Due to the importance of DnaK in cellular proteostasis, there have been efforts to generate molecules that modulate its function. In nature, both protein substrates and antimicrobial peptides interact with DnaK. However, many of these ligands interact with other cellular machinery as well. Recent work has sought to modify these peptide scaffolds to create DnaK-selective and species-specific probes. Others have reported protein domain mimics of interaction partners to disrupt cellular DnaK function and high-throughput screening approaches to discover clinically-relevant peptidomimetics that inhibit DnaK. The described work provides a foundation for the design of new assays and molecules to regulate DnaK activity.
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Affiliation(s)
- Aweon Richards
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, NY 10003, USA.
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Abstract
Understanding the factors that shape viral evolution is critical for developing effective antiviral strategies, accurately predicting viral evolution, and preventing pandemics. One fundamental determinant of viral evolution is the interplay between viral protein biophysics and the host machineries that regulate protein folding and quality control. Most adaptive mutations in viruses are biophysically deleterious, resulting in a viral protein product with folding defects. In cells, protein folding is assisted by a dynamic system of chaperones and quality control processes known as the proteostasis network. Host proteostasis networks can determine the fates of viral proteins with biophysical defects, either by assisting with folding or by targeting them for degradation. In this review, we discuss and analyze new discoveries revealing that host proteostasis factors can profoundly shape the sequence space accessible to evolving viral proteins. We also discuss the many opportunities for research progress proffered by the proteostasis perspective on viral evolution and adaptation.
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Affiliation(s)
- Jimin Yoon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Jessica E Patrick
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - C Brandon Ogbunugafor
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
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Zahra NUA, Vagiona AC, Uddin R, Andrade-Navarro MA. Selection of Multi-Drug Targets against Drug-Resistant Mycobacterium tuberculosis XDR1219 Using the Hyperbolic Mapping of the Protein Interaction Network. Int J Mol Sci 2023; 24:14050. [PMID: 37762354 PMCID: PMC10530867 DOI: 10.3390/ijms241814050] [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] [Received: 07/19/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Tuberculosis remains the leading cause of death from a single pathogen. On the other hand, antimicrobial resistance (AMR) makes it increasingly difficult to deal with this disease. We present the hyperbolic embedding of the Mycobacterium tuberculosis protein interaction network (mtbPIN) of resistant strain (MTB XDR1219) to determine the biological relevance of its latent geometry. In this hypermap, proteins with similar interacting partners occupy close positions. An analysis of the hypermap of available drug targets (DTs) and their direct and intermediate interactors was used to identify potentially useful drug combinations and drug targets. We identify rpsA and rpsL as close DTs targeted by different drugs (pyrazinamide and aminoglycosides, respectively) and propose that the combination of these drugs could have a synergistic effect. We also used the hypermap to explain the effects of drugs that affect multiple DTs, for example, forcing the bacteria to deal with multiple stresses like ethambutol, which affects the synthesis of both arabinogalactan and lipoarabinomannan. Our strategy uncovers novel potential DTs, such as dprE1 and dnaK proteins, which interact with two close DT pairs: arabinosyltransferases (embC and embB), Ser/Thr protein kinase (pknB) and RNA polymerase (rpoB), respectively. Our approach provides mechanistic explanations for existing drugs and suggests new DTs. This strategy can also be applied to the study of other resistant strains.
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Affiliation(s)
- Noor ul Ain Zahra
- Lab 103 PCMD ext., Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan;
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany;
| | - Aimilia-Christina Vagiona
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany;
| | - Reaz Uddin
- Lab 103 PCMD ext., Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan;
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany;
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Tonui R, John RO, Edkins AL. Optimized Microscale Protein Aggregation Suppression Assay: A Method for Evaluating the Holdase Activity of Chaperones. Methods Mol Biol 2023; 2693:113-123. [PMID: 37540431 DOI: 10.1007/978-1-0716-3342-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Many molecular chaperones act as holdases by binding hydrophobic regions of substrates to prevent aggregation. Therefore, measuring holdase activity is an amenable method to determine chaperone activity. The holdase function is reliably and easily achieved by monitoring the suppression of heat-induced aggregation of well-characterized model protein substrates. However, the standard assay format requires large amounts of protein and hence is not applicable to all proteins. Using DnaK from Escherichia coli and heat-induced aggregation of malate dehydrogenase, we describe a protocol for absorbance and fluorescence-based miniaturized versions of the standard aggregation suppression assay that are affordable and have wide application for low abundance holdases. The assay can be used for both fundamental characterization of holdase function in proteins and screening of inhibitors of holdase activity.
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Affiliation(s)
- Ronald Tonui
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Ruth O John
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Adrienne L Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa.
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Protein Quality Control in Glioblastoma: A Review of the Current Literature with New Perspectives on Therapeutic Targets. Int J Mol Sci 2022; 23:ijms23179734. [PMID: 36077131 PMCID: PMC9456419 DOI: 10.3390/ijms23179734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/12/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Protein quality control allows eukaryotes to maintain proteostasis under the stress of constantly changing conditions. In this review, we discuss the current literature on PQC, highlighting flaws that must exist for malignancy to occur. At the nidus of PQC, the expression of BAG1-6 reflects the cell environment; each isoform directs proteins toward different, parallel branches of the quality control cascade. The sum of these branches creates a net shift toward either homeostasis or apoptosis. With an established role in ALP, Bag3 is necessary for cell survival in stress conditions including those of the cancerous niche (i.e., hypoxia, hypermutation). Evidence suggests that excessive Bag3–HSP70 activity not only sustains, but also propagates cancers. Its role is anti-apoptotic—which allows malignant cells to persist—and intercellular—with the production of infectious ‘oncosomes’ enabling cancer expansion and recurrence. While Bag3 has been identified as a key prognostic indicator in several cancer types, its investigation is limited regarding glioblastoma. The cochaperone HSP70 has been strongly linked with GBM, while ALP inhibitors have been shown to improve GBM susceptibility to chemotherapeutics. Given the highly resilient, frequently recurrent nature of GBM, the targeting of Bag3 is a necessary consideration for the successful and definitive treatment of GBM.
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9
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Richards A, Yawson GK, Nelson B, Lupoli TJ. Complementary protocols to evaluate inhibitors against the DnaK chaperone network. STAR Protoc 2022; 3:101381. [PMID: 35600924 PMCID: PMC9114682 DOI: 10.1016/j.xpro.2022.101381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Bacterial DnaK belongs to the Hsp70 chaperone family, which plays a critical role in maintaining proteostasis by catalyzing protein folding, and is a proposed antibacterial target in the pathogen Mycobacterium tuberculosis. Here, we describe an experimental toolbox for evaluating inhibitors against the mycobacterial DnaK chaperone network: a coupled-enzymatic assay to monitor ATPase activity, a proteolytic cleavage assay to study DnaK conformational changes upon ligand addition, as well as a protein renaturation assay to assess chaperone function. For complete details on the use and execution of this protocol, please refer to Hosfelt et al. (2021). Measurement of ATPase activation of mycobacterial DnaK by cofactors DnaJ2 and GrpE Evaluation of compound inhibition of the chaperone network using IC50 values Using SDS-PAGE to detect conformational changes of DnaK in the presence of ligands Assay of protein folding activity in response to inhibitors
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10
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Nelson B, Hong SH, Lupoli TJ. Protein Cofactor Mimics Disrupt Essential Chaperone Function in Stressed Mycobacteria. ACS Infect Dis 2022; 8:901-910. [PMID: 35412813 DOI: 10.1021/acsinfecdis.1c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial DnaK is an ATP-dependent molecular chaperone important for maintaining cellular proteostasis in concert with cofactor proteins. The cofactor DnaJ delivers non-native client proteins to DnaK and activates its ATPase activity, which is required for protein folding. In the bacterial pathogen Mycobacterium tuberculosis, DnaK is assisted by two DnaJs, DnaJ1 and DnaJ2. Functional protein-protein interactions (PPIs) between DnaK and at least one DnaJ are essential for survival of mycobacteria; hence, these PPIs represent untapped antibacterial targets. Here, we synthesize peptide-based mimetics of DnaJ1 and DnaJ2 N-terminal domains as rational inhibitors of DnaK-cofactor interactions. We find that covalently stabilized DnaJ mimetics are capable of disrupting DnaK-cofactor activity in vitro and prevent mycobacterial recovery from proteotoxic stress in vivo, leading to cell death. Since chaperones and cofactors are highly conserved, we anticipate these results will inform the design of other mimetics to modulate chaperone function across cell types.
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Affiliation(s)
- Brock Nelson
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Seong Ho Hong
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, New York 10003, United States
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