1
|
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.
Collapse
|
2
|
Brown EM, Arellano-Santoyo H, Temple ER, Costliow ZA, Pichaud M, Hall AB, Liu K, Durney MA, Gu X, Plichta DR, Clish CA, Porter JA, Vlamakis H, Xavier RJ. Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors. Cell Host Microbe 2021; 29:1351-1365.e11. [PMID: 34403684 DOI: 10.1016/j.chom.2021.07.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 06/23/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022]
Abstract
Bacterial ADP-ribosyltransferases (ADPRTs) have been described as toxins involved in pathogenesis through the modification of host proteins. Here, we report that ADPRTs are not pathogen restricted but widely prevalent in the human gut microbiome and often associated with phage elements. We validated their biochemical activity in a large clinical isolate collection and further examined Bxa, a highly abundant ADPRT in Bacteroides. Bxa is expressed, secreted, and enzymatically active in Bacteroides and can ADP-ribosylate non-muscle myosin II proteins. Addition of Bxa to epithelial cells remodeled the actin cytoskeleton and induced secretion of inosine. Bxa-encoding B. stercoris can use inosine as a carbon source and colonizes the gut to significantly greater numbers than a bxa-deleted strain in germ-free and altered Schaedler flora (ASF) mice. Colonization correlated with increased inosine concentrations in the feces and tissues. Altogether, our results show that ADPRTs are abundant in the microbiome and act as bacterial fitness factors.
Collapse
Affiliation(s)
- Eric M Brown
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hugo Arellano-Santoyo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novartis Institutes for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Emily R Temple
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Matthieu Pichaud
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novartis Institutes for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - A Brantley Hall
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kai Liu
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Xiebin Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Clary A Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey A Porter
- Novartis Institutes for Biomedical Research Inc., Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
3
|
Chaoprasid P, Lukat P, Mühlen S, Heidler T, Gazdag E, Dong S, Bi W, Rüter C, Kirchenwitz M, Steffen A, Jänsch L, Stradal TEB, Dersch P, Blankenfeldt W. Crystal structure of bacterial cytotoxic necrotizing factor CNF Y reveals molecular building blocks for intoxication. EMBO J 2021; 40:e105202. [PMID: 33410511 PMCID: PMC7883292 DOI: 10.15252/embj.2020105202] [Citation(s) in RCA: 10] [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: 04/06/2020] [Revised: 11/12/2020] [Accepted: 11/23/2020] [Indexed: 12/30/2022] Open
Abstract
Cytotoxic necrotizing factors (CNFs) are bacterial single-chain exotoxins that modulate cytokinetic/oncogenic and inflammatory processes through activation of host cell Rho GTPases. To achieve this, they are secreted, bind surface receptors to induce endocytosis and translocate a catalytic unit into the cytosol to intoxicate host cells. A three-dimensional structure that provides insight into the underlying mechanisms is still lacking. Here, we determined the crystal structure of full-length Yersinia pseudotuberculosis CNFY . CNFY consists of five domains (D1-D5), and by integrating structural and functional data, we demonstrate that D1-3 act as export and translocation module for the catalytic unit (D4-5) and for a fused β-lactamase reporter protein. We further found that D4, which possesses structural similarity to ADP-ribosyl transferases, but had no equivalent catalytic activity, changed its position to interact extensively with D5 in the crystal structure of the free D4-5 fragment. This liberates D5 from a semi-blocked conformation in full-length CNFY , leading to higher deamidation activity. Finally, we identify CNF translocation modules in several uncharacterized fusion proteins, which suggests their usability as a broad-specificity protein delivery tool.
Collapse
Affiliation(s)
- Paweena Chaoprasid
- Institute of InfectiologyCenter for Molecular Biology of Inflammation (ZMBE)University of MünsterMünsterGermany
- Molecular Infection BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Peer Lukat
- Structure and Function of ProteinsHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Sabrina Mühlen
- Institute of InfectiologyCenter for Molecular Biology of Inflammation (ZMBE)University of MünsterMünsterGermany
- Molecular Infection BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
- Deutsches Zentrum für InfektionsforschungBraunschweigGermany
| | - Thomas Heidler
- Molecular Structural BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Emerich‐Mihai Gazdag
- Structure and Function of ProteinsHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Shuangshuang Dong
- Structure and Function of ProteinsHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Wenjie Bi
- Cellular ProteomicsHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Christian Rüter
- Institute of InfectiologyCenter for Molecular Biology of Inflammation (ZMBE)University of MünsterMünsterGermany
| | - Marco Kirchenwitz
- Cell BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Anika Steffen
- Cell BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
| | - Lothar Jänsch
- Cellular ProteomicsHelmholtz Centre for Infection ResearchBraunschweigGermany
- Institute of ZoologyTechnische Universität BraunschweigBraunschweigGermany
| | - Theresia E B Stradal
- Cell BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
- Institute of ZoologyTechnische Universität BraunschweigBraunschweigGermany
| | - Petra Dersch
- Institute of InfectiologyCenter for Molecular Biology of Inflammation (ZMBE)University of MünsterMünsterGermany
- Molecular Infection BiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
- Deutsches Zentrum für InfektionsforschungBraunschweigGermany
- Institute of MicrobiologyTechnische Universität BraunschweigBraunschweigGermany
| | - Wulf Blankenfeldt
- Structure and Function of ProteinsHelmholtz Centre for Infection ResearchBraunschweigGermany
- Institute for Biochemistry, Biotechnology and BioinformaticsTechnische Universität BraunschweigBraunschweigGermany
| |
Collapse
|
4
|
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.
Collapse
|
5
|
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.
Collapse
Affiliation(s)
| | | | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (O.T.); (Z.T.)
| |
Collapse
|
6
|
Chutshela A, Masamba P, Oyinloye BE, Kappo AP. Molecular Context of ADP-ribosylation in Schistosomes for Drug Discovery and Vaccine Development. Curr Drug Discov Technol 2020; 18:473-484. [PMID: 32767945 DOI: 10.2174/1570163817666200806170654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022]
Abstract
Schistosome infection is regarded as one of the most important and neglected tropical diseases associated with poor sanitation. Like other living organisms, schistosomes employ multiple biological processes, of which some are regulated by a post-translational modification called Adenosine Diphosphate-ribosylation (ADP-ribosylation), catalyzed by ADP-ribosyltransferases. ADP-ribosylation is the addition of ADP-ribose moieties from Nicotinamide Adenine Dinucleotide (NAD+) to various targets, which include proteins and nucleotides. It is crucial in biological processes such as DNA repair, apoptosis, carbohydrate metabolism and catabolism. In the absence of a vaccine against schistosomiasis, this becomes a promising pathway in the identification of drug targets against various forms of this infection. The tegument of the worm is an encouraging immunogenic target for anti-schistosomal vaccine development. Vaccinology, molecular modeling and target-based drug discovery strategies have been used for years in drug discovery and for vaccine development. In this paper, we outline ADP-ribosylation and other different approaches to drug discovery and vaccine development against schistosomiasis.
Collapse
Affiliation(s)
- Amandla Chutshela
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa 3886, South Africa
| | - Priscilla Masamba
- Molecular Biophysics and Structural Biology Group, Department of Biochemistry, University of Johannesburg, Kingsway Campus, Auckland Park 2006, South Africa
| | | | - Abidemi Paul Kappo
- Molecular Biophysics and Structural Biology Group, Department of Biochemistry, University of Johannesburg, Kingsway Campus, Auckland Park 2006, South Africa
| |
Collapse
|
7
|
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: 2] [Impact Index Per Article: 0.5] [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.
Collapse
Affiliation(s)
- Geoffrey Masuyer
- Department of Pharmacy and Pharmacology, Centre for Therapeutic Innovation, University of Bath, Bath BA2 7AY, UK
| |
Collapse
|
8
|
Rajkovic A, Jovanovic J, Monteiro S, Decleer M, Andjelkovic M, Foubert A, Beloglazova N, Tsilla V, Sas B, Madder A, De Saeger S, Uyttendaele M. Detection of toxins involved in foodborne diseases caused by Gram‐positive bacteria. Compr Rev Food Sci Food Saf 2020; 19:1605-1657. [DOI: 10.1111/1541-4337.12571] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Andreja Rajkovic
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Jelena Jovanovic
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Silvia Monteiro
- Laboratorio Analises, Instituto Superior TecnicoUniversidade de Lisboa Lisbon Portugal
| | - Marlies Decleer
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Mirjana Andjelkovic
- Operational Directorate Food, Medicines and Consumer SafetyService for Chemical Residues and Contaminants Brussels Belgium
| | - Astrid Foubert
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Natalia Beloglazova
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
- Nanotechnology Education and Research CenterSouth Ural State University Chelyabinsk Russia
| | - Varvara Tsilla
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Benedikt Sas
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| | - Annemieke Madder
- Laboratorium for Organic and Biomimetic Chemistry, Department of Organic and Macromolecular ChemistryGhent University Ghent Belgium
| | - Sarah De Saeger
- Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical SciencesGhent University Ghent Belgium
| | - Mieke Uyttendaele
- Laboratory of Food Microbiology and Food Preservation, Department of Food Technology, Safety and Health, Faculty of Bioscience EngineeringGhent University Ghent Belgium
| |
Collapse
|
9
|
Lugo MR, Merrill AR. An In-Silico Sequence-Structure-Function Analysis of the N-Terminal Lobe in CT Group Bacterial ADP-Ribosyltransferase Toxins. Toxins (Basel) 2019; 11:toxins11060365. [PMID: 31234283 PMCID: PMC6628389 DOI: 10.3390/toxins11060365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 01/02/2023] Open
Abstract
The C3-like toxins are single-domain proteins that represent a minimal mono-ADP-ribosyl transferase (mART) enzyme with a simple model scaffold for the entire cholera toxin (CT)-group. These proteins possess a single (A-domain) that modifies Rho proteins. In contrast, C2-like toxins require a binding/translocation partner (B-component) for intoxication. These are A-only toxins that contain the E-x-E motif, modify G-actin, but are two-domains with a C-domain possessing enzymatic activity. The N-domain of the C2-like toxins is unstructured, and its function is currently unknown. A sequence-structure-function comparison was performed on the N-terminal region of the mART domain of the enzymatic component of the CT toxin group in the CATCH fold (3.90.210.10). Special consideration was given to the N-domain distal segment, the α-lobe (α1–α4), and its different roles in these toxin sub-groups. These results show that the role of the N-terminal α-lobe is to provide a suitable configuration (i) of the α2–α3 helices to feature the α3-motif that has a role in NAD+ substrate binding and possibly in the interaction with the protein target; (ii) the α3–α4 helices to provide the α3/4-loop with protein-protein interaction capability; and (iii) the α1-Ntail that features specialized motif(s) according to the toxin type (A-only or A-B toxins) exhibiting an effect on the catalytic activity via the ARTT-loop, with a role in the inter-domain stability, and with a function in the binding and/or translocation steps during the internalization process.
Collapse
Affiliation(s)
- Miguel R Lugo
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G 2W1, Canada.
| | - A Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G 2W1, Canada.
| |
Collapse
|
10
|
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.
Collapse
|
11
|
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.
Collapse
|
12
|
Tang JY, Bullen NP, Ahmad S, Whitney JC. Diverse NADase effector families mediate interbacterial antagonism via the type VI secretion system. J Biol Chem 2017; 293:1504-1514. [PMID: 29237732 DOI: 10.1074/jbc.ra117.000178] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/06/2017] [Indexed: 11/06/2022] Open
Abstract
The bacterial type VI secretion system (T6SS) mediates antagonistic cell-cell interactions between competing Gram-negative bacteria. In plant-beneficial bacteria, this pathway has been shown to suppress the growth of bacterial pathogens; however, the identification and mode of action of T6SS effector proteins that mediate this protective effect remain poorly defined. Here, we identify two previously uncharacterized effectors required for interbacterial antagonism by the plant commensal bacterium Pseudomonas protegens Consistent with the established effector-immunity paradigm for antibacterial T6SS substrates, the toxic activities of these effectors are neutralized by adjacently encoded cognate immunity determinants. Although one of these effectors, RhsA, belongs to the family of DNase enzymes, the activity of the other was not apparent from its sequence. To determine the mechanism of toxicity of this latter effector, we determined its 1.3 Å crystal structure in complex with its immunity protein and found that it resembles NAD(P)+-degrading enzymes. In line with this structural similarity, biochemical characterization of this effector, termed Tne2 (Type VI secretion NADase effector family 2), demonstrates that it possesses potent NAD(P)+ hydrolase activity. Tne2 is the founding member of a widespread family of interbacterial NADases predicted to transit not only the Gram-negative T6SS but also the Gram-positive type VII secretion system, a pathway recently implicated in interbacterial competition among Firmicutes. Together, this work identifies new T6SS effectors employed by a plant commensal bacterium to antagonize its competitors and broadly implicates NAD(P)+-hydrolyzing enzymes as substrates of interbacterial conflict pathways found in diverse bacterial phyla.
Collapse
Affiliation(s)
- Jenny Y Tang
- From the Michael DeGroote Institute for Infectious Disease Research and.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Nathan P Bullen
- From the Michael DeGroote Institute for Infectious Disease Research and.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Shehryar Ahmad
- From the Michael DeGroote Institute for Infectious Disease Research and.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - John C Whitney
- From the Michael DeGroote Institute for Infectious Disease Research and .,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| |
Collapse
|
13
|
Ebeling J, Fünfhaus A, Knispel H, Krska D, Ravulapalli R, Heney KA, Lugo MR, Merrill AR, Genersch E. Characterization of the toxin Plx2A, a RhoA-targeting ADP-ribosyltransferase produced by the honey bee pathogenPaenibacillus larvae. Environ Microbiol 2017; 19:5100-5116. [DOI: 10.1111/1462-2920.13989] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/24/2017] [Accepted: 11/04/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Julia Ebeling
- Department of Molecular Microbiology and Bee Diseases; Institute for Bee Research; 16540 Hohen Neuendorf Germany
| | - Anne Fünfhaus
- Department of Molecular Microbiology and Bee Diseases; Institute for Bee Research; 16540 Hohen Neuendorf Germany
| | - Henriette Knispel
- Department of Molecular Microbiology and Bee Diseases; Institute for Bee Research; 16540 Hohen Neuendorf Germany
| | - Daniel Krska
- Department of Molecular and Cellular Biology; Guelph ON Canada N1G 2W1
| | | | - Kayla A. Heney
- Department of Molecular and Cellular Biology; Guelph ON Canada N1G 2W1
| | - Miguel R. Lugo
- Department of Molecular and Cellular Biology; Guelph ON Canada N1G 2W1
| | - A. Rod Merrill
- Department of Molecular and Cellular Biology; Guelph ON Canada N1G 2W1
| | - Elke Genersch
- Department of Molecular Microbiology and Bee Diseases; Institute for Bee Research; 16540 Hohen Neuendorf Germany
- Fachbereich Veterinärmedizin, Institut für Mikrobiologie und Tierseuchen; Freie Universität Berlin; 14163 Berlin Germany
| |
Collapse
|
14
|
CagL from Helicobacter pylori has ADP-ribosylation activity and exerts partial protective efficacy in mice. Arch Biochem Biophys 2017; 635:102-109. [DOI: 10.1016/j.abb.2017.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/20/2017] [Accepted: 10/26/2017] [Indexed: 12/26/2022]
|
15
|
Aktories K, Schwan C, Lang AE. ADP-Ribosylation and Cross-Linking of Actin by Bacterial Protein Toxins. Handb Exp Pharmacol 2017; 235:179-206. [PMID: 27316913 DOI: 10.1007/164_2016_26] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Actin and the actin cytoskeleton play fundamental roles in host-pathogen interactions. Proper function of the actin cytoskeleton is crucial for innate and acquired immune defense. Bacterial toxins attack the actin cytoskeleton by targeting regulators of actin. Moreover, actin is directly modified by various bacterial protein toxins and effectors, which cause ADP-ribosylation or cross-linking of actin. Modification of actin can result in inhibition or stimulation of actin polymerization. Toxins, acting directly on actin, are reviewed.
Collapse
Affiliation(s)
- Klaus Aktories
- Institute for Experimental and Clinical Pharmacology and Toxicology, Albert-Ludwigs-Universität Freiburg, Freiburg, 79104, Germany. .,Freiburg Institute of Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Freiburg, 79104, Germany.
| | - Carsten Schwan
- Institute for Experimental and Clinical Pharmacology and Toxicology, Albert-Ludwigs-Universität Freiburg, Freiburg, 79104, Germany
| | - Alexander E Lang
- Institute for Experimental and Clinical Pharmacology and Toxicology, Albert-Ludwigs-Universität Freiburg, Freiburg, 79104, Germany
| |
Collapse
|
16
|
Biology of Paenibacillus larvae, a deadly pathogen of honey bee larvae. Appl Microbiol Biotechnol 2016; 100:7387-95. [PMID: 27394713 DOI: 10.1007/s00253-016-7716-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 01/23/2023]
Abstract
The gram-positive bacterium Paenibacillus larvae is the etiological agent of American Foulbrood of honey bees, a notifiable disease in many countries. Hence, P. larvae can be considered as an entomopathogen of considerable relevance in veterinary medicine. P. larvae is a highly specialized pathogen with only one established host, the honey bee larva. No other natural environment supporting germination and proliferation of P. larvae is known. Over the last decade, tremendous progress in the understanding of P. larvae and its interactions with honey bee larvae at a molecular level has been made. In this review, we will present the recent highlights and developments in P. larvae research and discuss the impact of some of the findings in a broader context to demonstrate what we can learn from studying "exotic" pathogens.
Collapse
|
17
|
Lyons B, Ravulapalli R, Lanoue J, Lugo MR, Dutta D, Carlin S, Merrill AR. Scabin, a Novel DNA-acting ADP-ribosyltransferase from Streptomyces scabies. J Biol Chem 2016; 291:11198-215. [PMID: 27002155 PMCID: PMC4900268 DOI: 10.1074/jbc.m115.707653] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/12/2016] [Indexed: 11/06/2022] Open
Abstract
A bioinformatics strategy was used to identify Scabin, a novel DNA-targeting enzyme from the plant pathogen 87.22 strain of Streptomyces scabies Scabin shares nearly 40% sequence identity with the Pierisin family of mono-ADP-ribosyltransferase toxins. Scabin was purified to homogeneity as a 22-kDa single-domain enzyme and was shown to possess high NAD(+)-glycohydrolase (Km (NAD) = 68 ± 3 μm; kcat = 94 ± 2 min(-1)) activity with an RSQXE motif; it was also shown to target deoxyguanosine and showed sigmoidal enzyme kinetics (K0.5(deoxyguanosine) = 302 ± 12 μm; kcat = 14 min(-1)). Mass spectrometry analysis revealed that Scabin labels the exocyclic amino group on guanine bases in either single-stranded or double-stranded DNA. Several small molecule inhibitors were identified, and the most potent compounds were found to inhibit the enzyme activity with Ki values ranging from 3 to 24 μm PJ34, a well known inhibitor of poly-ADP-ribosyltransferases, was shown to be the most potent inhibitor of Scabin. Scabin was crystallized, representing the first structure of a DNA-targeting mono-ADP-ribosyltransferase enzyme; the structures of the apo-form (1.45 Å) and with two inhibitors (P6-E, 1.4 Å; PJ34, 1.6 Å) were solved. These x-ray structures are also the first high resolution structures of the Pierisin subgroup of the mono-ADP-ribosyltransferase toxin family. A model of Scabin with its DNA substrate is also proposed.
Collapse
Affiliation(s)
- Bronwyn Lyons
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Ravikiran Ravulapalli
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Jason Lanoue
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Miguel R Lugo
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Debajyoti Dutta
- the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Stephanie Carlin
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - A Rod Merrill
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| |
Collapse
|
18
|
Affiliation(s)
- C. Satheesan Babu
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan R.O.C
| | - Carmay Lim
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan R.O.C
- Department
of Chemistry, National Tsing-Hua University, Hsinchu 300, Taiwan R.O.C
| |
Collapse
|
19
|
Robb C, Robb M, Nano F, Boraston A. The Structure of the Toxin and Type Six Secretion System Substrate Tse2 in Complex with Its Immunity Protein. Structure 2016; 24:277-84. [DOI: 10.1016/j.str.2015.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/04/2015] [Accepted: 11/23/2015] [Indexed: 01/11/2023]
|
20
|
Sheets J, Aktories K. Insecticidal Toxin Complexes from Photorhabdus luminescens. Curr Top Microbiol Immunol 2016; 402:3-23. [DOI: 10.1007/82_2016_55] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
21
|
Whitney JC, Quentin D, Sawai S, LeRoux M, Harding BN, Ledvina HE, Tran BQ, Robinson H, Goo YA, Goodlett DR, Raunser S, Mougous JD. An interbacterial NAD(P)(+) glycohydrolase toxin requires elongation factor Tu for delivery to target cells. Cell 2015; 163:607-19. [PMID: 26456113 DOI: 10.1016/j.cell.2015.09.027] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/15/2015] [Accepted: 08/19/2015] [Indexed: 11/17/2022]
Abstract
Type VI secretion (T6S) influences the composition of microbial communities by catalyzing the delivery of toxins between adjacent bacterial cells. Here, we demonstrate that a T6S integral membrane toxin from Pseudomonas aeruginosa, Tse6, acts on target cells by degrading the universally essential dinucleotides NAD(+) and NADP(+). Structural analyses of Tse6 show that it resembles mono-ADP-ribosyltransferase proteins, such as diphtheria toxin, with the exception of a unique loop that both excludes proteinaceous ADP-ribose acceptors and contributes to hydrolysis. We find that entry of Tse6 into target cells requires its binding to an essential housekeeping protein, translation elongation factor Tu (EF-Tu). These proteins participate in a larger assembly that additionally directs toxin export and provides chaperone activity. Visualization of this complex by electron microscopy defines the architecture of a toxin-loaded T6S apparatus and provides mechanistic insight into intercellular membrane protein delivery between bacteria.
Collapse
Affiliation(s)
- John C Whitney
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Dennis Quentin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Shin Sawai
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Michele LeRoux
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Brittany N Harding
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Hannah E Ledvina
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Bao Q Tran
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Howard Robinson
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Young Ah Goo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - David R Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
| |
Collapse
|
22
|
Ravulapalli R, Lugo MR, Pfoh R, Visschedyk D, Poole A, Fieldhouse RJ, Pai EF, Merrill AR. Characterization of Vis Toxin, a Novel ADP-Ribosyltransferase from Vibrio splendidus. Biochemistry 2015; 54:5920-36. [PMID: 26352925 DOI: 10.1021/acs.biochem.5b00921] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vis toxin was identified by a bioinformatics strategy as a putative virulence factor produced by Vibrio splendidus with mono-ADP-ribosyltransferase activity. Vis was purified to homogeneity as a 28 kDa single-domain enzyme and was shown to possess NAD(+)-glycohydrolase [KM(NAD(+)) = 276 ± 12 μM] activity and with an R-S-E-X-E motif; it targets arginine-related compounds [KM(agmatine) = 272 ± 18 mM]. Mass spectrometry analysis revealed that Vis labels l-arginine with ADP-ribose from the NAD(+) substrate at the amino nitrogen of the guanidinium side chain. Vis is toxic to yeast when expressed in the cytoplasm under control of the CUP1 promotor, and catalytic variants lost the ability to kill the yeast host, indicating that the toxin exerts its lethality through its enzyme activity. Several small molecule inhibitors were identified from a virtual screen, and the most potent compounds were found to inhibit the transferase activity of the enzyme with Ki values ranging from 25 to 134 μM. Inhibitor compound M6 bears the necessary attributes of a solid candidate as a lead compound for therapeutic development. Vis toxin was crystallized, and the structures of the apoenzyme (1.4 Å) and the enzyme bound with NAD(+) (1.8 Å) and with the M6 inhibitor (1.5 Å) were determined. The structures revealed that Vis represents a new subgroup within the mono-ADP-ribosyltransferase toxin family.
Collapse
Affiliation(s)
- Ravikiran Ravulapalli
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Miguel R Lugo
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Roland Pfoh
- Department of Biology, York University , Toronto, ON, Canada M3J 1P3.,Department of Biochemistry, University of Toronto , Toronto, ON, Canada M5S 1A8.,Campbell Family Institute for Cancer Research, Princess Margaret Hospital , Toronto, ON, Canada M5G 1L7
| | - Danielle Visschedyk
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Amanda Poole
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Robert J Fieldhouse
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center , New York, New York 10065, United States.,Department of Systems Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Emil F Pai
- Department of Biochemistry, University of Toronto , Toronto, ON, Canada M5S 1A8.,Campbell Family Institute for Cancer Research, Princess Margaret Hospital , Toronto, ON, Canada M5G 1L7.,Departments of Medical Biophysics and Molecular Genetics, University of Toronto , Toronto, ON, Canada M5S 1A8
| | - A Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| |
Collapse
|
23
|
Lugo MR, Merrill AR. The Father, Son and Cholix Toxin: The Third Member of the DT Group Mono-ADP-Ribosyltransferase Toxin Family. Toxins (Basel) 2015. [PMID: 26213968 PMCID: PMC4549722 DOI: 10.3390/toxins7082757] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The cholix toxin gene (chxA) was first identified in V. cholerae strains in 2007, and the protein was identified by bioinformatics analysis in 2008. It was identified as the third member of the diphtheria toxin group of mono-ADP-ribosyltransferase toxins along with P. aeruginosa exotoxin A and C. diphtheriae diphtheria toxin. Our group determined the structure of the full-length, three-domain cholix toxin at 2.1 Å and its C-terminal catalytic domain (cholixc) at 1.25 Å resolution. We showed that cholix toxin is specific for elongation factor 2 (diphthamide residue), similar to exotoxin A and diphtheria toxin. Cholix toxin possesses molecular features required for infection of eukaryotes by receptor-mediated endocytosis, translocation to the host cytoplasm and inhibition of protein synthesis. More recently, we also solved the structure of full-length cholix toxin in complex with NAD+ and proposed a new kinetic model for cholix enzyme activity. In addition, we have taken a computational approach that revealed some important properties of the NAD+-binding pocket at the residue level, including the role of crystallographic water molecules in the NAD+ substrate interaction. We developed a pharmacophore model of cholix toxin, which revealed a cationic feature in the side chain of cholix toxin active-site inhibitors that may determine the active pose. Notably, several recent reports have been published on the role of cholix toxin as a major virulence factor in V. cholerae (non-O1/O139 strains). Additionally, FitzGerald and coworkers prepared an immunotoxin constructed from domains II and III as a cancer treatment strategy to complement successful immunotoxins derived from P. aeruginosa exotoxin A.
Collapse
Affiliation(s)
- Miguel R Lugo
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - A Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| |
Collapse
|
24
|
Structure of CARDS toxin, a unique ADP-ribosylating and vacuolating cytotoxin from Mycoplasma pneumoniae. Proc Natl Acad Sci U S A 2015; 112:5165-70. [PMID: 25848012 DOI: 10.1073/pnas.1420308112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycoplasma pneumoniae (Mp) infections cause tracheobronchitis and "walking" pneumonia, and are linked to asthma and other reactive airway diseases. As part of the infectious process, the bacterium expresses a 591-aa virulence factor with both mono-ADP ribosyltransferase (mART) and vacuolating activities known as Community-Acquired Respiratory Distress Syndrome Toxin (CARDS TX). CARDS TX binds to human surfactant protein A and annexin A2 on airway epithelial cells and is internalized, leading to a range of pathogenetic events. Here we present the structure of CARDS TX, a triangular molecule in which N-terminal mART and C-terminal tandem β-trefoil domains associate to form an overall architecture distinct from other well-recognized ADP-ribosylating bacterial toxins. We demonstrate that CARDS TX binds phosphatidylcholine and sphingomyelin specifically over other membrane lipids, and that cell surface binding and internalization activities are housed within the C-terminal β-trefoil domain. The results enhance our understanding of Mp pathogenicity and suggest a novel avenue for the development of therapies to treat Mp-associated asthma and other acute and chronic airway diseases.
Collapse
|
25
|
Lugo MR, Merrill AR. A comparative structure-function analysis of active-site inhibitors of Vibrio cholerae cholix toxin. J Mol Recognit 2015; 28:539-52. [PMID: 25756608 DOI: 10.1002/jmr.2469] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/26/2015] [Accepted: 01/27/2015] [Indexed: 01/27/2023]
Abstract
Cholix toxin from Vibrio cholerae is a novel mono-ADP-ribosyltransferase (mART) toxin that shares structural and functional properties with Pseudomonas aeruginosa exotoxin A and Corynebacterium diphtheriae diphtheria toxin. Herein, we have used the high-resolution X-ray structure of full-length cholix toxin in the apo form, NAD(+) bound, and 10 structures of the cholix catalytic domain (C-domain) complexed with several strong inhibitors of toxin enzyme activity (NAP, PJ34, and the P-series) to study the binding mode of the ligands. A pharmacophore model based on the active pose of NAD(+) was compared with the active conformation of the inhibitors, which revealed a cationic feature in the side chain of the inhibitors that may determine the active pose. Moreover, a conformational search was conducted for the missing coordinates of one of the main active-site loops (R-loop). The resulting structural models were used to evaluate the interaction energies and for 3D-QSAR modeling. Implications for a rational drug design approach for mART toxins were derived.
Collapse
Affiliation(s)
- Miguel R Lugo
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - A Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| |
Collapse
|
26
|
Lugo MR, Merrill AR. Pocket analysis of the full-length cholix toxin. An assessment of the structure-dynamics of the apo catalytic domain. J Biomol Struct Dyn 2015; 33:2452-68. [PMID: 25559625 DOI: 10.1080/07391102.2014.1000972] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cholix toxin from Vibrio cholerae is the third member of the diphtheria toxin (DT) group of mono-ADP-ribosyltransferase (mART) bacterial toxins. It shares structural and functional properties with Pseudomonas aeruginosa exotoxin A and Corynebacterium diphtheriae DT. Cholix toxin is an important model for the development of antivirulence approaches and therapeutics against these toxins from pathogenic bacteria. Herein, we have used the high-resolution X-ray structure of full-length cholix complexed with NAD(+) to describe the properties of the NAD(+)-binding pocket at the residue level, including the role of crystallographic water molecules in the NAD(+) substrate interaction. The full-length apo cholix structure is used to describe the putative NAD(+)-binding site(s) and to correlate biochemical with crystallographic data to study the stoichiometry and orientation of bound NAD(+) molecules. We quantitatively describe the NAD(+) substrate interactions on a residue basis for the main 22 pocket residues in cholixf, a glycerol and 5 contact water molecules as part of the recognition surface by the substrate according to the conditions of crystallization. In addition, the dynamic properties of an in silico version of the catalytic domain were investigated in order to understand the lack of electronic density for one of the main flexible loops (R-loop) in the pocket of X-ray complexes. Implications for a rational drug design approach for mART toxins are derived.
Collapse
Affiliation(s)
- Miguel R Lugo
- a Department of Molecular and Cellular Biology, Science Complex , University of Guelph , Guelph , ON , Canada N1G2W
| | - A Rod Merrill
- a Department of Molecular and Cellular Biology, Science Complex , University of Guelph , Guelph , ON , Canada N1G2W
| |
Collapse
|
27
|
|
28
|
Krska D, Ravulapalli R, Fieldhouse RJ, Lugo MR, Merrill AR. C3larvin toxin, an ADP-ribosyltransferase from Paenibacillus larvae. J Biol Chem 2014; 290:1639-53. [PMID: 25477523 DOI: 10.1074/jbc.m114.589846] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
C3larvin toxin was identified by a bioinformatic strategy as a putative mono-ADP-ribosyltransferase and a possible virulence factor from Paenibacillus larvae, which is the causative agent of American Foulbrood in honey bees. C3larvin targets RhoA as a substrate for its transferase reaction, and kinetics for both the NAD(+) (Km = 34 ± 12 μm) and RhoA (Km = 17 ± 3 μm) substrates were characterized for this enzyme from the mono-ADP-ribosyltransferase C3 toxin subgroup. C3larvin is toxic to yeast when expressed in the cytoplasm, and catalytic variants of the enzyme lost the ability to kill the yeast host, indicating that the toxin exerts its lethality through its enzyme activity. A small molecule inhibitor of C3larvin enzymatic activity was discovered called M3 (Ki = 11 ± 2 μm), and to our knowledge, is the first inhibitor of transferase activity of the C3 toxin family. C3larvin was crystallized, and its crystal structure (apoenzyme) was solved to 2.3 Å resolution. C3larvin was also shown to have a different mechanism of cell entry from other C3 toxins.
Collapse
Affiliation(s)
- Daniel Krska
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ravikiran Ravulapalli
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Robert J Fieldhouse
- the Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, and the Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel R Lugo
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - A Rod Merrill
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada,
| |
Collapse
|
29
|
Pfaumann V, Lang AE, Schwan C, Schmidt G, Aktories K. The actin and Rho-modifying toxins PTC3 and PTC5 ofPhotorhabdus luminescens: enzyme characterization and induction of MAL/SRF-dependent transcription. Cell Microbiol 2014; 17:579-94. [DOI: 10.1111/cmi.12386] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/11/2014] [Accepted: 10/19/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Vanda Pfaumann
- Institute of Experimental and Clinical Pharmacology and Toxicology; University of Freiburg; Freiburg Germany
| | - Alexander E. Lang
- Institute of Experimental and Clinical Pharmacology and Toxicology; University of Freiburg; Freiburg Germany
| | - Carsten Schwan
- Institute of Experimental and Clinical Pharmacology and Toxicology; University of Freiburg; Freiburg Germany
| | - Gudula Schmidt
- Institute of Experimental and Clinical Pharmacology and Toxicology; University of Freiburg; Freiburg Germany
| | - Klaus Aktories
- Institute of Experimental and Clinical Pharmacology and Toxicology; University of Freiburg; Freiburg Germany
- Centre for Biological Signalling Studies (BIOSS); University of Freiburg; Freiburg Germany
| |
Collapse
|
30
|
Aktories K, Schmidt G, Lang AE. Photorhabdus luminescens toxins TccC3 and TccC5: insecticidal ADP-ribosyltransferases that modify threonine and glutamine. Curr Top Microbiol Immunol 2014; 384:53-67. [PMID: 24908144 DOI: 10.1007/82_2014_382] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ADP-ribosyltransferases TccC3 and TccC5 are the biologically active TcC components of the tripartite Photorhabdus luminescens Tc toxin, which consist of TcA, TcB, and TcC components. TcA is the binding and membrane translocation component. TcB is a functional linker between TcC and TcA and also involved in the translocation of the toxin. While TccC3 ADP-ribosylates actin at threonine 148, TccC5 modifies Rho proteins at glutamine 61/63. Both modifications result in major alteration of the actin cytoskeleton. Here we discuss structure and function of the Tc toxin and compare its ADP-ribosyltransferase activities with other types of actin and Rho modifying toxins.
Collapse
Affiliation(s)
- Klaus Aktories
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany,
| | | | | |
Collapse
|
31
|
Picchianti M, Del Vecchio M, Di Marcello F, Biagini M, Veggi D, Norais N, Rappuoli R, Pizza M, Balducci E. Auto ADP-ribosylation of NarE, a Neisseria meningitidis ADP-ribosyltransferase, regulates its catalytic activities. FASEB J 2013; 27:4723-30. [PMID: 23964075 DOI: 10.1096/fj.13-229955] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
NarE is an arginine-specific mono-ADP-ribosyltransferase identified in Neisseria meningitidis that requires the presence of iron in a structured cluster for its enzymatic activities. In this study, we show that NarE can perform auto-ADP-ribosylation. This automodification occurred in a time- and NAD-concentration-dependent manner; was inhibited by novobiocin, an ADP-ribosyltransferase inhibitor; and did not occur when NarE was heat inactivated. No reduction in incorporation was evidenced in the presence of high concentrations of ATP, GTP, ADP-ribose, or nicotinamide, which inhibits NAD-glycohydrolase, impeding the formation of free ADP-ribose. Based on the electrophoretic profile of NarE on auto-ADP-ribosylation and on the results of mutagenesis and mass spectrometry analysis, the auto-ADP-ribosylation appeared to be restricted to the addition of a single ADP-ribose. Chemical stability experiments showed that the ADP-ribosyl linkage was sensitive to hydroxylamine, which breaks ADP-ribose-arginine bonds. Site-directed mutagenesis suggested that the auto-ADP-ribosylation site occurred preferentially on the R(7) residue, which is located in the region I of the ADP-ribosyltransferase family. After auto-ADP-ribosylation, NarE showed a reduction in ADP-ribosyltransferase activity, while NAD-glycohydrolase activity was increased. Overall, our findings provide evidence for a novel intramolecular mechanism used by NarE to regulate its enzymatic activities.
Collapse
Affiliation(s)
- Monica Picchianti
- 1Centro Ricerche Novartis Vaccines and Diagnostics, Via Fiorentina 1, 53100 Siena, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
|
33
|
Structural biology of the writers, readers, and erasers in mono- and poly(ADP-ribose) mediated signaling. Mol Aspects Med 2013; 34:1088-108. [PMID: 23458732 PMCID: PMC3726583 DOI: 10.1016/j.mam.2013.02.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/01/2013] [Accepted: 02/18/2013] [Indexed: 12/19/2022]
Abstract
ADP-ribosylation of proteins regulates protein activities in various processes including transcription control, chromatin organization, organelle assembly, protein degradation, and DNA repair. Modulating the proteins involved in the metabolism of ADP-ribosylation can have therapeutic benefits in various disease states. Protein crystal structures can help understand the biological functions, facilitate detailed analysis of single residues, as well as provide a basis for development of small molecule effectors. Here we review recent advances in our understanding of the structural biology of the writers, readers, and erasers of ADP-ribosylation.
Collapse
|
34
|
Visschedyk D, Rochon A, Tempel W, Dimov S, Park HW, Merrill AR. Certhrax toxin, an anthrax-related ADP-ribosyltransferase from Bacillus cereus. J Biol Chem 2012; 287:41089-102. [PMID: 22992735 DOI: 10.1074/jbc.m112.412809] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We identified Certhrax, the first anthrax-like mART toxin from the pathogenic G9241 strain of Bacillus cereus. Certhrax shares 31% sequence identity with anthrax lethal factor from Bacillus anthracis; however, we have shown that the toxicity of Certhrax resides in the mART domain, whereas anthrax uses a metalloprotease mechanism. Like anthrax lethal factor, Certhrax was found to require protective antigen for host cell entry. This two-domain enzyme was shown to be 60-fold more toxic to mammalian cells than anthrax lethal factor. Certhrax localizes to distinct regions within mouse RAW264.7 cells by 10 min postinfection and is extranuclear in its cellular location. Substitution of catalytic residues shows that the mART function is responsible for the toxicity, and it binds NAD(+) with high affinity (K(D) = 52.3 ± 12.2 μM). We report the 2.2 Å Certhrax structure, highlighting its structural similarities and differences with anthrax lethal factor. We also determined the crystal structures of two good inhibitors (P6 (K(D) = 1.7 ± 0.2 μM, K(i) = 1.8 ± 0.4 μM) and PJ34 (K(D) = 5.8 ± 2.6 μM, K(i) = 9.6 ± 0.3 μM)) in complex with Certhrax. As with other toxins in this family, the phosphate-nicotinamide loop moves toward the NAD(+) binding site with bound inhibitor. These results indicate that Certhrax may be important in the pathogenesis of B. cereus.
Collapse
Affiliation(s)
- Danielle Visschedyk
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | | | | | | | | | | |
Collapse
|
35
|
Shniffer A, Visschedyk DD, Ravulapalli R, Suarez G, Turgeon ZJ, Petrie AA, Chopra AK, Merrill AR. Characterization of an actin-targeting ADP-ribosyltransferase from Aeromonas hydrophila. J Biol Chem 2012; 287:37030-41. [PMID: 22969084 DOI: 10.1074/jbc.m112.397612] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The mono-ADP-ribosyltransferase (mART) toxins are contributing factors to a number of human diseases, including cholera, diphtheria, traveler's diarrhea, and whooping cough. VahC is a cytotoxic, actin-targeting mART from Aeromonas hydrophila PPD134/91. This bacterium is implicated primarily in diseases among freshwater fish species but also contributes to gastrointestinal and extraintestinal infections in humans. VahC was shown to ADP-ribosylate Arg-177 of actin, and the kinetic parameters were K(m)(NAD(+)) = 6 μM, K(m)(actin) = 24 μM, and k(cat) = 22 s(-1). VahC activity caused depolymerization of actin filaments, which induced caspase-mediated apoptosis in HeLa Tet-Off cells. Alanine-scanning mutagenesis of predicted catalytic residues showed the predicted loss of in vitro mART activity and cytotoxicity. Bioinformatic and kinetic analysis also identified three residues in the active site loop that were critical for the catalytic mechanism. A 1.9 Å crystal structure supported the proposed roles of these residues and their conserved nature among toxin homologues. Several small molecules were characterized as inhibitors of in vitro VahC mART activity and suramin was the best inhibitor (IC(50) = 20 μM). Inhibitor activity was also characterized against two other actin-targeting mART toxins. Notably, these inhibitors represent the first report of broad spectrum inhibition of actin-targeting mART toxins.
Collapse
Affiliation(s)
- Adin Shniffer
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Cherkis KA, Temple BRS, Chung EH, Sondek J, Dangl JL. AvrRpm1 missense mutations weakly activate RPS2-mediated immune response in Arabidopsis thaliana. PLoS One 2012; 7:e42633. [PMID: 22880057 PMCID: PMC3412798 DOI: 10.1371/journal.pone.0042633] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/09/2012] [Indexed: 02/04/2023] Open
Abstract
Plants recognize microbes via specific pattern recognition receptors that are activated by microbe-associated molecular patterns (MAMPs), resulting in MAMP-triggered immunity (MTI). Successful pathogens bypass MTI in genetically diverse hosts via deployment of effectors (virulence factors) that inhibit MTI responses, leading to pathogen proliferation. Plant pathogenic bacteria like Pseudomonas syringae utilize a type III secretion system to deliver effectors into cells. These effectors can contribute to pathogen virulence or elicit disease resistance, depending upon the host plant genotype. In disease resistant genotypes, intracellular immune receptors, typically belonging to the nucleotide binding leucine-rich repeat family of proteins, perceive bacterial effector(s) and initiate downstream defense responses (effector triggered immunity) that include the hypersensitive response, and transcriptional re-programming leading to various cellular outputs that collectively halt pathogen growth. Nucleotide binding leucine-rich repeat sensors can be indirectly activated via perturbation of a host protein acting as an effector target. AvrRpm1 is a P. syringae type III effector. Upon secretion into the host cell, AvrRpm1 is acylated by host enzymes and directed to the plasma membrane, where it contributes to virulence. This is correlated with phosphorylation of Arabidopsis RIN4 in vivo. RIN4 is a negative regulator of MAMP-triggered immunity, and its modification in the presence of four diverse type III effectors, including AvrRpm1, likely enhances this RIN4 regulatory function. The RPM1 nucleotide binding leucine-rich repeat sensor perceives RIN4 perturbation in disease resistant plants, leading to a successful immune response. Here, demonstrate that AvrRpm1 has a fold homologous to the catalytic domain of poly(ADP-ribosyl) polymerase. Site-directed mutagenesis of each residue in the putative catalytic triad, His63-Tyr122-Asp185 of AvrRpm1, results in loss of both AvrRpm1-dependent virulence and AvrRpm1-mediated activation of RPM1, but, surprisingly, causes a gain of function: the ability to activate the RPS2 nucleotide binding leucine-rich repeat sensor.
Collapse
Affiliation(s)
- Karen A. Cherkis
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Brenda R. S. Temple
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- R.L. Juliano Structural Bioinformatics Core Facility, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Eui-Hwan Chung
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - John Sondek
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeffery L. Dangl
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| |
Collapse
|
37
|
Yamamoto M, Takahashi-Nakaguchi A, Matsushima-Hibiya Y, Nakano T, Totsuka Y, Imanishi S, Mitsuhashi J, Watanabe M, Nakagama H, Sugimura T, Wakabayashi K. Nucleotide sequence and chromosomal localization of the gene for pierisin-1, a DNA ADP-ribosylating protein, in the cabbage butterfly Pieris rapae. Genetica 2012; 139:1251-8. [PMID: 22237414 DOI: 10.1007/s10709-011-9626-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 12/23/2011] [Indexed: 10/14/2022]
Abstract
Cabbage butterfly, Pieris rapae, contains a unique DNA ADP-ribosylating protein, pierisin-1, which transfers ADP-ribose moiety of NAD to guanine bases of DNA. Pierisin-like proteins are only distributed in subtribes Pierina, Aporiina and Appiadina of the family Pieridae. In this study, we obtained genomic clones carrying the pierisin-1 gene from adult samples of P. rapae by plaque hybridization. The pierisin-1 gene was found to consist of two exons, 0.1-kb exon 1 and 3.9-kb exon 2, and a 2.3-kb intron. In addition, we could demonstrate that the putative promoter in the about 3-kb upstream region from the transcription start site of the gene include a transcriptional activating motif involved in immune pathways and hormonal regulation. We also examined chromosomal localization of the pierisin-1 gene. Fluorescence in situ hybridization (FISH) analysis using Cy3-labeled pierisin-1 genomic clone demonstrated the localization of the gene near the kinetochore in chromosome 9. Thus, we confirmed that the pierisin-1 gene is located in the genome of P. rapae.
Collapse
Affiliation(s)
- Masafumi Yamamoto
- Division of Cancer Development System, Carcinogenesis Research Group, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Jeong BR, Lin Y, Joe A, Guo M, Korneli C, Yang H, Wang P, Yu M, Cerny RL, Staiger D, Alfano JR, Xu Y. Structure function analysis of an ADP-ribosyltransferase type III effector and its RNA-binding target in plant immunity. J Biol Chem 2011; 286:43272-81. [PMID: 22013065 DOI: 10.1074/jbc.m111.290122] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Pseudomonas syringae type III effector HopU1 is a mono-ADP-ribosyltransferase that is injected into plant cells by the type III protein secretion system. Inside the plant cell it suppresses immunity by modifying RNA-binding proteins including the glycine-rich RNA-binding protein GRP7. The crystal structure of HopU1 at 2.7-Å resolution reveals two unique protruding loops, L1 and L4, not found in other mono-ADP-ribosyltransferases. Site-directed mutagenesis demonstrates that these loops are essential for substrate recognition and enzymatic activity. HopU1 ADP-ribosylates the conserved arginine 49 of GRP7, and this reduces the ability of GRP7 to bind RNA in vitro. In vivo, expression of GRP7 with Arg-49 replaced with lysine does not complement the reduced immune responses of the Arabidopsis thaliana grp7-1 mutant demonstrating the importance of this residue for GRP7 function. These data provide mechanistic details how HopU1 recognizes this novel type of substrate and highlights the role of GRP7 in plant immunity.
Collapse
Affiliation(s)
- Byeong-ryool Jeong
- Center for Plant Science Innovation and the Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68588-0660, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Kuppuraj G, Sargsyan K, Hua YH, Merrill AR, Lim C. Linking distinct conformations of nicotinamide adenine dinucleotide with protein fold/function. J Phys Chem B 2011; 115:7932-9. [PMID: 21612228 DOI: 10.1021/jp1118663] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD or NADP) are essential cofactor/substrate for enzymes that catalyze redox or nonredox reactions. Because several enzymes involved in NAD(P) metabolism have been implicated in a wide array of diseases, there is great interest in designing inhibitors/activators of these NAD(P)-dependent enzymes based on their structures. Hence, we have elucidated the various distinct enzyme-bound NAD(P) conformations and their correlation with the respective protein fold and function using hierarchical clustering methods. Torsion angles distinguishing enzyme-bound NAD versus NADP conformations and NAD(P) conformations bound to redox versus nonredox enzymes were identified. Although an unusually small χ(N) in diphtheria toxin-bound NAD(+) had been postulated to strain the N-glycosidic bond, thus facilitating catalysis, toxin-bound NAD(+) molecules with χ(N) varying from 0 to 60° were found to exhibit similar C(1D)-N(1N) bond cleavage barriers in water. The findings herein provide useful guidelines in the design of inhibitors/activators of NAD(P)-dependent enzymes that are therapeutic targets.
Collapse
Affiliation(s)
- Gopi Kuppuraj
- Chemical Biology & Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
| | | | | | | | | |
Collapse
|
40
|
Fieldhouse RJ, Turgeon Z, White D, Merrill AR. Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases. PLoS Comput Biol 2010; 6:e1001029. [PMID: 21170356 PMCID: PMC3000352 DOI: 10.1371/journal.pcbi.1001029] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 11/10/2010] [Indexed: 11/19/2022] Open
Abstract
Chelt, a cholera-like toxin from Vibrio cholerae, and Certhrax, an anthrax-like toxin from Bacillus cereus, are among six new bacterial protein toxins we identified and characterized using in silico and cell-based techniques. We also uncovered medically relevant toxins from Mycobacterium avium and Enterococcus faecalis. We found agriculturally relevant toxins in Photorhabdus luminescens and Vibrio splendidus. These toxins belong to the ADP-ribosyltransferase family that has conserved structure despite low sequence identity. Therefore, our search for new toxins combined fold recognition with rules for filtering sequences--including a primary sequence pattern--to reduce reliance on sequence identity and identify toxins using structure. We used computers to build models and analyzed each new toxin to understand features including: structure, secretion, cell entry, activation, NAD+ substrate binding, intracellular target binding and the reaction mechanism. We confirmed activity using a yeast growth test. In this era where an expanding protein structure library complements abundant protein sequence data--and we need high-throughput validation--our approach provides insight into the newest toxin ADP-ribosyltransferases.
Collapse
Affiliation(s)
- Robert J. Fieldhouse
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Zachari Turgeon
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Dawn White
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
41
|
Newly discovered and characterized antivirulence compounds inhibit bacterial mono-ADP-ribosyltransferase toxins. Antimicrob Agents Chemother 2010; 55:983-91. [PMID: 21135177 DOI: 10.1128/aac.01164-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The mono-ADP-ribosyltransferase toxins are bacterial virulence factors that contribute to many disease states in plants, animals, and humans. These toxins function as enzymes that target various host proteins and covalently attach an ADP-ribose moiety that alters target protein function. We tested compounds from a virtual screen of commercially available compounds combined with a directed poly(ADP-ribose) polymerase (PARP) inhibitor library and found several compounds that bind tightly and inhibit toxins from Pseudomonas aeruginosa and Vibrio cholerae. The most efficacious compounds completely protected human lung epithelial cells against the cytotoxicity of these bacterial virulence factors. Moreover, we determined high-resolution crystal structures of the best inhibitors in complex with cholix toxin to reveal important criteria for inhibitor binding and mechanism of action. These results provide new insight into development of antivirulence compounds for treating many bacterial diseases.
Collapse
|
42
|
Lang AE, Schmidt G, Sheets JJ, Aktories K. Targeting of the actin cytoskeleton by insecticidal toxins from Photorhabdus luminescens. Naunyn Schmiedebergs Arch Pharmacol 2010; 383:227-35. [PMID: 21072628 DOI: 10.1007/s00210-010-0579-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 10/27/2010] [Indexed: 10/18/2022]
Abstract
Photorhabdus luminescens produces several types of protein toxins, which are essential for participation in a trilateral symbiosis with nematodes and insects. The nematodes, carrying the bacteria, invade insect larvae and release the bacteria, which kill the insects with their toxins. Recently, the molecular mechanisms of the toxin complexes PTC3 and PTC5 have been elucidated. The biologically active components of the toxin complexes are ADP-ribosyltransferases, which modify actin and Rho GTPases, respectively. The actions of the toxins are described and compared with other bacterial protein toxins acting on the cytoskeleton.
Collapse
Affiliation(s)
- Alexander E Lang
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | | | | | | |
Collapse
|
43
|
Söllner J, Heinzel A, Summer G, Fechete R, Stipkovits L, Szathmary S, Mayer B. Concept and application of a computational vaccinology workflow. Immunome Res 2010; 6 Suppl 2:S7. [PMID: 21067549 PMCID: PMC2981879 DOI: 10.1186/1745-7580-6-s2-s7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The last years have seen a renaissance of the vaccine area, driven by clinical needs in infectious diseases but also chronic diseases such as cancer and autoimmune disorders. Equally important are technological improvements involving nano-scale delivery platforms as well as third generation adjuvants. In parallel immunoinformatics routines have reached essential maturity for supporting central aspects in vaccinology going beyond prediction of antigenic determinants. On this basis computational vaccinology has emerged as a discipline aimed at ab-initio rational vaccine design.Here we present a computational workflow for implementing computational vaccinology covering aspects from vaccine target identification to functional characterization and epitope selection supported by a Systems Biology assessment of central aspects in host-pathogen interaction. We exemplify the procedures for Epstein Barr Virus (EBV), a clinically relevant pathogen causing chronic infection and suspected of triggering malignancies and autoimmune disorders. RESULTS We introduce pBone/pView as a computational workflow supporting design and execution of immunoinformatics workflow modules, additionally involving aspects of results visualization, knowledge sharing and re-use. Specific elements of the workflow involve identification of vaccine targets in the realm of a Systems Biology assessment of host-pathogen interaction for identifying functionally relevant targets, as well as various methodologies for delineating B- and T-cell epitopes with particular emphasis on broad coverage of viral isolates as well as MHC alleles.Applying the workflow on EBV specifically proposes sequences from the viral proteins LMP2, EBNA2 and BALF4 as vaccine targets holding specific B- and T-cell epitopes promising broad strain and allele coverage. CONCLUSION Based on advancements in the experimental assessment of genomes, transcriptomes and proteomes for both, pathogen and (human) host, the fundaments for rational design of vaccines have been laid out. In parallel, immunoinformatics modules have been designed and successfully applied for supporting specific aspects in vaccine design. Joining these advancements, further complemented by novel vaccine formulation and delivery aspects, have paved the way for implementing computational vaccinology for rational vaccine design tackling presently unmet vaccine challenges.
Collapse
Affiliation(s)
- Johannes Söllner
- emergentec biodevelopment GmbH, Rathausstrasse 5/3, 1010 Vienna, Austria
| | - Andreas Heinzel
- emergentec biodevelopment GmbH, Rathausstrasse 5/3, 1010 Vienna, Austria
- University of Applied Sciences, Softwarepark 11, 4232 Hagenberg, Austria
| | - Georg Summer
- University of Applied Sciences, Softwarepark 11, 4232 Hagenberg, Austria
| | - Raul Fechete
- emergentec biodevelopment GmbH, Rathausstrasse 5/3, 1010 Vienna, Austria
| | | | - Susan Szathmary
- Galenbio Kft., Erdőszél köz 21, 1037 Budapest, Hungary and GalenBio, Inc., 5922 Farnsworth Ct, Carlsbad, CA 92008, USA
| | - Bernd Mayer
- emergentec biodevelopment GmbH, Rathausstrasse 5/3, 1010 Vienna, Austria
- Institute for Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| |
Collapse
|
44
|
Dudev T, Lim C. Factors controlling the mechanism of NAD(+) non-redox reactions. J Am Chem Soc 2010; 132:16533-43. [PMID: 21047075 DOI: 10.1021/ja106600k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
β-Nicotinamide adenine dinucleotide (NAD(+)) is an indispensable coenzyme or substrate for enzymes involved in catalyzing redox and non-redox reactions. ADP-ribosylating enzymes catalyze cleavage of the nicotinamide-glycosyl bond of NAD(+) and addition of a nucleophilic group from their substrate proteins to the N-ribose anomeric carbon of NAD(+). Although the role of the nicotinamide-ribose fragment in the mechanism of NAD(+) hydrolysis has been examined, the role of the doubly negatively charged, flexible, and chemically reactive NAD(+) diphosphate moiety in the reaction process has largely been neglected. Thus, the participation of the pyrophosphate group in stabilizing intra- and intermolecular interactions in the ground state and transition state has not been explored. Furthermore, the roles of other factors such as the type/nucleophilicity of the attacking nucleophile and the medium in influencing the reaction pathway have not been systematically evaluated. In this study, we endeavor to fill in these gaps and elucidate the role of these factors in controlling the NAD(+) nicotinamide-glycosyl bond cleavage. Using density functional theory combined with continuum dielectric methods, we modeled both S(N)1 and S(N)2 reaction pathways and assessed the role of the diphosphate group in stabilizing the (i) NAD(+) ground state, (ii) oxocarbocation intermediate, (iii) reaction product, and (iv) nucleophile. We also assessed the chemical nature of the attacking nucleophile and the role of the protein matrix in affecting the reaction mechanism. Our results reveal an intricate interplay among various factors in controlling the reaction pathway, which in turn suggests ways in which the enzyme can accelerate the reaction.
Collapse
Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | |
Collapse
|
45
|
Laing S, Unger M, Koch-Nolte F, Haag F. ADP-ribosylation of arginine. Amino Acids 2010; 41:257-69. [PMID: 20652610 PMCID: PMC3102197 DOI: 10.1007/s00726-010-0676-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 06/24/2010] [Indexed: 12/16/2022]
Abstract
Arginine adenosine-5′-diphosphoribosylation (ADP-ribosylation) is an enzyme-catalyzed, potentially reversible posttranslational modification, in which the ADP-ribose moiety is transferred from NAD+ to the guanidino moiety of arginine. At 540 Da, ADP-ribose has the size of approximately five amino acid residues. In contrast to arginine, which, at neutral pH, is positively charged, ADP-ribose carries two negatively charged phosphate moieties. Arginine ADP-ribosylation, thus, causes a notable change in size and chemical property at the ADP-ribosylation site of the target protein. Often, this causes steric interference of the interaction of the target protein with binding partners, e.g. toxin-catalyzed ADP-ribosylation of actin at R177 sterically blocks actin polymerization. In case of the nucleotide-gated P2X7 ion channel, ADP-ribosylation at R125 in the vicinity of the ligand-binding site causes channel gating. Arginine-specific ADP-ribosyltransferases (ARTs) carry a characteristic R-S-EXE motif that distinguishes these enzymes from structurally related enzymes which catalyze ADP-ribosylation of other amino acid side chains, DNA, or small molecules. Arginine-specific ADP-ribosylation can be inhibited by small molecule arginine analogues such as agmatine or meta-iodobenzylguanidine (MIBG), which themselves can serve as targets for arginine-specific ARTs. ADP-ribosylarginine specific hydrolases (ARHs) can restore target protein function by hydrolytic removal of the entire ADP-ribose moiety. In some cases, ADP-ribosylarginine is processed into secondary posttranslational modifications, e.g. phosphoribosylarginine or ornithine. This review summarizes current knowledge on arginine-specific ADP-ribosylation, focussing on the methods available for its detection, its biological consequences, and the enzymes responsible for this modification and its reversal, and discusses future perspectives for research in this field.
Collapse
Affiliation(s)
- Sabrina Laing
- Campus Forschung, 2. OG Rm 02.0058, Institute of Immunology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | | | | | | |
Collapse
|
46
|
Lang AE, Schmidt G, Schlosser A, Hey TD, Larrinua IM, Sheets JJ, Mannherz HG, Aktories K. Photorhabdus luminescens toxins ADP-ribosylate actin and RhoA to force actin clustering. Science 2010; 327:1139-42. [PMID: 20185726 DOI: 10.1126/science.1184557] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The bacterium Photorhabdus luminescens is mutualistically associated with entomopathogenetic nematodes. These nematodes invade insect larvae and release the bacteria from their intestine, which kills the insects through the action of toxin complexes. We elucidated the mode of action of two of these insecticidal toxins from P. luminescens. We identified the biologically active components TccC3 and TccC5 as adenosine diphosphate (ADP)-ribosyltransferases, which modify unusual amino acids. TccC3 ADP-ribosylated threonine-148 of actin, resulting in actin polymerization. TccC5 ADP-ribosylated Rho guanosine triphosphatase proteins at glutamine-61 and glutamine-63, inducing their activation. The concerted action of both toxins inhibited phagocytosis of target insect cells and induced extensive intracellular polymerization and clustering of actin. Several human pathogenic bacteria produce related toxins.
Collapse
Affiliation(s)
- Alexander E Lang
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Visschedyk DD, Perieteanu AA, Turgeon ZJ, Fieldhouse RJ, Dawson JF, Merrill AR. Photox, a novel actin-targeting mono-ADP-ribosyltransferase from Photorhabdus luminescens. J Biol Chem 2010; 285:13525-34. [PMID: 20181945 DOI: 10.1074/jbc.m109.077339] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Photorhabdus luminescens is a pathogenic bacterium that produces many toxic proteins. The mono-ADP-ribosyltransferases (mARTs) are an enzyme class produced by numerous pathogenic bacteria and participate in disease in plants and animals, including humans. Herein we report a novel mART from P. luminescens called Photox. This 46-kDa toxin shows high homology to other actin-targeting mARTs in hallmark catalytic regions and a similar core catalytic fold. Furthermore, Photox shows in vivo cytotoxic activity against yeast, with protection occurring when catalytic residues are substituted with alanine. In vitro, enzymatic activity (k(cat), 1680 +/- 75 min(-1)) is higher than that of the related iota toxin, and diminishes by nearly 14,000-fold following substitution of the catalytic Glu (E355A). This toxin specifically ADP-ribosylates monomeric alpha-skeletal actin and nonmuscle beta- and gamma-actin at Arg(177), inhibiting regular polymerization of actin filaments. These results indicate that Photox is indeed an ADP-ribosyltransferase, making it the newest member of the actin-targeting mART family.
Collapse
Affiliation(s)
- Danielle D Visschedyk
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | | | | | | | | | | |
Collapse
|
48
|
Hottiger MO, Hassa PO, Lüscher B, Schüler H, Koch-Nolte F. Toward a unified nomenclature for mammalian ADP-ribosyltransferases. Trends Biochem Sci 2010; 35:208-19. [PMID: 20106667 DOI: 10.1016/j.tibs.2009.12.003] [Citation(s) in RCA: 643] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 12/07/2009] [Accepted: 12/10/2009] [Indexed: 10/19/2022]
Abstract
ADP-ribosylation is a post-translational modification of proteins catalyzed by ADP-ribosyltransferases. It comprises the transfer of the ADP-ribose moiety from NAD+ to specific amino acid residues on substrate proteins or to ADP-ribose itself. Currently, 22 human genes encoding proteins that possess an ADP-ribosyltransferase catalytic domain are known. Recent structural and enzymological evidence of poly(ADP-ribose)polymerase (PARP) family members demonstrate that earlier proposed names and classifications of these proteins are no longer accurate. Here we summarize these new findings and propose a new consensus nomenclature for all ADP-ribosyltransferases (ARTs) based on the catalyzed reaction and on structural features. A unified nomenclature would facilitate communication between researchers both inside and outside the ADP-ribosylation field.
Collapse
Affiliation(s)
- Michael O Hottiger
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | | | | | | | | |
Collapse
|