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Zhang Q, Alter T, Fleischmann S. Non-O1/Non-O139 Vibrio cholerae-An Underestimated Foodborne Pathogen? An Overview of Its Virulence Genes and Regulatory Systems Involved in Pathogenesis. Microorganisms 2024; 12:818. [PMID: 38674762 PMCID: PMC11052320 DOI: 10.3390/microorganisms12040818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
In recent years, the number of foodborne infections with non-O1 and non-O139 Vibrio cholerae (NOVC) has increased worldwide. These have ranged from sporadic infection cases to localized outbreaks. The majority of case reports describe self-limiting gastroenteritis. However, severe gastroenteritis and even cholera-like symptoms have also been described. All reported diarrheal cases can be traced back to the consumption of contaminated seafood. As climate change alters the habitats and distribution patterns of aquatic bacteria, there is a possibility that the number of infections and outbreaks caused by Vibrio spp. will further increase, especially in countries where raw or undercooked seafood is consumed or clean drinking water is lacking. Against this background, this review article focuses on a possible infection pathway and how NOVC can survive in the human host after oral ingestion, colonize intestinal epithelial cells, express virulence factors causing diarrhea, and is excreted by the human host to return to the environment.
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Affiliation(s)
| | | | - Susanne Fleischmann
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany; (Q.Z.); (T.A.)
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2
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Sajeevan A, Ramamurthy T, Solomon AP. Vibrio cholerae virulence and its suppression through the quorum-sensing system. Crit Rev Microbiol 2024:1-22. [PMID: 38441045 DOI: 10.1080/1040841x.2024.2320823] [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: 07/30/2023] [Accepted: 02/10/2024] [Indexed: 03/06/2024]
Abstract
Vibrio cholerae is a cholera-causing pathogen known to instigate severe contagious diarrhea that affects millions globally. Survival of vibrios depend on a combination of multicellular responses and adapt to changes that prevail in the environment. This process is achieved through a strong communication at the cellular level, the process has been recognized as quorum sensing (QS). The severity of infection is highly dependent on the QS of vibrios in the gut milieu. The quorum may exist in a low/high cell density (LCD/HCD) state to exert a positive or negative response to control the regulatory pathogenic networks. The impact of this regulation reflects on the transition of pathogenic V. cholerae from the environment to infect humans and cause outbreaks or epidemics of cholera. In this context, the review portrays various regulatory processes and associated virulent pathways, which maneuver and control LCD and HCD states for their survival in the host. Although several treatment options are existing, promotion of therapeutics by exploiting the virulence network may potentiate ineffective antibiotics to manage cholera. In addition, this approach is also useful in resource-limited settings, where the accessibility to antibiotics or conventional therapeutic options is limited.
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Affiliation(s)
- Anusree Sajeevan
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Disease, Kolkata, India
| | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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3
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Schaffrath R, Brinkmann U. Diphthamide - a conserved modification of eEF2 with clinical relevance. Trends Mol Med 2024; 30:164-177. [PMID: 38097404 DOI: 10.1016/j.molmed.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 02/17/2024]
Abstract
Diphthamide, a complex modification on eukaryotic translation elongation factor 2 (eEF2), assures reading-frame fidelity during translation. Diphthamide and enzymes for its synthesis are conserved in eukaryotes and archaea. Originally identified as target for diphtheria toxin (DT) in humans, its clinical relevance now proves to be broader than the link to pathogenic bacteria. Diphthamide synthesis enzymes (DPH1 and DPH3) are associated with cancer, and DPH gene mutations can cause diphthamide deficiency syndrome (DDS). Finally, new analyses provide evidence that diphthamide may restrict propagation of viruses including SARS-CoV-2 and HIV-1, and that DPH enzymes are targeted by viruses for degradation to overcome this restriction. This review describes how diphthamide is synthesized and functions in translation, and covers its clinical relevance in human development, cancer, and infectious diseases.
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Affiliation(s)
- Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany.
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany.
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4
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Zhang Z, Rondon-Cordero HM, Das C. Crystal structure of bacterial ubiquitin ADP-ribosyltransferase CteC reveals a substrate-recruiting insertion. J Biol Chem 2024; 300:105604. [PMID: 38159861 PMCID: PMC10810742 DOI: 10.1016/j.jbc.2023.105604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024] Open
Abstract
ADP-ribosylation is a post-translational modification involved in regulation of diverse cellular pathways. Interestingly, many pathogens have been identified to utilize ADP-ribosylation as a way for host manipulation. A recent study found that CteC, an effector from the bacterial pathogen Chromobacterium violaceum, hinders host ubiquitin (Ub) signaling pathways via installing mono-ADP-ribosylation on threonine 66 of Ub. However, the molecular basis of substrate recognition by CteC is not well understood. In this article, we probed the substrate specificity of this effector at protein and residue levels. We also determined the crystal structure of CteC in complex with NAD+, which revealed a canonical mono-ADP-ribosyltransferase fold with an additional insertion domain. The AlphaFold-predicted model differed significantly from the experimentally determined structure, even in regions not used in crystal packing. Biochemical and biophysical studies indicated unique features of the NAD+ binding pocket, while showing selectivity distinction between Ub and structurally close Ub-like modifiers and the role of the insertion domain in substrate recognition. Together, this study provides insights into the enzymatic specificities and the key structural features of a novel bacterial ADP-ribosyltransferase involved in host-pathogen interaction.
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Affiliation(s)
- Zhengrui Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.
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5
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Rehm C, Kolm C, Pleininger S, Heger F, Indra A, Reischer GH, Farnleitner AAH, Kirschner AKT. Vibrio cholerae-An emerging pathogen in Austrian bathing waters? Wien Klin Wochenschr 2023; 135:597-608. [PMID: 37530997 PMCID: PMC10651712 DOI: 10.1007/s00508-023-02241-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/11/2023] [Indexed: 08/03/2023]
Abstract
Vibrio cholerae, an important human pathogen, is naturally occurring in specific aquatic ecosystems. With very few exceptions, only the cholera-toxigenic strains belonging to the serogroups O1 and O139 are responsible for severe cholera outbreaks with epidemic or pandemic potential. All other nontoxigenic, non-O1/non-O139 V. cholerae (NTVC) strains may cause various other diseases, such as mild to severe infections of the ears, of the gastrointestinal and urinary tracts as well as wound and bloodstream infections. Older, immunocompromised people and patients with specific preconditions have an elevated risk. In recent years, worldwide reports demonstrated that NTVC infections are on the rise, caused amongst others by elevated water temperatures due to global warming.The aim of this review is to summarize the knowledge gained during the past two decades on V. cholerae infections and its occurrence in bathing waters in Austria, with a special focus on the lake Neusiedler See. We investigated whether NTVC infections have increased and which specific environmental conditions favor the occurrence of NTVC. We present an overview of state of the art methods that are currently available for clinical and environmental diagnostics. A preliminary public health risk assessment concerning NTVC infections related to the Neusiedler See was established. In order to raise awareness of healthcare professionals for NTVC infections, typical symptoms, possible treatment options and the antibiotic resistance status of Austrian NTVC isolates are discussed.
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Affiliation(s)
- Carmen Rehm
- Division Water Quality and Health, Karl-Landsteiner University of Health Sciences, Krems, Austria
- Institute for Hygiene and Applied Immunology - Water Microbiology, Medical University Vienna, Vienna, Austria
- Interuniversity Cooperation Centre Water & Health
| | - Claudia Kolm
- Division Water Quality and Health, Karl-Landsteiner University of Health Sciences, Krems, Austria
- Interuniversity Cooperation Centre Water & Health
- Institute for Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics 166/5/3, Technische Universität Wien, Vienna, Austria
| | - Sonja Pleininger
- Institute for Medical Microbiology and Hygiene, National Reference Centre for Vibrio cholerae, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Florian Heger
- Institute for Medical Microbiology and Hygiene, National Reference Centre for Vibrio cholerae, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Alexander Indra
- Institute for Medical Microbiology and Hygiene, National Reference Centre for Vibrio cholerae, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
- Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Georg H Reischer
- Interuniversity Cooperation Centre Water & Health
- Institute for Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics 166/5/3, Technische Universität Wien, Vienna, Austria
| | - Andreas A H Farnleitner
- Division Water Quality and Health, Karl-Landsteiner University of Health Sciences, Krems, Austria
- Interuniversity Cooperation Centre Water & Health
- Institute for Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics 166/5/3, Technische Universität Wien, Vienna, Austria
| | - Alexander K T Kirschner
- Division Water Quality and Health, Karl-Landsteiner University of Health Sciences, Krems, Austria.
- Institute for Hygiene and Applied Immunology - Water Microbiology, Medical University Vienna, Vienna, Austria.
- Interuniversity Cooperation Centre Water & Health, .
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Challa S, Nandu T, Kim HB, Gong A, Renshaw CW, Li WC, Tan X, Camacho CV, Chen J, Kraus WL. A PARP14/TARG1-Regulated RACK1 MARylation Cycle Drives Stress Granule Dynamics in Ovarian Cancer Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562273. [PMID: 37873085 PMCID: PMC10592810 DOI: 10.1101/2023.10.13.562273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Mono(ADP-ribosyl)ation (MARylation), a post-translational modification (PTM) of proteins, is emerging as a critical regulator of ribosome function and translation. Herein, we demonstrate that RACK1, a member of the tryptophan-aspartate repeat (WD-repeat) family of proteins and an integral component of the ribosome, is MARylated by the mono(ADP-ribosyl) transferase (MART) PARP14 in ovarian cancer cells. We mapped and confirmed the sites of MARylation, which occur on three acidic residues within blades 4 and 5 of β-propeller domain of RACK1, a chaperone that shuttles and anchors proteins where needed. Site-specific MARylation of RACK1 is required for stress granule formation and promotes the colocalization of RACK1 to stress granules with key components, such as G3BP1, eIF3η, and 40S ribosomal proteins. In parallel, we observed reduced translation of a subset of mRNAs, including those encoding key cancer regulators (e.g., AKT). Treatment with a PARP14 inhibitor or mutation of the sites of MARylation on RACK1 blocks these outcomes. To re-set the system after prolonged stress and recovery, the ADP-ribosyl hydrolase TARG1 deMARylates RACK1 to dissociate the stress granules and return RACK1 and the 40S ribosomal subunit to the cytoplasm, allowing for a restoration of translation. Collectively, our results highlight the discovery of a PARP14/TARG1-regulated RACK1 MARylation cycle that controls stress granule assembly and disassembly in ovarian cancer cells.
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Affiliation(s)
- Sridevi Challa
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hyung Bum Kim
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Graduate Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Amy Gong
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Charles W. Renshaw
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wan-Chen Li
- Altos Labs, Bay Area Institute of Science, Redwood City, CA 94403
| | - Xinrui Tan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cristel V. Camacho
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jin Chen
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Altos Labs, Bay Area Institute of Science, Redwood City, CA 94403
| | - W. Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Graduate Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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7
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Pinilla M, Mazars R, Vergé R, Gorse L, Paradis M, Suire B, Santoni K, Robinson KS, Toh GA, Prouvensier L, Leon-Icaza SA, Hessel A, Péricat D, Murris M, Guet-Revillet H, Henras A, Buyck J, Ravet E, Zhong FL, Cougoule C, Planès R, Meunier E. EEF2-inactivating toxins engage the NLRP1 inflammasome and promote epithelial barrier disruption. J Exp Med 2023; 220:e20230104. [PMID: 37642996 PMCID: PMC10465324 DOI: 10.1084/jem.20230104] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023] Open
Abstract
Human airway and corneal epithelial cells, which are critically altered during chronic infections mediated by Pseudomonas aeruginosa, specifically express the inflammasome sensor NLRP1. Here, together with a companion study, we report that the NLRP1 inflammasome detects exotoxin A (EXOA), a ribotoxin released by P. aeruginosa type 2 secretion system (T2SS), during chronic infection. Mechanistically, EXOA-driven eukaryotic elongation factor 2 (EEF2) ribosylation and covalent inactivation promote ribotoxic stress and subsequent NLRP1 inflammasome activation, a process shared with other EEF2-inactivating toxins, diphtheria toxin and cholix toxin. Biochemically, irreversible EEF2 inactivation triggers ribosome stress-associated kinases ZAKα- and P38-dependent NLRP1 phosphorylation and subsequent proteasome-driven functional degradation. Finally, cystic fibrosis cells from patients exhibit exacerbated P38 activity and hypersensitivity to EXOA-induced ribotoxic stress-dependent NLRP1 inflammasome activation, a process inhibited by the use of ZAKα inhibitors. Altogether, our results show the importance of P. aeruginosa virulence factor EXOA at promoting NLRP1-dependent epithelial damage and identify ZAKα as a critical sensor of virulence-inactivated EEF2.
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Affiliation(s)
- Miriam Pinilla
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Raoul Mazars
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Romain Vergé
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Leana Gorse
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Margaux Paradis
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Bastien Suire
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Karin Santoni
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Kim Samirah Robinson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Gee Ann Toh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Laure Prouvensier
- UFR Medicine and Pharmacy, INSERM U1070, University of Poitiers, Poitiers, France
| | | | - Audrey Hessel
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - David Péricat
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Marlène Murris
- Department of Pneumology, Hospital Larrey, Toulouse, France
- University Hospital of Toulouse, Toulouse, France
| | | | - Anthony Henras
- Center of Integrative Biology, University of Toulouse, CNRS, Toulouse, France
| | - Julien Buyck
- UFR Medicine and Pharmacy, INSERM U1070, University of Poitiers, Poitiers, France
| | | | - Franklin L. Zhong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Céline Cougoule
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Rémi Planès
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
- Invivogen, Toulouse, France
| | - Etienne Meunier
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
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8
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Mittal M, Tripathi S, Saini A, Mani I. Phage for treatment of Vibrio cholerae infection. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:21-39. [PMID: 37770173 DOI: 10.1016/bs.pmbts.2023.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Bacteriophages (or "phages") are ubiquitous and the amplest biological entities on our planet. It is a natural enemy of bacteria. Cholera is one of the most known diseases to cause multiple pandemics around the world, killing millions of people. The pathogen of cholera is Vibrio species. Up until the emergence of multidrug resistance, preventive therapeutics like antibiotics were the most effective means of battling bacteria. Globally, one of the most significant challenges in treating microbial infections is the development of drug-resistant strains. Based on their antibacterial properties and unique characteristics, phages are being comprehensively evaluated taxonomically. Moreover, phage-based vaccination is evolving as one of the most encouraging preventive approaches. Due to this, its related research got remarkable recognition. However, due to the rapid emergence of bacterial resistance to antibiotics, the use of phages (phage therapy) could be a major motive for research because the most promising solution lies in bacteriophages. This chapter briefly highlights the promising use of bacteriophages to combat Vibrio-related infectious diseases.
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Affiliation(s)
- Milky Mittal
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, New Delhi, India
| | - Surbhi Tripathi
- Dr. B.R. Ambedkar Centre for Biomedical Research, University of Delhi, New Delhi, India
| | - Ashok Saini
- Department of Microbiology, Institute of Home Economics, University of Delhi, New Delhi, India.
| | - Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
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9
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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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10
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Liu K, Hunter T, Taverner A, Yin K, MacKay J, Colebrook K, Correia M, Rapp A, Mrsny RJ. GRP75 as a functional element of cholix transcytosis. Tissue Barriers 2023; 11:2039003. [PMID: 35262466 PMCID: PMC9870019 DOI: 10.1080/21688370.2022.2039003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cholix (Chx) is secreted by non-pandemic strains of Vibrio cholerae in the intestinal lumen. For this exotoxin to induce cell death in non-polarized cells in the intestinal lamina propria, it must traverse the epithelium in the fully intact form. We identified host cell elements in polarized enterocytes associated with Chx endocytosis and apical to basal (A→B) vesicular transcytosis. This pathway overcomes endogenous mechanisms of apical vesicle recycling and lysosomal targeting by interacting with several host cell proteins that include the 75 kDa glucose-regulated protein (GRP75). Apical endocytosis of Chx appears to involve the single membrane spanning protein TMEM132A, and interaction with furin before it engages GRP75 in apical vesicular structures. Sorting within these apical vesicles results in Chx being trafficked to the basal region of cells in association with the Lectin, Mannose Binding 1 protein LMAN1. In this location, Chx interacts with the basement membrane-specific heparan sulfate proteoglycan perlecan in recycling endosomes prior to its release from this basal vesicular compartment to enter the underlying lamina propria. While the furin and LMAN1 elements of this Chx transcytosis pathway undergo cellular redistribution that are reflective of the polarity shifts noted for coatamer complexes COPI and COPII, GRP75 and perlecan fail to show these dramatic rearrangements. Together, these data define essential steps in the A→B transcytosis pathway accessed by Chx to reach the intestinal lamina propria where it can engage and intoxicate certain non-polarized cells.
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Affiliation(s)
- Keyi Liu
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Tom Hunter
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Alistair Taverner
- Department of Pharmacy and Pharmacology, University of Bath, Bath, UK
| | - Kevin Yin
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Julia MacKay
- Department of Pharmacy and Pharmacology, University of Bath, Bath, UK
| | - Kate Colebrook
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Morgan Correia
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Amandine Rapp
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Randall J. Mrsny
- Applied Molecular Transport, South San Francisco, CA, USA,Department of Pharmacy and Pharmacology, University of Bath, Bath, UK,CONTACT Randall J. Mrsny Applied Molecular Transport, 450 East Jamie Court, South San Francisco, CA94080USA
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11
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Gemler BT, Mukherjee C, Howland CA, Huk D, Shank Z, Harbo LJ, Tabbaa OP, Bartling CM. Function-based classification of hazardous biological sequences: Demonstration of a new paradigm for biohazard assessments. Front Bioeng Biotechnol 2022; 10:979497. [PMID: 36277394 PMCID: PMC9585941 DOI: 10.3389/fbioe.2022.979497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/31/2022] [Indexed: 12/04/2022] Open
Abstract
Bioengineering applies analytical and engineering principles to identify functional biological building blocks for biotechnology applications. While these building blocks are leveraged to improve the human condition, the lack of simplistic, machine-readable definition of biohazards at the function level is creating a gap for biosafety practices. More specifically, traditional safety practices focus on the biohazards of known pathogens at the organism-level and may not accurately consider novel biodesigns with engineered functionalities at the genetic component-level. This gap is motivating the need for a paradigm shift from organism-centric procedures to function-centric biohazard identification and classification practices. To address this challenge, we present a novel methodology for classifying biohazards at the individual sequence level, which we then compiled to distinguish the biohazardous property of pathogenicity at the whole genome level. Our methodology is rooted in compilation of hazardous functions, defined as a set of sequences and associated metadata that describe coarse-level functions associated with pathogens (e.g., adherence, immune subversion). We demonstrate that the resulting database can be used to develop hazardous “fingerprints” based on the functional metadata categories. We verified that these hazardous functions are found at higher levels in pathogens compared to non-pathogens, and hierarchical clustering of the fingerprints can distinguish between these two groups. The methodology presented here defines the hazardous functions associated with bioengineering functional building blocks at the sequence level, which provide a foundational framework for classifying biological hazards at the organism level, thus leading to the improvement and standardization of current biosecurity and biosafety practices.
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12
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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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13
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Abstract
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The paradigm of antivirulence
therapy dictates that bacterial pathogens
are specifically disarmed but not killed by neutralizing their virulence
factors. Clearance of the invading pathogen by the immune system is
promoted. As compared to antibiotics, the pathogen-selective antivirulence
drugs hold promise to minimize collateral damage to the beneficial
microbiome. Also, selective pressure for resistance is expected to
be lower because bacterial viability is not directly affected. Antivirulence
drugs are being developed for stand-alone prophylactic and therapeutic
treatments but also for combinatorial use with antibiotics. This Review
focuses on drug modalities that target bacterial exotoxins after the
secretion or release-upon-lysis. Exotoxins have a significant and
sometimes the primary role as the disease-causing virulence factor,
and thereby they are attractive targets for drug development. We describe
the key pre-clinical and clinical trial data that have led to the
approval of currently used exotoxin-targeted drugs, namely the monoclonal
antibodies bezlotoxumab (toxin B/TcdB, Clostridioides difficile), raxibacumab (anthrax toxin, Bacillus anthracis), and obiltoxaximab (anthrax toxin, Bacillus anthracis), but also to challenges with some of the promising leads. We also
highlight the recent developments in pre-clinical research sector
to develop exotoxin-targeted drug modalities, i.e., monoclonal antibodies,
antibody fragments, antibody mimetics, receptor analogs, neutralizing
scaffolds, dominant-negative mutants, and small molecules. We describe
how these exotoxin-targeted drug modalities work with high-resolution
structural knowledge and highlight their advantages and disadvantages
as antibiotic alternatives.
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Affiliation(s)
- Moona Sakari
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Arttu Laisi
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Arto T. Pulliainen
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
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14
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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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15
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Challa S, Khulpateea BR, Nandu T, Camacho CV, Ryu KW, Chen H, Peng Y, Lea JS, Kraus WL. Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers. Cell 2021; 184:4531-4546.e26. [PMID: 34314702 PMCID: PMC8380725 DOI: 10.1016/j.cell.2021.07.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/11/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
Defects in translation lead to changes in the expression of proteins that can serve as drivers of cancer formation. Here, we show that cytosolic NAD+ synthesis plays an essential role in ovarian cancer by regulating translation and maintaining protein homeostasis. Expression of NMNAT-2, a cytosolic NAD+ synthase, is highly upregulated in ovarian cancers. NMNAT-2 supports the catalytic activity of the mono(ADP-ribosyl) transferase (MART) PARP-16, which mono(ADP-ribosyl)ates (MARylates) ribosomal proteins. Depletion of NMNAT-2 or PARP-16 leads to inhibition of MARylation, increased polysome association and enhanced translation of specific mRNAs, aggregation of their translated protein products, and reduced growth of ovarian cancer cells. Furthermore, MARylation of the ribosomal proteins, such as RPL24 and RPS6, inhibits polysome assembly by stabilizing eIF6 binding to ribosomes. Collectively, our results demonstrate that ribosome MARylation promotes protein homeostasis in cancers by fine-tuning the levels of protein synthesis and preventing toxic protein aggregation.
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Affiliation(s)
- Sridevi Challa
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Beman R Khulpateea
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cristel V Camacho
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Keun W Ryu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hao Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yan Peng
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jayanthi S Lea
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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16
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Roussin M, Salcedo SP. NAD+-targeting by bacteria: an emerging weapon in pathogenesis. FEMS Microbiol Rev 2021; 45:6315328. [PMID: 34223888 DOI: 10.1093/femsre/fuab037] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 07/01/2021] [Indexed: 11/14/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is a major cofactor in redox reactions in all lifeforms. A stable level of NAD+ is vital to ensure cellular homeostasis. Some pathogens can modulate NAD+ metabolism to their advantage and even utilize or cleave NAD+ from the host using specialized effectors known as ADP-ribosyltransferase toxins and NADases, leading to energy store depletion, immune evasion, or even cell death. This review explores recent advances in the field of bacterial NAD+-targeting toxins, highlighting the relevance of NAD+ modulation as an emerging pathogenesis strategy. In addition, we discuss the role of specific NAD+-targeting toxins in niche colonization and bacterial lifestyle as components of Toxin/Antitoxin systems and key players in inter-bacterial competition. Understanding the mechanisms of toxicity, regulation, and secretion of these toxins will provide interesting leads in the search for new antimicrobial treatments in the fight against infectious diseases.
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Affiliation(s)
- Morgane Roussin
- Laboratory of Molecular Microbiology and Structural Biochemistry, Centre National de la Recherche Scientifique UMR5086, Université de Lyon, Lyon, France
| | - Suzana P Salcedo
- Laboratory of Molecular Microbiology and Structural Biochemistry, Centre National de la Recherche Scientifique UMR5086, Université de Lyon, Lyon, France
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17
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Awasthi SP, Chowdhury N, Hatanaka N, Hinenoya A, Ramamurthy T, Asakura M, Yamasaki S. Quantification of Vibrio cholerae cholix exotoxin by sandwich bead-ELISA. J Med Microbiol 2021; 70. [PMID: 33830907 DOI: 10.1099/jmm.0.001311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Cholix toxin (ChxA) is an ADP-ribosylating exotoxin produced by Vibrio cholerae. However, to date, there is no quantitative assay available for ChxA, which makes it difficult to detect and estimate the level of ChxA produced by V. cholerae.Hypothesis/Gap Statement. It is important to develop a reliable and specific quantitative assay to measure the production level of ChxA, which will help us to understand the role of ChxA in V. cholerae pathogenesis.Aim. The aim of this study was to develop a bead-based sandwich ELISA (bead-ELISA) for the quantification of ChxA and to evaluate the importance of ChxA in the pathogenesis of V. cholerae infection.Methodology. Anti-rChxA was raised in New Zealand white rabbits, and Fab-horse radish peroxidase conjugate was prepared by the maleimide method to use in the bead-ELISA. This anti-ChxA bead-ELISA was applied to quantify the ChxA produced by various V. cholerae strains. The production of ChxA was examined in different growth media such as alkaline peptone water (APW), Luria-Bertani broth and AKI. Finally, the assay was evaluated using a mouse lethality assay with representative V. cholerae strains categorized as low to high ChxA-producers based on anti-ChxA bead-ELISA.Results. A sensitive bead-ELISA assay, which can quantify from 0.6 to 60 ng ml-1 of ChxA, was developed. ChxA was mostly detected in the extracellular cell-free supernatant and its production level varied from 1.2 ng ml-1 to 1.6 µg ml-1. The highest ChxA production was observed when V. cholerae strains were cultured in LB broth, but not in APW or AKI medium. The ChxA-producer V. cholerae strains showed 20-80 % lethality and only the high ChxA II-producer was statistically more lethal than a non-ChxA-producer, in the mice model assay. ChxA I and II production levels were not well correlated with mice lethality, and this could be due to the heterogeneity of the strains tested.Conclusion. ChxA I to III was produced mostly extracellularly at various levels depending on strains and culture conditions. The bead-ELISA developed in this study is useful for the detection and quantification of ChxA in V. cholerae strains.
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Affiliation(s)
- Sharda Prasad Awasthi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Nityananda Chowdhury
- Present address: Medical University of South Carolina, 173 Ashley Ave., BSB 246, Charleston, SC, USA.,Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Noritoshi Hatanaka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | | | - Masahiro Asakura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
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18
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Mikolčević P, Hloušek-Kasun A, Ahel I, Mikoč A. ADP-ribosylation systems in bacteria and viruses. Comput Struct Biotechnol J 2021; 19:2366-2383. [PMID: 34025930 PMCID: PMC8120803 DOI: 10.1016/j.csbj.2021.04.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/30/2022] Open
Abstract
ADP-ribosylation is an ancient posttranslational modification present in all kingdoms of life. The system likely originated in bacteria where it functions in inter- and intra-species conflict, stress response and pathogenicity. It was repeatedly adopted via lateral transfer by eukaryotes, including humans, where it has a pivotal role in epigenetics, DNA-damage repair, apoptosis, and other crucial pathways including the immune response to pathogenic bacteria and viruses. In other words, the same ammunition used by pathogens is adapted by eukaryotes to fight back. While we know quite a lot about the eukaryotic system, expanding rather patchy knowledge on bacterial and viral ADP-ribosylation would give us not only a better understanding of the system as a whole but a fighting advantage in this constant arms race. By writing this review we hope to put into focus the available information and give a perspective on how this system works and can be exploited in the search for therapeutic targets in the future. The relevance of the subject is especially highlighted by the current situation of being amid the world pandemic caused by a virus harbouring and dependent on a representative of such a system.
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Affiliation(s)
- Petra Mikolčević
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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19
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Vatta M, Lyons B, Heney KA, Lidster T, Merrill AR. Mapping the DNA-Binding Motif of Scabin Toxin, a Guanine Modifying Enzyme from Streptomyces scabies. Toxins (Basel) 2021; 13:toxins13010055. [PMID: 33450958 PMCID: PMC7828395 DOI: 10.3390/toxins13010055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 01/09/2021] [Indexed: 11/16/2022] Open
Abstract
Scabin is a mono-ADP-ribosyltransferase toxin/enzyme and possible virulence factor produced by the agriculture pathogen, Streptomyces scabies. Recently, molecular dynamic approaches and MD simulations revealed its interaction with both NAD+ and DNA substrates. An Essential Dynamics Analysis identified a crab-claw-like mechanism, including coupled changes in the exposed motifs, and the Rβ1-RLa-NLc-STTβ2-WPN-WARTT-(QxE)ARTT sequence motif was proposed as a catalytic signature of the Pierisin family of DNA-acting toxins. A new fluorescence assay was devised to measure the kinetics for both RNA and DNA substrates. Several protein variants were prepared to probe the Scabin-NAD-DNA molecular model and to reveal the reaction mechanism for the transfer of ADP-ribose to the guanine base in the DNA substrate. The results revealed that there are several lysine and arginine residues in Scabin that are important for binding the DNA substrate; also, key residues such as Asn110 in the mechanism of ADP-ribose transfer to the guanine base were identified. The DNA-binding residues are shared with ScARP from Streptomyces coelicolor but are not conserved with Pierisin-1, suggesting that the modification of guanine bases by ADP-ribosyltransferases is divergent even in the Pierisin family.
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Affiliation(s)
- Maritza Vatta
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Bronwyn Lyons
- Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada;
| | - Kayla A. Heney
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada;
| | - Taylor Lidster
- Department of Biological Sciences, Brock University, St. Catherines, ON L2S 3A1, Canada;
| | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Correspondence: ; Fax: +1-519-837-1802
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20
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Yoshida T, Tsuge H. Common Mechanism for Target Specificity of Protein- and DNA-Targeting ADP-Ribosyltransferases. Toxins (Basel) 2021; 13:toxins13010040. [PMID: 33430384 PMCID: PMC7827354 DOI: 10.3390/toxins13010040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 12/14/2022] Open
Abstract
Many bacterial pathogens utilize ADP-ribosyltransferases (ARTs) as virulence factors. The critical aspect of ARTs is their target specificity. Each individual ART modifies a specific residue of its substrates, which could be proteins, DNA, or antibiotics. However, the mechanism underlying this specificity is poorly understood. Here, we review the substrate recognition mechanism and target residue specificity based on the available complex structures of ARTs and their substrates. We show that there are common mechanisms of target residue specificity among protein- and DNA-targeting ARTs.
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Affiliation(s)
- Toru Yoshida
- Faculty of Science, Japan Women’s University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan;
| | - Hideaki Tsuge
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Center for Molecular Research in Infectious Diseases, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan
- Correspondence: ; Tel.: +81-75-705-3117
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21
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The N-terminus of Paenibacillus larvae C3larvinA modulates catalytic efficiency. Biosci Rep 2021; 41:227200. [PMID: 33289829 PMCID: PMC7789906 DOI: 10.1042/bsr20203727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 01/21/2023] Open
Abstract
C3larvinA was recently described as a mono-ADP-ribosyltransferase (mART) toxin from the enterobacterial repetitive intergenic consensus (ERIC) III genotype of the agricultural pathogen, Paenibacillus larvae. It was shown to be the full-length, functional version of the previously described C3larvintrunc toxin, due to a 33-residue extension of the N-terminus of the protein. In the present study, a series of deletions and substitutions were made to the N-terminus of C3larvinA to assess the contribution of the α1-helix to toxin structure and function. Catalytic characterization of these variants identified Asp23 and Ala31 residues as supportive to enzymatic function. A third residue, Lys36, was also found to contribute to the catalytic activity of the enzyme. Analysis of the C3larvinA homology model revealed that these three residues were participating in a series of interactions to properly orient both the Q-X-E and S-T-S motifs. Ala31 and Lys36 were found to associate with a structural network of residues previously identified in silico, whereas Asp23 forms novel interactions not previously described. At last, the membrane translocation activity into host target cells of each variant was assessed, highlighting a possible relationship between protein dipole and target cell entry.
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22
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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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23
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Ogura K, Yahiro K, Moss J. Cell Death Signaling Pathway Induced by Cholix Toxin, a Cytotoxin and eEF2 ADP-Ribosyltransferase Produced by Vibrio cholerae. Toxins (Basel) 2020; 13:toxins13010012. [PMID: 33374361 PMCID: PMC7824611 DOI: 10.3390/toxins13010012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Pathogenic microorganisms produce various virulence factors, e.g., enzymes, cytotoxins, effectors, which trigger development of pathologies in infectious diseases. Cholera toxin (CT) produced by O1 and O139 serotypes of Vibrio cholerae (V. cholerae) is a major cytotoxin causing severe diarrhea. Cholix cytotoxin (Cholix) was identified as a novel eukaryotic elongation factor 2 (eEF2) adenosine-diphosphate (ADP)-ribosyltransferase produced mainly in non-O1/non-O139 V. cholerae. The function and role of Cholix in infectious disease caused by V. cholerae remain unknown. The crystal structure of Cholix is similar to Pseudomonas exotoxin A (PEA) which is composed of an N-terminal receptor-recognition domain and a C-terminal ADP-ribosyltransferase domain. The endocytosed Cholix catalyzes ADP-ribosylation of eEF2 in host cells and inhibits protein synthesis, resulting in cell death. In a mouse model, Cholix caused lethality with severe liver damage. In this review, we describe the mechanism underlying Cholix-induced cytotoxicity. Cholix-induced apoptosis was regulated by mitogen-activated protein kinase (MAPK) and protein kinase C (PKC) signaling pathways, which dramatically enhanced tumor necrosis factor-α (TNF-α) production in human liver, as well as the amount of epithelial-like HepG2 cancer cells. In contrast, Cholix induced apoptosis in hepatocytes through a mitochondrial-dependent pathway, which was not stimulated by TNF-α. These findings suggest that sensitivity to Cholix depends on the target cell. A substantial amount of information on PEA is provided in order to compare/contrast this well-characterized mono-ADP-ribosyltransferase (mART) with Cholix.
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Affiliation(s)
- Kohei Ogura
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-0942, Japan
- Correspondence: (K.O.); (K.Y.); Tel.: +81-76-265-2590 (K.O.); +81-43-226-2048 (K.Y.)
| | - Kinnosuke Yahiro
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
- Correspondence: (K.O.); (K.Y.); Tel.: +81-76-265-2590 (K.O.); +81-43-226-2048 (K.Y.)
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1590, USA;
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24
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Tremblay O, Thow Z, Merrill AR. Several New Putative Bacterial ADP-Ribosyltransferase Toxins Are Revealed from In Silico Data Mining, Including the Novel Toxin Vorin, Encoded by the Fire Blight Pathogen Erwinia amylovora. Toxins (Basel) 2020; 12:E792. [PMID: 33322547 PMCID: PMC7764402 DOI: 10.3390/toxins12120792] [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: 11/10/2020] [Revised: 11/28/2020] [Accepted: 12/10/2020] [Indexed: 12/31/2022] Open
Abstract
Mono-ADP-ribosyltransferase (mART) toxins are secreted by several pathogenic bacteria that disrupt vital host cell processes in deadly diseases like cholera and whooping cough. In the last two decades, the discovery of mART toxins has helped uncover the mechanisms of disease employed by pathogens impacting agriculture, aquaculture, and human health. Due to the current abundance of mARTs in bacterial genomes, and an unprecedented availability of genomic sequence data, mART toxins are amenable to discovery using an in silico strategy involving a series of sequence pattern filters and structural predictions. In this work, a bioinformatics approach was used to discover six bacterial mART sequences, one of which was a functional mART toxin encoded by the plant pathogen, Erwinia amylovora, called Vorin. Using a yeast growth-deficiency assay, we show that wild-type Vorin inhibited yeast cell growth, while catalytic variants reversed the growth-defective phenotype. Quantitative mass spectrometry analysis revealed that Vorin may cause eukaryotic host cell death by suppressing the initiation of autophagic processes. The genomic neighbourhood of Vorin indicated that it is a Type-VI-secreted effector, and co-expression experiments showed that Vorin is neutralized by binding of a cognate immunity protein, VorinI. We demonstrate that Vorin may also act as an antibacterial effector, since bacterial expression of Vorin was not achieved in the absence of VorinI. Vorin is the newest member of the mART family; further characterization of the Vorin/VorinI complex may help refine inhibitor design for mART toxins from other deadly pathogens.
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Affiliation(s)
| | | | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (O.T.); (Z.T.)
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25
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Vasquez-Rifo A, Ricci EP, Ambros V. Pseudomonas aeruginosa cleaves the decoding center of Caenorhabditis elegans ribosomes. PLoS Biol 2020; 18:e3000969. [PMID: 33259473 PMCID: PMC7707567 DOI: 10.1371/journal.pbio.3000969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/22/2020] [Indexed: 11/27/2022] Open
Abstract
Pathogens such as Pseudomonas aeruginosa advantageously modify animal host physiology, for example, by inhibiting host protein synthesis. Translational inhibition of insects and mammalian hosts by P. aeruginosa utilizes the well-known exotoxin A effector. However, for the infection of Caenorhabditis elegans by P. aeruginosa, the precise pathways and mechanism(s) of translational inhibition are not well understood. We found that upon exposure to P. aeruginosa PA14, C. elegans undergoes a rapid loss of intact ribosomes accompanied by the accumulation of ribosomes cleaved at helix 69 (H69) of the 26S ribosomal RNA (rRNA), a key part of ribosome decoding center. H69 cleavage is elicited by certain virulent P. aeruginosa isolates in a quorum sensing (QS)–dependent manner and independently of exotoxin A–mediated translational repression. H69 cleavage is antagonized by the 3 major host defense pathways defined by the pmk-1, fshr-1, and zip-2 genes. The level of H69 cleavage increases with the bacterial exposure time, and it is predominantly localized in the worm’s intestinal tissue. Genetic and genomic analysis suggests that H69 cleavage leads to the activation of the worm’s zip-2-mediated defense response pathway, consistent with translational inhibition. Taken together, our observations suggest that P. aeruginosa deploys a virulence mechanism to induce ribosome degradation and H69 cleavage of host ribosomes. In this manner, P. aeruginosa would impair host translation and block antibacterial responses. During infection of the nematode Caenorhabditis elegans by the bacterium Pseudomonas aeruginosa, a bacterial virulence mechanism leads to the cleavage of host ribosomal RNAs at the decoding center, thereby shutting down translation.
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Affiliation(s)
- Alejandro Vasquez-Rifo
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (AV-R); (VA)
| | - Emiliano P. Ricci
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École normale supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239, INSERM U1210 Lyon, France
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (AV-R); (VA)
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26
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Fay NC, Muthusamy BP, Nyugen LP, Desai RC, Taverner A, MacKay J, Seung M, Hunter T, Liu K, Chandalia A, Coyle MP, Kim HL, Postlethwaite S, Mangat K, Song L, Seto E, Alam A, Olson CV, Feng W, Saberi M, Mahmood TA, Mrsny RJ. A Novel Fusion of IL-10 Engineered to Traffic across Intestinal Epithelium to Treat Colitis. THE JOURNAL OF IMMUNOLOGY 2020; 205:3191-3204. [PMID: 33148717 DOI: 10.4049/jimmunol.2000848] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/03/2020] [Indexed: 01/08/2023]
Abstract
IL-10 is a potent anti-inflammatory cytokine capable of suppressing a number of proinflammatory signals associated with intestinal inflammatory diseases, such as ulcerative colitis and Crohn's disease. Clinical use of human IL-10 (hIL-10) has been limited by anemia and thrombocytopenia following systemic injection, side effects that might be eliminated by a gut-restricted distribution. We have identified a transcytosis pathway used by cholix, an exotoxin secreted by nonpandemic forms of the intestinal pathogen Vibrio cholerae A nontoxic fragment of the first 386 aa of cholix was genetically fused to hIL-10 to produce recombinant AMT-101. In vitro and in vivo characterization of AMT-101 showed it to efficiently cross healthy human intestinal epithelium (SMI-100) by a vesicular transcytosis process, activate hIL-10 receptors in an engineered U2OS osteosarcoma cell line, and increase cellular phospho-STAT3 levels in J774.2 mouse macrophage cells. AMT-101 was taken up by inflamed intestinal mucosa and activated pSTAT3 in the lamina propria with limited systemic distribution. AMT-101 administered to healthy mice by oral gavage or to cynomolgus monkeys (nonhuman primates) by colonic spray increased circulating levels of IL-1R antagonist (IL-1Ra). Oral gavage of AMT-101 in two mouse models of induced colitis prevented associated pathological events and plasma cytokine changes. Overall, these studies suggest that AMT-101 can efficiently overcome the epithelial barrier to focus biologically active IL-10 to the intestinal lamina propria.
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Affiliation(s)
- Nicole C Fay
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | | | - Linh P Nyugen
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Radhika C Desai
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Alistair Taverner
- Department of Pharmacy and Pharmacology, University of Bath, BA2 7AY Bath, United Kingdom
| | - Julia MacKay
- Department of Pharmacy and Pharmacology, University of Bath, BA2 7AY Bath, United Kingdom
| | - Minji Seung
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Tom Hunter
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Keyi Liu
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | | | - Michael P Coyle
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Hyojin L Kim
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | | | | | - Lisa Song
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Elbert Seto
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Aatif Alam
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Charles V Olson
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Weijun Feng
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Maziyar Saberi
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Tahir A Mahmood
- Applied Molecular Transport, South San Francisco, CA 94080; and
| | - Randall J Mrsny
- Applied Molecular Transport, South San Francisco, CA 94080; and .,Department of Pharmacy and Pharmacology, University of Bath, BA2 7AY Bath, United Kingdom
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27
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Liu J, Zuo Z, Zou M, Finkel T, Liu S. Identification of the transcription factor Miz1 as an essential regulator of diphthamide biosynthesis using a CRISPR-mediated genome-wide screen. PLoS Genet 2020; 16:e1009068. [PMID: 33057331 PMCID: PMC7591051 DOI: 10.1371/journal.pgen.1009068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/27/2020] [Accepted: 08/20/2020] [Indexed: 12/15/2022] Open
Abstract
Diphthamide is a unique post-translationally modified histidine residue (His715 in all mammals) found only in eukaryotic elongation factor-2 (eEF-2). The biosynthesis of diphthamide represents one of the most complex modifications, executed by protein factors conserved from yeast to humans. Diphthamide is not only essential for normal physiology (such as ensuring fidelity of mRNA translation), but is also exploited by bacterial ADP-ribosylating toxins (e.g., diphtheria toxin) as their molecular target in pathogenesis. Taking advantage of the observation that cells defective in diphthamide biosynthesis are resistant to ADP-ribosylating toxins, in the past four decades, seven essential genes (Dph1 to Dph7) have been identified for diphthamide biosynthesis. These technically unsaturated screens raise the question as to whether additional genes are required for diphthamide biosynthesis. In this study, we performed two independent, saturating, genome-wide CRISPR knockout screens in human cells. These screens identified all previously known Dph genes, as well as further identifying the BTB/POZ domain-containing transcription factor Miz1. We found that Miz1 is absolutely required for diphthamide biosynthesis via its role in the transcriptional regulation of Dph1 expression. Mechanistically, Miz1 binds to the Dph1 proximal promoter via an evolutionarily conserved consensus binding site to activate Dph1 transcription. Therefore, this work demonstrates that Dph1-7, along with the newly identified Miz1 transcription factor, are likely to represent the essential protein factors required for diphthamide modification on eEF2. Diphthamide is a unique post-translationally modified histidine residue (His699 in yeast, His715 in all mammals) found only in eukaryotic elongation factor-2 (eEF-2). Mice that are deficient in diphthamide biosynthesis are embryonic lethal, attesting to the importance of diphthamide in normal physiology. It has taken four decades to identify the seven non-redundant genes in diphthamide biosynthesis, but whether additional factors are required and how the pathway is regulated remained elusive. To address these issues, we performed two saturating, independent, and unbiased genome-wide CRISPR knockout screens. The screens concluded independently that Dph1-Dph7 and additionally transcription factor Miz1 are the key factors required for diphthamide biosynthesis. Mechanistically, Miz1 binds to the Dph1 proximal promoter via an evolutionarily conserved consensus binding site to activate Dph1 transcription. While diphthamide biosynthesis machinery (Dph1-Dph7) exists across eukaryotes, Miz1 orthologues do not exist in lower species such as yeast, C. elegans, and Drosophila, indicating that the regulation of diphthamide modification by Miz1 emerged much later in evolution. The work opens a new avenue for understanding the role that diphthamide modification plays in normal physiology and bacterial toxin pathogenesis.
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Affiliation(s)
- Jie Liu
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
- Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Zehua Zuo
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
| | - Meijuan Zou
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
| | - Toren Finkel
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
- Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Shihui Liu
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- * E-mail:
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28
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Ramamurthy T, Nandy RK, Mukhopadhyay AK, Dutta S, Mutreja A, Okamoto K, Miyoshi SI, Nair GB, Ghosh A. Virulence Regulation and Innate Host Response in the Pathogenicity of Vibrio cholerae. Front Cell Infect Microbiol 2020; 10:572096. [PMID: 33102256 PMCID: PMC7554612 DOI: 10.3389/fcimb.2020.572096] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
The human pathogen Vibrio cholerae is the causative agent of severe diarrheal disease known as cholera. Of the more than 200 "O" serogroups of this pathogen, O1 and O139 cause cholera outbreaks and epidemics. The rest of the serogroups, collectively known as non-O1/non-O139 cause sporadic moderate or mild diarrhea and also systemic infections. Pathogenic V. cholerae circulates between nutrient-rich human gut and nutrient-deprived aquatic environment. As an autochthonous bacterium in the environment and as a human pathogen, V. cholerae maintains its survival and proliferation in these two niches. Growth in the gastrointestinal tract involves expression of several genes that provide bacterial resistance against host factors. An intricate regulatory program involving extracellular signaling inputs is also controlling this function. On the other hand, the ability to store carbon as glycogen facilitates bacterial fitness in the aquatic environment. To initiate the infection, V. cholerae must colonize the small intestine after successfully passing through the acid barrier in the stomach and survive in the presence of bile and antimicrobial peptides in the intestinal lumen and mucus, respectively. In V. cholerae, virulence is a multilocus phenomenon with a large functionally associated network. More than 200 proteins have been identified that are functionally linked to the virulence-associated genes of the pathogen. Several of these genes have a role to play in virulence and/or in functions that have importance in the human host or the environment. A total of 524 genes are differentially expressed in classical and El Tor strains, the two biotypes of V. cholerae serogroup O1. Within the host, many immune and biological factors are able to induce genes that are responsible for survival, colonization, and virulence. The innate host immune response to V. cholerae infection includes activation of several immune protein complexes, receptor-mediated signaling pathways, and other bactericidal proteins. This article presents an overview of regulation of important virulence factors in V. cholerae and host response in the context of pathogenesis.
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Affiliation(s)
| | - Ranjan K Nandy
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K Mukhopadhyay
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Ankur Mutreja
- Global Health-Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Keinosuke Okamoto
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.,Collaborative Research Center of Okayama University for Infectious Diseases in India, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - G Balakrish Nair
- Microbiome Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Amit Ghosh
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
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29
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Tangestani MG, Alinezhad J, Khajeian A, Gharibi S, Haghighi MA. Identification of cholix toxin gene in Vibrio cholerae non-O1/non-O139 isolated from diarrhea patients in Bushehr, Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2020; 12:273-280. [PMID: 32994897 PMCID: PMC7502140 DOI: 10.18502/ijm.v12i4.3929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background and Objectives: Cholixin (cholix toxin) is a novel exotoxin in Vibrio cholerae identified as an elongation factor II specific ADP-ribosyltransferase which inhibits protein synthesis in the eukaryotic cell. Previous researches have suggested that cholixin probably is an important virulence factor in non-O1/non-O139 V. cholerae (NAG) serotypes that could be related to extra-intestinal rather than intestinal infections. This study was aimed to investigate the frequency and genetic diversity of colixin gene (chxA) in clinical V. cholerae NAG isolates. Materials and Methods: The presence of chxA gene in 44 clinical V. cholerae NAG isolates were screened using PCR through specific primers designed for the receptor-binding domain (RBD) of chxA gene. The five PCR products of chxA gene were sequenced. Results: This study showed that chxA gene presented in 19 V. cholerae NAG isolates. The sequences analysis of 5 out of 19 the partial chxA genes amplicon showed that 4 of them belonged to chxA I and the other one belonged to chxA II subtypes. Two distinct clusters were revealed for these isolates by phylogenic analysis, too. Conclusion: The chxA gene contained high frequency among V. cholerae NAG isolates in Bushehr, Iran. The polymorphism study on RBD of cholixin gene is suggested as an appropriate method for phylogenic characterization of the various chxA gene subtypes.
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Affiliation(s)
- Marziyeh Gholizadeh Tangestani
- Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran.,The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Jafar Alinezhad
- Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran.,The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Abdolmohammad Khajeian
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Somayyeh Gharibi
- Department of Microbiology, School of Sciences, Kherad Institute of Higher Education, Bushehr, Iran
| | - Mohammad Ali Haghighi
- Department of Microbiology and Parasitology, School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran.,The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
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30
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Masuyer G. Crystal Structure of Exotoxin A from Aeromonas Pathogenic Species. Toxins (Basel) 2020; 12:toxins12060397. [PMID: 32549399 PMCID: PMC7354439 DOI: 10.3390/toxins12060397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023] Open
Abstract
Aeromonas exotoxin A (AE) is a bacterial virulence factor recently discovered in a clinical case of necrotising fasciitis caused by the flesh-eating Aeromonas hydrophila. Here, database mining shows that AE is present in the genome of several emerging Aeromonas pathogenic species. The X-ray crystal structure of AE was solved at 2.3 Å and presents all the hallmarks common to diphthamide-specific mono-ADP-ribosylating toxins, suggesting AE is a fourth member of this family alongside the diphtheria toxin, Pseudomonas exotoxin A and cholix. Structural homology indicates AE may use a similar mechanism of cytotoxicity that targets eukaryotic elongation factor 2 and thus inhibition of protein synthesis. The structure of AE also highlights unique features including a metal binding site, and a negatively charged cleft that could play a role in interdomain interactions and may affect toxicity. This study raises new opportunities to engineer alternative toxin-based molecules with pharmaceutical potential.
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Affiliation(s)
- Geoffrey Masuyer
- Department of Pharmacy and Pharmacology, Centre for Therapeutic Innovation, University of Bath, Bath BA2 7AY, UK
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31
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Ashok Y, Miettinen M, Oliveira DKHD, Tamirat MZ, Näreoja K, Tiwari A, Hottiger MO, Johnson MS, Lehtiö L, Pulliainen AT. Discovery of Compounds Inhibiting the ADP-Ribosyltransferase Activity of Pertussis Toxin. ACS Infect Dis 2020; 6:588-602. [PMID: 31899865 DOI: 10.1021/acsinfecdis.9b00412] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The targeted pathogen-selective approach to drug development holds promise to minimize collateral damage to the beneficial microbiome. The AB5-topology pertussis toxin (PtxS1-S5) is a major virulence factor of Bordetella pertussis, the causative agent of the highly contagious respiratory disease whooping cough. Once internalized into the host cell, PtxS1 ADP-ribosylates α-subunits of the heterotrimeric Gαi-superfamily, thereby disrupting G-protein-coupled receptor signaling. Here, we report the discovery of the first small molecules inhibiting the ADP-ribosyltransferase activity of pertussis toxin. We developed protocols to purify milligram-levels of active recombinant B. pertussis PtxS1 from Escherichia coli and an in vitro high throughput-compatible assay to quantify NAD+ consumption during PtxS1-catalyzed ADP-ribosylation of Gαi. Two inhibitory compounds (NSC228155 and NSC29193) with low micromolar IC50-values (3.0 μM and 6.8 μM) were identified in the in vitro NAD+ consumption assay that also were potent in an independent in vitro assay monitoring conjugation of ADP-ribose to Gαi. Docking and molecular dynamics simulations identified plausible binding poses of NSC228155 and in particular of NSC29193, most likely owing to the rigidity of the latter ligand, at the NAD+-binding pocket of PtxS1. NSC228155 inhibited the pertussis AB5 holotoxin-catalyzed ADP-ribosylation of Gαi in living human cells with a low micromolar IC50-value (2.4 μM). NSC228155 and NSC29193 might prove to be useful hit compounds in targeted B. pertussis-selective drug development.
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Affiliation(s)
- Yashwanth Ashok
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Aapistie 7A, P.O. Box 5400, FI-90014, Oulu, Finland
| | - Moona Miettinen
- Institute of Biomedicine, Research Center for Cancer, Infections, and Immunity, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
- Turku Doctoral Programme of Molecular Medicine (TuDMM), University of Turku, Turku, Finland
| | - Danilo Kimio Hirabae de Oliveira
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Aapistie 7A, P.O. Box 5400, FI-90014, Oulu, Finland
| | - Mahlet Z. Tamirat
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6A, FI-20520 Turku, Finland
| | - Katja Näreoja
- Institute of Biomedicine, Research Center for Cancer, Infections, and Immunity, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Avlokita Tiwari
- Institute of Biomedicine, Research Center for Cancer, Infections, and Immunity, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Michael O. Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Tykistökatu 6A, FI-20520 Turku, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Aapistie 7A, P.O. Box 5400, FI-90014, Oulu, Finland
| | - Arto T. Pulliainen
- Institute of Biomedicine, Research Center for Cancer, Infections, and Immunity, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
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32
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Hackbusch S, Wichels A, Gimenez L, Döpke H, Gerdts G. Potentially human pathogenic Vibrio spp. in a coastal transect: Occurrence and multiple virulence factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 707:136113. [PMID: 31864001 DOI: 10.1016/j.scitotenv.2019.136113] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/19/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
An increase in human Vibrio spp. infections has been linked to climate change related events, in particular to seawater warming and heatwaves. However, there is a distinct lack of research of pathogenic Vibrio spp. occurrences in the temperate North Sea, one of the fastest warming seas globally. Particularly in the German Bight, Vibrio investigations are still scarce. This study focuses on the spatio-temporal quantification and pathogenic characterization of V. parahaemolyticus, V. vulnificus and V. cholerae over the course of 14 months. Species-specific MPN-PCR (Most probable number - polymerase chain reaction) conducted on selectively enriched surface water samples revealed seasonal patterns of all three species with increased abundances during summer months. The extended period of warm seawater coincided with prolonged Vibrio spp. occurrences in the German Bight. Temperature and nitrite were the factors explaining variations in Vibrio spp. abundances after generalized additive mixed models. The specific detection of pathogenic markers via PCR revealed trh-positive V. parahaemolyticus, pathogenic V. vulnificus (nanA, manIIA, PRXII) and V. cholerae serotype O139 presence. Additionally, spatio-temporally varying virulence profiles of V. cholerae with multiple accessory virulence-associated genes, such as the El Tor variant hemolysin (hlyAET), acyltransferase of the repeats-in-toxin cluster (rtxC), Vibrio 7th pandemic island II (VSP-II), Type III Secretion System (TTSS) and the Cholix Toxin (chxA) were detected. Overall, this study highlights that environmental human pathogenic Vibrio spp. comprise a reservoir of virulence-associated genes in the German Bight, especially in estuarine regions. Due to their known vast genetic plasticity, we point to the possible emergence of highly pathogenic V. cholerae strains. Particularly, the presence of V. cholerae serotype O139 is unusual and needs urgent continuous surveillance. Given the predictions of further warming and more frequent heatwave events, human pathogenic Vibrio spp. should be seriously considered as a developing risk to human health in the German Bight.
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Affiliation(s)
- Sidika Hackbusch
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany.
| | - Antje Wichels
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Luis Gimenez
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany; School of Ocean Sciences, Bangor University, LL50 5AB Menai Bridge, Anglesey, UK
| | - Hilke Döpke
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Gunnar Gerdts
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
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33
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Taverner A, MacKay J, Laurent F, Hunter T, Liu K, Mangat K, Song L, Seto E, Postlethwaite S, Alam A, Chandalia A, Seung M, Saberi M, Feng W, Mrsny RJ. Cholix protein domain I functions as a carrier element for efficient apical to basal epithelial transcytosis. Tissue Barriers 2020; 8:1710429. [PMID: 31928299 PMCID: PMC7063863 DOI: 10.1080/21688370.2019.1710429] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cholix (Chx) is expressed by the intestinal pathogen Vibrio cholerae as a single chain of 634 amino acids (~70.7 kDa protein) that folds into three distinct domains, with elements of the second and third domains being involved in accessing the cytoplasm of nonpolarized cells and inciting cell death via ADP-ribosylation of elongation factor 2, respectively. In order to reach nonpolarized cells within the intestinal lamina propria, however, Chx must cross the polarized epithelial barrier in an intact form. Here, we provide in vitro and in vivo demonstrations that a nontoxic Chx transports across intestinal epithelium via a vesicular trafficking pathway that rapidly achieves vesicular apical to basal (A→B) transcytosis and avoids routing to lysosomes. Specifically, Chx traffics in apical endocytic Rab7+ vesicles and in basal exocytic Rab11+ vesicles with a transition between these domains occurring in the ER-Golgi intermediate compartment (ERGIC) through interactions with the lectin mannose-binding protein 1 (LMAN1) protein that undergoes an intracellular re-distribution that coincides with the re-organization of COPI+ and COPII+ vesicular structures. Truncation studies demonstrated that domain I of Chx alone was sufficient to efficiently complete A→B transcytosis and capable of ferrying genetically conjoined human growth hormone (hGH). These studies provide evidence for a pathophysiological strategy where native Chx exotoxin secreted in the intestinal lumen by nonpandemic V. cholerae can reach nonpolarized cells within the lamina propria in an intact form by using a nondestructive pathway to cross in the intestinal epithelial that appears useful for oral delivery of biopharmaceuticals.One-Sentence Summary: Elements within the first domain of the Cholix exotoxin protein are essential and sufficient for the apical to basal transcytosis of this Vibrio cholerae-derived virulence factor across polarized intestinal epithelial cells.
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Affiliation(s)
- Alistair Taverner
- Department of Pharmacy and Pharmacology, University of Bath, Bath, England
| | - Julia MacKay
- Department of Pharmacy and Pharmacology, University of Bath, Bath, England
| | - Floriane Laurent
- Department of Pharmacy and Pharmacology, University of Bath, Bath, England
| | - Tom Hunter
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Keyi Liu
- Applied Molecular Transport, South San Francisco, CA, USA
| | | | - Lisa Song
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Elbert Seto
- Applied Molecular Transport, South San Francisco, CA, USA
| | | | - Aatif Alam
- Applied Molecular Transport, South San Francisco, CA, USA
| | | | - Minji Seung
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Mazi Saberi
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Weijun Feng
- Applied Molecular Transport, South San Francisco, CA, USA
| | - Randall J Mrsny
- Department of Pharmacy and Pharmacology, University of Bath, Bath, England.,Applied Molecular Transport, South San Francisco, CA, USA
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34
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Yahiro K, Ogura K, Terasaki Y, Satoh M, Miyagi S, Terasaki M, Yamasaki E, Moss J. Cholix toxin, an eukaryotic elongation factor 2 ADP-ribosyltransferase, interacts with Prohibitins and induces apoptosis with mitochondrial dysfunction in human hepatocytes. Cell Microbiol 2019; 21:e13033. [PMID: 31009148 PMCID: PMC9986844 DOI: 10.1111/cmi.13033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/16/2019] [Indexed: 12/12/2022]
Abstract
Vibrio cholerae produced-Cholix toxin (Cholix) is a cytotoxin that ADP-ribosylates eukaryotic elongation factor 2, inhibiting protein synthesis, and inducing apoptosis. Here, we identified prohibitin (PHB) 1 and 2 as novel Cholix-interacting membrane proteins in immortalised human hepatocytes and HepG2 cells by Cholix immunoprecipitation assays. The expression level of PHB1 was decreased by Cholix after a 12hr incubation. Cholix-induced poly (ADP-ribose) polymerase (PARP) cleavage was significantly enhanced in PHB (PHB1 or PHB2) knockdown cells. In contrast, transiently overexpressed PHB in hepatocytes attenuated Cholix-induced Bax/Bak conformational changes and PARP cleavage. In addition, Cholix-induced reactive oxygen species production and accumulation of fragmented mitochondria were enhanced in PHB-knockdown cells. Furthermore, Cholix induced activation of Rho-associated coiled coil-containing protein kinase 1 (ROCK1), which was enhanced in PHB-knockdown cells, followed by actin filament depolymerisation and accumulation of tubulin in the blebbing cells. Inhibition of ROCK1 by siRNA or its inhibitor suppressed Cholix-induced PARP cleavage and reactive oxygen species generation. Our findings identify PHB as a new protein that interacts with Cholix and is involved in Cholix-induced mitochondrial dysfunction and cytoskeletal rearrangement by ROCK1 activation during apoptosis.
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Affiliation(s)
- Kinnosuke Yahiro
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kohei Ogura
- Advanced Health Care Science Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Yasuhiro Terasaki
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan
| | - Satoru Miyagi
- Department of Life Science, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Mika Terasaki
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Eiki Yamasaki
- Diagnostic Center for Animal Health and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, Japan
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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35
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Abstract
ADP-ribosylation (ADPr) is an ancient reversible modification of cellular macromolecules controlling major biological processes as diverse as DNA damage repair, transcriptional regulation, intracellular transport, immune and stress responses, cell survival and proliferation. Furthermore, enzymatic reactions of ADPr are central in the pathogenesis of many human diseases, including infectious conditions. By providing a review of ADPr signalling in bacterial systems, we highlight the relevance of this chemical modification in the pathogenesis of human diseases depending on host-pathogen interactions. The post-antibiotic era has raised the need to find alternative approaches to antibiotic administration, as major pathogens becoming resistant to antibiotics. An in-depth understanding of ADPr reactions provides the rationale for designing novel antimicrobial strategies for treatment of infectious diseases. In addition, the understanding of mechanisms of ADPr by bacterial virulence factors offers important hints to improve our knowledge on cellular processes regulated by eukaryotic homologous enzymes, which are often involved in the pathogenesis of human diseases.
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36
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Wahlich J, Desai A, Greco F, Hill K, Jones AT, Mrsny RJ, Pasut G, Perrie Y, Seib FP, Seymour LW, Uchegbu IF. Nanomedicines for the Delivery of Biologics. Pharmaceutics 2019; 11:E210. [PMID: 31058802 PMCID: PMC6572454 DOI: 10.3390/pharmaceutics11050210] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 01/24/2023] Open
Abstract
A special symposium of the Academy of Pharmaceutical Sciences Nanomedicines Focus Group reviewed the current status of the use of nanomedicines for the delivery of biologics drugs. This meeting was particularly timely with the recent approval of the first siRNA-containing product Onpattro™ (patisiran), which is formulated as a lipid nanoparticle for intravenous infusion, and the increasing interest in the use of nanomedicines for the oral delivery of biologics. The challenges in delivering such molecules were discussed with specific emphasis on the delivery both across and into cells. The latest developments in Molecular Envelope Technology® (Nanomerics Ltd, London, UK), liposomal drug delivery (both from an academic and industrial perspective), opportunities offered by the endocytic pathway, delivery using genetically engineered viral vectors (PsiOxus Technologies Ltd, Abingdon, UK), Transint™ technology (Applied Molecular Transport Inc., South San Francisco, CA, USA), which has the potential to deliver a wide range of macromolecules, and AstraZeneca's initiatives in mRNA delivery were covered with a focus on their uses in difficult to treat diseases, including cancers. Preclinical data were presented for each of the technologies and where sufficiently advanced, plans for clinical studies as well as early clinical data. The meeting covered the work in progress in this exciting area and highlighted some key technologies to look out for in the future.
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Affiliation(s)
- John Wahlich
- The Academy of Pharmaceutical Sciences, 4 Heydon Road, Great Chishill, Royston SG8 8SR, UK.
| | - Arpan Desai
- Advanced Drug Delivery, Pharmaceutical Sciences, IMED Biotech Unit, AstraZeneca, Granta Park, Cambridge CB21 6GH, UK.
| | - Francesca Greco
- Reading School of Pharmacy, University of Reading, Whiteknights, Reading RG6 6AP, UK.
| | - Kathryn Hill
- Global Product Development, Pharmaceutical Technology and Development, Operations, AstraZeneca, Macclesfield SK10 2NA, UK.
| | - Arwyn T Jones
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff CF10 3NB, UK.
| | - Randall J Mrsny
- Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, UK.
| | - Gianfranco Pasut
- Pharmaceutical and Pharmacological Sciences Department, University of Padova, F. Marzolo 5, 35131 Padova, Italy.
| | - Yvonne Perrie
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK.
| | - F Philipp Seib
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK.
| | - Leonard W Seymour
- Department of Oncology, Old Road Campus Research Building, Oxford OX3 7DQ, UK.
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37
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Purification and characterization of native human elongation factor 2. Protein Expr Purif 2019; 158:15-19. [PMID: 30742898 DOI: 10.1016/j.pep.2019.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/04/2018] [Accepted: 02/05/2019] [Indexed: 11/20/2022]
Abstract
Human elongation factor 2 is the translocase that is responsible for the movement of tRNA from the A- to P- and P- to E-site on the ribosome during the elongation phase of translation. Being a vital factor of protein biosynthesis, its function is highly controlled and regulated. It has been implicated in numerous diseases and pathologies, and as such it is important to have a source for isolated pure and active protein for biomedical and biochemical studies. Here we report development of a purification protocol for native human elongation factor 2 from HEK-293S cells. The resulting protein is active, pure, has an intact diphtamide and is obtainable in yields suitable for functional and structural studies.
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38
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Awasthi SP, Chowdhury N, Neogi SB, Hinenoya A, Hatanaka N, Chowdhury G, Ramamurthy T, Yamasaki S. Development of a multiplex PCR assay for the detection of major virulence genes in Vibrio cholerae including non-O1 and non-O139 serogroups. J Microbiol Methods 2019; 157:54-58. [DOI: 10.1016/j.mimet.2018.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/09/2018] [Accepted: 12/13/2018] [Indexed: 01/29/2023]
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39
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Tsuda-Sakurai K, Miura M. The hidden nature of protein translational control by diphthamide: the secrets under the leather. J Biochem 2019; 165:1-8. [PMID: 30204891 DOI: 10.1093/jb/mvy071] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/27/2018] [Indexed: 01/16/2023] Open
Abstract
The protein translation elongation factor eEF2 undergoes a unique posttranslational modification called diphthamidation. eEF2 is an essential factor in protein translation, and the diphthamide modification has been a famous target of the diphtheria toxin for a long time. On the other hand, the physiological function of this rare modification in vivo remains unknown. Recent studies have suggested that diphthamide has specific functions for the cellular stress response and active proliferation. In this review, we summarize the history and findings of diphthamide obtained to date and discuss the possibility of a specific function for diphthamide in regulating protein translation.
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Affiliation(s)
- Kayoko Tsuda-Sakurai
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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40
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ParST is a widespread toxin-antitoxin module that targets nucleotide metabolism. Proc Natl Acad Sci U S A 2018; 116:826-834. [PMID: 30598453 DOI: 10.1073/pnas.1814633116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Toxin-antitoxin (TA) systems interfere with essential cellular processes and are implicated in bacterial lifestyle adaptations such as persistence and the biofilm formation. Here, we present structural, biochemical, and functional data on an uncharacterized TA system, the COG5654-COG5642 pair. Bioinformatic analysis showed that this TA pair is found in 2,942 of the 16,286 distinct bacterial species in the RefSeq database. We solved a structure of the toxin bound to a fragment of the antitoxin to 1.50 Å. This structure suggested that the toxin is a mono-ADP-ribosyltransferase (mART). The toxin specifically modifies phosphoribosyl pyrophosphate synthetase (Prs), an essential enzyme in nucleotide biosynthesis conserved in all organisms. We propose renaming the toxin ParT for Prs ADP-ribosylating toxin and ParS for the cognate antitoxin. ParT is a unique example of an intracellular protein mART in bacteria and is the smallest known mART. This work demonstrates that TA systems can induce bacteriostasis through interference with nucleotide biosynthesis.
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41
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Pérez-Reytor D, Jaña V, Pavez L, Navarrete P, García K. Accessory Toxins of Vibrio Pathogens and Their Role in Epithelial Disruption During Infection. Front Microbiol 2018; 9:2248. [PMID: 30294318 PMCID: PMC6158335 DOI: 10.3389/fmicb.2018.02248] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/03/2018] [Indexed: 01/21/2023] Open
Abstract
Gastrointestinal episodes associated with Vibrio species have been rising worldwide in the last few years. Consequently, it is important to comprehend how occurs the production of diarrhea, to establish new preventive and therapeutic measures. Besides the classical CT and TCP toxins, Zot, RTX, and Ace among others have been deeply studied in V. cholerae. However, in other Vibrio species of clinical interest, where some of these toxins have been reported, there is practically no information. Zot activates a cascade of signals inside of the cell that increase the permeability of epithelial barrier, while RTX causes depolymerization of the actin cytoskeleton and Ace increases the permeability of intestinal cell monolayers. The goal of this study is to acquire information about the distribution of these toxins in human pathogenic Vibrios and to review the progress in the study of their role in the intestinal epithelium during infection.
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Affiliation(s)
- Diliana Pérez-Reytor
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Victor Jaña
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Leonardo Pavez
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile.,Departamento de Ciencias Químicas y Biológicas, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Paola Navarrete
- Laboratorio de Microbiología y Probióticos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Katherine García
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
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42
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Narrowe AB, Spang A, Stairs CW, Caceres EF, Baker BJ, Miller CS, Ettema TJG. Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids. Genome Biol Evol 2018; 10:2380-2393. [PMID: 30060184 PMCID: PMC6143161 DOI: 10.1093/gbe/evy154] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.
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Affiliation(s)
- Adrienne B Narrowe
- Department of Integrative Biology, University of Colorado Denver, Denver
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, AB Den Burg, The Netherlands
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Courtney W Stairs
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Eva F Caceres
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas
| | | | - Thijs J G Ettema
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
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43
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Sakib SN, Reddi G, Almagro-Moreno S. Environmental role of pathogenic traits in Vibrio cholerae. J Bacteriol 2018; 200:e00795-17. [PMID: 29581410 PMCID: PMC6040180 DOI: 10.1128/jb.00795-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Vibrio cholerae is a natural inhabitant of aquatic ecosystems. Some strains of V. cholerae can colonize the human host and cause cholera, a profuse watery diarrhea. The major pathogenicity factors and virulence regulators of V. cholerae are either encoded in mobile genetic elements acquired in the environment (e.g. pathogenicity islands or lysogenic phages) or in the core genome. Several lines of evidence indicate that the emergence of numerous virulence traits of V. cholerae occurred in its natural environment due to biotic and abiotic pressures. Here, we discuss the connection between the human host and the potential ecological role of these virulent traits. Unraveling these connections will help us understand the emergence of this organism and other facultative bacterial pathogens.
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Affiliation(s)
- S Nazmus Sakib
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida 32816, USA
| | - Geethika Reddi
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida 32816, USA
| | - Salvador Almagro-Moreno
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida 32816, USA.
- National Center for Integrated Coastal Research, University of Central Florida, Orlando, Florida 32816, USA
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44
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Hossain ZZ, Farhana I, Tulsiani SM, Begum A, Jensen PKM. Transmission and Toxigenic Potential of Vibrio cholerae in Hilsha Fish ( Tenualosa ilisha) for Human Consumption in Bangladesh. Front Microbiol 2018. [PMID: 29515532 PMCID: PMC5826273 DOI: 10.3389/fmicb.2018.00222] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fish have been considered natural reservoirs of Vibrio cholerae, the deadly diarrheal pathogen. However, little is known about the role of fish in the transmission of V. cholerae from the Bay of Bengal to the households of rural and urban Bangladesh. This study analyzes the incidence and pathogenic potential of V. cholerae in Hilsha (Tenualosa ilisha), a commonly caught and consumed fish that exhibits a life cycle in both freshwater and marine environments in Bangladesh. During the period from October 2014 to October 2015, samples from the gills, recta, intestines, and scale swabs of a total of 48 fish were analyzed. The fish were collected both at local markets in the capital city Dhaka and directly from fishermen at the river. PCR analysis by targeting V. cholerae species-specific ompW gene revealed that 39 of 48 (81%) fish were positive in at least one of the sample types. Real-time PCR analysis demonstrated that the cholera-causing ctxA gene was detected in 20% (8 of 39) of V. cholerae-positive fish. A total of 158 V. cholerae isolates were obtained which were categorized into 35 genotypic groups. Altogether, 25 O1 and 133 non-O1/O139 strains were isolated, which were negative for the cholera toxin gene. Other pathogenic genes such as stn/sto, hlyA, chxA, SXT, rtxC, and HA-P were detected. The type three secretion system gene cluster (TTSS) was present in 18% (24 of 133) of non-O1/O139 isolates. The antibiotic susceptibility test revealed that the isolates conferred high resistance to sulfamethoxazole-trimethoprim and kanamycin. Both O1 and non-O1/O139 strains were able to accumulate fluid in rabbit ileal loops and caused distinctive cell death in HeLa cell. Multilocus sequence typing (MLST) showed clonal diversity among fish isolates with pandemic clones. Our data suggest a high prevalence of V. cholerae in Hilsha fish, which indicates that this fish could serve as a potential vehicle for V. cholerae transmission. Moreover, the indigenous V. cholerae strains isolated from Hilsha fish possess considerable virulence potential despite being quite diverse from current epidemic strains. This represents the first study of the population structure of V. cholerae associated with fish in Bangladesh.
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Affiliation(s)
- Zenat Z Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Institute of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Israt Farhana
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Suhella M Tulsiani
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark.,Copenhagen Centre for Disaster Research, University of Copenhagen, Copenhagen, Denmark
| | - Anowara Begum
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Peter K M Jensen
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark.,Copenhagen Centre for Disaster Research, University of Copenhagen, Copenhagen, Denmark
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45
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Susorov D, Zakharov N, Shuvalova E, Ivanov A, Egorova T, Shuvalov A, Shatsky IN, Alkalaeva E. Eukaryotic translation elongation factor 2 (eEF2) catalyzes reverse translocation of the eukaryotic ribosome. J Biol Chem 2018; 293:5220-5229. [PMID: 29453282 DOI: 10.1074/jbc.ra117.000761] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/22/2018] [Indexed: 01/10/2023] Open
Abstract
During protein synthesis, a ribosome moves along the mRNA template and, using aminoacyl-tRNAs, decodes the template nucleotide triplets to assemble a protein amino acid sequence. This movement is accompanied by shifting of mRNA-tRNA complexes within the ribosome in a process called translocation. In living cells, this process proceeds in a unidirectional manner, bringing the ribosome to the 3' end of mRNA, and is catalyzed by the GTPase translation elongation factor 2 (EF-G in prokaryotes and eEF2 in eukaryotes). Interestingly, the possibility of spontaneous backward translocation has been shown in vitro for bacterial ribosomes, suggesting a potential reversibility of this reaction. However, this possibility has not yet been tested for eukaryotic ribosomes. Here, using a reconstituted mammalian translation system, we show that the eukaryotic elongation factor eEF2 catalyzes ribosomal reverse translocation at one mRNA triplet. We found that this process requires a cognate tRNA in the ribosomal E-site and cannot occur spontaneously without eEF2. The efficiency of this reaction depended on the concentrations of eEF2 and cognate tRNAs and increased in the presence of nonhydrolyzable GTP analogues. Of note, ADP-ribosylation of eEF2 domain IV blocked reverse translocation, suggesting a crucial role of interactions of this domain with the ribosome for the catalysis of the reaction. In summary, our findings indicate that eEF2 is able to induce ribosomal translocation in forward and backward directions, highlighting the universal mechanism of tRNA-mRNA movements within the ribosome.
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Affiliation(s)
- Denis Susorov
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,the Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Nikita Zakharov
- the Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia 141700
| | - Ekaterina Shuvalova
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander Ivanov
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,the Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Tatiana Egorova
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,the Pirogov Russian National Research Medical University, Moscow 117997, Russia, and
| | - Alexey Shuvalov
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ivan N Shatsky
- the Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia
| | - Elena Alkalaeva
- From the Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia,
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46
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Discovery of novel bacterial toxins by genomics and computational biology. Toxicon 2018; 147:2-12. [PMID: 29438679 DOI: 10.1016/j.toxicon.2018.02.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/23/2017] [Accepted: 02/07/2018] [Indexed: 12/13/2022]
Abstract
Hundreds and hundreds of bacterial protein toxins are presently known. Traditionally, toxin identification begins with pathological studies of bacterial infectious disease. Following identification and cultivation of a bacterial pathogen, the protein toxin is purified from the culture medium and its pathogenic activity is studied using the methods of biochemistry and structural biology, cell biology, tissue and organ biology, and appropriate animal models, supplemented by bioimaging techniques. The ongoing and explosive development of high-throughput DNA sequencing and bioinformatic approaches have set in motion a revolution in many fields of biology, including microbiology. One consequence is that genes encoding novel bacterial toxins can be identified by bioinformatic and computational methods based on previous knowledge accumulated from studies of the biology and pathology of thousands of known bacterial protein toxins. Starting from the paradigmatic cases of diphtheria toxin, tetanus and botulinum neurotoxins, this review discusses traditional experimental approaches as well as bioinformatics and genomics-driven approaches that facilitate the discovery of novel bacterial toxins. We discuss recent work on the identification of novel botulinum-like toxins from genera such as Weissella, Chryseobacterium, and Enteroccocus, and the implications of these computationally identified toxins in the field. Finally, we discuss the promise of metagenomics in the discovery of novel toxins and their ecological niches, and present data suggesting the existence of uncharacterized, botulinum-like toxin genes in insect gut metagenomes.
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47
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Vibrio cholerae embraces two major evolutionary traits as revealed by targeted gene sequencing. Sci Rep 2018; 8:1631. [PMID: 29374205 PMCID: PMC5785995 DOI: 10.1038/s41598-018-19995-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/11/2018] [Indexed: 01/27/2023] Open
Abstract
Vibrio cholerae inhabits aquatic environments worldwide and has over 200 recognized serogroups classified by O-polysaccharide specificity. Here, we report that V. cholerae selects either of two genetic traits during their evolution. Sequencing of the specific gene locus MS6_A0927 revealed that 339 of 341 strains of V. cholerae and closely related Vibrio species originating from 34 countries over a century carried either metY (M) (~1,269 bp) or luxR-hchA (LH) (~1,600 bp) genes, and consequently those vibrios were separated into two clusters, M (45.4%) and LH (54.6%). Only two strains contained both M and LH in the same locus. Moreover, extensive polymorphisms in those genes were detected in M and LH with 79 and 46 sequence variations, respectively. V. cholerae O1 strains isolated from cholera outbreaks worldwide, and some non-O1 strains evolving from O1 via exchange of genes encoding cell surface polysaccharides possessed LH alleles. Analysis of polymorphisms in the gene locus implicated a high degree of genetic diversity and identical subpopulations among the V. cholerae species.
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48
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Ogura K, Terasaki Y, Miyoshi-Akiyama T, Terasaki M, Moss J, Noda M, Yahiro K. Vibrio cholerae Cholix Toxin-Induced HepG2 Cell Death is Enhanced by Tumor Necrosis Factor-Alpha Through ROS and Intracellular Signal-Regulated Kinases. Toxicol Sci 2018; 156:455-468. [PMID: 28087840 DOI: 10.1093/toxsci/kfx009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cholix toxin (Cholix) from Vibrio cholerae is a potent virulence factor exhibiting ADP-ribosyltransferase activity on eukaryotic elongation factor 2 (eEF2) of host cells, resulting in the inhibition of protein synthesis. Administration of Cholix or its homologue Pseudomonas exotoxin A (PEA) to mice causes lethal hepatocyte damage. In this study, we demonstrate cytotoxicity of Cholix on human hepatocytes in the presence of tumor necrosis factor α (TNF-α), which has been reported to play a fatal role in PEA administered to mice. Compared with incubating HepG2 cells with Cholix alone, co-treatment with TNF-α and Cholix (TNF-α/Cholix) significantly enhanced the activation of caspases, cytochrome c release from mitochondria into cytoplasm, and poly-ADP-ribose polymerase (PARP) cleavage, while incubation with TNF-α alone or co-treatment with TNF-α/catalytically inactive Cholix did not. In the early stage of cell death, Cholix increased phosphorylation of mitogen-activated protein kinases (e.g., p38, ERK, JNK) and Akt, which was not affected by TNF-α alone. MAPK inhibitors (SP600125, SB20852, and U0126) suppressed PARP cleavage induced by TNF-α/Cholix. Protein kinase inhibitor Go6976 suppressed JNK phosphorylation and PARP cleavage by TNF-α/Cholix. In contrast, PKC activator PMA in the absence of TNF-α promoted Cholix-induced PARP cleavage. Reactive oxygen species (ROS) inhibitor, N-acetyl cysteine (NAC), suppressed TNF-α/Cholix-induced JNK and ERK phosphorylation, resulting in inhibition of PARP cleavage. These data suggest that ROS and JNK pathways are important mediators of TNF-α/Cholix-induced HepG2 cell death.
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Affiliation(s)
- Kohei Ogura
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yasuhiro Terasaki
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Mika Terasaki
- Department of Analytic Human Pathology, Nippon Medical School, Tokyo, Japan
| | - Joel Moss
- Cardiovascular and Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-1590
| | - Masatoshi Noda
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kinnosuke Yahiro
- Department of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Abstract
Nowadays it is widely accepted that one compound can be able to hit several targets at once. This "magic shotgun" approach for drug development properly describes the mechanism of biomolecular recognition. The need to take into account the polypharmacology in structure-based drug design has led to the development of several computational tools. Here we present a computational protocol to identify promising compounds against several biological targets, a protocol known as inverse docking.
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Affiliation(s)
- Patricia Saenz-Méndez
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden. .,Computational Chemistry and Biology Group, Facultad de Química, UdelaR, Montevideo, Uruguay.
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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50
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Kober KM, Pogson GH. Genome-wide signals of positive selection in strongylocentrotid sea urchins. BMC Genomics 2017; 18:555. [PMID: 28732465 PMCID: PMC5521101 DOI: 10.1186/s12864-017-3944-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/13/2017] [Indexed: 12/21/2022] Open
Abstract
Background Comparative genomics studies investigating the signals of positive selection among groups of closely related species are still rare and limited in taxonomic breadth. Such studies show great promise in advancing our knowledge about the proportion and the identity of genes experiencing diversifying selection. However, methodological challenges have led to high levels of false positives in past studies. Here, we use the well-annotated genome of the purple sea urchin, Strongylocentrotus purpuratus, as a reference to investigate the signals of positive selection at 6520 single-copy orthologs from nine sea urchin species belonging to the family Strongylocentrotidae paying careful attention to minimizing false positives. Results We identified 1008 (15.5%) candidate positive selection genes (PSGs). Tests for positive selection along the nine terminal branches of the phylogeny identified 824 genes that showed lineage-specific adaptive diversification (1.67% of branch-sites tests performed). Positively selected codons were not enriched at exon borders or near regions containing missing data, suggesting a limited contribution of false positives caused by alignment or annotation errors. Alignments were validated at 10 loci with re-sequencing using Sanger methods. No differences were observed in the rates of synonymous substitution (dS), GC content, and codon bias between the candidate PSGs and those not showing positive selection. However, the candidate PSGs had 68% higher rates of nonsynonymous substitution (dN) and 33% lower levels of heterozygosity, consistent with selective sweeps and opposite to that expected by a relaxation of selective constraint. Although positive selection was identified at reproductive proteins and innate immunity genes, the strongest signals of adaptive diversification were observed at extracellular matrix proteins, cell adhesion molecules, membrane receptors, and ion channels. Many candidate PSGs have been widely implicated as targets of pathogen binding, inactivation, mimicry, or exploitation in other groups (notably mammals). Conclusions Our study confirmed the widespread action of positive selection across sea urchin genomes and allowed us to reject the possibility that annotation and alignment errors (including paralogs) were responsible for creating false signals of adaptive molecular divergence. The candidate PSGs identified in our study represent promising targets for future research into the selective agents responsible for their adaptive diversification and their contribution to speciation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3944-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kord M Kober
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, USA. .,Institute for Computational Health Sciences, University of California, San Francisco, USA. .,Present address: Department of Physiological Nursing, University of California, San Francisco, USA.
| | - Grant H Pogson
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, USA
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