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Mol M, de Maayer P. Elucidating the biotechnological potential of the genera Parageobacillus and Saccharococcus through comparative genomic and pan-genome analysis. BMC Genomics 2024; 25:723. [PMID: 39054411 PMCID: PMC11270796 DOI: 10.1186/s12864-024-10635-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND The genus Geobacillus and its associated taxa have been the focal point of numerous thermophilic biotechnological investigations, both at the whole cell and enzyme level. By contrast, comparatively little research has been done on its recently delineated sister genus, Parageobacillus. Here we performed pan-genomic analyses on a subset of publicly available Parageobacillus and Saccharococcus genomes to elucidate their biotechnological potential. RESULTS Phylogenomic analysis delineated the compared taxa into two distinct genera, Parageobacillus and Saccharococcus, with P. caldoxylosilyticus isolates clustering with S. thermophilus in the latter genus. Both genera present open pan-genomes, with the species P. toebii being characterized with the highest novel gene accrual. Diversification of the two genera is driven through the variable presence of plasmids, bacteriophages and transposable elements. Both genera present a range of potentially biotechnologically relevant features, including a source of novel antimicrobials, thermostable enzymes including DNA-active enzymes, carbohydrate active enzymes, proteases, lipases and carboxylesterases. Furthermore, they present a number of metabolic pathways pertinent to degradation of complex hydrocarbons and xenobiotics and for green energy production. CONCLUSIONS Comparative genomic analyses of Parageobacillus and Saccharococcus suggest that taxa in both of these genera can serve as a rich source of biotechnologically and industrially relevant secondary metabolites, thermostable enzymes and metabolic pathways that warrant further investigation.
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Affiliation(s)
- Michael Mol
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Pieter de Maayer
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, 2000, South Africa.
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Ge S, Yang H, Li Y, Chen X, Yang R, Dong X. Mitigation of biofouling in membrane bioreactors by quorum-quenching bacteria during the treatment of metal-containing wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:32126-32135. [PMID: 38649608 DOI: 10.1007/s11356-024-33336-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024]
Abstract
Quorum quenching (QQ) is an efficient way to mitigate membrane biofouling in a membrane bioreactor (MBR) during wastewater treatment. A QQ bacterium, Lysinibacillus sp. A4, was isolated and used to mitigate biofouling in an MBR during the treatment of wastewater containing metals. A QQ enzyme (named AilY) was cloned from A4 and identified as a metallo-β-lactamase-like lactonase. The QQ activity of A4 and that of Escherichia coli BL21 (DE3) overexpressing AilY could be promoted by Fe2+, Mn2+, and Zn2+ while remaining unaffected by other metals tested. The two bacteria effectively mitigated biofouling by reducing the transmembrane pressure from around 30 to 20 kPa without negative influence on the COD, NH4+-N, or total phosphorus of the effluent. The relative abundance of Lysinibacillus sp. A4 increased greatly from 0.04 to 8.29% in the MBR with metal-containing wastewater, suggesting that Lysinibacillus sp. A4 could multiply quickly and adapt to this environment. Taken together, the findings suggested that A4 could tolerate metal to a certain degree, and this property could allow A4 to adapt well to metal-containing wastewater, making it a valuable strain for mitigating biofouling in MBR during the treatment of metal-containing wastewater.
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Affiliation(s)
- Shimei Ge
- College of Life and Environmental Science, Wenzhou University, Ou-Hai District, Cha-Shan Town, Wenzhou, Zhejiang Province, 325035, People's Republic of China
- National & Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, Wenzhou University, Wenzhou, 325035, China
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China
| | - Huiting Yang
- College of Life and Environmental Science, Wenzhou University, Ou-Hai District, Cha-Shan Town, Wenzhou, Zhejiang Province, 325035, People's Republic of China
| | - Yaru Li
- College of Life and Environmental Science, Wenzhou University, Ou-Hai District, Cha-Shan Town, Wenzhou, Zhejiang Province, 325035, People's Republic of China
- National & Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, Wenzhou University, Wenzhou, 325035, China
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China
| | - Xiaohui Chen
- College of Life and Environmental Science, Wenzhou University, Ou-Hai District, Cha-Shan Town, Wenzhou, Zhejiang Province, 325035, People's Republic of China
| | - Ruixue Yang
- College of Life and Environmental Science, Wenzhou University, Ou-Hai District, Cha-Shan Town, Wenzhou, Zhejiang Province, 325035, People's Republic of China
| | - Xinjiao Dong
- College of Life and Environmental Science, Wenzhou University, Ou-Hai District, Cha-Shan Town, Wenzhou, Zhejiang Province, 325035, People's Republic of China.
- National & Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, Wenzhou University, Wenzhou, 325035, China.
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China.
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Bhat N, Nutho B, Hanpaibool C, Hadsadee S, Vangnai A, Rungrotmongkol T. Molecular binding of different classes of organophosphates to methyl parathion hydrolase from Ochrobactrum species. Proteins 2024; 92:96-105. [PMID: 37646471 DOI: 10.1002/prot.26579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/04/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Methyl parathion hydrolase (MPH) is an enzyme of the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphates (OPs). Recently, MPH has attracted attention as a promising enzymatic bioremediator. The crystal structure of MPH enzyme shows a dimeric form, with each subunit containing a binuclear metal ion center. MPH also demonstrates metal ion-dependent selectivity patterns. The origins of these patterns remain unclear but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. We aimed to investigate and compare the binding of different OP pesticides to MPH with cobalt(II) metal ions. In this study, MPH was modeled from Ochrobactrum sp. with different OP pesticides bound, including methyl paraoxon and dichlorvos and profenofos. The docked structures for each substrate optimized by DFT calculation were selected and subjected to atomistic molecular dynamics simulations for 500 ns. It was found that alpha metal ions did not coordinate with all the pesticides. Rather, the pesticides coordinated with less buried beta metal ions. It was also observed that the coordination of beta metal ions was perturbed to accommodate the pesticides. The binding free energy calculations and structure-based pharmacophore model revealed that all the three substrates could bind well at the active site. However, profenofos exhibit a stronger binding affinity to MPH in comparison to the other two substrates. Therefore, our findings provide molecular insight on the binding of different OP pesticides which could help us design the enzyme for OP pesticides degradation.
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Affiliation(s)
- Nayana Bhat
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Bodee Nutho
- Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Chonnikan Hanpaibool
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Sarinya Hadsadee
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Alisa Vangnai
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Hazardous Substance Management, Chulalongkorn University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
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Marone M, Porzio E, Lampitella EA, Manco G. A mesophilic phosphotriesterase-like lactonase shows high stability and proficiency as quorum quenching enzyme. Chem Biol Interact 2023; 383:110657. [PMID: 37573927 DOI: 10.1016/j.cbi.2023.110657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023]
Abstract
The problem of biofilm formation is a serious concern under various pathological conditions such as extensive burns, wounds in diabetic patients, bedsores, cystic fibrosis, nosocomial infections from implantable medical devices such as catheters, valves, etc. Environmental diffusion of biofilm (in pools, wet floors, industrial food plants) that could represent a reservoir of antibiotic resistant bacteria constitues an additional issue. In this work is described a lactonase from Rhodococcus erythropolis, a phosphotriesterase-like lactonase (PLL) enzyme, which has already been studied in the past and can be used for containment of biofilm formation. The protein is 28% and 40% identical with respect to the Pseudomonas diminuta PTE and the thermostable Saccharolobus solfataricus SsoPox respectively. The protein was obtained starting from a synthetic His-tagged gene, expressed in E. coli, purified and further characterized. New properties, not previously known or deducible from its sequence, have been highlighted. These properties are: the enzyme is thermophilic and thermostable even though it originates from a mesophilic bacterium; the enzyme has a long (months) shelf life at 4 °C; the enzyme is not only stable to low concentrations of the oxidant H2O2 but even activated by it at high concentrations; the enzyme proved to be a proficient quorum quenching enzyme, able to hydrolase acyl-homoserine lactones 3oxoC12-HSL and C4-HSL, and can inhibit up to 60% the formation of Pseudomonas aeruginosa (PAO1) biofilm. These different properties make the lactonase useful to fight resistant bacteria that induce inflammatory and infectious processes mediated by the quorum sensing mechanism.
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Affiliation(s)
- Maria Marone
- Institute of Biochemistry and Cell Biology. National Research Council of Italy, Via P. Castellino 111, Naples, Italy
| | - Elena Porzio
- Institute of Biochemistry and Cell Biology. National Research Council of Italy, Via P. Castellino 111, Naples, Italy
| | - Eros Antonio Lampitella
- Institute of Biochemistry and Cell Biology. National Research Council of Italy, Via P. Castellino 111, Naples, Italy
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology. National Research Council of Italy, Via P. Castellino 111, Naples, Italy.
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5
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Wang D, Cui F, Ren L, Li J, Li T. Quorum-quenching enzymes: Promising bioresources and their opportunities and challenges as alternative bacteriostatic agents in food industry. Compr Rev Food Sci Food Saf 2023; 22:1104-1127. [PMID: 36636773 DOI: 10.1111/1541-4337.13104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023]
Abstract
The problems of spoilage, disease, and biofilm caused by bacterial quorum-sensing (QS) systems have posed a significant challenge to the development of the food industry. Quorum-quenching (QQ) enzymes can block QS by hydrolyzing or modifying the signal molecule, making these enzymes promising new candidates for use as antimicrobials. With many recent studies of QQ enzymes and their potential to target foodborne bacteria, an updated and systematic review is necessary. Thus, the goals of this review were to summarize what is known about the effects of bacterial QS on the food industry; discuss the current understanding of the catalytic mechanisms of QQ enzymes, including lactonase, acylase, and oxidoreductase; and describe strategies for the engineering and evolution of QQ enzymes for practical use. In particular, this review focuses on the latest progress in the application of QQ enzymes in the field of food. Finally, the current challenges limiting the systematic application of QQ enzymes in the food industry are discussed to help guide the future development of these important enzymes.
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Affiliation(s)
- Dangfeng Wang
- College of Food Science and Technology, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Bohai University, Jinzhou, China
| | - Fangchao Cui
- College of Food Science and Technology, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Bohai University, Jinzhou, China
| | - Likun Ren
- College of Food Science and Technology, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Bohai University, Jinzhou, China
- Key Laboratory of Food Science and Engineering of Heilongjiang Province, College of Food Engineering, Harbin University of Commerce, Harbin, China
| | - Jianrong Li
- College of Food Science and Technology, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Bohai University, Jinzhou, China
| | - Tingting Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian, China
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6
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Liao J, Li Z, Xiong D, Shen D, Wang L, Shao X, Li T, Qian G. A Novel and Efficient Platform for Discovering Noncanonical Quorum-Quenching Proteins. Microbiol Spectr 2023; 11:e0343722. [PMID: 36475880 PMCID: PMC9927378 DOI: 10.1128/spectrum.03437-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Quorum sensing (QS) is a well-known chemical signaling system responsible for intercellular communication that is widespread in bacteria. Acyl-homoserine lactone (AHL) is the most-studied QS signal. Previously, bacterially encoded AHL-degrading enzymes were considered to be canonical quorum-quenching proteins that have been widely used to control pathogenic infections. Here, we report a novel platform that enabled the efficient discovery of noncanonical AHL quorum-quenching proteins. This platform initially asked bacteriologists to carry out comparative genomic analyses between phylogenetically related AHL-producing and non-AHL-producing members to identify genes that are conservatively shared by non-AHL-producing members but absent in AHL-producing species. These candidate genes were then introduced into recombinant AHL-producing E. coli to screen for target proteins with the ability to block AHL production. Via this platform, we found that non-AHL-producing Lysobacter containing numerous environmentally ubiquitous members encoded a conserved glycosyltransferase-like protein Le4759, which was experimentally shown to be a noncanonical AHL-quenching protein. Le4759 could not directly degrade exogenous AHL but rather recognized and altered the activities of multiple AHL synthases through protein-protein interactions. This versatile capability enabled Le4759 to block specific AHL synthase such as CarI from Pectobacterium carotovorum to reduce its protein abundance to suppress AHL synthesis, thereby impairing bacterial infection. Thus, this study provided bacteriologists with a unique platform to discover noncanonical quorum-quenching proteins that could be developed as promising next-generation drug candidates to overcome emerging bacterial antibiotic resistance. IMPORTANCE Targeting and blocking bacterial quorum sensing (QS), the process known as quorum quenching (QQ) is an effective mean to control bacterial infection and overcome the emerging antibiotic resistance. Previously, diverse QS signal-degradation enzymes are identified as canonical QQ proteins. Here, we provided a novel and universal platform that enabled to discover previously unidentified noncanonical QQ proteins that were unable to degrade acyl-homoserine lactone (AHL) but could block AHL generation by recognizing multiple AHL synthases via direct protein-protein interactions. Our findings are believed to trigger broad interest for bacteriologists to identify potentially widely distributed noncanonical QQ proteins that have great potential for developing next-generation anti-infectious drugs.
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Affiliation(s)
- Jinxing Liao
- College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Zihan Li
- College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Dan Xiong
- College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Danyu Shen
- College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Lu Wang
- Medical College, China Three Gorges University, Yichang, People’s Republic of China
| | - Xiaolong Shao
- College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Tao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Guoliang Qian
- College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
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Targeting Multidrug-Recalcitrant Pseudomonas aeruginosa Biofilms: Combined-Enzyme Treatment Enhances Antibiotic Efficacy. Antimicrob Agents Chemother 2023; 67:e0135822. [PMID: 36602373 PMCID: PMC9872604 DOI: 10.1128/aac.01358-22] [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] [Indexed: 01/06/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that forms biofilms during infection, resulting in recalcitrance to antibiotic treatment. Biofilm inhibition is a promising research direction for the treatment of biofilm-associated infections. Here, a combined-enzyme biofilm-targeted strategy was put forward for the first time to simultaneously prevent biofilm formation and break down preformed biofilms. The N-acylhomoserine lactonase AidH was used as a quorum-sensing inhibitor and was modified to enhance the inhibitory effect on biofilms by rational design. Mutant AidHA147G exerted maximum activity at the human body temperature and pH and could reduce the expression of virulence factors as well as biofilm-related genes of P. aeruginosa. Subsequently, the P. aeruginosa self-produced glycosyl hydrolase PslG joined with AidHA147G to disrupt biofilms. Interestingly, under the combined-enzyme intervention for P. aeruginosa wild-type strain PAO1 and clinical strains, no biofilm was observed on the bottom of NEST glass-bottom cell culture dishes. The combination strategy also helped multidrug-resistant clinical strains change from resistant to intermediate or sensitive to many antibiotics commonly used in clinical practice. These results demonstrated that the combined-enzyme approach for inhibiting biofilms is a potential clinical treatment for P. aeruginosa infection.
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Zhu X, Chen WJ, Bhatt K, Zhou Z, Huang Y, Zhang LH, Chen S, Wang J. Innovative microbial disease biocontrol strategies mediated by quorum quenching and their multifaceted applications: A review. FRONTIERS IN PLANT SCIENCE 2023; 13:1063393. [PMID: 36714722 PMCID: PMC9878147 DOI: 10.3389/fpls.2022.1063393] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/15/2022] [Indexed: 06/12/2023]
Abstract
With the increasing resistance exhibited by undesirable bacteria to traditional antibiotics, the need to discover alternative (or, at least, supplementary) treatments to combat chemically resistant bacteria is becoming urgent. Quorum sensing (QS) refers to a novel bacterial communication system for monitoring cell density and regulation of a network of gene expression that is mediated by a group of signaling molecules called autoinducers (AIs). QS-regulated multicellular behaviors include biofilm formation, horizontal gene transfer, and antibiotic synthesis, which are demonstrating increasing pathogenicity to plants and aquacultural animals as well as contamination of wastewater treatment devices. To inhibit QS-regulated microbial behaviors, the strategy of quorum quenching (QQ) has been developed. Different quorum quenchers interfere with QS through different mechanisms, such as competitively inhibiting AI perception (e.g., by QS inhibitors) and AI degradation (e.g., by QQ enzymes). In this review, we first introduce different signaling molecules, including diffusible signal factor (DSF) and acyl homoserine lactones (AHLs) for Gram-negative bacteria, AIPs for Gram-positive bacteria, and AI-2 for interspecies communication, thus demonstrating the mode of action of the QS system. We next exemplify the QQ mechanisms of various quorum quenchers, such as chemical QS inhibitors, and the physical/enzymatic degradation of QS signals. We devote special attention to AHL-degrading enzymes, which are categorized in detail according to their diverse catalytic mechanisms and enzymatic properties. In the final part, the applications and advantages of quorum quenchers (especially QQ enzymes and bacteria) are summarized in the context of agricultural/aquacultural pathogen biocontrol, membrane bioreactors for wastewater treatment, and the attenuation of human pathogenic bacteria. Taken together, we present the state-of-the-art in research considering QS and QQ, providing theoretical evidence and support for wider application of this promising environmentally friendly biocontrol strategy.
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Affiliation(s)
- Xixian Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Wen-Juan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, United States
| | - Zhe Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Lian-Hui Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Junxia Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Plant Protection, South China Agricultural University, Guangzhou, 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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10
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Mining marine metagenomes revealed a quorum-quenching lactonase with improved biochemical properties that inhibits the food spoilage bacteria Pseudomonas fluorescens. Appl Environ Microbiol 2021; 88:e0168021. [PMID: 34910563 DOI: 10.1128/aem.01680-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine environment presents great potential as a source of microorganisms that possess novel enzymes with unique activities and biochemical properties. Examples of such are the quorum-quenching (QQ) enzymes that hydrolyze bacterial quorum-sensing (QS) signaling molecules, such as N-acyl-homoserine lactones (AHLs). QS is a form of cell-to-cell communication that enables bacteria to synchronize gene expression in correlation with population density. Searching marine metagenomes for sequences homologous to an AHL lactonase from the phosphotriesterase-like lactonase (PLL) family, we identified new putative AHL lactonases (sharing 30-40% amino acid identity to a thermostable PLL member). Phylogenetic analysis indicated that these putative AHL lactonases comprise a new clade of marine enzymes in the PLL family. Following recombinant expression and purification, we verified the AHL lactonase activity for one of these proteins, named marine originated Lactonase Related Protein (moLRP). This enzyme presented greater activity and stability at a broad range of temperatures and pH, and tolerance to high salinity levels (up to 5M NaCl), as well as higher durability in bacterial culture, compared to another PLL member. The addition of purified moLRP to cultures of Pseudomonas fluorescens inhibited its extracellular protease activity, expression of the protease encoding gene, biofilm formation, and the sedimentation process in milk-based medium. These findings suggest that moLRP is adapted to the marine environment, and can potentially serve as an effective QQ enzyme, inhibiting the QS process in gram-negative bacteria involved in food spoilage. Importance Our results emphasize the potential of sequence and structure-based identification of new quorum-quenching (QQ) enzymes from environmental metagenomes, such as from the ocean, with improved stability or activity. The findings also suggest that purified QQ enzymes can present new strategies against food spoilage, in addition to their recognized involvement in inhibiting bacterial pathogen virulence factors. Future studies on the delivery and safety of enzymatic QQ strategy against bacterial food spoilage should be performed.
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Paidi MK, Satapute P, Haider MS, Udikeri SS, Ramachandra YL, Vo DVN, Govarthanan M, Jogaiah S. Mitigation of organophosphorus insecticides from environment: Residual detoxification by bioweapon catalytic scavengers. ENVIRONMENTAL RESEARCH 2021; 200:111368. [PMID: 34081974 DOI: 10.1016/j.envres.2021.111368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/09/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Organophosphorus insecticides (OPIs) have low persistence and are easily biodegradable in nature. The United States and India are the major countries producing OPIs of about 25% and 17% of the world, respectively. OPIs commonly used for agricultural practices occupy a major share in the global market, which leads to the increasing contamination of OPIs residues in various food chains. To overcome this issue, an enzymatic degradation method has been approved by several environmental toxic, and controlling agencies, including United States Environmental Protection Agency (USEPA). Different catalytic enzymes have been isolated and identified from various microbial sources to neutralize the toxic pesticides and/or insecticides. In this review, we have gathered information on OPIs biotransformation and their residual toxicity in the environment. Particularly, it focuses on OPIs degrading enzymes such as chlorpyrifos hydrolase, diisopropylfluorophosphatase, organophosphate acid anhydrolase, organophosphate hydrolases, and phosphotriesterases like lactonasesspecific activity either P-O link group type or P-S link group of pesticides. To summarize, the catalytic degradation of organophosphorus insecticides is not only profitable but also environmentally friendly. Hence, the enzymatic catalyst is an ultimate and super bio-weapon to mitigate or decontaminate various OPIs residues in both terrestrial and aqueous environments.
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Affiliation(s)
- Murali Krishna Paidi
- AcSIR, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Gijubhai Badheka Marg, Bhavnagar, Gujarat, 364002, India
| | - Praveen Satapute
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad, Karnataka, 580003, India
| | - Muhammad Salman Haider
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Shashikant Shiddappa Udikeri
- Agricultural Research Station, Dharwad Farm, University of Agricultural Sciences, Dharwad, 580005, Karnataka, India
| | | | - Dai-Viet N Vo
- Center of Excellence for Green Energy and Environmental Nanomaterials (CE@GrEEN), Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, South Korea.
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad, Karnataka, 580003, India.
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Lazar V, Holban AM, Curutiu C, Chifiriuc MC. Modulation of Quorum Sensing and Biofilms in Less Investigated Gram-Negative ESKAPE Pathogens. Front Microbiol 2021; 12:676510. [PMID: 34394026 PMCID: PMC8359898 DOI: 10.3389/fmicb.2021.676510] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/30/2021] [Indexed: 01/20/2023] Open
Abstract
Pathogenic bacteria have the ability to sense their versatile environment and adapt by behavioral changes both to the external reservoirs and the infected host, which, in response to microbial colonization, mobilizes equally sophisticated anti-infectious strategies. One of the most important adaptive processes is the ability of pathogenic bacteria to turn from the free, floating, or planktonic state to the adherent one and to develop biofilms on alive and inert substrata; this social lifestyle, based on very complex communication networks, namely, the quorum sensing (QS) and response system, confers them an increased phenotypic or behavioral resistance to different stress factors, including host defense mechanisms and antibiotics. As a consequence, biofilm infections can be difficult to diagnose and treat, requiring complex multidrug therapeutic regimens, which often fail to resolve the infection. One of the most promising avenues for discovering novel and efficient antibiofilm strategies is targeting individual cells and their QS mechanisms. A huge amount of data related to the inhibition of QS and biofilm formation in pathogenic bacteria have been obtained using the well-established gram-positive Staphylococcus aureus and gram-negative Pseudomonas aeruginosa models. The purpose of this paper was to revise the progress on the development of antibiofilm and anti-QS strategies in the less investigated gram-negative ESKAPE pathogens Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter sp. and identify promising leads for the therapeutic management of these clinically significant and highly resistant opportunistic pathogens.
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Affiliation(s)
- Veronica Lazar
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Alina Maria Holban
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Carmen Curutiu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
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Gurevich D, Dor S, Erov M, Dan Y, Moy JC, Mairesse O, Dafny-Yelin M, Adler-Abramovich L, Afriat-Jurnou L. Directed Enzyme Evolution and Encapsulation in Peptide Nanospheres of Quorum Quenching Lactonase as an Antibacterial Treatment against Plant Pathogen. ACS APPLIED MATERIALS & INTERFACES 2021; 13:2179-2188. [PMID: 33405501 DOI: 10.1021/acsami.0c15808] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The need to increase agricultural yield has led to an extensive use of antibiotics against plant pathogens, which has resulted in the emergence of resistant strains. Therefore, there is an increasing demand for new methods, preferably with lower chances of developing resistant strains and a lower risk to the environment or public health. Many Gram-negative bacterial pathogens use quorum sensing, a population-density-dependent regulatory mechanism, to monitor the secretion of N-acyl-homoserine lactones (AHLs) and pathogenicity. Therefore, quorum sensing represents an attractive antivirulence target. AHL lactonases hydrolyze AHLs and have potential antibacterial properties; however, their use is limited by thermal instability and durability, or low activity. Here, we demonstrate that an AHL lactonase from the phosphotriesterase-like lactonase family exhibits high activity with the AHL secreted from the plant pathogen Erwinia amylovora and attenuates infection in planta. Using directed enzyme evolution, we were able to increase the enzyme's temperature resistance (T50, the temperature at which 50% of the activity is retained) by 8 °C. Then, by performing enzyme encapsulation in nanospherical capsules composed of tertbutoxycarbonyl-Phe-Phe-OH peptide, the shelf life was extended for more than 5 weeks. Furthermore, the encapsulated and free mutant were able to significantly inhibit up to 70% blossom's infection in the field, achieving the same efficacy as seen with antibiotics commonly used today to treat the plant pathogen. We conclude that specific AHL lactonase can inhibit E. amylovora infection in the field, as it degrades the AHL secreted by this plant pathogen. The combination of directed enzyme evolution and peptide nanostructure encapsulation significantly improved the thermal resistance and shelf life of the enzyme, respectively, increasing its potential in future development as antibacterial treatment.
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Affiliation(s)
- David Gurevich
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Shlomit Dor
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Mayan Erov
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Yoav Dan
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jehudith Clara Moy
- Northern Agriculture Research & Development, Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Orly Mairesse
- Northern Agriculture Research & Development, Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Mery Dafny-Yelin
- Northern Agriculture Research & Development, Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The ADAMA Center for Novel Delivery Systems in Crop Protection, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Livnat Afriat-Jurnou
- Migal-Galilee Research Institute, Kiryat Shmona 11016, Israel
- The Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
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Sikdar R, Elias M. Quorum quenching enzymes and their effects on virulence, biofilm, and microbiomes: a review of recent advances. Expert Rev Anti Infect Ther 2020; 18:1221-1233. [PMID: 32749905 DOI: 10.1080/14787210.2020.1794815] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Numerous bacterial behaviors are regulated by a cell-density dependent mechanism known as Quorum Sensing (QS). QS relies on communication between bacterial cells using diffusible signaling molecules known as autoinducers. QS regulates physiological processes such as metabolism, virulence, and biofilm formation. Quorum Quenching (QQ) is the inhibition of QS using chemical or enzymatic means to counteract behaviors regulated by QS. AREAS COVERED We examine the main, diverse QS mechanisms present in bacterial species, with a special emphasis on AHL-mediated QS. We also discuss key in vitro and in vivo systems in which interference in QS was investigated. Additionally, we highlight promising developments, such as the substrate preference of the used enzymatic quencher, in the application of interference in QS to counter bacterial virulence. EXPERT OPINION Enabled via the recent isolation of highly stable quorum quenching enzymes and/or molecular engineering efforts, the effects of the interference in QS were recently evaluated outside of the traditional model of single species culture. Signal disruption in complex microbial communities was shown to result in the disruption of complex microbial behaviors, and changes in population structures. These new findings, and future studies, may result in significant changes in the traditional views about QS.
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Affiliation(s)
- Rakesh Sikdar
- Biochemistry, Molecular Biology & Biophysics Department and BioTechnology Institute, University of Minnesota , Saint Paul, Minnesota, USA
| | - Mikael Elias
- Biochemistry, Molecular Biology & Biophysics Department and BioTechnology Institute, University of Minnesota , Saint Paul, Minnesota, USA
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Billot R, Plener L, Jacquet P, Elias M, Chabrière E, Daudé D. Engineering acyl-homoserine lactone-interfering enzymes toward bacterial control. J Biol Chem 2020; 295:12993-13007. [PMID: 32690609 DOI: 10.1074/jbc.rev120.013531] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/17/2020] [Indexed: 12/20/2022] Open
Abstract
Enzymes able to degrade or modify acyl-homoserine lactones (AHLs) have drawn considerable interest for their ability to interfere with the bacterial communication process referred to as quorum sensing. Many proteobacteria use AHL to coordinate virulence and biofilm formation in a cell density-dependent manner; thus, AHL-interfering enzymes constitute new promising antimicrobial candidates. Among these, lactonases and acylases have been particularly studied. These enzymes have been isolated from various bacterial, archaeal, or eukaryotic organisms and have been evaluated for their ability to control several pathogens. Engineering studies on these enzymes were carried out and successfully modulated their capacity to interact with specific AHL, increase their catalytic activity and stability, or enhance their biotechnological potential. In this review, special attention is paid to the screening, engineering, and applications of AHL-modifying enzymes. Prospects and future opportunities are also discussed with a view to developing potent candidates for bacterial control.
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Affiliation(s)
- Raphaël Billot
- Gene&GreenTK, Marseille, France; IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | | | | | - Mikael Elias
- Molecular Biology and Biophysics and Biotechnology Institute, Department of Biochemistry, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric Chabrière
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France.
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Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily. Structure 2020; 28:635-642.e3. [DOI: 10.1016/j.str.2020.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 03/02/2020] [Accepted: 03/23/2020] [Indexed: 11/19/2022]
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Structural and Functional Characterization of New SsoPox Variant Points to the Dimer Interface as a Driver for the Increase in Promiscuous Paraoxonase Activity. Int J Mol Sci 2020; 21:ijms21051683. [PMID: 32121487 PMCID: PMC7084321 DOI: 10.3390/ijms21051683] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/02/2020] [Accepted: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
Increasing attention is more and more directed toward the thermostable Phosphotriesterase-Like-Lactonase (PLL) family of enzymes, for the efficient and reliable decontamination of toxic nerve agents. In the present study, the DNA Staggered Extension Process (StEP) technique was utilized to obtain new variants of PLL enzymes. Divergent homologous genes encoding PLL enzymes were utilized as templates for gene recombination and yielded a new variant of SsoPox from Saccharolobus solfataricus. The new mutant, V82L/C258L/I261F/W263A (4Mut) exhibited catalytic efficiency of 1.6 × 105 M−1 s−1 against paraoxon hydrolysis at 70°C, which is more than 3.5-fold and 42-fold improved in comparison with C258L/I261F/W263A (3Mut) and wild type SsoPox, respectively. 4Mut was also tested with chemical warfare nerve agents including tabun, sarin, soman, cyclosarin and VX. In particular, 4Mut showed about 10-fold enhancement in the hydrolysis of tabun and soman with respect to 3Mut. The crystal structure of 4Mut has been solved at the resolution of 2.8 Å. We propose that, reorganization of dimer conformation that led to increased central groove volume and dimer flexibility could be the major determinant for the improvement in hydrolytic activity in the 4Mut.
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Gupta K, Daroch P, Harjai K, Chhibber S. Parallels among natural and synthetically modified quorum-quenching strategies as convoy to future therapy. Microbiology (Reading) 2019; 165:1265-1281. [DOI: 10.1099/mic.0.000826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Kshitiz Gupta
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Priya Daroch
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Kusum Harjai
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjay Chhibber
- Department of Microbiology, Panjab University, Chandigarh, India
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AidB, a Novel Thermostable N-Acylhomoserine Lactonase from the Bacterium Bosea sp. Appl Environ Microbiol 2019; 85:AEM.02065-19. [PMID: 31604771 DOI: 10.1128/aem.02065-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/04/2019] [Indexed: 11/20/2022] Open
Abstract
Many Gram-negative bacteria employ N-acylhomoserine lactones (AHLs) as quorum-sensing (QS) signal molecules to regulate virulence expression in a density-dependent manner. Quorum quenching (QQ) via enzymatic inactivation of AHLs is a promising strategy to reduce bacterial infections and drug resistance. Herein, a thermostable AHL lactonase (AidB), which could degrade different AHLs, with or without a substitution of carbonyl or hydroxyl at the C-3 position, was identified from the soil bacterium Bosea sp. strain F3-2. Ultrahigh-performance liquid chromatography analysis demonstrated that AidB is an AHL lactonase that hydrolyzes the ester bond of the homoserine lactone (HSL) ring. AidB was thermostable in the range 30 to 80°C and showed maximum activity after preincubation at 60°C for 30 min. The optimum temperature of AidB was 60°C, and the enzyme could be stably stored in double-distilled water (ddH2O) at 4°C or room temperature. AidB homologs were found only in Rhizobiales and Rhodospirillales of the Alphaproteobacteria AidB from Agrobacterium tumefaciens and AidB from Rhizobium multihospitium (with amino acid identities of 50.6% and 52.8% to AidB, respectively) also showed thermostable AHL degradation activity. When introduced into bacteria, plasmid-expressed AidB attenuated pyocyanin production by Pseudomonas aeruginosa PAO1 and the pathogenicity of Pectobacterium carotovorum subsp. carotovorum Z3-3, suggesting that AidB is a potential therapeutic agent by degrading AHLs.IMPORTANCE A quorum-sensing system using AHLs as the signal in many bacterial pathogens is a critical virulence regulator and an attractive target for anti-infective drugs. In this work, we identified a novel AHL lactonase, AidB, from a soil bacterial strain, Bosea sp. F3-2. The expression of aidB reduced the production of AHL signals and QS-dependent virulence factors in Pseudomonas aeruginosa and Pectobacterium carotovorum The homologs of AidB with AHL-degrading activities were found only in several genera belonging to the Alphaproteobacteria Remarkably, AidB is a thermostable enzyme that retained its catalytic activity after treatment at 80°C for 30 min and exhibits reliable storage stability at both 4°C and room temperature. These properties might make it more suitable for practical application.
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Wang Y, Feng T, Li H, Yu Y, Han Y, Zhang J, Li X, Li Y, Zhang XH. A novel heterologous expression strategy for the quorum-quenching enzyme MomL in Lysobacter enzymogenes to the inhibit pathogenicity of Pectobacterium. Appl Microbiol Biotechnol 2019; 103:8889-8898. [PMID: 31656979 DOI: 10.1007/s00253-019-10166-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/20/2019] [Accepted: 09/28/2019] [Indexed: 01/28/2023]
Abstract
Quorum-quenching (QQ) enzymes can block the quorum-sensing (QS) system and prevent the expression of QS-controlled pathogenic factors in bacteria. However, the low expression levels of QQ proteins in the original host bacteria have affected their widespread application. In this study, we heterologously expressed momL, encoding a QQ enzyme with high activity, in Lysobacter enzymogenes. A "yellow-to-white" selection marker and the high-constitutive-expression promoter PgroEL were used in this novel heterologous expression system. In addition, we optimized the spacer between the SD sequence and the initiator to improve the efficiency of the expression system by 1.54-fold. The engineered strain LeMomL degraded the AHL molecule and the virulence factors of Pectobacterium carotovorum subsp. carotovora (Pcc). Additionally, LeMomL significantly decreased the disease caused by Pcc in Chinese cabbages and carrot root tissues. In conclusion, this novel and facile L. enzymogenes expression strategy has good prospects and is an ideal approach for foreign protein expression.
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Affiliation(s)
- Yan Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China. .,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Tao Feng
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hui Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yameng Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yong Han
- Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA
| | - Jingjing Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiaoyu Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yaoyao Li
- Key Laboratory of Chemical Biology, School of Pharmaceutical Sciences, Shandong University, Jinan, 250100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China. .,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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Xiang L, Lu Y, Wang H, Wang M, Zhang G. Improving the specific activity and pH stability of xylanase XynHBN188A by directed evolution. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0262-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Murugayah SA, Gerth ML. Engineering quorum quenching enzymes: progress and perspectives. Biochem Soc Trans 2019; 47:793-800. [PMID: 31064863 PMCID: PMC6599154 DOI: 10.1042/bst20180165] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Abstract
Quorum sensing is a key contributor to the virulence of many important plant, animal and human pathogens. The disruption of this signalling-a process referred to as 'quorum quenching'-is a promising new approach for controlling microbial pathogens. In this mini-review, we have focused on efforts to engineer enzymes that disrupt quorum sensing by inactivating acyl-homoserine lactone signalling molecules. We review different approaches for protein engineering and provide examples of how these engineering approaches have been used to tailor the stability, specificity and activities of quorum quenching enzymes. Finally, we grapple with some of the issues around these approaches-including the disconnect between in vitro biochemistry and potential in vivo applications.
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Affiliation(s)
- Shereen A Murugayah
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Monica L Gerth
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Huang S, Bergonzi C, Schwab M, Elias M, Hicks RE. Evaluation of biological and enzymatic quorum quencher coating additives to reduce biocorrosion of steel. PLoS One 2019; 14:e0217059. [PMID: 31095643 PMCID: PMC6522020 DOI: 10.1371/journal.pone.0217059] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/05/2019] [Indexed: 11/24/2022] Open
Abstract
Microbial colonization can be detrimental to the integrity of metal surfaces and lead to microbiologically influenced corrosion (MIC). Biocorrosion is a serious problem for aquatic and marine industries in the world. In Minnesota (USA), where this study was conducted, biocorrosion severely affects the maritime transportation industry. The anticorrosion activity of a variety of compounds, including chemical (magnesium peroxide) and biological (surfactin, capsaicin, and gramicidin) molecules were investigated as coating additives. We also evaluated a previously engineered, extremely stable, non-biocidal enzyme known to interfere in bacterial signaling, SsoPox (a quorum quenching lactonase). Experimental steel coupons were submerged in water from the Duluth Superior Harbor (DSH) for 8 weeks in the laboratory. Biocorrosion was evaluated by counting the number and the coverage of corrosion tubercles on coupons and also by ESEM imaging of the coupon surface. Three experimental coating additives significantly reduced the formation of corrosion tubercles: surfactin, magnesium peroxide and the quorum quenching lactonase by 31%, 36% and 50%, respectively. DNA sequence analysis of the V4 region of the bacterial 16S rRNA gene revealed that these decreases in corrosion were associated with significant changes in the composition of bacterial communities on the steel surfaces. These results demonstrate the potential of highly stable quorum quenching lactonases to provide a reliable, cost-effective method to treat steel structures and prevent biocorrosion.
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Affiliation(s)
- Siqian Huang
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, United States of America
- * E-mail: (SH); (ME); (REH)
| | - Celine Bergonzi
- Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Michael Schwab
- Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail: (SH); (ME); (REH)
| | - Randall E. Hicks
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, United States of America
- * E-mail: (SH); (ME); (REH)
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Vadakkan K, Choudhury AA, Gunasekaran R, Hemapriya J, Vijayanand S. Quorum sensing intervened bacterial signaling: Pursuit of its cognizance and repression. J Genet Eng Biotechnol 2018; 16:239-252. [PMID: 30733731 PMCID: PMC6353778 DOI: 10.1016/j.jgeb.2018.07.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/09/2018] [Accepted: 07/03/2018] [Indexed: 01/24/2023]
Abstract
Bacteria communicate within a system by means of a density dependent mechanism known as quorum sensing which regulate the metabolic and behavioral activities of a bacterial community. This sort of interaction occurs through a dialect of chemical signals called as autoinducers synthesized by bacteria. Bacterial quorum sensing occurs through various complex pathways depending upon specious diversity. Therefore the cognizance of quorum sensing mechanism will enable the regulation and thereby constrain bacterial communication. Inhibition strategies of quorum sensing are collectively called as quorum quenching; through which bacteria are incapacitated of its interaction with each other. Many virulence mechanism such as sporulation, biofilm formation, toxin production can be blocked by quorum quenching. Usually quorum quenching mechanisms can be broadly classified into enzymatic methods and non-enzymatic methods. Substantial understanding of bacterial communication and its inhibition enhances the development of novel antibacterial therapeutic drugs. In this review we have discussed the types and mechanisms of quorum sensing and various methods to inhibit and regulate density dependent bacterial communication.
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Affiliation(s)
- Kayeen Vadakkan
- Bioresource Technology Lab, Department of Biotechnology, Thiruvalluvar University, Vellore, TN 632115, India
| | - Abbas Alam Choudhury
- Bioresource Technology Lab, Department of Biotechnology, Thiruvalluvar University, Vellore, TN 632115, India
| | - Ramya Gunasekaran
- Bioresource Technology Lab, Department of Biotechnology, Thiruvalluvar University, Vellore, TN 632115, India
| | | | - Selvaraj Vijayanand
- Bioresource Technology Lab, Department of Biotechnology, Thiruvalluvar University, Vellore, TN 632115, India
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25
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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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26
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Highly active enzymes by automated combinatorial backbone assembly and sequence design. Nat Commun 2018; 9:2780. [PMID: 30018322 PMCID: PMC6050298 DOI: 10.1038/s41467-018-05205-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/13/2018] [Indexed: 12/05/2022] Open
Abstract
Automated design of enzymes with wild-type-like catalytic properties has been a long-standing but elusive goal. Here, we present a general, automated method for enzyme design through combinatorial backbone assembly. Starting from a set of homologous yet structurally diverse enzyme structures, the method assembles new backbone combinations and uses Rosetta to optimize the amino acid sequence, while conserving key catalytic residues. We apply this method to two unrelated enzyme families with TIM-barrel folds, glycoside hydrolase 10 (GH10) xylanases and phosphotriesterase-like lactonases (PLLs), designing 43 and 34 proteins, respectively. Twenty-one GH10 and seven PLL designs are active, including designs derived from templates with <25% sequence identity. Moreover, four designs are as active as natural enzymes in these families. Atomic accuracy in a high-activity GH10 design is further confirmed by crystallographic analysis. Thus, combinatorial-backbone assembly and design may be used to generate stable, active, and structurally diverse enzymes with altered selectivity or activity. Computationally designed enzymes often show lower activity or stability than their natural counterparts. Here, the authors present an evolution-inspired method for automated enzyme design, creating stable enzymes with accurate active site architectures and wild-type-like activities.
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27
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Jacquet P, Hiblot J, Daudé D, Bergonzi C, Gotthard G, Armstrong N, Chabrière E, Elias M. Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase. Sci Rep 2017; 7:16745. [PMID: 29196634 PMCID: PMC5711954 DOI: 10.1038/s41598-017-16841-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
The redesign of enzyme active sites to alter their function or specificity is a difficult yet appealing challenge. Here we used a structure-based design approach to engineer the lactonase SsoPox from Sulfolobus solfataricus into a phosphotriesterase. The five best variants were characterized and their structure was solved. The most active variant, αsD6 (V27A-Y97W-L228M-W263M) demonstrates a large increase in catalytic efficiencies over the wild-type enzyme, with increases of 2,210-fold, 163-fold, 58-fold, 16-fold against methyl-parathion, malathion, ethyl-paraoxon, and methyl-paraoxon, respectively. Interestingly, the best mutants are also capable of degrading fensulfothion, which is reported to be an inhibitor for the wild-type enzyme, as well as others that are not substrates of the starting template or previously reported W263 mutants. The broad specificity of these engineered variants makes them promising candidates for the bioremediation of organophosphorus compounds. Analysis of their structures reveals that the increase in activity mainly occurs through the destabilization of the active site loop involved in substrate binding, and it has been observed that the level of disorder correlates with the width of the enzyme specificity spectrum. This finding supports the idea that active site conformational flexibility is essential to the acquisition of broader substrate specificity.
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Affiliation(s)
- Pauline Jacquet
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Julien Hiblot
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
- MPI for Medical Research, Chemical Biology department (EPFL), Heidelberg, Germany
| | - David Daudé
- Gene&GreenTK, IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Céline Bergonzi
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Guillaume Gotthard
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Nicholas Armstrong
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Eric Chabrière
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France.
| | - Mikael Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA.
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28
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Hoque MA, Zhang Y, Chen L, Yang G, Khatun MA, Chen H, Hao L, Feng Y. Stepwise Loop Insertion Strategy for Active Site Remodeling to Generate Novel Enzyme Functions. ACS Chem Biol 2017; 12:1188-1193. [PMID: 28323400 DOI: 10.1021/acschembio.7b00018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The remodeling of active sites to generate novel biocatalysts is an attractive and challenging task. We developed a stepwise loop insertion strategy (StLois), in which randomized residue pairs are inserted into active site loops. The phosphotriesterase-like lactonase from Geobacillus kaustophilus (GkaP-PLL) was used to investigate StLois's potential for changing enzyme function. By inserting six residues into active site loop 7, the best variant ML7-B6 demonstrated a 16-fold further increase in catalytic efficiency toward ethyl-paraoxon compared with its initial template, that is a 609-fold higher, >107 fold substrate specificity shift relative to that of wild-type lactonase. The remodeled variants displayed 760-fold greater organophosphate hydrolysis activity toward the organophosphates parathion, diazinon, and chlorpyrifos. Structure and docking computations support the source of notably inverted enzyme specificity. Considering the fundamental importance of active site loops, the strategy has potential for the rapid generation of novel enzyme functions by loop remodeling.
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Affiliation(s)
- Md Anarul Hoque
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Zhang
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liuqing Chen
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guangyu Yang
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mst Afroza Khatun
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haifeng Chen
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liu Hao
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial
Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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29
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See-Too WS, Ee R, Lim YL, Convey P, Pearce DA, Yin WF, Chan KG. AidP, a novel N-Acyl homoserine lactonase gene from Antarctic Planococcus sp. Sci Rep 2017; 7:42968. [PMID: 28225085 PMCID: PMC5320481 DOI: 10.1038/srep42968] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/17/2017] [Indexed: 11/29/2022] Open
Abstract
Planococcus is a Gram-positive halotolerant bacterial genus in the phylum Firmicutes, commonly found in various habitats in Antarctica. Quorum quenching (QQ) is the disruption of bacterial cell-to-cell communication (known as quorum sensing), which has previously been described in mesophilic bacteria. This study demonstrated the QQ activity of a psychrotolerant strain, Planococcus versutus strain L10.15T, isolated from a soil sample obtained near an elephant seal wallow in Antarctica. Whole genome analysis of this bacterial strain revealed the presence of an N-acyl homoserine lactonase, an enzyme that hydrolyzes the ester bond of the homoserine lactone of N-acyl homoserine lactone (AHLs). Heterologous gene expression in E. coli confirmed its functions for hydrolysis of AHLs, and the gene was designated as aidP (autoinducer degrading gene from Planococcus sp.). The low temperature activity of this enzyme suggested that it is a novel and uncharacterized class of AHL lactonase. This study is the first report on QQ activity of bacteria isolated from the polar regions.
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Affiliation(s)
- Wah Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Peter Convey
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - David A. Pearce
- National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science University of Malaya, 50603 Kuala Lumpur, Malaysia
- UM Omics Centre, University of Malaya, Kuala Lumpur, Malaysia
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30
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Quorum Sensing and the Use of Quorum Quenchers as Natural Biocides to Inhibit Sulfate-Reducing Bacteria. Antibiotics (Basel) 2016; 5:antibiotics5040039. [PMID: 27983678 PMCID: PMC5187520 DOI: 10.3390/antibiotics5040039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/23/2016] [Accepted: 12/06/2016] [Indexed: 11/17/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) are one of the main protagonist groups of biocorrosion in the seawater environment. Given their principal role in biocorrosion, it remains a crucial task to develop strategies to reduce the abundance of SRBs. Conventional approaches include the use of biocides and antibiotics, which can impose health, safety, and environmental concerns. This review examines an alternative approach to this problem. This is achieved by reviewing the role of quorum sensing (QS) in SRB populations and its impact on the biofilm formation process. Genome databases of SRBs are mined to look for putative QS systems and homologous protein sequences representative of autoinducer receptors or synthases. Subsequently, this review puts forward the potential use of quorum quenchers as natural biocides against SRBs and outlines the potential strategies for the implementation of this approach.
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31
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Gómez-Garzón C, Dussán J. Evidence-based validation of quorum quenching from Lysinibacillus sphaericus and Geobacillus sp. in bioremediation of oil sludge. Can J Microbiol 2016; 63:74-82. [PMID: 27905820 DOI: 10.1139/cjm-2016-0323] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many studies on quorum quenching focus on the discovery and characterization of novel acyl-homoserine lactonases (AHL-lactonases) because these enzymes could be used in the control of diseases caused by Gram-negative bacteria. The effects of quorum quenching are also remarkable in the performance of bacterial consortia in applications such as bioremediation. In the current work, we demonstrated the presence of a potential novel AHL-lactonase-encoding locus (Bsph_3377) from Lysinibacillus sphaericus and Geobacillus sp. The deduced amino acid sequences for this enzyme possess the characteristic domains and motifs involved in Zn-binding from AHL lactonases and were grouped into 1 clade within the phylogeny of the lactonases from firmicutes, showing 70% of identity with the lactonase AhlS from Solibacillus silvestris. We demonstrated the locus transcription by RT-qPCR and its relationship with the suppression of the pathogenicity of Pectobacterium carotovorum. Additionally, we analyzed the interaction of these bacilli with a commercial consortium in the bioremediation of a hydrocarbon-contaminated soil, showing inhibitory effects on its establishment. These results represent a new contribution in the understanding of the potential biotechnological applications of L. sphaericus and Geobacillus sp. as well as in the research on antibacterial techniques based on quorum-sensing disruption.
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Affiliation(s)
- Camilo Gómez-Garzón
- Centro de Investigaciones Microbiológicas (CIMIC), Universidad de los Andes, Cra 1 No. 18A-10, Colombia.,Centro de Investigaciones Microbiológicas (CIMIC), Universidad de los Andes, Cra 1 No. 18A-10, Colombia
| | - Jenny Dussán
- Centro de Investigaciones Microbiológicas (CIMIC), Universidad de los Andes, Cra 1 No. 18A-10, Colombia.,Centro de Investigaciones Microbiológicas (CIMIC), Universidad de los Andes, Cra 1 No. 18A-10, Colombia
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32
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Liu X, Cao LC, Fan XJ, Liu YH, Xie W. Engineering of a thermostable esterase Est816 to improve its quorum-quenching activity and the underlying structural basis. Sci Rep 2016; 6:38137. [PMID: 27909291 PMCID: PMC5133562 DOI: 10.1038/srep38137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/04/2016] [Indexed: 12/14/2022] Open
Abstract
N-acyl-homoserine lactones (AHLs) are small diffusible molecules called autoinducers that mediate cell-to-cell communications. Enzymatic degradation of AHLs is a promising bio-control strategy known as quorum-quenching. To improve the quorum-quenching activity of a thermostable esterase Est816, which had been previously cloned, we have engineered the enzyme by random mutagenesis. One of the mutants M2 with double amino acid substitutions (A216V/K238N) showed 3-fold improvement on catalytic efficiency. Based on the crystal structure determined at 2.64 Å, rational design of M2 was conducted, giving rise to the mutant M3 (A216V/K238N/L122A). The kcat/KM value of the mutant M3 is 21.6-fold higher than that of Est816. Furthermore, activity assays demonstrated that M3 reached 99% conversion of 10-μM N-octanoyl-DL-homoserine lactone (C8-HSL) to N-octanoyl- DL-homoserine (C8-Hse) in 20 min, in contrast to the 8 h required by wild type Est816. The dramatic activity enhancement may be attributed to the increased hydrophobic interactions with the lactone ring by the mutation A216V, and the reduced steric clashes between the long side chain of L122 and the aliphatic tail of HSL by the mutation L122A, according to the crystal structure. This study sheds lights on the activity-structure relationship of AHL-lactonases, and may provide useful information in engineering AHL-degrading enzymes.
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Affiliation(s)
- Xiwen Liu
- School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, P. R. China.,State Key Laboratory for Biocontrol, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, P. R. China
| | - Li-Chuang Cao
- School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, P. R. China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou 510275, P. R. China
| | - Xin-Jiong Fan
- School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Rd., Hefei, Anhui 230032, P. R, China
| | - Yu-Huan Liu
- School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, P. R. China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou 510275, P. R. China
| | - Wei Xie
- School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, P. R. China.,State Key Laboratory for Biocontrol, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, P. R. China
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33
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Li XC, Wang C, Mulchandani A, Ge X. Engineering Soluble Human Paraoxonase 2 for Quorum Quenching. ACS Chem Biol 2016; 11:3122-3131. [PMID: 27623343 DOI: 10.1021/acschembio.6b00527] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many pathogenic bacteria utilize quorum sensing (QS) systems to regulate the expression of their virulence genes and promote the formation of biofilm, which renders pathogens with extreme resistance to conventional antibiotic treatments. As a novel approach for attenuating antibiotic resistance and in turn fighting chronic infections, enzymatic inactivation of QS signaling molecules, such as N-acyl homoserine lactones (AHLs), holds great promises. Instead of using bacterial lactonases that can evoke immune response when administered, we focus on the human paraoxonase 2 (huPON2). However, insolubility when heterologously overexpressed hinders its application as anti-infection therapeutics. In this study, huPON2 was engineered for soluble expression with minimal introduction of foreign sequences. On the basis of structure modeling, degenerate linkers were exploited for the removal of hydrophobic helices of huPON2 without disrupting its folding structure and thus retaining its enzymatic function. High soluble expression levels were achieved with a yield of 76 mg of fully human PON2 variants per liter of culture media. Particularly, two clones, D2 and E3, showed significant quorum quenching (QQ) bioactivities and effectively impeded Pseudomonas aeruginosa swimming and swarming motilities, signs of an early stage of biofilm formation. In addition, by correlating QQ with luminescence signal readouts, quantitative analysis of QQ toward natural or non-natural AHL-regulator combinations suggested that D2 and E3 exhibited strong lactone hydrolysis activities toward five AHLs of different side chain lengths and modifications widely utilized by a variety of biomedically important pathogens.
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Affiliation(s)
- Xin Cathy Li
- Department of Biochemistry and Molecular Biology, ‡Department of Chemical
and Environmental
Engineering, University of California Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Christopher Wang
- Department of Biochemistry and Molecular Biology, ‡Department of Chemical
and Environmental
Engineering, University of California Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Ashok Mulchandani
- Department of Biochemistry and Molecular Biology, ‡Department of Chemical
and Environmental
Engineering, University of California Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Xin Ge
- Department of Biochemistry and Molecular Biology, ‡Department of Chemical
and Environmental
Engineering, University of California Riverside, 900 University Ave., Riverside, California 92521, United States
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34
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Tiwari V. In vitro Engineering of Novel Bioactivity in the Natural Enzymes. Front Chem 2016; 4:39. [PMID: 27774447 PMCID: PMC5054688 DOI: 10.3389/fchem.2016.00039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 09/21/2016] [Indexed: 11/23/2022] Open
Abstract
Enzymes catalyze various biochemical functions with high efficiency and specificity. In vitro design of the enzyme leads to novel bioactivity in this natural biomolecule that give answers of some vital questions like crucial residues in binding with substrate, molecular evolution, cofactor specificity etc. Enzyme engineering technology involves directed evolution, rational designing, semi-rational designing, and structure-based designing using chemical modifications. Similarly, combined computational and in vitro evolution approaches together help in artificial designing of novel bioactivity in the natural enzyme. DNA shuffling, error prone PCR and staggered extension process are used to artificially redesign active site of enzyme, which can alter its efficiency and specificity. Modifications of the enzyme can lead to the discovery of new path of molecular evolution, designing of efficient enzymes, locating active sites and crucial residues, shift in substrate, and cofactor specificity. The methods and thermodynamics of in vitro designing of the enzyme are also discussed. Similarly, engineered thermophilic and psychrophilic enzymes attain substrate specificity and activity of mesophilic enzymes that may also be beneficial for industry and therapeutics.
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Affiliation(s)
- Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan Ajmer, India
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35
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Bzdrenga J, Daudé D, Rémy B, Jacquet P, Plener L, Elias M, Chabrière E. Biotechnological applications of quorum quenching enzymes. Chem Biol Interact 2016; 267:104-115. [PMID: 27223408 DOI: 10.1016/j.cbi.2016.05.028] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/04/2016] [Accepted: 05/20/2016] [Indexed: 11/12/2022]
Abstract
Numerous bacteria use quorum sensing (QS) to synchronize their behavior and monitor their population density. They use signaling molecules known as autoinducers (AI's) that are synthesized and secreted into their local environment to regulate QS-dependent gene expression. Among QS-regulated pathways, biofilm formation and virulence factor secretion are particularly problematic as they are involved in surface-attachment, antimicrobial agent resistance, toxicity, and pathogenicity. Targeting QS represents a promising strategy to inhibit undesirable bacterial traits. This strategy, referred to as quorum quenching (QQ), includes QS-inhibitors and QQ enzymes. These approaches are appealing because they do not directly challenge bacterial survival, and consequently selection pressure may be low, yielding a lower occurrence of resistance. QQ enzymes are particularly promising because they act extracellularly to degrade AI's and can be used in catalytic quantities. This review draws an overview of QQ enzyme related applications, covering several economically important fields such as agriculture, aquaculture, biofouling and health issues. Finally, the possibility of resistance mechanism occurrence to QQ strategies is discussed.
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Affiliation(s)
- Janek Bzdrenga
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - David Daudé
- Gene&GreenTK, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Benjamin Rémy
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Gene&GreenTK, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Pauline Jacquet
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Laure Plener
- Gene&GreenTK, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Mikael Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN 55108, USA
| | - Eric Chabrière
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.
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Guan S, Zhao L, Jin H, Shan N, Han W, Wang S, Shan Y. Binding modes of phosphotriesterase-like lactonase complexed with δ-nonanoic lactone and paraoxon using molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:273-286. [DOI: 10.1080/07391102.2016.1142899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Shanshan Guan
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Li Zhao
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Hanyong Jin
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Ning Shan
- Editorial Department of Journal of Jilin University (Science Edition), Changchun, China
| | - Weiwei Han
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Song Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Yaming Shan
- National Engineering Laboratory For AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
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Tay SB, Chow JY, Go MK, Yew WS. Anti-virulent Disruption of Pathogenic Biofilms using Engineered Quorum-quenching Lactonases. J Vis Exp 2016. [PMID: 26779961 DOI: 10.3791/53243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The rapid emergence of multi-drug resistant bacteria has accelerated the need for novel therapeutic approaches to counter life-threatening infections. The persistence of bacterial infection is often associated with quorum-sensing-mediated biofilm formation. Thus, the disruption of this signaling circuit presents an attractive anti-virulence strategy. Quorum-quenching lactonases have been reported to be effective disrupters of quorum-sensing circuits. However, there have been very few reports of the effective use of these enzymes in disrupting bacterial biofilm formation. This protocol describes a method to disrupt biofilm formation in a clinically relevant A. baumannii S1 strain through the use of an engineered quorum-quenching lactonase. Acinetobacter baumannii is a major human pathogen implicated in serious hospital-acquired infections globally and its virulence is attributed predominantly to its biofilm's tenacity. The engineered lactonase treatment achieved significant A. baumannii S1 biofilm reduction. This study also showed the possibility of using engineered quorum-quenching enzymes in future treatment of biofilm-mediated bacterial diseases. Lastly, the method may be used to evaluate the competency of promising quorum-quenching enzymes.
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Affiliation(s)
- Song Buck Tay
- Department of Biochemistry, Yong Loo Lin School of Medicine; Synthetic Biology Research Consortium, National University of Singapore
| | | | - Maybelle Kho Go
- Department of Biochemistry, Yong Loo Lin School of Medicine; Synthetic Biology Research Consortium, National University of Singapore
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine; Synthetic Biology Research Consortium, National University of Singapore;
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38
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Subhadra B, Hwan Oh M, Hee Choi C. Quorum sensing in Acinetobacter: with special emphasis on antibiotic resistance, biofilm formation and quorum quenching. AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.1.27] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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39
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Han SS, Park WJ, Kim HS, Kim GJ. Antisense RNA-based High-Throughput Screen System for Directed Evolution of Quorum Quenching Enzymes. ACS Chem Biol 2015; 10:2598-605. [PMID: 26366664 DOI: 10.1021/acschembio.5b00714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Quorum quenching (QQ) enzymes, which disrupt the quorum sensing signaling process, have attracted considerable attention as new antimicrobial agents. However, their low catalytic efficiency for quorum sensing molecules remains a challenge. Herein, we present an antisense RNA-based high-throughput screen system for directed evolution of a quorum quenching enzyme. The screening system was constructed by incorporating an antisense RNA (RyhB) into a synthetic module to quantitatively regulate the expression of a reporter gene fused with a sense RNA (sodB). To control the expression of a reporter gene in response to the catalytic activity of a quorum quenching enzyme, the region of interaction and mode between a pair of antisense (RyhB) and sense (sodB) RNAs was designed and optimized through the prediction of the secondary structure of the RNA pair. The screening system constructed was shown to lead to a significant reduction in the false-positive rate (average 42%) in the screening of N-acyl-homoserine lactonase (AiiA) with increased catalytic activity, resulting in a true-positive frequency of up to 76%. The utility and efficiency of the screening system were demonstrated by selecting an AiiA with 31-fold higher catalytic efficiency than the wild-type in three rounds of directed evolution. The present approach can be widely used for the screening of quorum quenching enzymes with the desired catalytic property, as well as for a synthetic network for a stringent regulation of the gene expression.
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Affiliation(s)
- Sang-Soo Han
- Department
of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Gusung-dong, Yusung-gu, Daejon, 305-701, Korea
| | - Won-Ji Park
- Department
of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju 500-757, Korea
- Department
of Molecular Medicine (BK21plus), Chonnam National University Graduate School, Chonnam National University, Gwangju 500-757, Korea
| | - Hak-Sung Kim
- Department
of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Gusung-dong, Yusung-gu, Daejon, 305-701, Korea
| | - Geun-Joong Kim
- Department
of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju 500-757, Korea
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40
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Maisuria VB, Nerurkar AS. Interference of Quorum Sensing by Delftia sp. VM4 Depends on the Activity of a Novel N-Acylhomoserine Lactone-Acylase. PLoS One 2015; 10:e0138034. [PMID: 26384328 PMCID: PMC4575145 DOI: 10.1371/journal.pone.0138034] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/24/2015] [Indexed: 01/01/2023] Open
Abstract
Background Turf soil bacterial isolate Delftia sp. VM4 can degrade exogenous N-acyl homoserine lactone (AHL), hence it effectively attenuates the virulence of bacterial soft rot pathogen Pectobacterium carotovorum subsp. carotovorum strain BR1 (Pcc BR1) as a consequence of quorum sensing inhibition. Methodology/Principal Findings Isolated Delftia sp. VM4 can grow in minimal medium supplemented with AHL as a sole source of carbon and energy. It also possesses the ability to degrade various AHL molecules in a short time interval. Delftia sp. VM4 suppresses AHL accumulation and the production of virulence determinant enzymes by Pcc BR1 without interference of the growth during co-culture cultivation. The quorum quenching activity was lost after the treatment with trypsin and proteinase K. The protein with quorum quenching activity was purified by three step process. Matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) and Mass spectrometry (MS/MS) analysis revealed that the AHL degrading enzyme (82 kDa) demonstrates homology with the NCBI database hypothetical protein (Daci_4366) of D. acidovorans SPH-1. The purified AHL acylase of Delftia sp. VM4 demonstrated optimum activity at 20–40°C and pH 6.2 as well as AHL acylase type mode of action. It possesses similarity with an α/β-hydrolase fold protein, which makes it unique among the known AHL acylases with domains of the N-terminal nucleophile (Ntn)-hydrolase superfamily. In addition, the kinetic and thermodynamic parameters for hydrolysis of the different AHL substrates by purified AHL-acylase were estimated. Here we present the studies that investigate the mode of action and kinetics of AHL-degradation by purified AHL acylase from Delftia sp. VM4. Significance We characterized an AHL-inactivating enzyme from Delftia sp. VM4, identified as AHL acylase showing distinctive similarity with α/β-hydrolase fold protein, described its biochemical and thermodynamic properties for the first time and revealed its potential application as an anti-virulence agent against bacterial soft rot pathogen Pectobacterium carotovorum subsp. carotovorum based on quorum quenching mechanism.
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Affiliation(s)
- Vimal B. Maisuria
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
- School of Life Sciences, Faculty of Health and Human Science, University of Hertfordshire, College Lane, Hatfield, Hertfordshire, United Kingdom
| | - Anuradha S. Nerurkar
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
- * E-mail:
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Mascarenhas R, Thomas PW, Wu CX, Nocek BP, Hoang QQ, Liu D, Fast W. Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase with Atypical Selectivity. Biochemistry 2015; 54:4342-53. [PMID: 26115006 DOI: 10.1021/acs.biochem.5b00499] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-l-homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 10(6) M(-1) s(-1) for N-heptanoyl-l-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typical AHL lactonases (ca. >1 mM). X-ray crystal structures of AidC alone and with the product N-hexanoyl-l-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multiangle light scattering. The structures reveal two atypical features as compared to previously characterized AHL lactonases: a "kinked" α-helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. Implications for the catalytic mechanism of AHL lactonases are discussed.
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Affiliation(s)
- Romila Mascarenhas
- §Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | | | - Chun-Xiang Wu
- ∥Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Boguslaw P Nocek
- ⊥Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Quyen Q Hoang
- ∥Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Dali Liu
- §Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
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Mayer C, Romero M, Muras A, Otero A. Aii20J, a wide-spectrum thermostable N-acylhomoserine lactonase from the marine bacterium Tenacibaculum sp. 20J, can quench AHL-mediated acid resistance in Escherichia coli. Appl Microbiol Biotechnol 2015; 99:9523-39. [PMID: 26092757 DOI: 10.1007/s00253-015-6741-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/24/2015] [Accepted: 05/29/2015] [Indexed: 11/25/2022]
Abstract
Acyl homoserine lactones (AHLs) are produced by many Gram-negative bacteria to coordinate gene expression in cellular density dependent mechanisms known as quorum sensing (QS). Since the disruption of the communication systems significantly reduces virulence, the inhibition of quorumsensing processes or quorum quenching (QQ) represents an interesting anti-pathogenic strategy to control bacterial infections. Escherichia coli does not produce AHLs but possesses an orphan AHL receptor, SdiA, which is thought to be able to sense the QS signals produced by other bacteria and controls important traits as the expression of glutamate-dependent acid resistance mechanism, therefore constituting a putative target for QQ. A novel AHL-lactonase, named Aii20J, has been identified, cloned and over expressed from the marine bacterium Tenacibaculum sp. strain 20 J presenting a wide-spectrum QQ activity. The enzyme, belonging to the metallo-β-lactamase family, shares less than 31 % identity with the lactonase AiiA from Bacillus spp. Aii20J presents a much higher specific activity than the Bacillus enzyme, maintains its activity after incubation at 100 ºC for 10 minutes, is resistant to protease K and α-chymotrypsin, and is unaffected by wide ranges of pH. The addition of Aii20J (20 μg/mL) to cultures of E. coli K-12 to which OC6-HSL was added resulted in a significant reduction in cell viability in comparison with the acidresistant cultures derived from the presence of the signal. Results confirm the interaction between AHLs and SdiA in E. coli for the expression of virulence-related genes and reveal the potential use of Aii20J as anti-virulence strategy against important bacterial pathogens and in other biotechnological applications.
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Affiliation(s)
- C Mayer
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - M Romero
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - A Muras
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - A Otero
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain.
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43
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Zhang Y, An J, Yang GY, Bai A, Zheng B, Lou Z, Wu G, Ye W, Chen HF, Feng Y, Manco G. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426. PLoS One 2015; 10:e0115130. [PMID: 25706379 PMCID: PMC4338136 DOI: 10.1371/journal.pone.0115130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/19/2014] [Indexed: 02/02/2023] Open
Abstract
Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, People’s Republic of China
- Environmental Science Research and Design Institute of Zhejiang Province, Hangzhou, People’s Republic of China
| | - Jiao An
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, People’s Republic of China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Aixi Bai
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, People’s Republic of China
| | - Baisong Zheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, People’s Republic of China
| | - Zhiyong Lou
- Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Geng Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Wei Ye
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, People’s Republic of China
- * E-mail: (YF); (GM)
| | - Giuseppe Manco
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
- * E-mail: (YF); (GM)
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Crystal structure of VmoLac, a tentative quorum quenching lactonase from the extremophilic crenarchaeon Vulcanisaeta moutnovskia. Sci Rep 2015; 5:8372. [PMID: 25670483 PMCID: PMC4323659 DOI: 10.1038/srep08372] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/12/2015] [Indexed: 11/13/2022] Open
Abstract
A new representative of the Phosphotriesterase-Like Lactonases (PLLs) family from the hyperthermophilic crenarchaeon Vulcanisaeta moutnovskia has been characterized and crystallized. VmoLac is a native, proficient lactonase with promiscuous, low phosphotriesterase activity. VmoLac therefore represents an interesting candidate for engineering studies, with the aim of developing an efficient bacterial quorum-quenching agent. Here, we provide an extensive biochemical and kinetic characterization of VmoLac and describe the X-ray structures of the enzyme bound to a fatty acid and to its cognate substrate 3-oxo-C10 AHL (Acyl-Homoserine Lactone). The structures highlight possible structural determinants that may be involved in its extreme thermal stability (Tm = 128°C). Moreover, the structure reveals that the substrate binding mode of VmoLac significantly differs from those of its close homologues, possibly explaining the substrate specificity of the enzyme. Finally, we describe the specific interactions between the enzyme and its substrate, and discuss the possible lactone hydrolysis mechanism of VmoLac.
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45
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Fetzner S. Quorum quenching enzymes. J Biotechnol 2014; 201:2-14. [PMID: 25220028 DOI: 10.1016/j.jbiotec.2014.09.001] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/29/2014] [Accepted: 09/04/2014] [Indexed: 01/12/2023]
Abstract
Bacteria use cell-to-cell communication systems based on chemical signal molecules to coordinate their behavior within the population. These quorum sensing systems are potential targets for antivirulence therapies, because many bacterial pathogens control the expression of virulence factors via quorum sensing networks. Since biofilm maturation is also usually influenced by quorum sensing, quenching these systems may contribute to combat biofouling. One possibility to interfere with quorum sensing is signal inactivation by enzymatic degradation or modification. Such quorum quenching enzymes are wide-spread in the bacterial world and have also been found in eukaryotes. Lactonases and acylases that hydrolyze N-acyl homoserine lactone (AHL) signaling molecules have been investigated most intensively, however, different oxidoreductases active toward AHLs or 2-alkyl-4(1H)-quinolone signals as well as other signal-converting enzymes have been described. Several approaches have been assessed which aim at alleviating virulence, or biofilm formation, by reducing the signal concentration in the bacterial environment. These involve the application or stimulation of signal-degrading bacteria as biocontrol agents in the protection of crop plants against soft-rot disease, the use of signal-degrading bacteria as probiotics in aquaculture, and the immobilization or entrapment of quorum quenching enzymes or bacteria to control biofouling in membrane bioreactors. While most approaches to use quorum quenching as antivirulence strategy are still in the research phase, the growing number of organisms and enzymes known to interfere with quorum sensing opens up new perspectives for the development of innovative antibacterial strategies.
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Affiliation(s)
- Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Muenster, Corrensstrasse 3, D-48149 Muenster, Germany.
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46
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N-acyl homoserine lactone-mediated quorum sensing with special reference to use of quorum quenching bacteria in membrane biofouling control. BIOMED RESEARCH INTERNATIONAL 2014; 2014:162584. [PMID: 25147787 PMCID: PMC4131561 DOI: 10.1155/2014/162584] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/04/2014] [Accepted: 07/06/2014] [Indexed: 11/17/2022]
Abstract
Membrane biofouling remains a severe problem to be addressed in wastewater treatment systems affecting reactor performance and economy. The finding that many wastewater bacteria rely on N-acyl homoserine lactone-mediated quorum sensing to synchronize their activities essential for biofilm formations; the quenching bacterial quorum sensing suggests a promising approach for control of membrane biofouling. A variety of quorum quenching compounds of both synthetic and natural origin have been identified and found effective in inhibition of membrane biofouling with much less environmental impact than traditional antimicrobials. Work over the past few years has demonstrated that enzymatic quorum quenching mechanisms are widely conserved in several prokaryotic organisms and can be utilized as a potent tool for inhibition of membrane biofouling. Such naturally occurring bacterial quorum quenching mechanisms also play important roles in microbe-microbe interactions and have been used to develop sustainable nonantibiotic antifouling strategies. Advances in membrane fabrication and bacteria entrapment techniques have allowed the implication of such quorum quenching bacteria for better design of membrane bioreactor with improved antibiofouling efficacies. In view of this, the present paper is designed to review and discuss the recent developments in control of membrane biofouling with special emphasis on quorum quenching bacteria that are applied in membrane bioreactors.
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47
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Bzdrenga J, Hiblot J, Gotthard G, Champion C, Elias M, Chabriere E. SacPox from the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius is a proficient lactonase. BMC Res Notes 2014; 7:333. [PMID: 24894602 PMCID: PMC4068969 DOI: 10.1186/1756-0500-7-333] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/27/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND SacPox, an enzyme from the extremophilic crenarchaeal Sulfolobus acidocaldarius (Sac), was isolated by virtue of its phosphotriesterase (or paraoxonase; Pox) activity, i.e. its ability to hydrolyze the neurotoxic organophosphorus insecticides. Later on, SacPox was shown to belong to the Phosphotriesterase-Like Lactonase family that comprises natural lactonases, possibly involved in quorum sensing, and endowed with promiscuous, phosphotriesterase activity. RESULTS Here, we present a comprehensive and broad enzymatic characterization of the natural lactonase and promiscuous organophosphorus hydrolase activities of SacPox, as well as a structural analysis using a model. CONCLUSION Kinetic experiments show that SacPox is a proficient lactonase, including at room temperature. Moreover, we discuss the observed differences in substrate specificity between SacPox and its closest homologues SsoPox and SisLac together with the possible structural causes for these observations.
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Affiliation(s)
- Janek Bzdrenga
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Julien Hiblot
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Guillaume Gotthard
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Charlotte Champion
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Mikael Elias
- Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel
| | - Eric Chabriere
- URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
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48
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Lade H, Paul D, Kweon JH. Quorum quenching mediated approaches for control of membrane biofouling. Int J Biol Sci 2014; 10:550-65. [PMID: 24910534 PMCID: PMC4046882 DOI: 10.7150/ijbs.9028] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 04/29/2014] [Indexed: 12/24/2022] Open
Abstract
Membrane biofouling is widely acknowledged as the most frequent adverse event in wastewater treatment systems resulting in significant loss of treatment efficiency and economy. Different strategies including physical cleaning and use of antimicrobial chemicals or antibiotics have been tried for reducing membrane biofouling. Such traditional practices are aimed to eradicate biofilms or kill the bacteria involved, but the greater efficacy in membrane performance would be achieved by inhibiting biofouling without interfering with bacterial growth. As a result, the search for environmental friendly non-antibiotic antifouling strategies has received much greater attention among scientific community. The use of quorum quenching natural compounds and enzymes will be a potential approach for control of membrane biofouling. This approach has previously proven useful in diseases and membrane biofouling control by triggering the expression of desired phenotypes. In view of this, the present review is provided to give the updated information on quorum quenching compounds and elucidate the significance of quorum sensing inhibition in control of membrane biofouling.
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Affiliation(s)
| | - Diby Paul
- Department of Environmental Engineering, Konkuk University, Seoul-143-701, Korea
| | - Ji Hyang Kweon
- Department of Environmental Engineering, Konkuk University, Seoul-143-701, Korea
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Hiblot J, Gotthard G, Champion C, Chabriere E, Elias M. Crystallization and preliminary X-ray diffraction analysis of the lactonase VmoLac from Vulcanisaeta moutnovskia. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1235-8. [PMID: 24192357 DOI: 10.1107/s1744309113024846] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/05/2013] [Indexed: 02/03/2023]
Abstract
Phosphotriesterase-like lactonases (PLLs) are native lactonases that are capable of hydrolyzing lactones such as aliphatic lactones or acyl-homoserine lactones, which are involved in bacterial quorum sensing. Previously characterized PLLs are moreover endowed with a promiscuous phosphotriesterase activity and are therefore able to detoxify organophosphate insecticides. A novel PLL representative, dubbed VmoLac, has been identified from the hyperthermophilic crenarchaeon Vulcanisaeta moutnovskia. Because of its intrinsic high thermal stability, VmoLac may constitute an appealing candidate for engineering studies with the aim of producing an efficient biodecontaminant for organophosphorus compounds and a bacterial antivirulence agent. In combination with biochemical studies, structural information will allow the identification of the residues involved in substrate specificity and an understanding of the enzymatic catalytic mechanisms. Here, the expression, purification, crystallization and X-ray data collection at 2.4 Å resolution of VmoLac are reported.
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Affiliation(s)
- Julien Hiblot
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents (URMITE), UMR CNRS-IRD-INSERM, IHU Méditerranée Infection, Aix-Marseille Université, 7 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
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Hiblot J, Gotthard G, Elias M, Chabriere E. Differential active site loop conformations mediate promiscuous activities in the lactonase SsoPox. PLoS One 2013; 8:e75272. [PMID: 24086491 PMCID: PMC3781021 DOI: 10.1371/journal.pone.0075272] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 08/14/2013] [Indexed: 11/19/2022] Open
Abstract
Enzymes are proficient catalysts that enable fast rates of Michaelis-complex formation, the chemical step and products release. These different steps may require different conformational states of the active site that have distinct binding properties. Moreover, the conformational flexibility of the active site mediates alternative, promiscuous functions. Here we focused on the lactonase SsoPox from Sulfolobus solfataricus. SsoPox is a native lactonase endowed with promiscuous phosphotriesterase activity. We identified a position in the active site loop (W263) that governs its flexibility, and thereby affects the substrate specificity of the enzyme. We isolated two different sets of substitutions at position 263 that induce two distinct conformational sampling of the active loop and characterized the structural and kinetic effects of these substitutions. These sets of mutations selectively and distinctly mediate the improvement of the promiscuous phosphotriesterase and oxo-lactonase activities of SsoPox by increasing active-site loop flexibility. These observations corroborate the idea that conformational diversity governs enzymatic promiscuity and is a key feature of protein evolvability.
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Affiliation(s)
- Julien Hiblot
- URMITE UMR CNRS-IRD 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Guillaume Gotthard
- URMITE UMR CNRS-IRD 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Mikael Elias
- Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel
| | - Eric Chabriere
- URMITE UMR CNRS-IRD 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
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