1
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Mesas Vaz C, Guembe Mülberger A, Torrent Burgas M. The battle within: how Pseudomonas aeruginosa uses host-pathogen interactions to infect the human lung. Crit Rev Microbiol 2024:1-36. [PMID: 39381985 DOI: 10.1080/1040841x.2024.2407378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 08/11/2024] [Accepted: 09/17/2024] [Indexed: 10/10/2024]
Abstract
Pseudomonas aeruginosa is a versatile Gram-negative pathogen known for its ability to invade the respiratory tract, particularly in cystic fibrosis patients. This review provides a comprehensive analysis of the multifaceted strategies for colonization, virulence, and immune evasion used by P. aeruginosa to infect the host. We explore the extensive protein arsenal of P. aeruginosa, including adhesins, exotoxins, secreted proteases, and type III and VI secretion effectors, detailing their roles in the infective process. We also address the unique challenge of treating diverse lung conditions that provide a natural niche for P. aeruginosa on the airway surface, with a particular focus in cystic fibrosis. The review also discusses the current limitations in treatment options due to antibiotic resistance and highlights promising future approaches that target host-pathogen protein-protein interactions. These approaches include the development of new antimicrobials, anti-attachment therapies, and quorum-sensing inhibition molecules. In summary, this review aims to provide a holistic understanding of the pathogenesis of P. aeruginosa in the respiratory system, offering insights into the underlying molecular mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Carmen Mesas Vaz
- The Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Alba Guembe Mülberger
- The Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marc Torrent Burgas
- The Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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2
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The DarT/DarG Toxin-Antitoxin ADP-Ribosylation System as a Novel Target for a Rational Design of Innovative Antimicrobial Strategies. Pathogens 2023; 12:pathogens12020240. [PMID: 36839512 PMCID: PMC9967889 DOI: 10.3390/pathogens12020240] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The chemical modification of cellular macromolecules by the transfer of ADP-ribose unit(s), known as ADP-ribosylation, is an ancient homeostatic and stress response control system. Highly conserved across the evolution, ADP-ribosyltransferases and ADP-ribosylhydrolases control ADP-ribosylation signalling and cellular responses. In addition to proteins, both prokaryotic and eukaryotic transferases can covalently link ADP-ribosylation to different conformations of nucleic acids, thus highlighting the evolutionary conservation of archaic stress response mechanisms. Here, we report several structural and functional aspects of DNA ADP-ribosylation modification controlled by the prototype DarT and DarG pair, which show ADP-ribosyltransferase and hydrolase activity, respectively. DarT/DarG is a toxin-antitoxin system conserved in many bacterial pathogens, for example in Mycobacterium tuberculosis, which regulates two clinically important processes for human health, namely, growth control and the anti-phage response. The chemical modulation of the DarT/DarG system by selective inhibitors may thus represent an exciting strategy to tackle resistance to current antimicrobial therapies.
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3
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Krebs SK, Stech M, Jorde F, Rakotoarinoro N, Ramm F, Marinoff S, Bahrke S, Danielczyk A, Wüstenhagen DA, Kubick S. Synthesis of an Anti-CD7 Recombinant Immunotoxin Based on PE24 in CHO and E. coli Cell-Free Systems. Int J Mol Sci 2022; 23:ijms232213697. [PMID: 36430170 PMCID: PMC9697001 DOI: 10.3390/ijms232213697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Recombinant immunotoxins (RITs) are an effective class of agents for targeted therapy in cancer treatment. In this article, we demonstrate the straight-forward production and testing of an anti-CD7 RIT based on PE24 in a prokaryotic and a eukaryotic cell-free system. The prokaryotic cell-free system was derived from Escherichia coli BL21 StarTM (DE3) cells transformed with a plasmid encoding the chaperones groEL/groES. The eukaryotic cell-free system was prepared from Chinese hamster ovary (CHO) cells that leave intact endoplasmic reticulum-derived microsomes in the cell-free reaction mix from which the RIT was extracted. The investigated RIT was built by fusing an anti-CD7 single-chain variable fragment (scFv) with the toxin domain PE24, a shortened variant of Pseudomonas Exotoxin A. The RIT was produced in both cell-free systems and tested for antigen binding against CD7 and cell killing on CD7-positive Jurkat, HSB-2, and ALL-SIL cells. CD7-positive cells were effectively killed by the anti-CD7 scFv-PE24 RIT with an IC50 value of 15 pM to 40 pM for CHO and 42 pM to 156 pM for E. coli cell-free-produced RIT. CD7-negative Raji cells were unaffected by the RIT. Toxin and antibody domain alone did not show cytotoxic effects on either CD7-positive or CD7-negative cells. To our knowledge, this report describes the production of an active RIT in E. coli and CHO cell-free systems for the first time. We provide the proof-of-concept that cell-free protein synthesis allows for on-demand testing of antibody−toxin conjugate activity in a time-efficient workflow without cell lysis or purification required.
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Affiliation(s)
- Simon K. Krebs
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute for Biotechnology, Technical University of Berlin, Ackerstrasse 76, 13355 Berlin, Germany
| | - Marlitt Stech
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Felix Jorde
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Nathanaël Rakotoarinoro
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Strasse 2 + 4, 14195 Berlin, Germany
| | - Franziska Ramm
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Sophie Marinoff
- Glycotope GmbH, Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Sven Bahrke
- Glycotope GmbH, Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Antje Danielczyk
- Glycotope GmbH, Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Doreen A. Wüstenhagen
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Stefan Kubick
- Branch Bioanalytics and Bioprocesses (IZI-BB), Fraunhofer Institute for Cell Therapy and Immunology (IZI), Am Mühlenberg 13, 14476 Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, 14476 Potsdam, Germany
- Correspondence:
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4
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Oberbach A, Schlichting N, Hagl C, Lehmann S, Kullnick Y, Friedrich M, Köhl U, Horn F, Kumbhari V, Löffler B, Schmidt F, Joskowiak D, Born F, Saha S, Bagaev E. Four decades of experience of prosthetic valve endocarditis reflect a high variety of diverse pathogens. Cardiovasc Res 2022; 119:410-428. [PMID: 35420122 DOI: 10.1093/cvr/cvac055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/04/2022] [Accepted: 03/23/2022] [Indexed: 01/18/2023] Open
Abstract
Prosthetic valve endocarditis (PVE) remains a serious condition with a high mortality rate. Precise identification of the PVE-associated pathogen/s and their virulence is essential for successful therapy, and patient survival. The commonly described PVE-associated pathogens are staphylococci, streptococci and enterococci, with Staphylococcus aureus being the most frequently diagnosed species. Furthermore, multi-drug resistance pathogens are increasing in prevalence, and continue to pose new challenges mandating a personalized approach. Blood cultures in combination with echocardiography are the most common methods to diagnose PVE, often being the only indication, it exists. In many cases, the diagnostic strategy recommended in the clinical guidelines does not identify the precise microbial agent and to frequently, false negative blood cultures are reported. Despite the fact that blood culture findings are not always a good indicator of the actual PVE agent in the valve tissue, only a minority of re-operated prostheses are subjected to microbiological diagnostic evaluation. In this review, we focus on the diversity and the complete spectrum of PVE-associated bacterial, fungal and viral pathogens in blood, and prosthetic heart valve, their possible virulence potential, and their challenges in making a microbial diagnosis. We are curious to understand if the unacceptable high mortality of PVE is associated with the high number of negative microbial findings in connection with a possible PVE. Herein, we discuss the possibilities and limits of the diagnostic methods conventionally used and make recommendations for enhanced pathogen identification. We also show possible virulence factors of the most common PVE-associated pathogens and their clinical effects. Based on blood culture, molecular biological diagnostics, and specific valve examination, better derivations for the antibiotic therapy as well as possible preventive intervention can be established in the future.
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Affiliation(s)
- Andreas Oberbach
- Department of Cardiac Surgery, Ludwig Maximilian University, Munich, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany
| | - Nadine Schlichting
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany.,Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Christian Hagl
- Department of Cardiac Surgery, Ludwig Maximilian University, Munich, Germany.,Munich Heart Alliance, Partner Site German Centre for Cardiovascular Disease (DZHK), Munich, Germany
| | - Stefanie Lehmann
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany.,Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Yvonne Kullnick
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany.,Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Maik Friedrich
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany.,Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Ulrike Köhl
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany.,Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Friedemann Horn
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany.,Institute of Clinical Immunology, University of Leipzig, Leipzig, Germany
| | - Vivek Kumbhari
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Florida, USA
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Frank Schmidt
- Proteomics Core, Weill Cornell Medical Centre Qatar, Doha, Qatar
| | - Dominik Joskowiak
- Department of Cardiac Surgery, Ludwig Maximilian University, Munich, Germany
| | - Frank Born
- Department of Cardiac Surgery, Ludwig Maximilian University, Munich, Germany
| | - Shekhar Saha
- Department of Cardiac Surgery, Ludwig Maximilian University, Munich, Germany
| | - Erik Bagaev
- Department of Cardiac Surgery, Ludwig Maximilian University, Munich, Germany
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5
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Sakari M, Tran MT, Rossjohn J, Pulliainen AT, Beddoe T, Littler DR. Crystal structures of pertussis toxin with NAD+ and analogs provide structural insights into the mechanism of its cytosolic ADP-ribosylation activity. J Biol Chem 2022; 298:101892. [PMID: 35378130 PMCID: PMC9079181 DOI: 10.1016/j.jbc.2022.101892] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/19/2022] Open
Abstract
Bordetella pertussis is the causative agent of whooping cough, a highly contagious respiratory disease. Pertussis toxin (PT), a major virulence factor secreted by B. pertussis, is an AB5-type protein complex topologically related to cholera toxin. The PT protein complex is internalized by host cells and follows a retrograde trafficking route to the endoplasmic reticulum, where it subsequently dissociates. The released enzymatic S1 subunit is then translocated from the endoplasmic reticulum into the cytosol and subsequently ADP-ribosylates the inhibitory alpha-subunits (Gαi) of heterotrimeric G proteins, thus promoting dysregulation of G protein–coupled receptor signaling. However, the mechanistic details of the ADP-ribosylation activity of PT are not well understood. Here, we describe crystal structures of the S1 subunit in complex with nicotinamide adenine dinucleotide (NAD+), with NAD+ hydrolysis products ADP-ribose and nicotinamide, with NAD+ analog PJ34, and with a novel NAD+ analog formed upon S1 subunit crystallization with 3-amino benzamide and NAD+, which we name benzamide amino adenine dinucleotide. These crystal structures provide unprecedented insights into pre- and post-NAD+ hydrolysis steps of the ADP-ribosyltransferase activity of PT. We propose that these data may aid in rational drug design approaches and further development of PT-specific small-molecule inhibitors.
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Affiliation(s)
- Moona Sakari
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Turku, Finland
| | - Mai T Tran
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, Wales, United Kingdom
| | - Arto T Pulliainen
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Turku, Finland.
| | - Travis Beddoe
- Department of Animal, Plant and Soil Science and Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia.
| | - Dene R Littler
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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6
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McCarthy M, Goncalves M, Powell H, Morey B, Turner M, Merrill AR. A Structural Approach to Anti-Virulence: A Discovery Pipeline. Microorganisms 2021; 9:microorganisms9122514. [PMID: 34946116 PMCID: PMC8704661 DOI: 10.3390/microorganisms9122514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
The anti-virulence strategy is designed to prevent bacterial virulence factors produced by pathogenic bacteria from initiating and sustaining an infection. One family of bacterial virulence factors is the mono-ADP-ribosyltransferase toxins, which are produced by pathogens as tools to compromise the target host cell. These toxins are bacterial enzymes that exploit host cellular NAD+ as the donor substrate to modify an essential macromolecule acceptor target in the host cell. This biochemical reaction modifies the target macromolecule (often protein or DNA) and functions in a binary fashion to turn the target activity on or off by blocking or impairing a critical process or pathway in the host. A structural biology approach to the anti-virulence method to neutralize the cytotoxic effect of these factors requires the search and design of small molecules that bind tightly to the enzyme active site and prevent catalytic function essentially disarming the pathogen. This method requires a high-resolution structure to serve as the model for small molecule inhibitor development, which illuminates the path to drug development. This alternative strategy to antibiotic therapy represents a paradigm shift that may circumvent multi-drug resistance in the offending microbe through anti-virulence therapy. In this report, the rationale for the anti-virulence structural approach will be discussed along with recent efforts to apply this method to treat honey bee diseases using natural products.
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7
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Anti-Virulence Strategy against the Honey Bee Pathogenic Bacterium Paenibacillus larvae via Small Molecule Inhibitors of the Bacterial Toxin Plx2A. Toxins (Basel) 2021; 13:toxins13090607. [PMID: 34564612 PMCID: PMC8470879 DOI: 10.3390/toxins13090607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/07/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
American Foulbrood, caused by Paenibacillus larvae, is the most devastating bacterial honey bee brood disease. Finding a treatment against American Foulbrood would be a huge breakthrough in the battle against the disease. Recently, small molecule inhibitors against virulence factors have been suggested as candidates for the development of anti-virulence strategies against bacterial infections. We therefore screened an in-house library of synthetic small molecules and a library of flavonoid natural products, identifying the synthetic compound M3 and two natural, plant-derived small molecules, Acacetin and Baicalein, as putative inhibitors of the recently identified P. larvae toxin Plx2A. All three inhibitors were potent in in vitro enzyme activity assays and two compounds were shown to protect insect cells against Plx2A intoxication. However, when tested in exposure bioassays with honey bee larvae, no effect on mortality could be observed for the synthetic or the plant-derived inhibitors, thus suggesting that the pathogenesis strategies of P. larvae are likely to be too complex to be disarmed in an anti-virulence strategy aimed at a single virulence factor. Our study also underscores the importance of not only testing substances in in vitro or cell culture assays, but also testing the compounds in P. larvae-infected honey bee larvae.
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8
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Yachnin BJ, Mulligan VK, Khare SD, Bailey-Kellogg C. MHCEpitopeEnergy, a Flexible Rosetta-Based Biotherapeutic Deimmunization Platform. J Chem Inf Model 2021; 61:2368-2382. [PMID: 33900750 PMCID: PMC8225355 DOI: 10.1021/acs.jcim.1c00056] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As non-"self" macromolecules, biotherapeutics can trigger an immune response that can reduce drug efficacy, require patients to be taken off therapy, or even cause life-threatening reactions. To enable the flexible and facile design of protein biotherapeutics while reducing the prevalence of T-cell epitopes that drive immune recognition, we have integrated into the Rosetta protein design suite a new scoring term that allows design protocols to account for predicted or experimentally identified epitopes in the optimized objective function. This flexible scoring term can be used in any Rosetta design trajectory, can be targeted to specific regions of a protein, and can be readily extended to work with a variety of epitope predictors. By performing extensive design runs with varied design parameter choices for three case study proteins as well as a larger diverse benchmark, we show that the incorporation of this scoring term enables the effective exploration of an alternative, deimmunized sequence space to discover diverse proteins that are potentially highly deimmunized while retaining physical and chemical qualities similar to those yielded by equivalent nondeimmunizing sequence design protocols.
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Affiliation(s)
- Brahm J. Yachnin
- Department of Chemistry and Chemical Biology and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Vikram Khipple Mulligan
- Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY, 10010, USA
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
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9
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Lugo MR, Merrill AR. Development of Anti-Virulence Therapeutics against Mono-ADP-Ribosyltransferase Toxins. Toxins (Basel) 2020; 13:toxins13010016. [PMID: 33375750 PMCID: PMC7824265 DOI: 10.3390/toxins13010016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/27/2022] Open
Abstract
Mono-ADP-ribosyltransferase toxins are often key virulence factors produced by pathogenic bacteria as tools to compromise the target host cell. These toxins are enzymes that use host cellular NAD+ as the substrate to modify a critical macromolecule target in the host cell machinery. This post-translational modification of the target macromolecule (usually protein or DNA) acts like a switch to turn the target activity on or off resulting in impairment of a critical process or pathway in the host. One approach to stymie bacterial pathogens is to curtail the toxic action of these factors by designing small molecules that bind tightly to the enzyme active site and prevent catalytic function. The inactivation of these toxins/enzymes is targeted for the site of action within the host cell and small molecule therapeutics can function as anti-virulence agents by disarming the pathogen. This represents an alternative strategy to antibiotic therapy with the potential as a paradigm shift that may circumvent multi-drug resistance in the offending microbe. In this review, work that has been accomplished during the past two decades on this approach to develop anti-virulence compounds against mono-ADP-ribosyltransferase toxins will be discussed.
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10
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Ghazalibina M, Morshedi K, Farahani RK, Babadi M, Khaledi A. Study of virulence genes and related with biofilm formation in Pseudomonas aeruginosa isolated from clinical samples of Iranian patients; A systematic review. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Yaghoubi A, Khazaei M, Hasanian SM, Avan A, C. Cho W, Soleimanpour S. Bacteriotherapy in Breast Cancer. Int J Mol Sci 2019; 20:E5880. [PMID: 31771178 PMCID: PMC6928964 DOI: 10.3390/ijms20235880] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the second most common cause of cancer-related mortality among women around the world. Conventional treatments in the fight against breast cancer, such as chemotherapy, are being challenged regarding their effectiveness. Thus, strategies for the treatment of breast cancer need to be continuously refined to achieve a better patient outcome. We know that a number of bacteria are pathogenic and some are even associated with tumor development, however, recent studies have demonstrated interesting results suggesting some bacteria may have potential for cancer therapy. Therefore, the therapeutic role of bacteria has aroused attention in medical and pharmaceutical studies. Furthermore, genetic engineering has been used in bacterial therapy and may led to greater efficacy with few side effects. Some genetically modified non-pathogenic bacterial species are more successful due to their selectivity for cancer cells but with low toxicity for normal cells. Some live, attenuated, or genetically modified bacterias are capable to multiply in tumors and inhibit their growth. This article aims to review the role of bacteria and their products including bacterial peptides, bacteriocins, and toxins for the treatment of breast cancer.
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Affiliation(s)
- Atieh Yaghoubi
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad 91387-35499, Iran;
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91387-35499, Iran
| | - Majid Khazaei
- Department of Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 9138735499, Iran;
| | - Seyed Mahdi Hasanian
- Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical, Sciences, Mashhad 91387-35499, Iran;
| | - Amir Avan
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad 91387-35499, Iran;
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Saman Soleimanpour
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad 91387-35499, Iran;
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91387-35499, Iran
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12
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Pseudomonas aeruginosa Regulatory Protein AnvM Controls Pathogenicity in Anaerobic Environments and Impacts Host Defense. mBio 2019; 10:mBio.01362-19. [PMID: 31337721 PMCID: PMC6650552 DOI: 10.1128/mbio.01362-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Infections by Pseudomonas aeruginosa, one of the most frequently isolated human pathogens, can create huge financial burdens. However, knowledge of the molecular mechanisms involved in the pathogenesis of P. aeruginosa remains elusive. We identified AnvM as a novel regulator of virulence in P. aeruginosa. Deletion of anvM altered the expression levels of more than 700 genes under aerobic and anaerobic conditions, including quorum sensing system genes and oxidative stress resistance genes. AnvM directly interacted with MvfR and Anr, thus regulating their downstream genes. More importantly, AnvM directly bound to TLR2 and TLR5, which turn on the host immune response. These findings provide insights into the significance of AnvM homologs in pathogenic bacteria and suggest a potential drug target against bacterial infection. Pseudomonas aeruginosa, one of the most common pathogens in hospital-acquired infections, is tightly controlled by a multilayered regulatory network, including the quorum sensing system (QS), the type VI secretion system (T6SS), and resistance to host immunity. We found that the P. aeruginosa 3880 (PA3880) gene, which encodes an unknown protein, acts as a regulator of anaerobic metabolism in response to oxidative stress and virulence in P. aeruginosa. More than 30 PA3880 homologs were found in other bacterial genomes, indicating that PA3880 is widely distributed in the Bacteria kingdom as a highly conserved gene. Deletion of the PA3880 gene changed the expression levels of more than 700 genes, including a group of virulence genes, under both aerobic and anaerobic conditions. To further study the mechanisms of PA3880-mediated regulation in virulence, we utilized a bacterial two-hybrid assay and found that the PA3880 protein interacted directly with QS regulator MvfR and anaerobic regulator Anr. Loss of the PA3880 protein significantly blunted the pathogenicity of P. aeruginosa, resulting in increased host survival, decreased bacterial burdens, reduced inflammatory responses, and fewer lung injuries in challenged mice hosts. Mechanistically, we found that Cys44 was a critical site for the full function of PA3880 in influencing alveolar macrophage phagocytosis and bacterial clearance. We also found that AnvM directly interacted with host receptors Toll-like receptor 2 (TLR2) and TLR5, which might lead to activation of the host immune response. Hence, we gave the name AnvM (anaerobic and virulence modulator) to the PA3880 protein. This characterization of AnvM could help to uncover new targets and strategies to treat P. aeruginosa infections.
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13
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Moss DL, Park HW, Mettu RR, Landry SJ. Deimmunizing substitutions in Pseudomonas exotoxin domain III perturb antigen processing without eliminating T-cell epitopes. J Biol Chem 2019; 294:4667-4681. [PMID: 30683694 DOI: 10.1074/jbc.ra118.006704] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/23/2019] [Indexed: 11/06/2022] Open
Abstract
Effective adaptive immune responses depend on activation of CD4+ T cells via the presentation of antigen peptides in the context of major histocompatibility complex (MHC) class II. The structure of an antigen strongly influences its processing within the endolysosome and potentially controls the identity of peptides that are presented to T cells. A recombinant immunotoxin, comprising exotoxin A domain III (PE-III) from Pseudomonas aeruginosa and a cancer-specific antibody fragment, has been developed to manage cancer, but its effectiveness is limited by the induction of neutralizing antibodies. Here, we observed that this immunogenicity is substantially reduced by substituting six residues within PE-III. Although these substitutions targeted T-cell epitopes, we demonstrate that reduced conformational stability and protease resistance were responsible for the reduced antibody titer. Analysis of mouse T-cell responses coupled with biophysical studies on single-substitution versions of PE-III suggested that modest but comprehensible changes in T-cell priming can dramatically perturb antibody production. The most strongly responsive PE-III epitope was well-predicted by a structure-based algorithm. In summary, single-residue substitutions can drastically alter the processing and immunogenicity of PE-III but have only modest effects on CD4+ T-cell priming in mice. Our findings highlight the importance of structure-based processing constraints for accurate epitope prediction.
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Affiliation(s)
- Daniel L Moss
- From the Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112 and
| | - Hee-Won Park
- From the Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112 and
| | - Ramgopal R Mettu
- the Department of Computer Science, Tulane University, New Orleans, Louisiana 70118
| | - Samuel J Landry
- From the Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana 70112 and
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14
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Ali IH, Jabir MS, Al-Shmgani HSA, Sulaiman GM, Sadoon AH. Pathological And Immunological Study On Infection With Escherichia Coli In ale BALB/c mice. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/1742-6596/1003/1/012009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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15
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Saenz-Méndez P, Eriksson M, Eriksson LA. Ligand Selectivity between the ADP-Ribosylating Toxins: An Inverse-Docking Study for Multitarget Drug Discovery. ACS OMEGA 2017; 2:1710-1719. [PMID: 30023642 PMCID: PMC6044789 DOI: 10.1021/acsomega.7b00010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/17/2017] [Indexed: 06/02/2023]
Abstract
Bacterial adenosine 5'-diphosphate-ribosylating toxins are encoded by several human pathogens, such as Pseudomonas aeruginosa (exotoxin A (ETA)), Corynebacterium diphtheriae (diphtheria toxin (DT)), and Vibrio cholerae (cholix toxin (CT)). The toxins modify eukaryotic elongation factor 2, an essential human enzyme in protein synthesis, thereby causing cell death. Targeting external virulence factors, such as the above toxins, is a promising alternative for developing new antibiotics, while at the same time avoiding drug resistance. This study aims to establish a reliable computational methodology to find a "silver bullet" able to target all three toxins. Herein, we have undertaken a detailed analysis of the active sites of ETA, DT, and CT, followed by the determination of the most appropriate selection of the size of the docking sphere. Thereafter, we tested two different approaches for normalizing the docking scores and used these to verify the best target (toxin) for each ligand. The results indicate that the methodology is suitable for identifying selective as well as multitoxin inhibitors, further validating the robustness of inverse docking for target-fishing experiments.
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Affiliation(s)
- Patricia Saenz-Méndez
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, 405 30 Göteborg, Sweden
- Computational
Chemistry and Biology Group, Facultad de Química, Universidad de la República, 11800 Montevideo, Uruguay
| | - Martin Eriksson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, 405 30 Göteborg, Sweden
| | - Leif A. Eriksson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, 405 30 Göteborg, Sweden
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16
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Affiliation(s)
- Megan Garland
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Sebastian Loscher
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Matthew Bogyo
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
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17
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Thorsell AG, Ekblad T, Karlberg T, Löw M, Pinto AF, Trésaugues L, Moche M, Cohen MS, Schüler H. Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors. J Med Chem 2016; 60:1262-1271. [PMID: 28001384 DOI: 10.1021/acs.jmedchem.6b00990] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Selective inhibitors could help unveil the mechanisms by which inhibition of poly(ADP-ribose) polymerases (PARPs) elicits clinical benefits in cancer therapy. We profiled 10 clinical PARP inhibitors and commonly used research tools for their inhibition of multiple PARP enzymes. We also determined crystal structures of these compounds bound to PARP1 or PARP2. Veliparib and niraparib are selective inhibitors of PARP1 and PARP2; olaparib, rucaparib, and talazoparib are more potent inhibitors of PARP1 but are less selective. PJ34 and UPF1069 are broad PARP inhibitors; PJ34 inserts a flexible moiety into hydrophobic subpockets in various ADP-ribosyltransferases. XAV939 is a promiscuous tankyrase inhibitor and a potent inhibitor of PARP1 in vitro and in cells, whereas IWR1 and AZ-6102 are tankyrase selective. Our biochemical and structural analysis of PARP inhibitor potencies establishes a molecular basis for either selectivity or promiscuity and provides a benchmark for experimental design in assessment of PARP inhibitor effects.
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Affiliation(s)
| | | | | | | | | | | | | | - Michael S Cohen
- Program in Chemical Biology and Department of Physiology and Pharmacology, Health & Science University , Portland, Oregon 97210, United States
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18
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A versatile strategy for the design and synthesis of novel ADP conjugates and their evaluation as potential poly(ADP-ribose) polymerase 1 inhibitors. Mol Divers 2016; 21:101-113. [PMID: 27677737 DOI: 10.1007/s11030-016-9703-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/12/2016] [Indexed: 12/24/2022]
Abstract
A versatile strategy for the synthesis of [Formula: see text] mimetics was developed, involving an efficient pyrophosphate linkage formation in key conjugates containing a functional amino group which acts as useful reactive anchor for further derivatization. These [Formula: see text] mimetics consist of ADP conjugated through a diphosphate chain to an extended aliphatic linker bearing an aromatic acid residue. A number of conjugates containing aromatic carboxylic acids were found to inhibit poly(ADP-ribose) synthesis catalyzed by poly(ADP-ribose) polymerase-1 (PARP-1). A new class of potential PARP-1 inhibitors mimicking [Formula: see text], a substrate in the PARP-1 catalyzed reaction, was proposed.
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19
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Lyons B, Ravulapalli R, Lanoue J, Lugo MR, Dutta D, Carlin S, Merrill AR. Scabin, a Novel DNA-acting ADP-ribosyltransferase from Streptomyces scabies. J Biol Chem 2016; 291:11198-215. [PMID: 27002155 PMCID: PMC4900268 DOI: 10.1074/jbc.m115.707653] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/12/2016] [Indexed: 11/06/2022] Open
Abstract
A bioinformatics strategy was used to identify Scabin, a novel DNA-targeting enzyme from the plant pathogen 87.22 strain of Streptomyces scabies Scabin shares nearly 40% sequence identity with the Pierisin family of mono-ADP-ribosyltransferase toxins. Scabin was purified to homogeneity as a 22-kDa single-domain enzyme and was shown to possess high NAD(+)-glycohydrolase (Km (NAD) = 68 ± 3 μm; kcat = 94 ± 2 min(-1)) activity with an RSQXE motif; it was also shown to target deoxyguanosine and showed sigmoidal enzyme kinetics (K0.5(deoxyguanosine) = 302 ± 12 μm; kcat = 14 min(-1)). Mass spectrometry analysis revealed that Scabin labels the exocyclic amino group on guanine bases in either single-stranded or double-stranded DNA. Several small molecule inhibitors were identified, and the most potent compounds were found to inhibit the enzyme activity with Ki values ranging from 3 to 24 μm PJ34, a well known inhibitor of poly-ADP-ribosyltransferases, was shown to be the most potent inhibitor of Scabin. Scabin was crystallized, representing the first structure of a DNA-targeting mono-ADP-ribosyltransferase enzyme; the structures of the apo-form (1.45 Å) and with two inhibitors (P6-E, 1.4 Å; PJ34, 1.6 Å) were solved. These x-ray structures are also the first high resolution structures of the Pierisin subgroup of the mono-ADP-ribosyltransferase toxin family. A model of Scabin with its DNA substrate is also proposed.
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Affiliation(s)
- Bronwyn Lyons
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Ravikiran Ravulapalli
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Jason Lanoue
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Miguel R Lugo
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Debajyoti Dutta
- the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Stephanie Carlin
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - A Rod Merrill
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
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20
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Cross-talk among flesh-eating Aeromonas hydrophila strains in mixed infection leading to necrotizing fasciitis. Proc Natl Acad Sci U S A 2016; 113:722-7. [PMID: 26733683 DOI: 10.1073/pnas.1523817113] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Necrotizing fasciitis (NF) caused by flesh-eating bacteria is associated with high case fatality. In an earlier study, we reported infection of an immunocompetent individual with multiple strains of Aeromonas hydrophila (NF1-NF4), the latter three constituted a clonal group whereas NF1 was phylogenetically distinct. To understand the complex interactions of these strains in NF pathophysiology, a mouse model was used, whereby either single or mixed A. hydrophila strains were injected intramuscularly. NF2, which harbors exotoxin A (exoA) gene, was highly virulent when injected alone, but its virulence was attenuated in the presence of NF1 (exoA-minus). NF1 alone, although not lethal to animals, became highly virulent when combined with NF2, its virulence augmented by cis-exoA expression when injected alone in mice. Based on metagenomics and microbiological analyses, it was found that, in mixed infection, NF1 selectively disseminated to mouse peripheral organs, whereas the other strains (NF2, NF3, and NF4) were confined to the injection site and eventually cleared. In vitro studies showed NF2 to be more effectively phagocytized and killed by macrophages than NF1. NF1 inhibited growth of NF2 on solid media, but ExoA of NF2 augmented virulence of NF1 and the presence of NF1 facilitated clearance of NF2 from animals either by enhanced priming of host immune system or direct killing via a contact-dependent mechanism.
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21
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Ravulapalli R, Lugo MR, Pfoh R, Visschedyk D, Poole A, Fieldhouse RJ, Pai EF, Merrill AR. Characterization of Vis Toxin, a Novel ADP-Ribosyltransferase from Vibrio splendidus. Biochemistry 2015; 54:5920-36. [PMID: 26352925 DOI: 10.1021/acs.biochem.5b00921] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vis toxin was identified by a bioinformatics strategy as a putative virulence factor produced by Vibrio splendidus with mono-ADP-ribosyltransferase activity. Vis was purified to homogeneity as a 28 kDa single-domain enzyme and was shown to possess NAD(+)-glycohydrolase [KM(NAD(+)) = 276 ± 12 μM] activity and with an R-S-E-X-E motif; it targets arginine-related compounds [KM(agmatine) = 272 ± 18 mM]. Mass spectrometry analysis revealed that Vis labels l-arginine with ADP-ribose from the NAD(+) substrate at the amino nitrogen of the guanidinium side chain. Vis is toxic to yeast when expressed in the cytoplasm under control of the CUP1 promotor, and catalytic variants lost the ability to kill the yeast host, indicating that the toxin exerts its lethality through its enzyme activity. Several small molecule inhibitors were identified from a virtual screen, and the most potent compounds were found to inhibit the transferase activity of the enzyme with Ki values ranging from 25 to 134 μM. Inhibitor compound M6 bears the necessary attributes of a solid candidate as a lead compound for therapeutic development. Vis toxin was crystallized, and the structures of the apoenzyme (1.4 Å) and the enzyme bound with NAD(+) (1.8 Å) and with the M6 inhibitor (1.5 Å) were determined. The structures revealed that Vis represents a new subgroup within the mono-ADP-ribosyltransferase toxin family.
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Affiliation(s)
- Ravikiran Ravulapalli
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Miguel R Lugo
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Roland Pfoh
- Department of Biology, York University , Toronto, ON, Canada M3J 1P3.,Department of Biochemistry, University of Toronto , Toronto, ON, Canada M5S 1A8.,Campbell Family Institute for Cancer Research, Princess Margaret Hospital , Toronto, ON, Canada M5G 1L7
| | - Danielle Visschedyk
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Amanda Poole
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Robert J Fieldhouse
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center , New York, New York 10065, United States.,Department of Systems Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Emil F Pai
- Department of Biochemistry, University of Toronto , Toronto, ON, Canada M5S 1A8.,Campbell Family Institute for Cancer Research, Princess Margaret Hospital , Toronto, ON, Canada M5G 1L7.,Departments of Medical Biophysics and Molecular Genetics, University of Toronto , Toronto, ON, Canada M5S 1A8
| | - A Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
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22
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Lugo MR, Merrill AR. The Father, Son and Cholix Toxin: The Third Member of the DT Group Mono-ADP-Ribosyltransferase Toxin Family. Toxins (Basel) 2015. [PMID: 26213968 PMCID: PMC4549722 DOI: 10.3390/toxins7082757] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The cholix toxin gene (chxA) was first identified in V. cholerae strains in 2007, and the protein was identified by bioinformatics analysis in 2008. It was identified as the third member of the diphtheria toxin group of mono-ADP-ribosyltransferase toxins along with P. aeruginosa exotoxin A and C. diphtheriae diphtheria toxin. Our group determined the structure of the full-length, three-domain cholix toxin at 2.1 Å and its C-terminal catalytic domain (cholixc) at 1.25 Å resolution. We showed that cholix toxin is specific for elongation factor 2 (diphthamide residue), similar to exotoxin A and diphtheria toxin. Cholix toxin possesses molecular features required for infection of eukaryotes by receptor-mediated endocytosis, translocation to the host cytoplasm and inhibition of protein synthesis. More recently, we also solved the structure of full-length cholix toxin in complex with NAD+ and proposed a new kinetic model for cholix enzyme activity. In addition, we have taken a computational approach that revealed some important properties of the NAD+-binding pocket at the residue level, including the role of crystallographic water molecules in the NAD+ substrate interaction. We developed a pharmacophore model of cholix toxin, which revealed a cationic feature in the side chain of cholix toxin active-site inhibitors that may determine the active pose. Notably, several recent reports have been published on the role of cholix toxin as a major virulence factor in V. cholerae (non-O1/O139 strains). Additionally, FitzGerald and coworkers prepared an immunotoxin constructed from domains II and III as a cancer treatment strategy to complement successful immunotoxins derived from P. aeruginosa exotoxin A.
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Affiliation(s)
- Miguel R Lugo
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - A Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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23
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Di Girolamo M. Regulation of nucleocytoplasmic transport by ADP-ribosylation: the emerging role of karyopherin-β1 mono-ADP-ribosylation by ARTD15. Curr Top Microbiol Immunol 2015; 384:189-209. [PMID: 25037261 DOI: 10.1007/82_2014_421] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Post-translational modifications of a cellular protein by mono- and poly-ADP-ribosylation involve the cleavage of NAD (+) , with the release of its nicotinamide moiety. This is accompanied by the transfer of a single (mono-) or several (poly-) ADP-ribose molecules from NAD (+) to a specific amino-acid residue of the protein. Recent reports have shed new light on the correlation between NAD (+) -dependent ADP-ribosylation reactions and the endoplasmic reticulum, in addition to the well-documented roles of these reactions in the nucleus and mitochondria. We have demonstrated that ARTD15/PARP16 is a novel mono-ADP-ribosyltransferase with a new intracellular location, as it is associated with the endoplasmic reticulum. The endoplasmic reticulum, which is a membranous network of interconnected tubules and cisternae, is responsible for specialised cellular functions, including protein folding and protein transport. Maintenance of specialised cellular functions requires the correct flow of information between separate organelles that is made possible through the nucleocytoplasmic trafficking of proteins. ARTD15 appears to have a role in nucleocytoplasmic shuttling, through karyopherin-β1 mono-ADP-ribosylation. This is in line with the emerging role of ADP-ribosylation in the regulation of intracellular trafficking of cellular proteins. Indeed, other, ADP-ribosyltransferases like ARTD1/PARP1, have been reported to regulate nucleocytoplasmic trafficking of crucial proteins, including p53 and NF-κB, and as a consequence, to modulate the subcellular localisation of these proteins under both physiological and pathological conditions.
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Affiliation(s)
- Maria Di Girolamo
- G-Protein-Mediated Signalling Laboratory, Fondazione Mario Negri Sud, Via Nazionale 8/A, 66030, S. Maria Imbaro (CH), Italy,
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24
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Lugo MR, Merrill AR. A comparative structure-function analysis of active-site inhibitors of Vibrio cholerae cholix toxin. J Mol Recognit 2015; 28:539-52. [PMID: 25756608 DOI: 10.1002/jmr.2469] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/26/2015] [Accepted: 01/27/2015] [Indexed: 01/27/2023]
Abstract
Cholix toxin from Vibrio cholerae is a novel mono-ADP-ribosyltransferase (mART) toxin that shares structural and functional properties with Pseudomonas aeruginosa exotoxin A and Corynebacterium diphtheriae diphtheria toxin. Herein, we have used the high-resolution X-ray structure of full-length cholix toxin in the apo form, NAD(+) bound, and 10 structures of the cholix catalytic domain (C-domain) complexed with several strong inhibitors of toxin enzyme activity (NAP, PJ34, and the P-series) to study the binding mode of the ligands. A pharmacophore model based on the active pose of NAD(+) was compared with the active conformation of the inhibitors, which revealed a cationic feature in the side chain of the inhibitors that may determine the active pose. Moreover, a conformational search was conducted for the missing coordinates of one of the main active-site loops (R-loop). The resulting structural models were used to evaluate the interaction energies and for 3D-QSAR modeling. Implications for a rational drug design approach for mART toxins were derived.
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Affiliation(s)
- Miguel R Lugo
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - A Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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25
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Lugo MR, Merrill AR. Pocket analysis of the full-length cholix toxin. An assessment of the structure-dynamics of the apo catalytic domain. J Biomol Struct Dyn 2015; 33:2452-68. [PMID: 25559625 DOI: 10.1080/07391102.2014.1000972] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cholix toxin from Vibrio cholerae is the third member of the diphtheria toxin (DT) group of mono-ADP-ribosyltransferase (mART) bacterial toxins. It shares structural and functional properties with Pseudomonas aeruginosa exotoxin A and Corynebacterium diphtheriae DT. Cholix toxin is an important model for the development of antivirulence approaches and therapeutics against these toxins from pathogenic bacteria. Herein, we have used the high-resolution X-ray structure of full-length cholix complexed with NAD(+) to describe the properties of the NAD(+)-binding pocket at the residue level, including the role of crystallographic water molecules in the NAD(+) substrate interaction. The full-length apo cholix structure is used to describe the putative NAD(+)-binding site(s) and to correlate biochemical with crystallographic data to study the stoichiometry and orientation of bound NAD(+) molecules. We quantitatively describe the NAD(+) substrate interactions on a residue basis for the main 22 pocket residues in cholixf, a glycerol and 5 contact water molecules as part of the recognition surface by the substrate according to the conditions of crystallization. In addition, the dynamic properties of an in silico version of the catalytic domain were investigated in order to understand the lack of electronic density for one of the main flexible loops (R-loop) in the pocket of X-ray complexes. Implications for a rational drug design approach for mART toxins are derived.
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Affiliation(s)
- Miguel R Lugo
- a Department of Molecular and Cellular Biology, Science Complex , University of Guelph , Guelph , ON , Canada N1G2W
| | - A Rod Merrill
- a Department of Molecular and Cellular Biology, Science Complex , University of Guelph , Guelph , ON , Canada N1G2W
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26
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Krska D, Ravulapalli R, Fieldhouse RJ, Lugo MR, Merrill AR. C3larvin toxin, an ADP-ribosyltransferase from Paenibacillus larvae. J Biol Chem 2014; 290:1639-53. [PMID: 25477523 DOI: 10.1074/jbc.m114.589846] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
C3larvin toxin was identified by a bioinformatic strategy as a putative mono-ADP-ribosyltransferase and a possible virulence factor from Paenibacillus larvae, which is the causative agent of American Foulbrood in honey bees. C3larvin targets RhoA as a substrate for its transferase reaction, and kinetics for both the NAD(+) (Km = 34 ± 12 μm) and RhoA (Km = 17 ± 3 μm) substrates were characterized for this enzyme from the mono-ADP-ribosyltransferase C3 toxin subgroup. C3larvin is toxic to yeast when expressed in the cytoplasm, and catalytic variants of the enzyme lost the ability to kill the yeast host, indicating that the toxin exerts its lethality through its enzyme activity. A small molecule inhibitor of C3larvin enzymatic activity was discovered called M3 (Ki = 11 ± 2 μm), and to our knowledge, is the first inhibitor of transferase activity of the C3 toxin family. C3larvin was crystallized, and its crystal structure (apoenzyme) was solved to 2.3 Å resolution. C3larvin was also shown to have a different mechanism of cell entry from other C3 toxins.
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Affiliation(s)
- Daniel Krska
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ravikiran Ravulapalli
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Robert J Fieldhouse
- the Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, and the Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel R Lugo
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - A Rod Merrill
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada,
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27
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Tang GW, Altman RB. Knowledge-based fragment binding prediction. PLoS Comput Biol 2014; 10:e1003589. [PMID: 24762971 PMCID: PMC3998881 DOI: 10.1371/journal.pcbi.1003589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 03/11/2014] [Indexed: 11/18/2022] Open
Abstract
Target-based drug discovery must assess many drug-like compounds for potential activity. Focusing on low-molecular-weight compounds (fragments) can dramatically reduce the chemical search space. However, approaches for determining protein-fragment interactions have limitations. Experimental assays are time-consuming, expensive, and not always applicable. At the same time, computational approaches using physics-based methods have limited accuracy. With increasing high-resolution structural data for protein-ligand complexes, there is now an opportunity for data-driven approaches to fragment binding prediction. We present FragFEATURE, a machine learning approach to predict small molecule fragments preferred by a target protein structure. We first create a knowledge base of protein structural environments annotated with the small molecule substructures they bind. These substructures have low-molecular weight and serve as a proxy for fragments. FragFEATURE then compares the structural environments within a target protein to those in the knowledge base to retrieve statistically preferred fragments. It merges information across diverse ligands with shared substructures to generate predictions. Our results demonstrate FragFEATURE's ability to rediscover fragments corresponding to the ligand bound with 74% precision and 82% recall on average. For many protein targets, it identifies high scoring fragments that are substructures of known inhibitors. FragFEATURE thus predicts fragments that can serve as inputs to fragment-based drug design or serve as refinement criteria for creating target-specific compound libraries for experimental or computational screening.
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Affiliation(s)
- Grace W. Tang
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Russ B. Altman
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail:
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28
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Omori S, Kitao A. CyClus: A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys. Proteins 2013; 81:1005-16. [DOI: 10.1002/prot.24252] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 12/20/2012] [Accepted: 01/04/2013] [Indexed: 11/07/2022]
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Visschedyk D, Rochon A, Tempel W, Dimov S, Park HW, Merrill AR. Certhrax toxin, an anthrax-related ADP-ribosyltransferase from Bacillus cereus. J Biol Chem 2012; 287:41089-102. [PMID: 22992735 DOI: 10.1074/jbc.m112.412809] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We identified Certhrax, the first anthrax-like mART toxin from the pathogenic G9241 strain of Bacillus cereus. Certhrax shares 31% sequence identity with anthrax lethal factor from Bacillus anthracis; however, we have shown that the toxicity of Certhrax resides in the mART domain, whereas anthrax uses a metalloprotease mechanism. Like anthrax lethal factor, Certhrax was found to require protective antigen for host cell entry. This two-domain enzyme was shown to be 60-fold more toxic to mammalian cells than anthrax lethal factor. Certhrax localizes to distinct regions within mouse RAW264.7 cells by 10 min postinfection and is extranuclear in its cellular location. Substitution of catalytic residues shows that the mART function is responsible for the toxicity, and it binds NAD(+) with high affinity (K(D) = 52.3 ± 12.2 μM). We report the 2.2 Å Certhrax structure, highlighting its structural similarities and differences with anthrax lethal factor. We also determined the crystal structures of two good inhibitors (P6 (K(D) = 1.7 ± 0.2 μM, K(i) = 1.8 ± 0.4 μM) and PJ34 (K(D) = 5.8 ± 2.6 μM, K(i) = 9.6 ± 0.3 μM)) in complex with Certhrax. As with other toxins in this family, the phosphate-nicotinamide loop moves toward the NAD(+) binding site with bound inhibitor. These results indicate that Certhrax may be important in the pathogenesis of B. cereus.
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Affiliation(s)
- Danielle Visschedyk
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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D'Urzo N, Malito E, Biancucci M, Bottomley MJ, Maione D, Scarselli M, Martinelli M. The structure of Clostridium difficile toxin A glucosyltransferase domain bound to Mn2+ and UDP provides insights into glucosyltransferase activity and product release. FEBS J 2012; 279:3085-97. [PMID: 22747490 DOI: 10.1111/j.1742-4658.2012.08688.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Clostridiumdifficile toxin A (TcdA) is a member of the large clostridial toxin family, and is responsible, together with C. difficile toxin B (TcdB), for many clinical symptoms d ring human infections. Like other large clostridial toxins, TcdA catalyzes the glucosylation of GTPases, and is able to inactivate small GTPases within the host cell. Here, we report the crystal structures of the TcdA glucosyltransferase domain (TcdA-GT) in the apo form and in the presence of Mn(2+) and hydrolyzed UDP-glucose. These structures, together with the recently reported crystal structure of TcdA-GT bound to UDP-glucose, provide a detailed understanding of the conformational changes of TcdA that occur during the catalytic cycle. Indeed, we present a new intermediate conformation of a so-called 'lid' loop (residues 510-522 in TcdA), concomitant with the absence of glucose in the catalytic domain. The recombinant TcdA was expressed in Brevibacillus in the inactive apo form. High thermal stability of wild-type TcdA was observed only after the addition of both Mn(2+) and UDP-glucose. The glucosylhydrolase activity, which is readily restored after reconstitution with both these cofactors, was similar to that reported for TcdB. Interestingly, we found that ammonium, like K(+) , is able to activate the UDP-glucose hydrolase activities of TcdA. Consequently, the presence of ammonium in the crystallization buffer enabled us to obtain the first crystal structure of TcdA-GT bound to the hydrolysis product UDP.
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Di Paola S, Micaroni M, Di Tullio G, Buccione R, Di Girolamo M. PARP16/ARTD15 is a novel endoplasmic-reticulum-associated mono-ADP-ribosyltransferase that interacts with, and modifies karyopherin-ß1. PLoS One 2012; 7:e37352. [PMID: 22701565 PMCID: PMC3372510 DOI: 10.1371/journal.pone.0037352] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 04/20/2012] [Indexed: 11/18/2022] Open
Abstract
Background Protein mono-ADP-ribosylation is a reversible post-translational modification that modulates the function of target proteins. The enzymes that catalyze this reaction in mammalian cells are either bacterial pathogenic toxins or endogenous cellular ADP-ribosyltransferases. The latter include members of three different families of proteins: the well characterized arginine-specific ecto-enzymes ARTCs, two sirtuins and, more recently, novel members of the poly(ADP-ribose) polymerase (PARP/ARTD) family that have been suggested to act as cellular mono-ADP-ribosyltransferases. Here, we report on the characterisation of human ARTD15, the only known ARTD family member with a putative C-terminal transmembrane domain. Methodology/Principal Findings Immunofluorescence and electron microscopy were performed to characterise the sub-cellular localisation of ARTD15, which was found to be associated with membranes of the nuclear envelope and endoplasmic reticulum. The orientation of ARTD15 was determined using protease protection assay, and is shown to be a tail-anchored protein with a cytosolic catalytic domain. Importantly, by combining immunoprecipitation with mass spectrometry and using cell lysates from cells over-expressing FLAG-ARTD15, we have identified karyopherin-ß1, a component of the nuclear trafficking machinery, as a molecular partner of ARTD15. Finally, we demonstrate that ARTD15 is a mono-ADP-ribosyltransferase able to induce the ADP-ribosylation of karyopherin-ß1, thus defining the first substrate for this enzyme. Conclusions/Significance Our data reveal that ARTD15 is a novel ADP-ribosyltransferase enzyme with a new intracellular location. Finally, the identification of karyopherin-ß1 as a target of ARTD15-mediated ADP-ribosylation, hints at a novel regulatory mechanism of karyopherin-ß1 functions.
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Affiliation(s)
- Simone Di Paola
- Consorzio Mario Negri Sud, Santa Maria Imbaro (Chieti), Italy
| | | | | | | | - Maria Di Girolamo
- Consorzio Mario Negri Sud, Santa Maria Imbaro (Chieti), Italy
- * E-mail:
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Ivarsson ME, Leroux JC, Castagner B. Targeting bacterial toxins. Angew Chem Int Ed Engl 2012; 51:4024-45. [PMID: 22441768 DOI: 10.1002/anie.201104384] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/21/2011] [Indexed: 12/18/2022]
Abstract
Protein toxins constitute the main virulence factors of several species of bacteria and have proven to be attractive targets for drug development. Lead candidates that target bacterial toxins range from small molecules to polymeric binders, and act at each of the multiple steps in the process of toxin-mediated pathogenicity. Despite recent and significant advances in the field, a rationally designed drug that targets toxins has yet to reach the market. This Review presents the state of the art in bacterial toxin targeted drug development with a critical consideration of achieved breakthroughs and withstanding challenges. The discussion focuses on A-B-type protein toxins secreted by four species of bacteria, namely Clostridium difficile (toxins A and B), Vibrio cholerae (cholera toxin), enterohemorrhagic Escherichia coli (Shiga toxin), and Bacillus anthracis (anthrax toxin), which are the causative agents of diseases for which treatments need to be improved.
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Affiliation(s)
- Mattias E Ivarsson
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology Zurich, Wolfgang-Pauli-Strasse 10, Zurich, Switzerland
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34
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Lee D, de Beer TAP, Laskowski RA, Thornton JM, Orengo CA. 1,000 structures and more from the MCSG. BMC STRUCTURAL BIOLOGY 2011; 11:2. [PMID: 21219649 PMCID: PMC3024214 DOI: 10.1186/1472-6807-11-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 01/10/2011] [Indexed: 11/10/2022]
Abstract
Background The Midwest Center for Structural Genomics (MCSG) is one of the large-scale centres of the Protein Structure Initiative (PSI). During the first two phases of the PSI the MCSG has solved over a thousand protein structures. A criticism of structural genomics is that target selection strategies mean that some structures are solved without having a known function and thus are of little biomedical significance. Structures of unknown function have stimulated the development of methods for function prediction from structure. Results We show that the MCSG has met the stated goals of the PSI and use online resources and readily available function prediction methods to provide functional annotations for more than 90% of the MCSG structures. The structure-to-function prediction method ProFunc provides likely functions for many of the MCSG structures that cannot be annotated by sequence-based methods. Conclusions Although the focus of the PSI was structural coverage, many of the structures solved by the MCSG can also be associated with functional classes and biological roles of possible biomedical value.
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Affiliation(s)
- David Lee
- Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.
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35
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Wang M, Soyano T, Machida S, Yang JY, Jung C, Chua NH, Yuan YA. Molecular insights into plant cell proliferation disturbance by Agrobacterium protein 6b. Genes Dev 2010; 25:64-76. [PMID: 21156810 DOI: 10.1101/gad.1985511] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Agrobacterium Ti plasmid (T-DNA) 6b proteins interact with many different host proteins implicated in plant cell proliferation. Here, we show that Arabidopsis plants overexpressing 6b display microRNA (miRNA) deficiency by directly targeting SERRATE and AGO1 via a specific loop fragment (residues 40-55). In addition, we report the crystal structures of Agrobacterium tumefaciens AK6b at 2.1 Å, Agrobacterium vitis AB6b at 1.65 Å, and Arabidopsis ADP ribosylation factor (ARF) at 1.8 Å. The 6b structure adopts an ADP-ribosylating toxin fold closely related to cholera toxin. In vitro ADP ribosylation analysis demonstrates that 6b represents a new toxin family, with Tyr 66, Thr 93, and Tyr 153 as the ADP ribosylation catalytic residues in the presence of Arabidopsis ARF and GTP. Our work provides molecular insights, suggesting that 6b regulates plant cell growth by the disturbance of the miRNA pathway through its ADP ribosylation activity.
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Affiliation(s)
- Meimei Wang
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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Newly discovered and characterized antivirulence compounds inhibit bacterial mono-ADP-ribosyltransferase toxins. Antimicrob Agents Chemother 2010; 55:983-91. [PMID: 21135177 DOI: 10.1128/aac.01164-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The mono-ADP-ribosyltransferase toxins are bacterial virulence factors that contribute to many disease states in plants, animals, and humans. These toxins function as enzymes that target various host proteins and covalently attach an ADP-ribose moiety that alters target protein function. We tested compounds from a virtual screen of commercially available compounds combined with a directed poly(ADP-ribose) polymerase (PARP) inhibitor library and found several compounds that bind tightly and inhibit toxins from Pseudomonas aeruginosa and Vibrio cholerae. The most efficacious compounds completely protected human lung epithelial cells against the cytotoxicity of these bacterial virulence factors. Moreover, we determined high-resolution crystal structures of the best inhibitors in complex with cholix toxin to reveal important criteria for inhibitor binding and mechanism of action. These results provide new insight into development of antivirulence compounds for treating many bacterial diseases.
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The Mycobacterium tuberculosis phagosome is a HLA-I processing competent organelle. PLoS Pathog 2009; 5:e1000374. [PMID: 19360129 PMCID: PMC2661020 DOI: 10.1371/journal.ppat.1000374] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 03/10/2009] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) resides in a long-lived phagosomal compartment that resists maturation. The manner by which Mtb antigens are processed and presented on MHC Class I molecules is poorly understood. Using human dendritic cells and IFN-γ release by CD8+ T cell clones, we examined the processing and presentation pathway for two Mtb–derived antigens, each presented by a distinct HLA-I allele (HLA-Ia versus HLA-Ib). Presentation of both antigens is blocked by the retrotranslocation inhibitor exotoxin A. Inhibitor studies demonstrate that, after reaching the cytosol, both antigens require proteasomal degradation and TAP transport, but differ in the requirement for ER–golgi egress and new protein synthesis. Specifically, presentation by HLA-B8 but not HLA-E requires newly synthesized HLA-I and transport through the ER–golgi. Phenotypic analysis of the Mtb phagosome by flow organellometry revealed the presence of Class I and loading accessory molecules, including TAP and PDI. Furthermore, loaded HLA-I:peptide complexes are present within the Mtb phagosome, with a pronounced bias towards HLA-E:peptide complexes. In addition, protein analysis also reveals that HLA-E is enriched within the Mtb phagosome compared to HLA-A2. Together, these data suggest that the phagosome, through acquisition of ER–localized machinery and as a site of HLA-I loading, plays a vital role in the presentation of Mtb–derived antigens, similar to that described for presentation of latex bead-associated antigens. This is, to our knowledge, the first description of this presentation pathway for an intracellular pathogen. Moreover, these data suggest that HLA-E may play a unique role in the presentation of phagosomal antigens. Major Histocompatibility Complex Class I (MHC-I) generally serves to present peptides derived from cytosolic proteins to CD8+ T lymphocytes, thereby alerting the immune system that the cell is infected. The machinery required for MHC-I antigen processing and presentation is localized to the cytosol and endoplasmic reticulum (ER). After phagocytosis of bacteria, it is unclear how bacterial antigens are presented by MHC-I, as they are segregated from this machinery. In this report, we examine processing and presentation of two proteins derived from the intracellular pathogen, Mycobacterium tuberculosis (Mtb). We find that Mtb proteins are able to access the cytosol where they are degraded by the proteasome. Mtb proteins reach the cytosol by retrotranslocation, a process which normally functions to transport misfolded proteins from the ER to the cytosol. Furthermore, the Mtb phagosome contains ER–derived members of the MHC-I peptide loading complex, which aid in loading peptides onto MHC-I molecules. Finally, we detect loaded HLA-I:peptide complexes in the phagosome, demonstrating that loading can occur in the Mtb phagosome. Together, these findings suggest that the Mtb phagosome, through acquisition of ER–derived MHC-I machinery and as a site of MHC-I loading, plays a vital role in presentation of Mtb–derived peptides on MHC-I.
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Jørgensen R, Wang Y, Visschedyk D, Merrill AR. The nature and character of the transition state for the ADP-ribosyltransferase reaction. EMBO Rep 2008; 9:802-9. [PMID: 18583986 PMCID: PMC2515215 DOI: 10.1038/embor.2008.90] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Revised: 04/21/2008] [Accepted: 04/21/2008] [Indexed: 11/08/2022] Open
Abstract
Exotoxin A (ExoA) from Pseudomonas aeruginosa is an important virulence factor that belongs to a class of exotoxins that are secreted by pathogenic bacteria which cause human diseases such as cholera, diphtheria, pneumonia and whooping cough. We present the first crystal structures, to our knowledge, of ExoA in complex with elongation factor 2 (eEF2) and intact NAD(+), which indicate a direct role of two active-site loops in ExoA during the catalytic cycle. One loop moves to form a solvent cover for the active site of the enzyme and reaches towards the target residue (diphthamide) in eEF2 forming an important hydrogen bond. The NAD(+) substrate adopts a conformation remarkably different from that of the NAD(+) analogue, betaTAD, observed in previous structures, and fails to trigger any loop movements. Mutational studies of the two loops in the toxin identify several residues important for catalytic activity, in particular Glu 546 and Arg 551, clearly supporting the new complex structures. On the basis of these data, we propose a transition-state model for the toxin-catalysed reaction.
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Affiliation(s)
- René Jørgensen
- Department of Molecular and Cellular Biology, University of Guelph, Building No. 140, 50 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Yolanda Wang
- Department of Molecular and Cellular Biology, University of Guelph, Building No. 140, 50 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Danielle Visschedyk
- Department of Molecular and Cellular Biology, University of Guelph, Building No. 140, 50 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - A Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Building No. 140, 50 Gordon Street, Guelph, Ontario N1G 2W1, Canada
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Arnoldo A, Curak J, Kittanakom S, Chevelev I, Lee VT, Sahebol-Amri M, Koscik B, Ljuma L, Roy PJ, Bedalov A, Giaever G, Nislow C, Merrill RA, Lory S, Stagljar I. Identification of small molecule inhibitors of Pseudomonas aeruginosa exoenzyme S using a yeast phenotypic screen. PLoS Genet 2008; 4:e1000005. [PMID: 18454192 PMCID: PMC2265467 DOI: 10.1371/journal.pgen.1000005] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 01/17/2008] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that is a key factor in the mortality of cystic fibrosis patients, and infection represents an increased threat for human health worldwide. Because resistance of Pseudomonas aeruginosa to antibiotics is increasing, new inhibitors of pharmacologically validated targets of this bacterium are needed. Here we demonstrate that a cell-based yeast phenotypic assay, combined with a large-scale inhibitor screen, identified small molecule inhibitors that can suppress the toxicity caused by heterologous expression of selected Pseudomonas aeruginosa ORFs. We identified the first small molecule inhibitor of Exoenzyme S (ExoS), a toxin involved in Type III secretion. We show that this inhibitor, exosin, modulates ExoS ADP-ribosyltransferase activity in vitro, suggesting the inhibition is direct. Moreover, exosin and two of its analogues display a significant protective effect against Pseudomonas infection in vivo. Furthermore, because the assay was performed in yeast, we were able to demonstrate that several yeast homologues of the known human ExoS targets are likely ADP-ribosylated by the toxin. For example, using an in vitro enzymatic assay, we demonstrate that yeast Ras2p is directly modified by ExoS. Lastly, by surveying a collection of yeast deletion mutants, we identified Bmh1p, a yeast homologue of the human FAS, as an ExoS cofactor, revealing that portions of the bacterial toxin mode of action are conserved from yeast to human. Taken together, our integrated cell-based, chemical-genetic approach demonstrates that such screens can augment traditional drug screening approaches and facilitate the discovery of new compounds against a broad range of human pathogens.
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Affiliation(s)
- Anthony Arnoldo
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Jasna Curak
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Saranya Kittanakom
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Igor Chevelev
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Vincent T. Lee
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mehdi Sahebol-Amri
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Becky Koscik
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Lana Ljuma
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Peter J. Roy
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Antonio Bedalov
- Clinical Research and Human Biology Divisions, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Guri Giaever
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Ontario, Canada
| | - Corey Nislow
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Ontario, Canada
| | - Rod A. Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
| | - Stephen Lory
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Igor Stagljar
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- * E-mail:
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40
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Jørgensen R, Purdy AE, Fieldhouse RJ, Kimber MS, Bartlett DH, Merrill AR. Cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae. J Biol Chem 2008; 283:10671-8. [PMID: 18276581 DOI: 10.1074/jbc.m710008200] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ADP-ribosyltransferases are a class of enzymes that display activity in a variety of bacterial pathogens responsible for causing diseases in plants and animals, including those affecting mankind, such as diphtheria, cholera, and whooping cough. We report the characterization of a novel toxin from Vibrio cholerae, which we call cholix toxin. The toxin is active against mammalian cells (IC(50) = 4.6 +/- 0.4 ng/ml) and crustaceans (Artemia nauplii LD(50) = 10 +/- 2 mug/ml). Here we show that this toxin is the third member of the diphthamide-specific class of ADP-ribose transferases and that it possesses specific ADP-ribose transferase activity against ribosomal eukaryotic elongation factor 2. We also describe the high resolution crystal structures of the multidomain toxin and its catalytic domain at 2.1- and 1.25-A resolution, respectively. The new structural data show that cholix toxin possesses the necessary molecular features required for infection of eukaryotes by receptor-mediated endocytosis, translocation to the host cytoplasm, and inhibition of protein synthesis by specific modification of elongation factor 2. The crystal structures also provide important insight into the structural basis for activation of toxin ADP-ribosyltransferase activity. These results indicate that cholix toxin may be an important virulence factor of Vibrio cholerae that likely plays a significant role in the survival of the organism in an aquatic environment.
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Affiliation(s)
- René Jørgensen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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41
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Hassa PO, Haenni SS, Elser M, Hottiger MO. Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiol Mol Biol Rev 2006; 70:789-829. [PMID: 16959969 PMCID: PMC1594587 DOI: 10.1128/mmbr.00040-05] [Citation(s) in RCA: 508] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Since poly-ADP ribose was discovered over 40 years ago, there has been significant progress in research into the biology of mono- and poly-ADP-ribosylation reactions. During the last decade, it became clear that ADP-ribosylation reactions play important roles in a wide range of physiological and pathophysiological processes, including inter- and intracellular signaling, transcriptional regulation, DNA repair pathways and maintenance of genomic stability, telomere dynamics, cell differentiation and proliferation, and necrosis and apoptosis. ADP-ribosylation reactions are phylogenetically ancient and can be classified into four major groups: mono-ADP-ribosylation, poly-ADP-ribosylation, ADP-ribose cyclization, and formation of O-acetyl-ADP-ribose. In the human genome, more than 30 different genes coding for enzymes associated with distinct ADP-ribosylation activities have been identified. This review highlights the recent advances in the rapidly growing field of nuclear mono-ADP-ribosylation and poly-ADP-ribosylation reactions and the distinct ADP-ribosylating enzyme families involved in these processes, including the proposed family of novel poly-ADP-ribose polymerase-like mono-ADP-ribose transferases and the potential mono-ADP-ribosylation activities of the sirtuin family of NAD(+)-dependent histone deacetylases. A special focus is placed on the known roles of distinct mono- and poly-ADP-ribosylation reactions in physiological processes, such as mitosis, cellular differentiation and proliferation, telomere dynamics, and aging, as well as "programmed necrosis" (i.e., high-mobility-group protein B1 release) and apoptosis (i.e., apoptosis-inducing factor shuttling). The proposed molecular mechanisms involved in these processes, such as signaling, chromatin modification (i.e., "histone code"), and remodeling of chromatin structure (i.e., DNA damage response, transcriptional regulation, and insulator function), are described. A potential cross talk between nuclear ADP-ribosylation processes and other NAD(+)-dependent pathways is discussed.
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Affiliation(s)
- Paul O Hassa
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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42
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Yates SP, Jørgensen R, Andersen GR, Merrill AR. Stealth and mimicry by deadly bacterial toxins. Trends Biochem Sci 2006; 31:123-33. [PMID: 16406634 DOI: 10.1016/j.tibs.2005.12.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 11/21/2005] [Accepted: 12/21/2005] [Indexed: 11/19/2022]
Abstract
Diphtheria toxin and exotoxin A are well-characterized members of the ADP-ribosyltransferase toxin family that function as virulence factors in the pathogenic bacteria Corynebacterium diphtheriae and Pseudomonas aeruginosa. Recent high-resolution structural data of the Michaelis (enzyme-substrate) complex of the P. aeruginosa toxin with an NAD(+) analog and eukaryotic elongation factor 2 (eEF2) have provided insights into the mechanism of inactivation of protein synthesis caused by these protein factors. In addition, rigorous steady-state and stopped-flow kinetic analyses of the toxin-catalyzed reaction, in combination with inhibitor studies, have resulted in a quantum leap in our understanding of the mechanistic details of this deadly enzyme mechanism. It is now apparent that these toxins use stealth and molecular mimicry in unleashing their toxic strategy in the infected host eukaryotic cell.
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Affiliation(s)
- Susan P Yates
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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43
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Jørgensen R, Merrill AR, Yates SP, Marquez VE, Schwan AL, Boesen T, Andersen GR. Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry. Nature 2005; 436:979-84. [PMID: 16107839 DOI: 10.1038/nature03871] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Accepted: 06/03/2005] [Indexed: 11/09/2022]
Abstract
The bacteria causing diphtheria, whooping cough, cholera and other diseases secrete mono-ADP-ribosylating toxins that modify intracellular proteins. Here, we describe four structures of a catalytically active complex between a fragment of Pseudomonas aeruginosa exotoxin A (ETA) and its protein substrate, translation elongation factor 2 (eEF2). The target residue in eEF2, diphthamide (a modified histidine), spans across a cleft and faces the two phosphates and a ribose of the non-hydrolysable NAD+ analogue, betaTAD. This suggests that the diphthamide is involved in triggering NAD+ cleavage and interacting with the proposed oxacarbenium intermediate during the nucleophilic substitution reaction, explaining the requirement of diphthamide for ADP ribosylation. Diphtheria toxin may recognize eEF2 in a manner similar to ETA. Notably, the toxin-bound betaTAD phosphates mimic the phosphate backbone of two nucleotides in a conformational switch of 18S rRNA, thereby achieving universal recognition of eEF2 by ETA.
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Affiliation(s)
- René Jørgensen
- Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000, Denmark
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