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Teixeira Nunes M, Retailleau P, Raoux-Barbot D, Comisso M, Missinou AA, Velours C, Plancqueel S, Ladant D, Mechold U, Renault L. Functional and structural insights into the multi-step activation and catalytic mechanism of bacterial ExoY nucleotidyl cyclase toxins bound to actin-profilin. PLoS Pathog 2023; 19:e1011654. [PMID: 37747912 PMCID: PMC10553838 DOI: 10.1371/journal.ppat.1011654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/05/2023] [Accepted: 09/01/2023] [Indexed: 09/27/2023] Open
Abstract
ExoY virulence factors are members of a family of bacterial nucleotidyl cyclases (NCs) that are activated by specific eukaryotic cofactors and overproduce cyclic purine and pyrimidine nucleotides in host cells. ExoYs act as actin-activated NC toxins. Here, we explore the Vibrio nigripulchritudo Multifunctional-Autoprocessing Repeats-in-ToXin (MARTX) ExoY effector domain (Vn-ExoY) as a model for ExoY-type members that interact with monomeric (G-actin) instead of filamentous (F-actin) actin. Vn-ExoY exhibits moderate binding affinity to free or profilin-bound G-actin but can capture the G-actin:profilin complex, preventing its spontaneous or VASP- or formin-mediated assembly at F-actin barbed ends in vitro. This mechanism may prolong the activated cofactor-bound state of Vn-ExoY at sites of active actin cytoskeleton remodelling. We present a series of high-resolution crystal structures of nucleotide-free, 3'-deoxy-ATP- or 3'-deoxy-CTP-bound Vn-ExoY, activated by free or profilin-bound G-actin-ATP/-ADP, revealing that the cofactor only partially stabilises the nucleotide-binding pocket (NBP) of NC toxins. Substrate binding induces a large, previously-unidentified, closure of their NBP, confining catalytically important residues and metal cofactors around the substrate, and facilitating the recruitment of two metal ions to tightly coordinate the triphosphate moiety of purine or pyrimidine nucleotide substrates. We validate critical residues for both the purinyl and pyrimidinyl cyclase activity of NC toxins in Vn-ExoY and its distantly-related ExoY from Pseudomonas aeruginosa, which specifically interacts with F-actin. The data conclusively demonstrate that NC toxins employ a similar two-metal-ion mechanism for catalysing the cyclisation of nucleotides of different sizes. These structural insights into the dynamics of the actin-binding interface of actin-activated ExoYs and the multi-step activation of all NC toxins offer new perspectives for the specific inhibition of class II bacterial NC enzymes.
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Affiliation(s)
- Magda Teixeira Nunes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Pascal Retailleau
- Université Paris Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Dorothée Raoux-Barbot
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Biochimie des Interactions macromoléculaires, Département de Biologie Structurale et Chimie, Paris, France
| | - Martine Comisso
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Anani Amegan Missinou
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christophe Velours
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphane Plancqueel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Daniel Ladant
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Biochimie des Interactions macromoléculaires, Département de Biologie Structurale et Chimie, Paris, France
| | - Undine Mechold
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Biochimie des Interactions macromoléculaires, Département de Biologie Structurale et Chimie, Paris, France
| | - Louis Renault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Teixeira-Nunes M, Retailleau P, Comisso M, Deruelle V, Mechold U, Renault L. Bacterial Nucleotidyl Cyclases Activated by Calmodulin or Actin in Host Cells: Enzyme Specificities and Cytotoxicity Mechanisms Identified to Date. Int J Mol Sci 2022; 23:ijms23126743. [PMID: 35743184 PMCID: PMC9223806 DOI: 10.3390/ijms23126743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
Many pathogens manipulate host cell cAMP signaling pathways to promote their survival and proliferation. Bacterial Exoenzyme Y (ExoY) toxins belong to a family of invasive, structurally-related bacterial nucleotidyl cyclases (NC). Inactive in bacteria, they use proteins that are uniquely and abundantly present in eukaryotic cells to become potent, unregulated NC enzymes in host cells. Other well-known members of the family include Bacillus anthracis Edema Factor (EF) and Bordetella pertussis CyaA. Once bound to their eukaryotic protein cofactor, they can catalyze supra-physiological levels of various cyclic nucleotide monophosphates in infected cells. Originally identified in Pseudomonas aeruginosa, ExoY-related NC toxins appear now to be more widely distributed among various γ- and β-proteobacteria. ExoY-like toxins represent atypical, poorly characterized members within the NC toxin family. While the NC catalytic domains of EF and CyaA toxins use both calmodulin as cofactor, their counterparts in ExoY-like members from pathogens of the genus Pseudomonas or Vibrio use actin as a potent cofactor, in either its monomeric or polymerized form. This is an original subversion of actin for cytoskeleton-targeting toxins. Here, we review recent advances on the different members of the NC toxin family to highlight their common and distinct functional characteristics at the molecular, cytotoxic and enzymatic levels, and important aspects that need further characterizations.
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Affiliation(s)
- Magda Teixeira-Nunes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (M.T.-N.); (M.C.)
| | - Pascal Retailleau
- Institut de Chimie des Substances Naturelles (ICSN), CNRS-UPR2301, Université Paris-Saclay, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France;
| | - Martine Comisso
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (M.T.-N.); (M.C.)
| | - Vincent Deruelle
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, CNRS UMR 3528, Institut Pasteur, 75015 Paris, France; (V.D.); (U.M.)
| | - Undine Mechold
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, CNRS UMR 3528, Institut Pasteur, 75015 Paris, France; (V.D.); (U.M.)
| | - Louis Renault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (M.T.-N.); (M.C.)
- Correspondence:
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Zhao T, Zhao X, Liu J, Meng Y, Feng Y, Fang T, Zhang J, Yang X, Li J, Xu J, Chen W. Diminished but Not Abolished Effect of Two His351 Mutants of Anthrax Edema Factor in a Murine Model. Toxins (Basel) 2016; 8:35. [PMID: 26848687 PMCID: PMC4773788 DOI: 10.3390/toxins8020035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/08/2016] [Accepted: 01/15/2016] [Indexed: 01/14/2023] Open
Abstract
Edema toxin (ET), which is composed of a potent adenylate cyclase (AC), edema factor (EF), and protective antigen (PA), is one of the major toxicity factors of Bacillus anthracis. In this study, we introduced mutations in full-length EF to generate alanine EF(H351A) and arginine EF(H351R) variants. In vitro activity analysis displayed that the adenylyl cyclase activity of both the mutants was significantly diminished compared with the wild-type EF. When the native and mutant toxins were administered subcutaneously in a mouse footpad edema model, severe acute swelling was evoked by wild-type ET, while the symptoms induced by mutant toxins were very minor. Systemic administration of these EF variants caused non-lethal hepatotoxicity. In addition, EF(H351R) exhibited slightly higher activity in causing more severe edema than EF(H351A). Our findings demonstrate that the toxicity of ET is not abolished by substitution of EF residue His351 by alanine or arginine. These results also indicate the potential of the mouse footpad edema model as a sensitive method for evaluating both ET toxicity and the efficacy of candidate therapeutic agents.
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Affiliation(s)
- Taoran Zhao
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Xinghui Zhao
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Ju Liu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Yingying Meng
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Yingying Feng
- Department of Colorectal Surgery, the Second Artillery General Hospital, Beijing 100088, China.
| | - Ting Fang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Jinlong Zhang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Xiuxu Yang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Jianmin Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Junjie Xu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Wei Chen
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
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Laine É, Martínez L, Ladant D, Malliavin T, Blondel A. Molecular motions as a drug target: mechanistic simulations of anthrax toxin edema factor function led to the discovery of novel allosteric inhibitors. Toxins (Basel) 2012; 4:580-604. [PMID: 23012649 PMCID: PMC3446745 DOI: 10.3390/toxins4080580] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/04/2012] [Accepted: 07/18/2012] [Indexed: 01/14/2023] Open
Abstract
Edema Factor (EF) is a component of Bacillus anthracis toxin essential for virulence. Its adenylyl cyclase activity is induced by complexation with the ubiquitous eukaryotic cellular protein, calmodulin (CaM). EF and its complexes with CaM, nucleotides and/or ions, have been extensively characterized by X-ray crystallography. Those structural data allowed molecular simulations analysis of various aspects of EF action mechanism, including the delineation of EF and CaM domains through their association energetics, the impact of calcium binding on CaM, and the role of catalytic site ions. Furthermore, a transition path connecting the free inactive form to the CaM-complexed active form of EF was built to model the activation mechanism in an attempt to define an inhibition strategy. The cavities at the surface of EF were determined for each path intermediate to identify potential sites where the binding of a ligand could block activation. A non-catalytic cavity (allosteric) was found to shrink rapidly at early stages of the path and was chosen to perform virtual screening. Amongst 18 compounds selected in silico and tested in an enzymatic assay, 6 thiophen ureidoacid derivatives formed a new family of EF allosteric inhibitors with IC50 as low as 2 micromolars.
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Affiliation(s)
- Élodie Laine
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, 61, avenue du Président Wilson, 94235 Cachan cedex, France;
| | - Leandro Martínez
- The Molecular Biotechnology Group, Institute of Physics of São Carlos, University of São Paulo, Av. Trabalhador Sãocarlense, 400, 13566-590 São Carlos, SP, Brazil;
| | - Daniel Ladant
- Unité de Biochimie des Interactions Macromoléculaires and CNRS UMR 3528, Département de Biologie Structurale et Chimie, Institut Pasteur, 28, rue du Dr. Roux, 75724 Paris Cedex 15, France;
| | - Thérèse Malliavin
- Unité de Bioinformatique Structurale and CNRS UMR 3528, Département de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75724 Paris Cedex 15, France;
| | - Arnaud Blondel
- Unité de Bioinformatique Structurale and CNRS UMR 3528, Département de Biologie Structurale et Chimie, Institut Pasteur, 25, rue du Dr. Roux, 75724 Paris Cedex 15, France;
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Cloning, expression, and characterization of an adenylate cyclase from Arthrobacter sp. CGMCC 3584. Appl Microbiol Biotechnol 2012; 96:963-70. [DOI: 10.1007/s00253-012-3890-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 12/29/2011] [Accepted: 01/04/2012] [Indexed: 11/25/2022]
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Martínez L, Malliavin TE, Blondel A. Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study. Proteins 2011; 79:1649-61. [PMID: 21425348 DOI: 10.1002/prot.22991] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 12/14/2010] [Accepted: 12/30/2010] [Indexed: 11/07/2022]
Abstract
The anthrax edema factor is a toxin overproducing damaging levels of cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi) from ATP. Here, mechanisms of dissociation of ATP and products (cAMP, PPi) from the active site are studied using locally enhanced sampling (LES) and steered molecular dynamics simulations. Various substrate conformations and ionic binding modes found in crystallographic structures are considered. LES simulations show that PPi and cAMP dissociate through different solvent accessible channels, while ATP dissociation requires significant active site exposure to solvent. The ionic content of the active site directly affects the dissociation of ATP and products. Only one ion dissociates along with ATP in the two-Mg(2+) binding site, suggesting that the other ion binds EF prior to ATP association. Dissociation of reaction products cAMP and PPi is impaired by direct electrostatic interactions between products and Mg(2+) ions. This provides an explanation for the inhibitory effect of high Mg(2+) concentrations on EF enzymatic activity. Breaking of electrostatic interactions is dependent on a competitive binding of water molecules to the ions, and thus on the solvent accessibility of the active site. Consequently, product dissociation seems to be a two-step process. First, ligands are progressively solvated while preserving the most important electrostatic interactions, in a process that is dependent on the flexibility of the active site. Second, breakage of the electrostatic bonds follows, and ligands diffuse into solvent. In agreement with this mechanism, product protonation facilitates dissociation.
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Affiliation(s)
- Leandro Martínez
- Unité de Bioinformatique Structurale, URA CNRS 2185, Institut Pasteur, 25, rue du Dr Roux, F-75015 Paris, France.
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Gupta M, Alam S, Bhatnagar R. Catalytically inactive anthrax toxin(s) are potential prophylactic agents. Vaccine 2007; 25:8410-9. [PMID: 17980467 DOI: 10.1016/j.vaccine.2007.09.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2007] [Revised: 09/10/2007] [Accepted: 09/27/2007] [Indexed: 01/21/2023]
Abstract
The anthrax exotoxin, which is a key mediator of anthrax related pathogenesis, is composed of two separate toxins formed by pairwise combinations of three proteins that are encoded on the pXO1 plasmid of Bacillus anthracis. Lethal toxin is composed of protective antigen (PA) combined with lethal factor (LF) while edema toxin is composed of PA and edema factor (EF). The present study found that the catalytic mutants of LF (LFE687A) and EF (EFH351A) competitively inhibited lethal toxin and edema toxin-mediated activity in vitro and lethality in vivo and were non-toxic to sensitive cell lines when combined with PA. While PA combined with EFH351A was non-lethal in mice, PA combined with LFE687A was of reduced virulence. Full protection of mice against a lethal toxin challenge required injection of mice with PA combined with both LFE687A and EFH351A. The potential use of these full-length, biologically inactive mutant proteins combined with PA as prophylactics or therapeutics is discussed.
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Affiliation(s)
- Megha Gupta
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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