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Erol I, Kotil SE, Ortakci F, Durdagi S. Exploring the binding capacity of lactic acid bacteria derived bacteriocins against RBD of SARS-CoV-2 Omicron variant by molecular simulations. J Biomol Struct Dyn 2023; 41:10774-10784. [PMID: 36591650 DOI: 10.1080/07391102.2022.2158934] [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: 07/22/2022] [Accepted: 12/10/2022] [Indexed: 01/03/2023]
Abstract
The changes in the SARS-CoV-2 genome have resulted in the emergence of new variants. Some of the variants have been classified as variants of concern (VOC). These strains have higher transmission rate and improved fitness. One of the prevalent were the Omicron variant. Unlike previous VOCs, the Omicron possesses fifteen mutations on the spike protein's receptor binding domain (RBD). The modifications of spike protein's key amino acid residues facilitate the virus' binding capability against ACE2, resulting in an increase in the infectiousness of Omicron variant. Consequently, investigating the prevention and treatment of the Omicron variant is crucial. In the present study, we aim to explore the binding capacity of twenty-two bacteriocins derived from Lactic Acid Bacteria (LAB) against the Omicron variant by using protein-peptidedocking and molecular dynamics (MD) simulations. The Omicron variant RBD was prepared by introducing fifteen mutations using PyMol. The protein-peptide complexes were obtained using HADDOCK v2.4 docking webserver. Top scoring complexes obtained from HADDOCK webserver were retrieved and submitted to the PRODIGY server for the prediction of binding energies. RBD-bacteriocin complexes were subjected to MD simulations. We discovered promising peptide-based therapeutic candidates for the inhibition of Omicron variant for example Salivaricin B, Pediocin PA 1, Plantaricin W, Lactococcin mmfii and Enterocin A. The lead bacteriocins, except Enterocin A, are biosynthesized by food-grade lactic acid bacteria. Our study puts forth a preliminary information regarding potential utilization of food-grade LAB-derived bacteriocins, particularly Salivaricin B and Pediocin PA 1, for Covid-19 treatment and prophylaxis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Seyfullah Enes Kotil
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Fatih Ortakci
- Bioengineering Department, Faculty of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
- School of Pharmacy, Bahcesehir University, Istanbul, Turkey
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2
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Oftedal TF, Diep DB. Flow cytometric detection of vancomycin-resistant Enterococcus faecium in urine using fluorescently labelled enterocin K1. Sci Rep 2023; 13:10930. [PMID: 37414859 PMCID: PMC10325980 DOI: 10.1038/s41598-023-38114-9] [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: 12/22/2022] [Accepted: 07/03/2023] [Indexed: 07/08/2023] Open
Abstract
A urinary tract infection (UTI) occurs when bacteria enter and multiply in the urinary system. The infection is most often caused by enteric bacteria that normally live in the gut, which include Enterococcus faecium. Without antibiotic treatment, UTIs can progress to life-threatening septic shock. Early diagnosis and identification of the pathogen will reduce antibiotic use and improve patient outcomes. In this work, we develop and optimize a cost-effective and rapid (< 40 min) method for detecting E. faecium in urine. The method uses a fluorescently labelled bacteriocin enterocin K1 (FITC-EntK1) that binds specifically to E. faecium and is then detected using a conventional flow cytometer. Using this detection assay, urine containing E. faecium was identified by an increase in the fluorescent signals by 25-73-fold (median fluorescence intensity) compared to control samples containing Escherichia coli or Staphylococcus aureus. The method presented in this work is a proof of concept showing the potential of bacteriocins to act as specific probes for the detection of specific bacteria, such as pathogens, in biological samples.
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Affiliation(s)
- Thomas F Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Dzung B Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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3
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Li R, Duan J, Zhou Y, Wang J. Structural Basis of the Mechanisms of Action and Immunity of Lactococcin A, a Class IId Bacteriocin. Appl Environ Microbiol 2023; 89:e0006623. [PMID: 36840592 PMCID: PMC10056949 DOI: 10.1128/aem.00066-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 01/27/2023] [Indexed: 02/24/2023] Open
Abstract
Lactococcin A (LcnA), a class IId bacteriocin, induces membrane leakage and cell death by specifically binding to the membrane receptor-mannose phosphotransferase system (man-PTS), as is the case for pediocin-like (class IIa) bacteriocins. The cognate immunity protein of bacteriocins, which protects the producer cell from its own bacteriocin, recognizes and binds to the bacteriocin-man-PTS complex, consequently blocking membrane leakage. We previously deciphered the mode of action and immunity of class IIa bacteriocins. Here, we determined the structure of the ternary complex of LcnA, LciA (i.e., the immunity protein), and its receptor, i.e., the man-PTS of Lactococcus lactis (ll-man-PTS). An external loop on the membrane-located component IIC of ll-man-PTS was found to prevent specific binding of the N-terminal region of LcnA to the site recognized by pediocin-like bacteriocins. Thus, the N-terminal β-sheet region of LcnA recognized an adjacent site on the extracellular side of ll-man-PTS, with the LcnA C-terminal hydrophobic helix penetrating into the membrane. The cytoplasmic cleft formed within the man-PTS Core and Vmotif domains induced by embedded LcnA from the periplasmic side is adopted by the appropriate angle between helices H3 and H4 of the N terminus of LciA. The flexible C terminus of LciA then blocks membrane leakage. To summarize, our findings reveal the molecular mechanisms of action and immunity of LcnA and LciA, laying a foundation for further design of class IId bacteriocins. IMPORTANCE Class IId (lactococcin-like) bacteriocins and class IIa (pediocin-like) bacteriocins share a few similarities: (i) both induce membrane leakage and cell death by specifically binding the mannose phosphotransferase system (man-PTS) on their target cells, and (ii) cognate immunity proteins recognize and bind to the bacteriocin-man-PTS complex to block membrane leakage. However, class IId bacteriocins lack the "pediocin box" motif, which is typical of class IIa bacteriocins, and basically target only lactococcal cells; in contrast, class IIa bacteriocins target diverse bacterial cells, but not lactococcal cells. We previously solved the structure of class IIa bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei. Here, we determined the structure of the ternary complex of class IId bacteriocin LcnA, its cognate immunity protein LciA, and its receptor, the man-PTS of Lactococcus lactis. By comparing the interactions between man-PTS and class IIa and class IId bacteriocins, this study affords some clues to better understand the specificity of bacteriocins targeting the mannose phosphotransferase system.
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Affiliation(s)
- Ruilian Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Jinsong Duan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Yicheng Zhou
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
- Independent Researcher, Urbana, Illinois, USA
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
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4
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In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2. Probiotics Antimicrob Proteins 2023; 15:17-29. [PMID: 34837166 PMCID: PMC8626284 DOI: 10.1007/s12602-021-09879-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2021] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic caused by a novel coronavirus (SARS-CoV-2) is a serious health concern in the twenty-first century for scientists, health workers, and all humans. The absence of specific biotherapeutics requires new strategies to prevent the spread and prophylaxis of the novel virus and its variants. The SARS-CoV-2 virus shows pathogenesis by entering the host cells via spike protein and Angiotensin-Converting Enzyme 2 receptor protein. Thus, the present study aims to compute the binding energies between a wide range of bacteriocins with receptor-binding domain (RBD) on spike proteins of wild type (WT) and beta variant (lineage B.1.351). Molecular docking analyses were performed to evaluate binding energies. Upon achieving the best bio-peptides with the highest docking scores, further molecular dynamics (MD) simulations were performed to validate the structure and interaction stability. Protein-protein docking of the chosen 22 biopeptides with WT-RBD showed docking scores lower than -7.9 kcal/mol. Pediocin PA-1 and salivaricin P showed the lowest (best) docking scores of - 12 kcal/mol. Pediocin PA-1, salivaricin B, and salivaricin P showed a remarkable increase in the double mutant's predicted binding affinity with -13.8 kcal/mol, -13.0 kcal/mol, and -12.5 kcal/mol, respectively. Also, a better predicted binding affinity of pediocin PA-1 and salivaricin B against triple mutant was observed compared to the WT. Thus, pediocin PA-1 binds stronger to mutants of the RBD, particularly to double and triple mutants. Salivaricin B showed a better predicted binding affinity towards triple mutant compared to WT, showing that it might be another bacteriocin with potential activity against the SARS-CoV-2 beta variant. Overall, pediocin PA-1, salivaricin P, and salivaricin B are the most promising candidates for inhibiting SARS-CoV-2 (including lineage B.1.351) entrance into the human cells. These bacteriocins derived from lactic acid bacteria hold promising potential for paving an alternative way for treatment and prophylaxis of WT and beta variants.
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Pereira WA, Mendonça CMN, Urquiza AV, Marteinsson VÞ, LeBlanc JG, Cotter PD, Villalobos EF, Romero J, Oliveira RPS. Use of Probiotic Bacteria and Bacteriocins as an Alternative to Antibiotics in Aquaculture. Microorganisms 2022; 10:microorganisms10091705. [PMID: 36144306 PMCID: PMC9503917 DOI: 10.3390/microorganisms10091705] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/18/2022] Open
Abstract
In addition to their use in human medicine, antimicrobials are also used in food animals and aquaculture, and their use can be categorized as therapeutic against bacterial infections. The use of antimicrobials in aquaculture may involve a broad environmental application that affects a wide variety of bacteria, promoting the spread of bacterial resistance genes. Probiotics and bacteriocins, antimicrobial peptides produced by some types of lactic acid bacteria (LAB), have been successfully tested in aquatic animals as alternatives to control bacterial infections. Supplementation might have beneficial impacts on the intestinal microbiota, immune response, development, and/or weight gain, without the issues associated with antibiotic use. Thus, probiotics and bacteriocins represent feasible alternatives to antibiotics. Here, we provide an update with respect to the relevance of aquaculture in the animal protein production sector, as well as the present and future challenges generated by outbreaks and antimicrobial resistance, while highlighting the potential role of probiotics and bacteriocins to address these challenges. In addition, we conducted data analysis using a simple linear regression model to determine whether a linear relationship exists between probiotic dose added to feed and three variables of interest selected, including specific growth rate, feed conversion ratio, and lysozyme activity.
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Affiliation(s)
- Wellison Amorim Pereira
- Microbial Biomolecules Laboratory, Faculty of Pharmaceutical Sciences, São Paulo University, Rua do Lago 250, Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | - Carlos Miguel N. Mendonça
- Microbial Biomolecules Laboratory, Faculty of Pharmaceutical Sciences, São Paulo University, Rua do Lago 250, Cidade Universitária, São Paulo 05508-000, SP, Brazil
| | | | | | - Jean Guy LeBlanc
- Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucuman T4000, Argentina
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland, T12 K8AF Cork, Ireland
| | - Elías Figueroa Villalobos
- Nucleus of Research in Food Production, Faculty of Natural Resources, Catholic University of Temuco, Temuco 4780000, Chile
- Correspondence:
| | - Jaime Romero
- Laboratorio de Biotecnología de Alimentos, Instituto de Nutricion y Tecnologia de los Alimentos (INTA), Universidad de Chile, El Libano 5524, Santiago 783090, Chile
| | - Ricardo P. S. Oliveira
- Microbial Biomolecules Laboratory, Faculty of Pharmaceutical Sciences, São Paulo University, Rua do Lago 250, Cidade Universitária, São Paulo 05508-000, SP, Brazil
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6
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Liu G, Nie R, Liu Y, Mehmood A. Combined antimicrobial effect of bacteriocins with other hurdles of physicochemic and microbiome to prolong shelf life of food: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:154058. [PMID: 35217045 DOI: 10.1016/j.scitotenv.2022.154058] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/24/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Bacteriocins are ribosomally synthesized peptides to inhibit food spoilage bacteria, which are widely used as a kind of food biopreservation. The role of bacteriocins in therapeutics and food industries has received increasing attention across a number of disciplines in recent years. Despite their advantages as alternative therapeutics over existing strategies, the application of bacteriocins suffers from shortcomings such as the high isolation and purification cost, narrow spectrum of activity, low stability and solubility and easy enzymatic degradation. Previous studies have studied the synergistic or additive effects of bacteriocins when used in combination with other hurdles including physics, chemicals, and microbes. These combined treatments reduce the adverse effects of chemical additives, extending the shelf life of food products while guaranteeing food quality. This review highlights the advantages and disadvantages of bacteriocins in food preservation. It then reviews the combined effect and mechanism of different hurdles and bacteriocins in enhancing food preservation in detail. The combination of bacterioncins and other hurdles provide potential approaches for maintaining food quality and food safety.
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Affiliation(s)
- Guorong Liu
- Beijing Advance Innovation Center for Food Nutrition and Human Health, Beijing Laboratory of Food Quality and Safety, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing 100048, China.
| | - Rong Nie
- Beijing Advance Innovation Center for Food Nutrition and Human Health, Beijing Laboratory of Food Quality and Safety, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Yangshuo Liu
- Beijing Advance Innovation Center for Food Nutrition and Human Health, Beijing Laboratory of Food Quality and Safety, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Arshad Mehmood
- Beijing Advance Innovation Center for Food Nutrition and Human Health, Beijing Laboratory of Food Quality and Safety, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University (BTBU), Beijing 100048, China
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7
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Pereira WA, Piazentin ACM, de Oliveira RC, Mendonça CMN, Tabata YA, Mendes MA, Fock RA, Makiyama EN, Corrêa B, Vallejo M, Villalobos EF, de S Oliveira RP. Bacteriocinogenic probiotic bacteria isolated from an aquatic environment inhibit the growth of food and fish pathogens. Sci Rep 2022; 12:5530. [PMID: 35365686 PMCID: PMC8975912 DOI: 10.1038/s41598-022-09263-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/08/2022] [Indexed: 12/19/2022] Open
Abstract
The conditions of aquatic environments have a great influence on the microbiota of several animals, many of which are a potential source of microorganisms of biotechnological interest. In this study, bacterial strains isolated from aquatic environments were bioprospected to determine their probiotic profile and antimicrobial effect against fish and food pathogens. Two isolates, identified via 16S rRNA sequencing as Lactococcus lactis (L1 and L2) and one as Enterococcus faecium 135 (EF), produced a bacteriocin-like antimicrobial substance (BLIS), active against Listeria monocytogenes, Salmonella Choleraesuis and Salmonella Typhimurium. Antimicrobial activity of BLIS was reduced when exposed to high temperatures and proteolytic enzymes (trypsin, pepsin, papain and pancreatin). All strains were sensitive to 7 types of antibiotics (vancomycin, clindamycin, streptomycin, gentamicin, chloramphenicol, rifampicin and ampicillin), exhibited a high rate of adherence to Caco-2 cells and expressed no hemolysin and gelatinase virulence factors. EF showed some resistance at pH 2.5 and 3.0, and L2/EF showed higher resistance to the action of bile salts. Finally, the presence of bacteriocin genes encoding for proteins, including Nisin (L1 and L2), Enterocin A, B, P, and Mundticin KS (EF) was detected. The molecular and physiological evidence suggests that the bacterial isolates in this study could be used as natural antimicrobial agents and may be considered safe for probiotic application.
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Affiliation(s)
- Wellison Amorim Pereira
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo, 05508-000, Brazil
| | - Anna Carolina M Piazentin
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo, 05508-000, Brazil
| | - Rodrigo Cardoso de Oliveira
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo, 05508-000, Brazil
| | - Carlos Miguel N Mendonça
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo, 05508-000, Brazil
| | - Yara Aiko Tabata
- Fishing Institute of São Paulo/Salmoniculture Experimental Station, Av. Campos Do Jordão, Residencial Horto Florestal, Campos do Jordão, São Paulo, 12460-000, Brazil
| | - Maria Anita Mendes
- Chemical Engineering Department, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo, 05508-000, Brazil
| | - Ricardo Ambrósio Fock
- Laboratory of Experimental Hematology, University of São Paulo, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, 05508- 000, Brazil
| | - Edson Naoto Makiyama
- Laboratory of Experimental Hematology, University of São Paulo, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, 05508- 000, Brazil
| | - Benedito Corrêa
- Laboratory of Toxigenic Fungi and Mycotoxins, Av. Prof. Lineu Prestes, 1.374, Edifício Biomédicas II, 05508-900, São Paulo, Brasil
| | - Marisol Vallejo
- Bacterial Biotechnology Laboratory, Faculty of Natural Sciences and Health Sciences, UNPSJB, Sede Trelew, Chubut, Argentina
| | - Elias Figueroa Villalobos
- Nucleus of Research in Food Production, Faculty of Natural Resources, Catholic University of Temuco, Temuco, Chile
| | - Ricardo Pinheiro de S Oliveira
- Laboratory of Microbial Biomolecules, School of Pharmaceutical Sciences, University of São Paulo, Rua Do Lago, 250, Cidade Universitária, São Paulo, 05508-000, Brazil.
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8
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Darbandi A, Asadi A, Mahdizade Ari M, Ohadi E, Talebi M, Halaj Zadeh M, Darb Emamie A, Ghanavati R, Kakanj M. Bacteriocins: Properties and potential use as antimicrobials. J Clin Lab Anal 2021; 36:e24093. [PMID: 34851542 PMCID: PMC8761470 DOI: 10.1002/jcla.24093] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/03/2021] [Accepted: 10/24/2021] [Indexed: 12/12/2022] Open
Abstract
A variety of bacteriocins originate from lactic acid bacteria, which have recently been modified by scientists. Many strains of lactic acid bacteria related to food groups could produce bacteriocins or antibacterial proteins highly effective against foodborne pathogens such as Staphylococcus aureus, Pseudomonas fluorescens, P. aeruginosa, Salmonella typhi, Shigella flexneri, Listeria monocytogenes, Escherichia coli O157:H7, and Clostridium botulinum. A wide range of bacteria belonging primarily to the genera Bifidobacterium and Lactobacillus have been characterized with different health‐promoting attributes. Extensive studies and in‐depth understanding of these antimicrobials mechanisms of action could enable scientists to determine their production in specific probiotic lactic acid bacteria, as they are potentially crucial for the final preservation of functional foods or for medicinal applications. In this review study, the structure, classification, mode of operation, safety, and antibacterial properties of bacteriocins as well as their effect on foodborne pathogens and antibiotic‐resistant bacteria were extensively studied.
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Affiliation(s)
- Atieh Darbandi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Arezoo Asadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Elnaz Ohadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Malihe Talebi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Masoume Halaj Zadeh
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Darb Emamie
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Maryam Kakanj
- Food and Drug Laboratory Research Center, Food and Drug Administration, MOH&ME, Tehran, Iran
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9
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Pérez-Ramos A, Madi-Moussa D, Coucheney F, Drider D. Current Knowledge of the Mode of Action and Immunity Mechanisms of LAB-Bacteriocins. Microorganisms 2021; 9:2107. [PMID: 34683428 PMCID: PMC8538875 DOI: 10.3390/microorganisms9102107] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteriocins produced by lactic acid bacteria (LAB-bacteriocins) may serve as alternatives for aging antibiotics. LAB-bacteriocins can be used alone, or in some cases as potentiating agents to treat bacterial infections. This approach could meet the different calls and politics, which aim to reduce the use of traditional antibiotics and develop novel therapeutic options. Considering the clinical applications of LAB-bacteriocins as a reasonable and desirable therapeutic approach, it is therefore important to assess the advances achieved in understanding their modes of action, and the resistance mechanisms developed by the producing bacteria to their own bacteriocins. Most LAB-bacteriocins act by disturbing the cytoplasmic membrane through forming pores, or by cell wall degradation. Nevertheless, some of these peptides still have unknown modes of action, especially those that are active against Gram-negative bacteria. Regarding immunity, most bacteriocin-producing strains have an immunity mechanism involving an immunity protein and a dedicated ABC transporter system. However, these immunity mechanisms vary from one bacteriocin to another.
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Affiliation(s)
| | | | | | - Djamel Drider
- UMR Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV—Institut Charles Viollette, F-59000 Lille, France; (A.P.-R.); (D.M.-M.); (F.C.)
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10
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Cao L, Do T, Link AJ. Mechanisms of action of ribosomally synthesized and posttranslationally modified peptides (RiPPs). J Ind Microbiol Biotechnol 2021; 48:6121428. [PMID: 33928382 PMCID: PMC8183687 DOI: 10.1093/jimb/kuab005] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/22/2021] [Indexed: 12/19/2022]
Abstract
Natural products remain a critical source of medicines and drug leads. One of the most rapidly growing superclasses of natural products is RiPPs: ribosomally synthesized and posttranslationally modified peptides. RiPPs have rich and diverse bioactivities. This review highlights examples of the molecular mechanisms of action that underly those bioactivities. Particular emphasis is placed on RiPP/target interactions for which there is structural information. This detailed mechanism of action work is critical toward the development of RiPPs as therapeutics and can also be used to prioritize hits in RiPP genome mining studies.
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Affiliation(s)
- Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Truc Do
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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11
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He H, Guo J, Lin X, Xu B. Enzyme-Instructed Assemblies Enable Mitochondria Localization of Histone H2B in Cancer Cells. Angew Chem Int Ed Engl 2020; 59:9330-9334. [PMID: 32119754 PMCID: PMC7269854 DOI: 10.1002/anie.202000983] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Indexed: 01/11/2023]
Abstract
Presently, little is known of how the inter-organelle crosstalk impacts cancer cells owing to the lack of approaches that can manipulate inter-organelle communication in cancer cells. We found that a negatively charged, enzyme cleavable peptide (MitoFlag) enables the trafficking of histone protein H2B, a nuclear protein, to the mitochondria in cancer cells. MitoFlag interacts with the nuclear location sequence of H2B to block it from entering the nucleus. A protease on the mitochondria cleaves the Flag from the MitoFlag/H2B complex to form assemblies that retain H2B on the mitochondria and facilitate H2B entering the mitochondria. Adding NLS, replacing aspartic acid by glutamic acid residues, or changing the l- to d-aspartic acid residue on MitoFlag abolishes the trafficking of H2B into mitochondria of HeLa cells. As the first example of the enzyme-instructed self-assembly of a synthetic peptide for trafficking endogenous proteins, this work provides insights for understanding and manipulating inter-organelle communication in cells.
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Affiliation(s)
- Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Xingyi Lin
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
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12
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He H, Guo J, Lin X, Xu B. Enzyme‐Instructed Assemblies Enable Mitochondria Localization of Histone H2B in Cancer Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hongjian He
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Jiaqi Guo
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Xinyi Lin
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
| | - Bing Xu
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02453 USA
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13
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Ruan W, Engevik MA, Spinler JK, Versalovic J. Healthy Human Gastrointestinal Microbiome: Composition and Function After a Decade of Exploration. Dig Dis Sci 2020; 65:695-705. [PMID: 32067143 DOI: 10.1007/s10620-020-06118-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The human gastrointestinal (GI) tract contains communities of microbes (bacteria, fungi, viruses) that vary by anatomic location and impact human health. Microbial communities differ in composition based on age, diet, and location in the gastrointestinal tract. Differences in microbial composition have been associated with chronic disease states. In terms of function, microbial metabolites provide key signals that help maintain healthy human physiology. Alterations of the healthy gastrointestinal microbiome have been linked to the development of various disease states including inflammatory bowel disease, diabetes, and colorectal cancer. While the definition of a healthy GI microbiome cannot be precisely identified, features of a healthy gut microbiome include relatively greater biodiversity and relative abundances of specific phyla and genera. Microbes with desirable functional profiles for the human host have been identified, in addition to specific metabolic features of the microbiome. This article reviews the composition and function of the healthy human GI microbiome, including the relative abundances of different bacterial taxa and the specific metabolic pathways and classes of microbial metabolites contributing to human health and disease prevention.
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Affiliation(s)
- Wenly Ruan
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Gastroenterology, Hepatology, and Nutrition, Texas Children's Hospital, Houston, TX, USA
| | - Melinda A Engevik
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology, Texas Children's Hospital, 1102 Bates St., Feigin Tower Suite 830, Houston, TX, 77030, USA
| | - Jennifer K Spinler
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology, Texas Children's Hospital, 1102 Bates St., Feigin Tower Suite 830, Houston, TX, 77030, USA
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA. .,Department of Pathology, Texas Children's Hospital, 1102 Bates St., Feigin Tower Suite 830, Houston, TX, 77030, USA.
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Farizano JV, Masías E, Hsu FF, Salomón RA, Freitag NE, Hebert EM, Minahk C, Saavedra L. PrfA activation in Listeria monocytogenes increases the sensitivity to class IIa bacteriocins despite impaired expression of the bacteriocin receptor. Biochim Biophys Acta Gen Subj 2019; 1863:1283-1291. [DOI: 10.1016/j.bbagen.2019.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 10/26/2022]
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15
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Balandin SV, Sheremeteva EV, Ovchinnikova TV. Pediocin-Like Antimicrobial Peptides of Bacteria. BIOCHEMISTRY (MOSCOW) 2019; 84:464-478. [PMID: 31234762 DOI: 10.1134/s000629791905002x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bacteriocins are bacterial antimicrobial peptides that, unlike classical peptide antibiotics, are products of ribosomal synthesis and usually have a narrow spectrum of antibacterial activity against species closely related to the producers. Pediocin-like bacteriocins (PLBs) belong to the class IIa of the bacteriocins of Gram-positive bacteria. PLBs possess high activity against pathogenic bacteria from Listeria and Enterococcus genera. Molecular target for PLBs is a membrane protein complex - bacterial mannose-phosphotransferase. PLBs can be synthesized by components of symbiotic microflora and participate in the maintenance of homeostasis in various compartments of the digestive tract and on the surface of epithelial tissues contacting the external environment. PLBs could give a rise to a new group of antibiotics of narrow spectrum of activity.
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Affiliation(s)
- S V Balandin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - E V Sheremeteva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - T V Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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Vasilchenko AS, Valyshev AV. Pore-forming bacteriocins: structural–functional relationships. Arch Microbiol 2018; 201:147-154. [DOI: 10.1007/s00203-018-1610-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/19/2018] [Accepted: 12/11/2018] [Indexed: 12/21/2022]
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17
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Mousavi Khaneghah A, Hashemi SMB, Limbo S. Antimicrobial agents and packaging systems in antimicrobial active food packaging: An overview of approaches and interactions. FOOD AND BIOPRODUCTS PROCESSING 2018. [DOI: 10.1016/j.fbp.2018.05.001] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Pediocin-like bacteriocins: new perspectives on mechanism of action and immunity. Curr Genet 2017; 64:345-351. [PMID: 28983718 DOI: 10.1007/s00294-017-0757-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 01/26/2023]
Abstract
This review attempts to analyze the mechanism of action and immunity of class IIa bacteriocins. These peptides are promising alternative food preservatives and they have a great potential application in medical sciences. Class IIa bacteriocins act on the cytoplasmic membrane of Gram-positive cells dissipating the transmembrane electrical potential by forming pores. However, their toxicity and immunity mechanism remains elusive. Here we discuss the role of the mannose phosphotransferase system (man-PTS) as the receptor for class IIa bacteriocins and the influence of the membrane composition on the activity of these antimicrobial peptides. A model that is consistent with experimental results obtained by different researchers involves the non-specific binding of the bacteriocin to the negatively charged membrane of target bacteria. This step would facilitate a specific binding to the receptor protein, altering its functionality and forming an independent pore in which the bacteriocin is inserted in the membrane. An immunity protein could specifically recognize and block the pore. Bacteriocins function in bacterial ecosystems and energetic costs associated with their production are also discussed. Theoretical models based on solid experimental evidence are vital to understand bacteriocins mechanism of action and to promote new technological developments.
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Engevik MA, Versalovic J. Biochemical Features of Beneficial Microbes: Foundations for Therapeutic Microbiology. Microbiol Spectr 2017; 5:10.1128/microbiolspec.BAD-0012-2016. [PMID: 28984235 PMCID: PMC5873327 DOI: 10.1128/microbiolspec.bad-0012-2016] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Indexed: 12/15/2022] Open
Abstract
Commensal and beneficial microbes secrete myriad products which target the mammalian host and other microbes. These secreted substances aid in bacterial niche development, and select compounds beneficially modulate the host and promote health. Microbes produce unique compounds which can serve as signaling factors to the host, such as biogenic amine neuromodulators, or quorum-sensing molecules to facilitate inter-bacterial communication. Bacterial metabolites can also participate in functional enhancement of host metabolic capabilities, immunoregulation, and improvement of intestinal barrier function. Secreted products such as lactic acid, hydrogen peroxide, bacteriocins, and bacteriocin-like substances can also target the microbiome. Microbes differ greatly in their metabolic potential and subsequent host effects. As a result, knowledge about microbial metabolites will facilitate selection of next-generation probiotics and therapeutic compounds derived from the mammalian microbiome. In this article we describe prominent examples of microbial metabolites and their effects on microbial communities and the mammalian host.
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Affiliation(s)
- Melinda A Engevik
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030 and Department of Pathology, Texas Children's Hospital, Houston, TX 77030
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030 and Department of Pathology, Texas Children's Hospital, Houston, TX 77030
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Cintas LM, Casaus MP, Herranz C, Nes IF, Hernández PE. Review: Bacteriocins of Lactic Acid Bacteria. FOOD SCI TECHNOL INT 2016. [DOI: 10.1106/r8de-p6hu-clxp-5ryt] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During the last few years, a large number of new bacteriocins produced by lactic acid bacteria (LAB) have been identified and characterized. LAB-bacteriocins comprise a heterogeneous group of physicochemically diverse ribosomally-synthesized peptides or proteins showing a narrow or broad antimicrobial activity spectrum against Gram-positive bacteria. Bacteriocins are classified into separate groups such as the lantibiotics (Class I); the small (<10 kDa) heat-stable postranslationally unmodified non-lantibiotics (Class II), further subdivided in the pediocin-like and anti Listeria bacteriocins (subclass IIa), the two-peptide bacteriocins (subclass IIb), and the sec-dependent bacteriocins (subclass IIc); and the large (>30 kDa) heat-labile non-lantibiotics (Class III). Most bacteriocins characterized to date belong to Class II and are synthesized as precursor peptides (preprobacteriocins) containing an N-terminal double-glycine leader peptide, which is cleaved off concomitantly with externalization of biologically active bacteriocins by a dedicated ABC-transporter and its accessory protein. However, the recently identified sec-dependent bacteriocins contain an N-terminal signal peptide that directs bacteriocin secretion through the general secretory pathway (GSP). Most LAB-bacteriocins act on sensitive cells by destabilization and permeabilization of the cytoplasmic membrane through the formation of transitory poration complexes or ionic channels that cause the reduction or dissipation of the proton motive force (PMF). Bacteriocin producing LAB strains protect themselves against the toxicity of their own bacteriocins by the expression of a specific immunity protein which is generally encoded in the bacteriocin operon. Bacteriocin production in LAB is frequently regulated by a three-component signal transduction system consisting of an induction factor (IF), and histidine protein kinase (HPK) and a response regulator (RR). This paper presents an updated review on the general knowledge about physicochemical properties, molecular mode of action, biosynthesis, regulation and genetics of LAB-bacteriocins.
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Affiliation(s)
- L. M. Cintas
- Departamento de Nutrición y Bromatología III (Higiene y Tecnología de los Alimentos), Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - M. P. Casaus
- Carrefour, Departamento de Marcas Propias, Área de Calidad, Campezo 16, 28022 Madrid
| | - C. Herranz
- Departamento de Nutrición y Bromatología III (Higiene y Tecnología de los Alimentos), Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - I. F. Nes
- Laboratory of Microbial Gene Technology, Department of Chemistry and Biotechnology, Agricultural University of Norway, P.O. Box 5051, N-1432 Ås, Norway
| | - P. E. Hernández
- Departamento de Nutrición y Bromatología III (Higiene y Tecnología de los Alimentos), Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
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McClintock MK, Kaznessis YN, Hackel BJ. Enterocin A mutants identified by saturation mutagenesis enhance potency towards vancomycin-resistant Enterococci. Biotechnol Bioeng 2015; 113:414-23. [PMID: 26191783 DOI: 10.1002/bit.25710] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 12/31/2022]
Abstract
Vancomycin-resistant Enterococci infections are a significant clinical problem. One proposed solution is to use probiotics, such as lactic acid bacteria, to produce antimicrobial peptides at the site of infection. Enterocin A, a class 2a bacteriocin, exhibits inhibitory activity against E. faecium and E. faecalis, which account for 86% of vancomycin-resistant Enterococci infections. In this study, we aimed to engineer enterocin A mutants with enhanced potency within a lactic acid bacterial production system. Peptide mutants resulting from saturation mutagenesis at sites A24 and T27 were efficiently screened in a 96-well plate assay for inhibition of pathogen growth. Several mutants exhibit increased potency relative to wild-type enterocin A in both liquid- and solid-medium growth assays. In particular, A24P and T27G exhibit enhanced inhibition of multiple strains of E. faecium and E. faecalis, including clinically isolated vancomycin-resistant strains. A24P and T27G enhance killing of E. faecium 8 by 13 ± 3- and 18 ± 4-fold, respectively. The engineered enterocin A/lactic acid bacteria systems offer significant potential to combat antibiotic-resistant infections.
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Affiliation(s)
- Maria K McClintock
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Yiannis N Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, 55455.
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22
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Khitrin A, Khitrin K, Model M. A model for membrane potential and intracellular ion distribution. Chem Phys Lipids 2014; 184:76-81. [DOI: 10.1016/j.chemphyslip.2014.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/27/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
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Singh PK, Sharma S, Kumari A, Korpole S. A non-pediocin low molecular weight antimicrobial peptide produced by Pediococcus pentosaceus strain IE-3 shows increased activity under reducing environment. BMC Microbiol 2014; 14:226. [PMID: 25158757 PMCID: PMC4243815 DOI: 10.1186/s12866-014-0226-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 08/18/2014] [Indexed: 11/26/2022] Open
Abstract
Background Species of the genus Pediococcus are known to produce antimicrobial peptides such as pediocin-like bacteriocins that contain YGNGVXC as a conserved motif at their N-terminus. Until now, the molecular weight of various bacteriocins produced by different strains of the genus Pediococcus have been found to vary between 2.7 to 4.6 kD. In the present study, we characterized an antimicrobial peptide produced by P. pentosaceus strain IE-3. Results Antimicrobial peptide was isolated and purified from the supernatant of P. pentosaceus strain IE-3 grown for 48 h using cation exchange chromatography and reversed-phase high-performance liquid chromatography (RP-HPLC) techniques. While MALDI-TOF MS experiments determined the precise molecular mass of the peptide to be 1701.00 Da, the de novo sequence (APVPFSCTRGCLTHLV) of the peptide revealed no similarity with reported pediocins and did not contain the YGNGVXC conserved motif. Unlike pediocin-like bacteriocins, the low molecular weight peptide (LMW) showed resistance to different proteases. Moreover, peptide treated with reducing agent like dithiothreitol (DTT) exhibited increased activity against both Gram-positive and Gram-negative test strains in comparison to native peptide. However, peptide treated with oxidizing agent such as hydrogen peroxide (H2O2) did not show any antimicrobial activity. Conclusion To our knowledge this is the lowest molecular weight peptide produced by members of the genus Pediococcus. The low molecular weight peptide shared amino acid arrangement with N-terminal sequence of Class IIa, pediocin-like bacteriocins and showed increased activity under reducing conditions. Antimicrobial peptides active under reduced conditions are valuable for the preservation of processed foods like meat, dairy and canned foods where low redox potential prevails.
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Affiliation(s)
| | | | | | - Suresh Korpole
- MTCC and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, 160036, Chandigarh, India.
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Bodapati KC, Soudy R, Etayash H, Stiles M, Kaur K. Design, synthesis and evaluation of antimicrobial activity of N-terminal modified Leucocin A analogues. Bioorg Med Chem 2013; 21:3715-22. [DOI: 10.1016/j.bmc.2013.04.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/05/2013] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
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25
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Jiménez JJ, Borrero J, Diep DB, Gútiez L, Nes IF, Herranz C, Cintas LM, Hernández PE. Cloning, production, and functional expression of the bacteriocin sakacin A (SakA) and two SakA-derived chimeras in lactic acid bacteria (LAB) and the yeasts Pichia pastoris and Kluyveromyces lactis. J Ind Microbiol Biotechnol 2013; 40:977-93. [PMID: 23794087 DOI: 10.1007/s10295-013-1302-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 05/30/2013] [Indexed: 11/25/2022]
Abstract
Mature sakacin A (SakA, encoded by sapA) and its cognate immunity protein (SakI, encoded by sapiA), and two SakA-derived chimeras mimicking the N-terminal end of mature enterocin P (EntP/SakA) and mature enterocin A (EntA/SakA) together with SakI, were fused to different signal peptides (SP) and cloned into the protein expression vectors pNZ8048 and pMG36c for evaluation of their production and functional expression by different lactic acid bacteria. The amount, antimicrobial activity, and specific antimicrobial activity of SakA and its chimeras produced by Lactococcus lactis subsp. cremoris NZ9000 depended on the SP and the expression vector. Only L. lactis NZ9000 (pNUPS), producing EntP/SakA, showed higher bacteriocin production and antimicrobial activity than the natural SakA-producer Lactobacillus sakei Lb706. The lower antimicrobial activity of the SakA-producer L. lactis NZ9000 (pNUS) and that of the EntA/SakA-producer L. lactis NZ9000 (pNUAS) could be ascribed to secretion of truncated bacteriocins. On the other hand, of the Lb. sakei Lb706 cultures transformed with the pMG36c-derived vectors only Lb. sakei Lb706 (pGUS) overproducing SakA showed a higher antimicrobial activity than Lb. sakei Lb706. Finally, cloning of SakA and EntP/SakA into pPICZαA and pKLAC2 permitted the production of SakA and EntP/SakA by recombinant Pichia pastoris X-33 and Kluyveromyces lactis GG799 derivatives although their antimicrobial activity was lower than expected from their production.
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Affiliation(s)
- Juan J Jiménez
- Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
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Interaction with lipid II induces conformational changes in bovicin HC5 structure. Antimicrob Agents Chemother 2012; 56:4586-93. [PMID: 22687503 DOI: 10.1128/aac.00295-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bovicin HC5 is a lantibiotic produced by Streptococcus bovis HC5 that targets the cell wall precursor lipid II. An understanding of the modes of action against target bacteria can help broadening the clinical applicability of lantibiotics in human and veterinary medicine. In this study, the interaction of bovicin HC5 with lipid II was examined using tryptophan fluorescence and circular dichroism spectroscopy with model membrane systems that do or do not allow pore formation by bovicin HC5. In the presence of lipid II, a blue-shift of 12 nm could be observed for the fluorescence emission maximum of the tryptophan residue for all of the membrane systems tested. This change in fluorescence emission was paralleled by a decrease in accessibility toward acrylamide and phospholipids carrying a spin-label at the acyl chain; the tryptophan residue of bovicin HC5 was located near the twelfth position of the membrane phospholipid acyl chains. Moreover, the binding of lipid II by bovicin HC5 induced remarkable conformational changes in the bovicin HC5 structure. The interaction of bovicin HC5 with lipid II was highly stable even at pH 2.0. These results indicate that bovicin HC5 interacts directly with lipid II and that the topology of this interaction changes under different conditions, which is relevant for the biological activity of the peptide. To our knowledge, bovicin HC5 is the only bacteriocin described thus far that is able to interact with its target in extreme pH values, and this fact might be related to its unique structure and stability.
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Affiliation(s)
- Vijay K. Juneja
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania 19038;
| | | | - Xianghe Yan
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania 19038;
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Jacquet T, Cailliez-Grimal C, Borges F, Gaiani C, Francius G, Duval J, Waldvogel Y, Revol-Junelles AM. Surface properties of bacteria sensitive and resistant to the class IIa carnobacteriocin Cbn BM1. J Appl Microbiol 2011; 112:372-82. [DOI: 10.1111/j.1365-2672.2011.05195.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Development of Class IIa Bacteriocins as Therapeutic Agents. Int J Microbiol 2011; 2012:386410. [PMID: 22187559 PMCID: PMC3236453 DOI: 10.1155/2012/386410] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 10/08/2011] [Indexed: 12/02/2022] Open
Abstract
Class IIa bacteriocins have been primarily explored as natural food preservatives, but there is much interest in exploring the application of these peptides as therapeutic antimicrobial agents. Bacteriocins of this class possess antimicrobial activity against several important human pathogens. Therefore, the therapeutic development of these bacteriocins will be reviewed. Biological and chemical modifications to both stabilize and increase the potency of bacteriocins are discussed, as well as the optimization of their production and purification. The suitability of bacteriocins as pharmaceuticals is explored through determinations of cytotoxicity, effects on the natural microbiota, and in vivo efficacy in mouse models. Recent results suggest that class IIa bacteriocins show promise as a class of therapeutic agents.
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Castro M, Palavecino N, Herman C, Garro O, Campos C. Lactic acid bacteria isolated from artisanal dry sausages: Characterization of antibacterial compounds and study of the factors affecting bacteriocin production. Meat Sci 2011; 87:321-9. [DOI: 10.1016/j.meatsci.2010.11.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 10/03/2010] [Accepted: 11/06/2010] [Indexed: 11/29/2022]
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Synthesis of trypsin-resistant variants of the Listeria-active bacteriocin salivaricin P. Appl Environ Microbiol 2010; 76:5356-62. [PMID: 20581174 DOI: 10.1128/aem.00523-10] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two-component salivaricin P-like bacteriocins have demonstrated potential as antimicrobials capable of controlling infections in the gastrointestinal tract (GIT). The anti-Listeria activity of salivaricin P is optimal when the individual peptides Sln1 and Sln2 are added in succession at a 1:1 ratio. However, as degradation by digestive proteases may compromise the functionality of these peptides within the GIT, we investigated the potential to create salivaricin variants with enhanced resistance to the intestinal protease trypsin. A total of 11 variants of the salivaricin P components, in which conservative modifications at the trypsin-specific cleavage sites were explored in order to protect the peptides from trypsin degradation while maintaining their potent antimicrobial activity, were generated. Analysis of these variants revealed that eight were resistant to trypsin digestion while retaining antimicrobial activity. Combining the complementary trypsin-resistant variants Sln1-5 and Sln2-3 resulted in a MIC(50) of 300 nM against Listeria monocytogenes, a 3.75-fold reduction in activity compared to the level for wild-type salivaricin P. This study demonstrates the potential of engineering bacteriocin variants which are resistant to specific protease action but which retain significant antimicrobial activity.
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Todorov SD. Bacteriocins from Lactobacillus plantarum - production, genetic organization and mode of action: produção, organização genética e modo de ação. Braz J Microbiol 2009; 40:209-21. [PMID: 24031346 PMCID: PMC3769724 DOI: 10.1590/s1517-83822009000200001] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 09/29/2008] [Accepted: 02/14/2009] [Indexed: 11/30/2022] Open
Abstract
Bacteriocins are biologically active proteins or protein complexes that display a bactericidal mode of action towards usually closely related species. Numerous strains of bacteriocin producing Lactobacillus plantarum have been isolated in the last two decades from different ecological niches including meat, fish, fruits, vegetables, and milk and cereal products. Several of these plantaricins have been characterized and the aminoacid sequence determined. Different aspects of the mode of action, fermentation optimization and genetic organization of the bacteriocin operon have been studied. However, numerous of bacteriocins produced by different Lactobacillus plantarum strains have not been fully characterized. In this article, a brief overview of the classification, genetics, characterization, including mode of action and production optimization for bacteriocins from Lactic Acid Bacteria in general, and where appropriate, with focus on bacteriocins produced by Lactobacillus plantarum, is presented.
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Affiliation(s)
- Svetoslav D Todorov
- Department of Microbiology, University of Stellenbosch , 7600 Stellenbosch , South Africa
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33
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Papagianni M, Anastasiadou S. Pediocins: The bacteriocins of Pediococci. Sources, production, properties and applications. Microb Cell Fact 2009; 8:3. [PMID: 19133115 PMCID: PMC2634753 DOI: 10.1186/1475-2859-8-3] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 01/08/2009] [Indexed: 11/19/2022] Open
Abstract
Class IIa bacteriocins from lactic acid bacteria are small, cationic proteins with antilisterial activity. Within this class, the pediocins are those bacteriocins that share a highly conserved hydrophilic and charged N-terminal part harboring the consensus sequence -YGNGV- and a more variable hydrophobic and/or amphiphilic C-terminal part. Several pediocins have been isolated and characterized. Despite the structural similarities, their molecular weight varies, as well as their spectrum of antimicrobial activity. They exhibit important technological properties, e.g. thermostability and retaining of activity at a wide pH range, which along with the bactericidal action against Gram-positive food spoilage and pathogenic bacteria, make them an important class of biopreservatives. Much new information regarding the pediocins has emerged during the last years. In this review, we summarize and discuss all the available information regarding the sources of pediocins, the characteristics of their biosynthesis and production in fermentation systems, the characteristics of the known pediocin molecules, and their antibacterial action. The advances made by genetic engineering in improving the features of pediocins are also discussed, as well as their perspectives for future applications.
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Affiliation(s)
- Maria Papagianni
- Department of Hygiene and Technology of Food of Animal Origin, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54006, Greece
| | - Sofia Anastasiadou
- Department of Hygiene and Technology of Food of Animal Origin, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54006, Greece
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Jasniewski J, Cailliez-Grimal C, Younsi M, Millière JB, Revol-Junelles AM. Functional differences inLeuconostocsensitive and resistant strains to mesenterocin 52A, a class IIa bacteriocin. FEMS Microbiol Lett 2008; 289:193-201. [DOI: 10.1111/j.1574-6968.2008.01381.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Anastasiadou S, Papagianni M, Filiousis G, Ambrosiadis I, Koidis P. Growth and metabolism of a meat isolated strain of Pediococcus pentosaceus in submerged fermentation. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Mutational analysis of the class IIa bacteriocin curvacin A and its orientation in target cell membranes. Appl Environ Microbiol 2008; 74:6766-73. [PMID: 18791005 DOI: 10.1128/aem.01068-08] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To analyze the orientation in target cell membranes of the pediocin-like bacteriocin (antimicrobial peptide) curvacin A, 55 variants were generated by site-directed mutagenesis and their potencies against four different target cells determined. The result suggest that the somewhat hydrophilic short central helix (residues 19 to 24), along with the N-terminal beta-sheet-like structure (residues 1 to 16), inserts in the interface region of the target cell membrane, with Ala22 close to the hydrophobic core of the membrane. The following hinge region, with Gly28 as an important residue, may then form a turn wherein Gly28 becomes positioned near the border between the interface and the hydrophobic regions, thus permitting the longer and more-hydrophobic C-terminal helix (residues 29 to 41) to insert into the hydrophobic core of the membrane. This helix contains three glycine residues (G33, G37, and G40) that form a putative helix-helix-interacting GxxxGxxG motif. The replacement of any of these glycines with a larger residue was very detrimental, suggesting their possible involvement in helix-helix interactions with a membrane-embedded receptor protein.
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Tominaga T, Hatakeyama Y. Development of innovative pediocin PA-1 by DNA shuffling among class IIa bacteriocins. Appl Environ Microbiol 2007; 73:5292-9. [PMID: 17601819 PMCID: PMC1950993 DOI: 10.1128/aem.00558-07] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pediocin PA-1 is a member of the class IIa bacteriocins, which show antimicrobial effects against lactic acid bacteria. To develop an improved version of pediocin PA-1, reciprocal chimeras between pediocin PA-1 and enterocin A, another class IIa bacteriocin, were constructed. Chimera EP, which consisted of the C-terminal half of pediocin PA-1 fused to the N-terminal half of enterocin A, showed increased activity against a strain of Leuconostoc lactis isolated from a sour-spoiled dairy product. To develop an even more effective version of this chimera, a DNA-shuffling library was constructed, wherein four specific regions within the N-terminal half of pediocin PA-1 were shuffled with the corresponding sequences from 10 other class IIa bacteriocins. Activity screening indicated that 63 out of 280 shuffled mutants had antimicrobial activity. A colony overlay activity assay showed that one of the mutants (designated B1) produced a >7.8-mm growth inhibition circle on L. lactis, whereas the parent pediocin PA-1 did not produce any circle. Furthermore, the active shuffled mutants showed increased activity against various species of Lactobacillus, Pediococcus, and Carnobacterium. Sequence analysis revealed that the active mutants had novel N-terminal sequences; in active mutant B1, for example, the parental pediocin PA-1 sequence (KYYGNGVTCGKHSC) was changed to TKYYGNGVSCTKSGC. These new and improved DNA-shuffled bacteriocins could prove useful as food additives for inhibiting sour spoilage of dairy products.
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Affiliation(s)
- Tatsuya Tominaga
- Saitama Industrial Technology Center North Institute, 2-133 Suehiro, Kumagaya, Saitama 360-0031, Japan.
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High resolution crystal structure of PedB: a structural basis for the classification of pediocin-like immunity proteins. BMC STRUCTURAL BIOLOGY 2007; 7:35. [PMID: 17537233 PMCID: PMC1904221 DOI: 10.1186/1472-6807-7-35] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Accepted: 05/30/2007] [Indexed: 11/10/2022]
Abstract
BACKGROUND Pediocin-like bacteriocins, ribosomally-synthesized antimicrobial peptides, are generally coexpressed with cognate immunity proteins in order to protect the bacteriocin-producer from its own bacteriocin. As a step for understanding the mode of action of immunity proteins, we determined the crystal structure of PedB, a pediocin-like immunity protein conferring immunity to pediocin PP-1. RESULTS The 1.6 A crystal structure of PedB reveals that PedB consists of an antiparallel four-helix bundle with a flexible C-terminal end. PedB shows structural similarity to an immunity protein against enterocin A (EntA-im) but some disparity to an immunity protein against carnobacteriocin B2 (ImB2) in both the C-terminal conformation and the local structure constructed by alpha3, alpha4, and their connecting loop. Structure-inspired mutational studies reveal that deletion of the last seven residues of the C-terminus of PedB almost abolished its immunity activity. CONCLUSION The fact that PedB, EntA-im, and ImB2 share a four-helix bundle structure strongly suggests the structural conservation of this motif in the pediocin-like immunity proteins. The significant difference in the core structure and the C-terminal conformation provides a structural basis for the classification of pediocin-like immunity proteins. Our mutational study using C-terminal-shortened PedBs and the investigation of primary sequence of the C-terminal region, propose that several polar or charged residues in the extreme C-terminus of PedB which is crucial for the immunity are involved in the specific recognition of pediocin PP-1.
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Franz CMAP, van Belkum MJ, Holzapfel WH, Abriouel H, Gálvez A. Diversity of enterococcal bacteriocins and their grouping in a new classification scheme. FEMS Microbiol Rev 2007; 31:293-310. [PMID: 17298586 DOI: 10.1111/j.1574-6976.2007.00064.x] [Citation(s) in RCA: 275] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Enterococci are lactic acid bacteria of importance in food, public health and medical microbiology. Many strains produce bacteriocins, some of which have been well characterized. This review describes the structural and genetic characteristics of enterocins, the bacteriocins produced by enterococci. Some of these can be grouped with typical bacteriocins produced by lactic acid bacteria according to traditional classification, whereas others are atypical and structurally distinct from the general classes of bacteriocins. These atypical enterocins recently played an important role in and prompted reclassification of the class II bacteriocins into a new scheme. In this review, a more simplified classification scheme for enterocins based on amino acid sequence homologies is proposed. Enterocins are of interest for their diversity and potential for use as food biopreservatives. The emergence of multiple antibiotic-resistant enterococci among agents of nosocomial disease and the presence of virulence factors among food isolates requires a careful safety evaluation of isolates intended for potential biotechnical use. Nevertheless, enterococcal bacteriocins produced by heterologous hosts or added as cell-free preparations may still be attractive for application in food preservation.
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Affiliation(s)
- Charles M A P Franz
- Federal Research Centre for Nutrition and Food, Institute for Hygiene and Toxicology, Karlsruhe, Germany
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Drider D, Fimland G, Héchard Y, McMullen LM, Prévost H. The continuing story of class IIa bacteriocins. Microbiol Mol Biol Rev 2006; 70:564-82. [PMID: 16760314 PMCID: PMC1489543 DOI: 10.1128/mmbr.00016-05] [Citation(s) in RCA: 436] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many bacteria produce antimicrobial peptides, which are also referred to as peptide bacteriocins. The class IIa bacteriocins, often designated pediocin-like bacteriocins, constitute the most dominant group of antimicrobial peptides produced by lactic acid bacteria. The bacteriocins that belong to this class are structurally related and kill target cells by membrane permeabilization. Despite their structural similarity, class IIa bacteriocins display different target cell specificities. In the search for new antibiotic substances, the class IIa bacteriocins have been identified as promising new candidates and have thus received much attention. They kill some pathogenic bacteria (e.g., Listeria) with high efficiency, and they constitute a good model system for structure-function analyses of antimicrobial peptides in general. This review focuses on class IIa bacteriocins, especially on their structure, function, mode of action, biosynthesis, bacteriocin immunity, and current food applications. The genetics and biosynthesis of class IIa bacteriocins are well understood. The bacteriocins are ribosomally synthesized with an N-terminal leader sequence, which is cleaved off upon secretion. After externalization, the class IIa bacteriocins attach to potential target cells and, through electrostatic and hydrophobic interactions, subsequently permeabilize the cell membrane of sensitive cells. Recent observations suggest that a chiral interaction and possibly the presence of a mannose permease protein on the target cell surface are required for a bacteria to be sensitive to class IIa bacteriocins. There is also substantial evidence that the C-terminal half penetrates into the target cell membrane, and it plays an important role in determining the target cell specificity of these bacteriocins. Immunity proteins protect the bacteriocin producer from the bacteriocin it secretes. The three-dimensional structures of two class IIa immunity proteins have been determined, and it has been shown that the C-terminal halves of these cytosolic four-helix bundle proteins specify which class IIa bacteriocin they protect against.
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Affiliation(s)
- Djamel Drider
- Laboratoire de Microbiologie Alimentaire et Industrielle, ENITIAA, Rue de la Géraudière, BP82225, 44322 Nantes Cedex, France.
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Fimland G, Pirneskoski J, Kaewsrichan J, Jutila A, Kristiansen PE, Kinnunen PKJ, Nissen-Meyer J. Mutational analysis and membrane-interactions of the β-sheet-like N-terminal domain of the pediocin-like antimicrobial peptide sakacin P. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1132-40. [PMID: 16762606 DOI: 10.1016/j.bbapap.2006.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2006] [Revised: 04/03/2006] [Accepted: 04/03/2006] [Indexed: 11/16/2022]
Abstract
To gain insight into how the N-terminal three-stranded beta-sheet-like domain in pediocin-like antimicrobial peptides positions itself on membranes, residues in the well-conserved (Y)YGNGV-motif in the domain were substituted and the effect of the substitutions on antimicrobial activity and binding of peptides to liposomes was determined. Peptide-liposome interactions were detected by measuring tryptophan-fluorescence upon exposing liposomes to peptides in which a tryptophan residue had been introduced in the N-terminal domain. The results revealed that the N-terminal domain associates readily with anionic liposomes, but not with neutral liposomes. The electrostatic interactions between peptides and liposomes facilitated the penetration of some of the peptide residues into the liposomes. Measuring the antimicrobial activity of the mutated peptides revealed that the Tyr2Leu and Tyr3Leu mutations resulted in about a 10-fold reduction in activity, whereas the Tyr2Trp, Tyr2Phe, Tyr3Trp and Tyr3Phe mutations were tolerated fairly well, especially the mutations in position 3. The Val7Ile mutation did not have a marked detrimental effect on the activity. The Gly6Ala mutation was highly detrimental, consistent with Gly6 being in one of the turns in the beta-sheet-like N-terminal domain, whereas the Gly4Ala mutation was tolerated fairly well. All mutations involving Asn5, including the conservative mutations Asn5Gln and Asn5Asp, were very deleterious. Thus, both the polar amide group on the side chain of Asn5 and its exact position in space were crucial for the peptides to be fully active. Taken together, the results are consistent with Val7 positioning itself in the hydrophobic core of target membranes, thus forcing most of the other residues in the N-terminal domain into the membrane interface region: Tyr3 and Asn5 in the lower half with their side chains pointing downward and approaching the hydrophobic core, Tyr2, Gly4 and His8 and 12 in the upper half, Lys1 near the middle of the interface region, and the side chain of Lys11 pointing out toward the membrane surface.
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Affiliation(s)
- Gunnar Fimland
- Department of Molecular Biosciences, University of Oslo, Post box 1041, Blindern, 0316 Oslo, Norway.
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Tominaga T, Hatakeyama Y. Determination of essential and variable residues in pediocin PA-1 by NNK scanning. Appl Environ Microbiol 2006; 72:1141-7. [PMID: 16461660 PMCID: PMC1392896 DOI: 10.1128/aem.72.2.1141-1147.2006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pediocin PA-1 is an antimicrobial peptide (called bacteriocin) that shows inhibitory activity against the food-borne pathogen Listeria monocytogenes. To elucidate which residue(s) is responsible for this function, the antimicrobial activities of pediocin PA-1 mutants were evaluated and compared. Each of the 44 native codons was replaced with the NNK triplet oligonucleotide in a technique termed NNK scanning, and 35 mutations at each position were examined for antimicrobial activities using a modified colony overlay screening method. As a consequence, the functional responsibility of each residue was estimated by counting the number of active mutants, allowing us to identify candidate essential/variable residues. Activity was abrogated by many of the mutations at residues Y2, G6, C9, C14, C24, W33, G37, and C44, indicating that these residues may be essential. In contrast, activity was retained by almost all versions harboring mutations at K1, T8, G10, S13, G19, N28, and N41, indicating that these are functionally redundant residues. Sequence analysis revealed that only the wild type was active and 14 and 11 substitutions were inactive at G6 and C14, respectively, while 12 and 11 substitutions were active and 2 and 0 substitutions were inactive at T8 and K1, respectively. These findings suggest that NNK scanning is effective for determining essential and variable residues in pediocin PA-1, leading to an elucidation of structure-function relationships and to improvements in the antimicrobial function efficiently by peptide engineering.
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Affiliation(s)
- Tatsuya Tominaga
- Saitama Industrial Technology Center North Institute, 2-133 Suehiro, Kumagaya, Saitama 360-0031, Japan.
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Li J, Aroutcheva AA, Faro S, Chikindas ML. Mode of action of lactocin 160, a bacteriocin from vaginal Lactobacillus rhamnosus. Infect Dis Obstet Gynecol 2006; 13:135-40. [PMID: 16126497 PMCID: PMC1784572 DOI: 10.1080/10647440500148156] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES: To determine the mechanism of antimicrobial action of lactocin 160, a bacteriocin produced by the healthy vaginal strain of Lactobacillus rhamnosus, using an established model, with Micrococcus luteus ATCC 10420 as a test organism. METHODS: Sensitivity of M. luteus to lactocin 160 was determined by the diffusion assay. Loss of cellular ATP in the lactocin-treated cells was elucidated using a commercially available ATP determination kit (luciferin-luciferase bioluminescence assay). Luminescence intensity as a reflection of ATP quantity was determined using a luminometer. Dissipation of membrane potential (Deltapsi) was studied using fluorophore DiSC3(5) with the fluorescence spectrum sensitive to changes in Deltapsi. RESULTS: Lactocin 160 inhibited growth of M. luteus ATCC 10420 at a concentration of 5 microg/ml. There were no significant changes in the intracellular ATP level of M. luteus upon the addition of 20 microg/ml of lactocin 160. However, the extracellular ATP level increased significantly. This means that the treatment of cells with lactocin 160 resulted in an efflux of ATP from inside the cells. Therefore, a partially purified lactocin 160 preparation (16 microg /ml of the bacteriocin in the sample) killed sensitive cells and dissipated 3.12 +/- 0.36% of Deltapsi. CONCLUSION: Lactocin 160 has a mode of action typical for bacteriocins. It disturbs the cellular membrane (Deltapsi dissipation) and induces ATP efflux, most likely because of the pore formation, which is a common mechanism of action for many bacteriocins.
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Affiliation(s)
- Jie Li
- Rutgers, The State University of New Jersey, New Brunswick, NJ 08901-8520, USA
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Fimland G, Johnsen L, Dalhus B, Nissen-Meyer J. Pediocin-like antimicrobial peptides (class IIa bacteriocins) and their immunity proteins: biosynthesis, structure, and mode of action. J Pept Sci 2006; 11:688-96. [PMID: 16059970 DOI: 10.1002/psc.699] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Pediocin-like antimicrobial peptides (AMPs) form a group of lactic acid bacteria produced, cationic membrane-permeabilizing peptides with 37 to 48 residues. Upon exposure to membrane-mimicking entities, their hydrophilic, cationic, and highly conserved N-terminal region forms a three-stranded antiparallel beta-sheet supported by a conserved disulfide bridge. This N-terminal beta-sheet region is followed by a central amphiphilic alpha-helix and this in most (if not all) of these peptides is followed by a rather extended C-terminal tail that folds back onto the central alpha-helix, thereby creating a hairpin-like structure in the C-terminal half. There is a flexible hinge between the beta-sheet N-terminal region and the hairpin C-terminal region and one thus obtains two domains that may move relative to each other. The cationic N-terminal beta-sheet domain mediates binding of the pediocin-like AMPs to the target-cell surface through electrostatic interactions, while the more hydrophobic and amphiphilic C-terminal hairpin domain penetrates into the hydrophobic part of the target-cell membrane, thereby mediating leakage through the membrane. The hinge provides the structural flexibility that enables the C-terminal hairpin domain to dip into the hydrophobic part of the membrane. Despite extensive sequence similarities, these AMPs differ markedly in their target-cell specificity, and results obtained with hybrid AMPs indicate that the membrane-penetrating hairpin-like C-terminal domain is the major specificity determinant. Bacteria that produce pediocin-like AMPs also produce a 11-kDa cognate immunity protein that protects the producer. The immunity proteins are well-structured, 4-helix bundle cytosolic proteins. They show a high degree of specificity in that they largely recognize and confer immunity only to their cognate AMP and in some cases to a few AMPs that are closely related to their cognate AMP. The C-terminal half of the immunity proteins contains a domain that is involved in specific recognition of the C-terminal membrane-penetrating specificity-determining hairpin domain of the cognate AMP.
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Affiliation(s)
- Gunnar Fimland
- Department of Molecular Biosciences, University of Oslo, Norway
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45
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Beaulieu L, Groleau D, Miguez CB, Jetté JF, Aomari H, Subirade M. Production of pediocin PA-1 in the methylotrophic yeast Pichia pastoris reveals unexpected inhibition of its biological activity due to the presence of collagen-like material. Protein Expr Purif 2005; 43:111-25. [PMID: 16023368 DOI: 10.1016/j.pep.2005.05.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Revised: 05/18/2005] [Accepted: 05/20/2005] [Indexed: 10/25/2022]
Abstract
Expression of the pedA gene from Pediococcus acidilactici, coding for mature bacteriocin Pediocin PA-1, was investigated using the yeast Pichia pastoris to obtain larger quantities of pediocin to support additional studies, including structure-function research. Following various cloning strategies, a KM71H (Mut(s)) strain was selected. A significant concentration (74 microg/ml) of extracellular recombinant pediocin was obtained but the pediocin showed no biological activity. Supernatant fluids from P. pastoris cultures, harboring or not pedA, inhibited the biological activity of natural pediocin PA-1. The recombinant pediocin appeared as a mixture of three main fractions (7-8, 11, 20 kDa vs. 4.6 kDa for natural pediocin PA-1). The recombinant pediocin was also less hydrophobic and behaved differently when subjected to isoelectric focusing. Strong evidence indicated that some "collagen-like" material was tightly associated, most probably via covalent binding, to the recombinant pediocin. The "collagen-like" material was most probably responsible for the lack of biological activity of the recombinant pediocin and for the differences observed regarding some of the physico-chemical properties. Both the recombinant pediocin and natural pediocin were sensitive to collagenase, suggesting that pediocin PA-1 may possess a somewhat "collagen-like" nature. Interestingly, recombinant pediocin preparations showed the ability to assemble into fibrils.
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Affiliation(s)
- Lucie Beaulieu
- Biotechnology Research Institute, National Research Council, 6100 Royalmount Avenue, Montreal, Que., Canada
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Abstract
Bacteriocins are bacterially produced antimicrobial peptides with narrow or broad host ranges. Many bacteriocins are produced by food-grade lactic acid bacteria, a phenomenon which offers food scientists the possibility of directing or preventing the development of specific bacterial species in food. This can be particularly useful in preservation or food safety applications, but also has implications for the development of desirable flora in fermented food. In this sense, bacteriocins can be used to confer a rudimentary form of innate immunity to foodstuffs, helping processors extend their control over the food flora long after manufacture.
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Affiliation(s)
- Paul D Cotter
- Alimentary Pharmabiotic Centre, Microbiology Department, University College Cork, Cork, Ireland
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Suzuki M, Yamamoto T, Kawai Y, Inoue N, Yamazaki K. Mode of action of piscicocin CS526 produced by Carnobacterium piscicola CS526. J Appl Microbiol 2005; 98:1146-51. [PMID: 15836484 DOI: 10.1111/j.1365-2672.2005.02546.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Piscicocin CS526 is a unique class IIa bacteriocin produced by Carnobacterium piscicola CS526. The mode of action against the sensitive strain Listeria monocytogenes IID581 was evaluated. METHODS AND RESULTS Piscicocin CS526 was adsorbed on both sensitive and insensitive gram-positive and gram-negative bacterial cells. Treatment of L. monocytogenes cells with trypsin, lipase and Triton X-100 did not reduce subsequent adsorption of piscicocin CS526. The activity of piscicocin CS526 against L. monocytogenes cells was bactericidal rather than bacteriostatic, but did not cause bacteriolysis. Piscicocin CS526 induced the efflux of K+ ions from the target cells which cause dissipation of the transmembrane potential (DeltaPsi) of the cell membrane. Moreover, after exposure to piscicocin CS526, intracellular adenosine 5'-triphosphate (ATP) level of the target cells rapidly reduced without leakage of ATP from the cells, indicating that ATP depletion occurred in the cells. CONCLUSIONS Pore formation by piscicocin CS526 caused a rapid efflux of small molecules such as K+ from the indicator cells and dissipation of proton motive force (PMF), which lead to the cell death. SIGNIFICANCE AND IMPACT OF THE STUDY Molecular mechanism of action of piscicocin CS526 is very similar to that of other pediocin-like bacteriocins, although piscicocin CS526 possesses a unique N-terminal sequence in which Val is substituted for by Leu in the amino acid at position 7.
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Affiliation(s)
- M Suzuki
- Laboratory of Marine Food Science, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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48
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Yamazaki K, Suzuki M, Kawai Y, Inoue N, Montville TJ. Purification and characterization of a novel class IIa bacteriocin, piscicocin CS526, from surimi-associated Carnobacterium piscicola CS526. Appl Environ Microbiol 2005; 71:554-7. [PMID: 15640235 PMCID: PMC544203 DOI: 10.1128/aem.71.1.554-557.2005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacteriocin piscicocin CS526 was inactivated by proteolytic enzymes, was stable at 100 degrees C for 30 min, had a pH range of 2 to 8, and was active against Enterococcus, Listeria, Pediococcus, and Leuconostoc. The N-terminal sequence was YGNGL, not the YGNGV consensus motif common in class IIa bacteriocins (alternate residues underlined). The molecular mass of piscicocin CS526, which had a bactericidal mode of action, was approximately 4,430 Da.
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Affiliation(s)
- Koji Yamazaki
- Laboratory of Marine Food Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato, Hakodate 041-8611, Japan.
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Castano S, Desbat B, Delfour A, Dumas JM, da Silva A, Dufourcq J. Study of structure and orientation of mesentericin Y105, a bacteriocin from Gram-positive Leuconostoc mesenteroides, and its Trp-substituted analogues in phospholipid environments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1668:87-98. [PMID: 15670734 DOI: 10.1016/j.bbamem.2004.11.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Revised: 11/16/2004] [Accepted: 11/16/2004] [Indexed: 11/19/2022]
Abstract
Mesentericin Y105 (Mes-Y105) is a bacteriocin secreted by Leuconostoc mesenteroides which is particularly active on Listeria. It is constituted by 37 residues and reticulated by one disulfide bridge. It has two W residues, W18 and W37, which can be studied by fluorescence. Two single substituted W/F analogues were synthesized (Mes-Y105/W18 and Mes-Y105/W37) to differentiate the local environment around each W and to study their changes in the presence of lipid vesicles. Fluorescence experiments show that, for the pure Trp-analogues, W18 and W37 are fully exposed to solvent whatever pH and buffer conditions. In the presence of lipid vesicles, both became buried. Lipid affinities were estimated: they are weak for zwitterionic phospholipids but an order of magnitude higher for negatively charged phosphatidylserine (PS) and phosphatidylglycerol (PG) lipids. On negatively charged PG lipids, Mes-Y105 and Mes-Y105/W37 display comparable lipid affinities. A decrease in lipid affinity is observed for Mes-Y105/W18 compared to Mes-Y105, which means that W37 would seem to be required for increased lipid selectivity. In the lipid-bound state W18 is strongly dehydrated, probably embedded into the acyl chains, while W37 stands more at the interface. Mes-Y105 was also studied by polarization modulation infrared reflection absorption spectroscopy (PMIRRAS), alone and in various phospholipid environments, to obtain structural information and to assess lipid perturbations. At nanomolar concentrations close to those required for anti-Listeria activity, Mes-Y105 forms films at the air/water interface and inserts into negatively charged lipid monolayers. In situ infrared data show that Mes-Y105 binding only affects the polar head group vibrations while the lipid order of the acyl chains remains unaffected. The PMIRRAS show that Mes-Y105 folds into an N-terminal antiparallel beta-sheet followed by an alpha-helix, both structures being tilted (40 degrees) compared to the normal at the interface, which is in agreement with the thickness estimated by Brewster angle microscopy (BAM). All these data support the proposal of a new model for Mes-Y105 at the membrane interface.
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Affiliation(s)
- Sabine Castano
- Laboratoire de Physico-Chimie Moléculaire, Université de Bordeaux I, 351 cours de la Libération, 33405 Talence, France.
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Johnsen L, Fimland G, Nissen-Meyer J. The C-terminal domain of pediocin-like antimicrobial peptides (class IIa bacteriocins) is involved in specific recognition of the C-terminal part of cognate immunity proteins and in determining the antimicrobial spectrum. J Biol Chem 2005; 280:9243-50. [PMID: 15611086 DOI: 10.1074/jbc.m412712200] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pediocin-like bacteriocins contain two domains: a cationic N-terminal beta-sheet domain that mediates binding of the bacteriocin to the target cell surface and a more hydrophobic C-terminal hairpin-like domain that penetrates into the hydrophobic part of the target cell membrane. The two domains are joined by a hinge, which enables movement of the domains relative to each other. In this study, 12 different hybrid bacteriocins were constructed by exchanging domains between 5 different bacteriocins. The hybrid bacteriocins were by and large highly potent (i.e. similar potencies as the parental bacteriocins) when constructed such that the recombination point was in the hinge region, indicating that the two domains function independently. The use of optimal recombination points was, however, crucial. Shifting the recombination point just one residue from the hinge could reduce the activity of the hybrid by 3-4 orders of magnitude. Most interestingly, the active hybrids displayed target cell specificities similar to those of the parental bacteriocin from which their membrane-penetrating C-terminal hairpin domain was derived. The results also indicate that the negatively charged aspartate reside in the hinge of most pediocin-like bacteriocins interacts with the C-terminal hairpin domain, perhaps by interacting with the positively charged residue that is present at one of the last three positions in the C-terminal end of most pediocin-like bacteriocins. Bacteria that produce pediocin-like bacteriocins also produce a cognate immunity protein that protects the producer from being killed by its own bacteriocin. Four different active hybrid immunity proteins constructed by exchanging regions between three different immunity proteins were tested for their ability to confer immunity to the hybrid bacteriocins. The results showed that the C-terminal half of the immunity proteins contains a region that directly or indirectly specifically recognizes the membrane-penetrating C-terminal hairpin domain of pediocin-like bacteriocins. The implications these results have on how pediocin-like bacteriocins and their immunity proteins interact with cellular specificity determinants (for instance a putative bacteriocin receptor) are discussed.
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Affiliation(s)
- Line Johnsen
- Program for Biochemistry and Molecular Biology, Department of Molecular Biosciences, University of Oslo, Oslo 0316, Norway.
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