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Hao L, Liang J, Chen S, Zhang J, Zhang Y, Xu Y. MzmL, a novel marine derived N-acyl homoserine lactonase from Mesoflavibacter zeaxanthinifaciens that attenuates Pectobacterium carotovorum subsp. carotovorum virulence. Front Microbiol 2024; 15:1353711. [PMID: 38784800 PMCID: PMC11112094 DOI: 10.3389/fmicb.2024.1353711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Quorum sensing (QS) is a conserved cell-cell communication mechanism widely distributed in bacteria, and is oftentimes tightly correlated with pathogen virulence. Quorum quenching enzymes, which interfere with QS through degrading the QS signaling molecules, could attenuate virulence instead of killing the pathogens, and thus are less likely to induce drug resistance. Many Gram-negative bacteria produce N-acyl homoserine lactones (AHLs) for interspecies communication. In this study, we isolated and identified a bacterial strain, Mesoflavibacter zeaxanthinifaciens XY-85, from an Onchidium sp. collected from the intertidal zone of Dapeng Reserve in Shenzhen, China, and found it had strong AHL degradative activity. Whole genome sequencing and blast analysis revealed that XY-85 harbors an AHL lactonase (designated MzmL), which is predicted to have an N-terminal signal peptide and share the "HXHXDH" motif with known AHL lactonases belonging to the Metallo-β-lactamase superfamily. Phylogenetic studies showed MzmL was closest to marine lactonase cluster members, MomL and Aii20J, instead of the AiiA type lactonases. Ultra performance liquid chromatography-mass spectrometry analysis confirmed that MzmL functions as an AHL lactonase catalyzing AHL degradation through lactone hydrolysis. MzmL could degrade both short- and long-chain AHLs with or without a substitution of oxo-group at the C-3 position, and retained full bioactivity under a wide range of temperatures (28-100°C) and pHs (4-11). Furthermore, MzmL significantly reduced Pectobacterium carotovorum subsp. carotovorum virulence factor production in vitro, such as biofilm formation and plant cell wall degrading enzyme production, and inhibited soft rot development on potato slices. These results demonstrated that MzmL may be a novel type of AHL lactonase with good environmental stability, and has great potential to be developed into a novel biological control agent for bacterial disease management.
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Affiliation(s)
- Lingyun Hao
- Center for Plant Environmental Sensing, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jinyou Liang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Shuotian Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Junliang Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yu Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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Chen Y, Liu P, Wu J, Yan W, Xie S, Sun X, Ye BC, Chu X. N-acylhomoserine lactonase-based hybrid nanoflowers: a novel and practical strategy to control plant bacterial diseases. J Nanobiotechnology 2022; 20:347. [PMID: 35883097 PMCID: PMC9327166 DOI: 10.1186/s12951-022-01557-9] [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: 05/07/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The disease caused by plant pathogenic bacteria in the production, transportation, and storage of many crops has brought huge losses to agricultural production. N-acylhomoserine lactonases (AHLases) can quench quorum-sensing (QS) by hydrolyzing acylhomoserine lactones (AHLs), which makes them the promising candidates for controlling infections of QS-dependent pathogenic bacteria. Although many AHLases have been isolated and considered as a potentially effective preventive and therapeutic agents for bacterial diseases, the intrinsically poor ambient stability has seriously restricted its application. RESULTS Herein, we showed that a spheroid enzyme-based hybrid nanoflower (EHNF), AhlX@Ni3(PO4)2, can be easily synthesized, and it exhibited 10 times AHL (3OC8-HSL) degradation activity than that with free AhlX (a thermostable AHL lactonase). In addition, it showed intriguing stability even at the working concentration, and retained ~ 100% activity after incubation at room temperature (25 °C) for 40 days and approximately 80% activity after incubation at 60 °C for 48 h. Furthermore, it exhibited better organic solvent tolerance and long-term stability in a complicated ecological environment than that of AhlX. To reduce the cost and streamline production processes, CSA@Ni3(PO4)2, which was assembled from the crude supernatants of AhlX and Ni3(PO4)2, was synthesized. Both AhlX@Ni3(PO4)2 and CSA@Ni3(PO4)2 efficiently attenuated pathogenic bacterial infection. CONCLUSIONS In this study, we have developed N-acylhomoserine lactonase-based hybrid nanoflowers as a novel and efficient biocontrol reagent with significant control effect, outstanding environmental adaptability and tolerance. It was expected to overcome the bottlenecks of poor stability and limited environmental tolerance that have existed for over two decades and pioneered the practical application of EHNFs in the field of biological control.
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Affiliation(s)
- Yan Chen
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Pengfu Liu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Jiequn Wu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Wanqing Yan
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Saixue Xie
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Xuanrong Sun
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Bang-Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China.
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China.
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Anandan K, Vittal RR. Quorum quenching activity of AiiA lactonase KMMI17 from endophytic Bacillus thuringiensis KMCL07 on AHL- mediated pathogenic phenotype in Pseudomonas aeruginosa. Microb Pathog 2019; 132:230-242. [PMID: 31082528 DOI: 10.1016/j.micpath.2019.05.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/25/2022]
Abstract
Virulence pathways in gram-negative pathogenic bacteria are regulated by quorum sensing mechanisms, through the production and sensing of N-acylhomoserine lactone (AHL) signal molecules. Enzymatic degradation to disrupt quorum-sensing in these bacteria could pave the way for the new development in decreasing resistance strains and are of significant interest for clinical, agricultural, and industrial applications. Isolated endophytic Bacillus thuringiensis strain KMCL07 showing quorum quenching activity on Pseudomonas aeruginosa PAO1 has been studied. AiiA lactonase KMMI17 identified belongs to metallo- β-lactamase superfamily preserving conserved regions of 106HXDH-59 amino acids-H169-21 amino acids-D191 motif, significantly inhibits the biofilm formation and attenuates virulence factor pyocyanin production of PAO1. Insilico molecular docking analysis of lactonase KMMI17 using alternative catalytic site (PDB entry: 3DHA) with the AHL-based QS system regulators of PAO-1, C4 AHL, C6 AHL and 3-oxo-C12 AHL molecules showed good binding affinity between the protein and ligands, Phe111 and Tyr198 residues plays an important role in binding them. Crude enzyme extract was found to have Km value for C6-HSL: 134.2702 ± 34.83 μM-1, C4-HSL: 308.217 ± 139.9 μM-1 and 3-oxo-C12-HSL: 760.463 ± 251.3 μM-1. LCMS analysis confirms the degradation activity of lactonase KMMI17 on AHL molecules and its hydrolytic process, which indicates the potential application of lactonase KMMI17 as a biocontrol agent or an anti-pathogenic drug.
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Affiliation(s)
- Kanmani Anandan
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore, 570006, India
| | - Ravishankar Rai Vittal
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore, 570006, India.
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Liu Y, Ebalunode JO, Briggs JM. Insights into the substrate binding specificity of quorum-quenching acylase PvdQ. J Mol Graph Model 2019; 88:104-120. [PMID: 30703686 DOI: 10.1016/j.jmgm.2019.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 01/19/2023]
Abstract
Quorum sensing is a cell to cell signaling mechanism that enables them to coordinate their behaviors in a density-dependent manner mediated by small diffusible signaling molecules, which can control the virulence and biofilm gene expression in many Gram-negative and positive bacteria. N-acyl homoserine lactone acylase PvdQ from human opportunistic pathogen Pseudomonas aeruginosa is a quorum-quenching enzyme that can hydrolyze the amide bond of the quorum signaling N-acyl homoserine lactones (AHLs) thereby degrading the signaling molecules, turning off the biofilm phenotype and resulting in a reduction of bacterial virulence. Previous studies demonstrated that PvdQ has different preferences for N-acyl substrates with different acyl chain lengths and substituents. However, the substrate binding specificity determinants of the quorum-quenching enzyme PvdQ with the different bacterial ligands are unknown and unintuitive. Further, elucidation of these determinants can lead to mutants with efficiency and broader substrate promiscuity. To investigate this question, a computational study was carried out combining multiple molecular docking methods, molecular dynamics simulations, residue interaction network analysis, and binding free energy calculations. The main findings are: firstly, the results from pKa predictions support that the pKa of the N-terminus of Serβ1 was depressed due to the surrounding residues. Multiple molecular docking studies provide useful information about the detailed binding modes and binding affinities. Secondly, 300 ns molecular dynamics simulations were carried out to analyze the overall molecular motions of substrate-bound and substrate-free PvdQ. The specific interactions between the active site of PvdQ and different ligands revealed the determinants for the preference among the ligands. A systematic comparison and analysis of the protein dynamic fingerprint of each complex demonstrated that binding of the most favorable ligand, C12-homoserine lactone (C12-HSL), reduced the global motions of the complex and maintained the correct arrangement of the catalytic site. Further, the residue interaction network analysis of each system illustrated that there are more communication contacts and pathways between the residues in the C12-HSL complex as compared to complexes with the other ligands. The binding of the C12-HSL ligand facilitates structural communication between the two knobs and the active site. While the binding of the other ligands tend to impair specific communication pathways between the two knobs and the active site, and lead to a catalytically inefficient state. Finally, simulation results from free energy landscape and binding free energy analysis revealed that the C12-HSL ligand has the lowest binding free energy and greater stability than the less favored ligands. Each of the following residues: Serβ1, Hisβ23, Pheβ24, Metβ30, Pheβ32, Leuβ50, Asnβ57, Thrβ69, Valβ70, Trpβ162, Trpβ186, Asnβ269, Argβ297 and Leuα146, play different roles in substrate binding specificity. This is the first computational study that provides molecular information for structure-dynamic-function relationships of PvdQ with different ligands and demonstrates determinants of bacterial substrate binding specificity.
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Affiliation(s)
- Yanyun Liu
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | - Jerry O Ebalunode
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
| | - James M Briggs
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA.
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Bergonzi C, Schwab M, Naik T, Daudé D, Chabrière E, Elias M. Structural and Biochemical Characterization of AaL, a Quorum Quenching Lactonase with Unusual Kinetic Properties. Sci Rep 2018; 8:11262. [PMID: 30050039 PMCID: PMC6062542 DOI: 10.1038/s41598-018-28988-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/29/2018] [Indexed: 11/10/2022] Open
Abstract
Quorum quenching lactonases are enzymes that are capable of disrupting bacterial signaling based on acyl homoserine lactones (AHL) via their enzymatic degradation. In particular, lactonases have therefore been demonstrated to inhibit bacterial behaviors that depend on these chemicals, such as the formation of biofilms or the expression of virulence factors. Here we characterized biochemically and structurally a novel representative from the metallo-β-lactamase superfamily, named AaL that was isolated from the thermoacidophilic bacterium Alicyclobacillus acidoterrestris. AaL is a potent quorum quenching enzyme as demonstrated by its ability to inhibit the biofilm formation of Acinetobacter baumannii. Kinetic studies demonstrate that AaL is both a proficient and a broad spectrum enzyme, being capable of hydrolyzing a wide range of lactones with high rates (kcat/KM > 105 M-1.s-1). Additionally, AaL exhibits unusually low KM values, ranging from 10 to 80 µM. Analysis of AaL structures bound to phosphate, glycerol, and C6-AHL reveals a unique hydrophobic patch (W26, F87 and I237), involved in substrate binding, possibly accounting for the enzyme's high specificity. Identifying the specificity determinants will aid the development of highly specific quorum quenching enzymes as potential therapeutics.
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Affiliation(s)
- Celine Bergonzi
- Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA
| | - Michael Schwab
- Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA
| | - Tanushree Naik
- Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA
| | - David Daudé
- Gene&GreenTK, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Eric Chabrière
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Mikael Elias
- Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA.
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