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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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Khrenova MG, Kulakova AM, Nemukhin AV. Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase. J Chem Inf Model 2021; 61:1215-1225. [PMID: 33677973 DOI: 10.1021/acs.jcim.0c01308] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report the first computational characterization of an optogenetic system composed of two photosensing BLUF (blue light sensor using flavin adenine dinucleotide) domains and two catalytic adenylyl cyclase (AC) domains. Conversion of adenosine triphosphate (ATP) to the reaction products, cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi), catalyzed by ACs initiated by excitation in photosensing domains has emerged in the focus of modern optogenetic applications because of the request in photoregulated enzymes that modulate cellular concentrations of signaling messengers. The photoactivated AC from the soil bacterium Beggiatoa sp. (bPAC) is an important model showing a considerable increase in the ATP to cAMP conversion rate in the catalytic domain after the illumination of the BLUF domain. The 1 μs classical molecular dynamics simulations reveal that the activation of the BLUF domain leading to tautomerization of Gln49 in the chromophore-binding pocket results in switching of the position of the side chain of Arg278 in the active site of AC. Allosteric signal transmission pathways between Gln49 from BLUF and Arg278 from AC were revealed by the dynamical network analysis. The Gibbs energy profiles of the ATP → cAMP + PPi reaction computed using QM(DFT(ωB97X-D3/6-31G**))/MM(CHARMM) molecular dynamics simulations for both Arg278 conformations in AC clarify the reaction mechanism. In the light-activated system, the corresponding arginine conformation stabilizes the pentacoordinated phosphorus of the α-phosphate group in the transition state, thus lowering the activation energy. Simulations of the bPAC system with the Tyr7Phe replacement in the BLUF demonstrate occurrence of both arginine conformations in an equal ratio, explaining the experimentally observed intermediate catalytic activity of the bPAC-Y7F variant as compared with the dark and light states of the wild-type bPAC.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071 Russian Federation
| | - Anna M Kulakova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
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Grigorenko B, Polyakov I, Nemukhin A. Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires. J Phys Chem B 2020; 124:451-460. [PMID: 31881811 DOI: 10.1021/acs.jpcb.9b07349] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report a mechanism of adenosine triphosphate (ATP) to cyclic adenosine monophosphate (cAMP) conversion by the mammalian type V adenylyl cyclase revealed in molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) simulations. We characterize a set of computationally derived enzyme-substrate (ES) structures showing an important role of coordination shells of magnesium ions in the solvent accessible active site. In the lowest energy ES conformation, the coordination shell of MgA2+ does not include the Oδ1 atom of the conserved Asp440 residue. Starting from this conformation, a one-step reaction mechanism is characterized that includes proton transfer from the ribose O3'H3' group in ATP to Asp440 via a shuttling water molecule concerted with PA-O3A bond cleavage and O3'-PA bond formation. The energy profile of this route is consistent with the observed reaction kinetics. The computed energy profiles initiated from higher energy ES complexes are characterized by larger energy expenses to complete the reaction. Consistent with experimental data, we show that the Asp440Ala mutant of the enzyme should exhibit a reduced but retained activity. All considered reaction pathways include proton wires from the O3'H3' group via shuttling water molecules.
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Affiliation(s)
- Bella Grigorenko
- Chemistry Department , M. V. Lomonosov Moscow State University , 1-3 Leninskiye Gory , Moscow 119991 , Russia.,N. M. Emanuel Institute of Biochemical Physics , Russian Academy of Sciences , 4 Kosygin Street , Moscow 119334 , Russia
| | - Igor Polyakov
- Chemistry Department , M. V. Lomonosov Moscow State University , 1-3 Leninskiye Gory , Moscow 119991 , Russia.,N. M. Emanuel Institute of Biochemical Physics , Russian Academy of Sciences , 4 Kosygin Street , Moscow 119334 , Russia
| | - Alexander Nemukhin
- Chemistry Department , M. V. Lomonosov Moscow State University , 1-3 Leninskiye Gory , Moscow 119991 , Russia.,N. M. Emanuel Institute of Biochemical Physics , Russian Academy of Sciences , 4 Kosygin Street , Moscow 119334 , Russia
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Dashnyam P, Mudududdla R, Hsieh TJ, Lin TC, Lin HY, Chen PY, Hsu CY, Lin CH. β-Glucuronidases of opportunistic bacteria are the major contributors to xenobiotic-induced toxicity in the gut. Sci Rep 2018; 8:16372. [PMID: 30401818 PMCID: PMC6219552 DOI: 10.1038/s41598-018-34678-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/23/2018] [Indexed: 02/07/2023] Open
Abstract
Gut bacterial β-D-glucuronidases (GUSs) catalyze the removal of glucuronic acid from liver-produced β-D-glucuronides. These reactions can have deleterious consequences when they reverse xenobiotic metabolism. The human gut contains hundreds of GUSs of variable sequences and structures. To understand how any particular bacterial GUS(s) contributes to global GUS activity and affects human health, the individual substrate preference(s) must be known. Herein, we report that representative GUSs vary in their ability to produce various xenobiotics from their respective glucuronides. To attempt to explain the distinct substrate preference, we solved the structure of a bacterial GUS complexed with coumarin-3-β-D-glucuronide. Comparisons of this structure with other GUS structures identified differences in loop 3 (or the α2-helix loop) and loop 5 at the aglycone-binding site, where differences in their conformations, hydrophobicities and flexibilities appear to underlie the distinct substrate preference(s) of the GUSs. Additional sequence, structural and functional analysis indicated that several groups of functionally related gut bacterial GUSs exist. Our results pinpoint opportunistic gut bacterial GUSs as those that cause xenobiotic-induced toxicity. We propose a structure-activity relationship that should allow both the prediction of the functional roles of GUSs and the design of selective inhibitors.
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Affiliation(s)
- Punsaldulam Dashnyam
- 0000 0000 9360 4962grid.469086.5Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, 11529 Taiwan ,0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan ,0000 0004 0532 3749grid.260542.7Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 40227 Taiwan
| | - Ramesh Mudududdla
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Tung-Ju Hsieh
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Ting-Chien Lin
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Hsien-Ya Lin
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Peng-Yuan Chen
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Chia-Yi Hsu
- 0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan
| | - Chun-Hung Lin
- 0000 0000 9360 4962grid.469086.5Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, 11529 Taiwan ,0000 0001 2287 1366grid.28665.3fInstitute of Biological Chemistry, Academia Sinica, Taipei, 11529 Taiwan ,0000 0004 0532 3749grid.260542.7Biotechnology Center, National Chung-Hsing University, Taichung, 40227 Taiwan ,0000 0004 0546 0241grid.19188.39Department of Chemistry and Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617 Taiwan
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