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Hernández M, Areche C, Castañeta G, Rojas D, Varas MA, Marcoleta AE, Chávez FP. Dictyostelium discoideum-assisted pharmacognosy of plant resources for discovering antivirulence molecules targeting Klebsiella pneumoniae. Nat Prod Res 2024:1-8. [PMID: 38829280 DOI: 10.1080/14786419.2024.2360166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/21/2024] [Indexed: 06/05/2024]
Abstract
The rise of antibiotic-resistant bacterial strains represents an important challenge for global health, underscoring the critical need for innovative strategies to confront this threat. Natural products and their derivatives have emerged as a promising reservoir for drug discovery. The social amoeba Dictyostelium discoideum is a potent model organism in this effort. Employing this invertebrate model, we introduce a novel perspective to investigate natural plant extracts in search of molecules with potential antivirulence activity. Our work established an easy-scalable developmental assay targeting a virulent strain of Klebsiella pneumoniae, with Helenium aromaticum as the representative plant. The main objective was to identify tentative compounds from the Helenium aromaticum extract that attenuate the virulence of K. pneumoniae virulence without inducing cytotoxic effects on amoeba cells. Notably, the methanolic root extract of H. aromaticum fulfilled these prerequisites compared to the dichloromethane extract. Using UHPLC Q/Orbitrap/ESI/MS/MS, 63 compounds were tentatively identified in both extracts, 47 in the methanolic and 29 in the dichloromethane, with 13 compounds in common. This research underscores the potential of employing D. discoideum-assisted pharmacognosy to discover new antivirulence agents against multidrug-resistant pathogens.
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Affiliation(s)
- Marcos Hernández
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Carlos Areche
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Grover Castañeta
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Diego Rojas
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Macarena A Varas
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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2
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Baquero F, Beis K, Craik DJ, Li Y, Link AJ, Rebuffat S, Salomón R, Severinov K, Zirah S, Hegemann JD. The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide. Nat Prod Rep 2024; 41:469-511. [PMID: 38164764 DOI: 10.1039/d3np00046j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, 4072 Brisbane, Queensland, Australia
| | - Yanyan Li
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - A James Link
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Raúl Salomón
- Instituto de Química Biológica "Dr Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany.
- Department of Pharmacy, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
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3
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Pfeiffer IPM, Schröder MP, Mordhorst S. Opportunities and challenges of RiPP-based therapeutics. Nat Prod Rep 2024. [PMID: 38411278 DOI: 10.1039/d3np00057e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: up to 2024Ribosomally synthesised and post-translationally modified peptides (RiPPs) comprise a substantial group of peptide natural products exhibiting noteworthy bioactivities ranging from antiinfective to anticancer and analgesic effects. Furthermore, RiPP biosynthetic pathways represent promising production routes for complex peptide drugs, and the RiPP technology is well-suited for peptide engineering to produce derivatives with specific functions. Thus, RiPP natural products possess features that render them potentially ideal candidates for drug discovery and development. Nonetheless, only a small number of RiPP-derived compounds have successfully reached the market thus far. This review initially outlines the therapeutic opportunities that RiPP-based compounds can offer, whilst subsequently discussing the limitations that require resolution in order to fully exploit the potential of RiPPs towards the development of innovative drugs.
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Affiliation(s)
- Isabel P-M Pfeiffer
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Maria-Paula Schröder
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Silja Mordhorst
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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4
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Eslami SM, van der Donk WA. Proteases Involved in Leader Peptide Removal during RiPP Biosynthesis. ACS BIO & MED CHEM AU 2024; 4:20-36. [PMID: 38404746 PMCID: PMC10885120 DOI: 10.1021/acsbiomedchemau.3c00059] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 02/27/2024]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) have received much attention in recent years because of their promising bioactivities and the portability of their biosynthetic pathways. Heterologous expression studies of RiPP biosynthetic enzymes identified by genome mining often leave a leader peptide on the final product to prevent toxicity to the host and to allow the attachment of a genetically encoded affinity purification tag. Removal of the leader peptide to produce the mature natural product is then carried out in vitro with either a commercial protease or a protease that fulfills this task in the producing organism. This review covers the advances in characterizing these latter cognate proteases from bacterial RiPPs and their utility as sequence-dependent proteases. The strategies employed for leader peptide removal have been shown to be remarkably diverse. They include one-step removal by a single protease, two-step removal by two dedicated proteases, and endoproteinase activity followed by aminopeptidase activity by the same protease. Similarly, the localization of the proteolytic step varies from cytoplasmic cleavage to leader peptide removal during secretion to extracellular leader peptide removal. Finally, substrate recognition ranges from highly sequence specific with respect to the leader and/or modified core peptide to nonsequence specific mechanisms.
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Affiliation(s)
- Sara M. Eslami
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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5
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Baquero F, Rodríguez-Beltrán J, Coque TM, del Campo R. Boosting Fitness Costs Associated with Antibiotic Resistance in the Gut: On the Way to Biorestoration of Susceptible Populations. Biomolecules 2024; 14:76. [PMID: 38254676 PMCID: PMC10812938 DOI: 10.3390/biom14010076] [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: 11/25/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
The acquisition and expression of antibiotic resistance implies changes in bacterial cell physiology, imposing fitness costs. Many human opportunistic pathogenic bacteria, such as those causing urinary tract or bloodstream infections, colonize the gut. In this opinionated review, we will examine the various types of stress that these bacteria might suffer during their intestinal stay. These stresses, and their compensatory responses, probably have a fitness cost, which might be additive to the cost of expressing antibiotic resistance. Such an effect could result in a disadvantage relative to antibiotic susceptible populations that might replace the resistant ones. The opinion proposed in this paper is that the effect of these combinations of fitness costs should be tested in antibiotic resistant bacteria with susceptible ones as controls. This testing might provide opportunities to increase the bacterial gut stress boosting physiological biomolecules or using dietary interventions. This approach to reduce the burden of antibiotic-resistant populations certainly must be answered empirically. In the end, the battle against antibiotic resistance should be won by antibiotic-susceptible organisms. Let us help them prevail.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- Network Center for Biomedical Research in Infectious Diseases (CIBER-INFEC), 28034 Madrid, Spain
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6
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Choi GH, Holzapfel WH, Todorov SD. Diversity of the bacteriocins, their classification and potential applications in combat of antibiotic resistant and clinically relevant pathogens. Crit Rev Microbiol 2023; 49:578-597. [PMID: 35731254 DOI: 10.1080/1040841x.2022.2090227] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 12/19/2022]
Abstract
There is almost a century since discovery of penicillin by Alexander Fleming, a century of enthusiasm, abuse, facing development of antibiotic-resistance and clear conclusion that the modern medicine needs a new type of antimicrobials. Bacteriocins produced by Gram-positive and Gram-negative bacteria, Archaea and Eukaryotes were widely explored as potential antimicrobials with several applications in food industry. In last two decades bacteriocins showed their potential as promising alternative therapeutic for the treatment of antibiotic-resistant pathogens. Bacteriocins can be characterised as highly selective antimicrobials and therapeutics with low cytotoxicity. Most probably in order to solve the problems associated with the increasing number of antibiotic-resistant bacteria, the application of natural or bioengineered bacteriocins in addition to synergistically acting preparations of bacteriocins and conventional antibiotics, can be the next step in combat versus drug-resistant pathogens. In this overview we focussed on diversity of specific lactic acid bacteria and their bacteriocins. Moreover, some additional examples of bacteriocins from non-lactic acid, Gram-positive and Gram-negative bacteria, Archaea and eukaryotic organisms are presented and discussed. Therapeutic properties of bacteriocins, their bioengineering and combined applications, together with conventional antibiotics, were evaluated with the scope of application in human and veterinary medicine for combating (multi-)drug-resistant pathogens.
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Affiliation(s)
- Gee-Hyeun Choi
- ProBacLab, Department of Advanced Convergence, Handong Global University, Pohang, Republic of Korea
| | - Wilhelm Heinrich Holzapfel
- Human Effective Microbes, Department of Advanced Convergence, Handong Global University, Pohang, Republic of Korea
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7
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Ma Y, Fu W, Hong B, Wang X, Jiang S, Wang J. Antibacterial MccM as the Major Microcin in Escherichia coli Nissle 1917 against Pathogenic Enterobacteria. Int J Mol Sci 2023; 24:11688. [PMID: 37511446 PMCID: PMC10380612 DOI: 10.3390/ijms241411688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Probiotic Escherichia coli Nissle 1917 (EcN) possesses excellent antibacterial effects on pathogenic enterobacteria. The microcins MccM and MccH47 produced in EcN played critical roles, but they are understudied and poorly characterized, and the individual antibacterial mechanisms are still unclear. In this study, three EcN mutants (ΔmcmA, ΔmchB, and ΔmcmAΔmchB) were constructed and compared with wild-type EcN (EcN wt) to test for inhibitory effects on the growth of Escherichia coli O157: H7, Salmonella enterica (SE), and Salmonella typhimurium (ST). The antibacterial effects on O157: H7 were not affected by the knockout of mcmA (MccM) and mchB (MccH47) in EcN. However, the antibacterial effect on Salmonella declined sharply in EcN mutants ΔmcmA. The overexpressed mcmA gene in EcN::mcmA showed more efficient antibacterial activity on Salmonella than that of EcN wt. Furthermore, the EcN::mcmA strain significantly reduced the abilities of adhesion and invasion of Salmonella to intestinal epithelial cells, decreasing the invasion ability of ST by 56.31% (62.57 times more than that of EcN wt) while reducing the adhesion ability of ST by 50.14% (2.41 times more than that of EcN wt). In addition, the supernatant of EcN::mcmA culture significantly decreased the mRNA expression and secretion of IL-1β, TNF-α, and IL-6 on macrophages induced by LPS. The EcN::mcmA strain generated twice as much orange halo as EcN wt by CAS agar diffusion assay by producing more siderophores. MccM was more closely related to the activity of EcN against Salmonella, and MccM-overproducing EcN inhibited Salmonella growth by producing more siderophores-MccM to compete for iron, which was critical to pathogen growth. Based on the above, EcN::mcmA can be developed as engineered probiotics to fight against pathogenic enterobacteria colonization in the gut.
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Affiliation(s)
- Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Wei Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Bin Hong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xinfeng Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shoujin Jiang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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8
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Abstract
Microcins are a class of antimicrobial peptides produced by certain Gram-negative bacterial species to kill or inhibit the growth of competing bacteria. Only 10 unique, experimentally validated class II microcins have been identified, and the majority of these come from Escherichia coli. Although the current representation of microcins is sparse, they exhibit a diverse array of molecular functionalities, uptake mechanisms, and target specificities. This broad diversity from such a small representation suggests that microcins may have untapped potential for bioprospecting peptide antibiotics from genomic data sets. We used a systematic bioinformatics approach to search for verified and novel class II microcins in E. coli and other species within its family, Enterobacteriaceae. Nearly one-quarter of the E. coli genome assemblies contained one or more microcins, where the prevalence of hits to specific microcins varied by isolate phylogroup. E. coli isolates from human extraintestinal and poultry meat sources were enriched for microcins, while those from freshwater were depleted. Putative microcins were found in various abundances across all five distinct phylogenetic lineages of Enterobacteriaceae, with a particularly high prevalence in the "Klebsiella" clade. Representative genome assemblies from species across the Enterobacterales order, as well as a few outgroup species, also contained putative microcin sequences. This study suggests that microcins have a complicated evolutionary history, spanning far beyond our limited knowledge of the currently validated microcins. Efforts to functionally characterize these newly identified microcins have great potential to open a new field of peptide antibiotics and microbiome modulators and elucidate the ways in which bacteria compete with each other. IMPORTANCE Class II microcins are small bacteriocins produced by strains of Gram-negative bacteria in the Enterobacteriaceae. They are generally understood to play a role in interbacterial competition, although direct evidence of this is limited, and they could prove informative in developing new peptide antibiotics. However, few examples of verified class II microcins exist, and novel microcins are difficult to identify due to their sequence diversity, making it complicated to study them as a group. Here, we overcome this limitation by developing a bioinformatics pipeline to detect microcins in silico. Using this pipeline, we demonstrate that both verified and novel class II microcins are widespread within and outside the Enterobacteriaceae, which has not been systematically shown previously. The observed prevalence of class II microcins suggests that they are ecologically important, and the elucidation of novel microcins provides a resource that can be used to expand our knowledge of the structure and function of microcins as antibacterials.
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9
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Johnston CW, Badran AH. Natural and engineered precision antibiotics in the context of resistance. Curr Opin Chem Biol 2022; 69:102160. [PMID: 35660248 DOI: 10.1016/j.cbpa.2022.102160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Antibiotics are essential weapons in our fight against infectious disease, yet the consequences of broad-spectrum antibiotic use on microbiome stability and pathogen resistance are prompting investigations into more selective alternatives. Echoing the advent of precision medicine in oncology, precision antibiotics with focused activities are emerging as a means of addressing infections without damaging microbiomes or incentivizing resistance. Historically, antibiotic design principles have been gleaned from Nature, and reinvestigation of overlooked antibacterials is now providing scaffolds and targets for the design of pathogen-specific drugs. In this perspective, we summarize the biosynthetic and antibacterial mechanisms used to access these activities, and discuss how such strategies may be co-opted through engineering approaches to afford precision antibiotics.
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Affiliation(s)
- Chad W Johnston
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ahmed H Badran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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10
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Parker JK, Davies BW. Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001175. [PMID: 35438625 PMCID: PMC10233263 DOI: 10.1099/mic.0.001175] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/17/2022] [Indexed: 12/20/2022]
Abstract
Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.
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Affiliation(s)
| | - Bryan William Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
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11
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LAMBERTI MÓNICAFTORREZ, LÓPEZ FABIÁNE, PESCARETTI MARÍADELASMERCEDES, DELGADO MÓNICAA. Characterization of a bacteriocin produced by a clinical isolate of Shigella flexneri 2. AN ACAD BRAS CIENC 2022. [DOI: 10.1590/0001-3765202220200982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | - FABIÁN E. LÓPEZ
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Argentina; Universidad Nacional de Chilecito (UNdeC), Argentina
| | | | - MÓNICA A. DELGADO
- Instituto Superior de Investigaciones Biológicas (INSIBIO), Argentina
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12
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Mcc1229, an Stx2a-amplifying microcin, is produced in vivo and requires CirA for activity. Infect Immun 2021; 90:e0058721. [PMID: 34871041 PMCID: PMC8853679 DOI: 10.1128/iai.00587-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) strains, including the foodborne pathogen E. coli O157:H7, are responsible for thousands of hospitalizations each year. Various environmental triggers can modulate pathogenicity in EHEC by inducing the expression of Shiga toxin (Stx), which is encoded on a lambdoid prophage and transcribed together with phage late genes. Cell-free supernatants of the sequence type 73 (ST73) E. coli strain 0.1229 are potent inducers of Stx2a production in EHEC, suggesting that 0.1229 secretes a factor that activates the SOS response and leads to phage lysis. We previously demonstrated that this factor, designated microcin 1229 (Mcc1229), was proteinaceous and plasmid-encoded. To further characterize Mcc1229 and support its classification as a microcin, we investigated its regulation, determined its receptor, and identified loci providing immunity. The production of Mcc1229 was increased upon iron limitation, as determined by an enzyme-linked immunosorbent assay (ELISA), lacZ fusions, and quantitative real-time PCR (qRT-PCR). Spontaneous Mcc1229-resistant mutants and targeted gene deletion revealed that CirA was the Mcc1229 receptor. TonB, which interacts with CirA in the periplasm, was also essential for Mcc1229 import. Subcloning of the Mcc1229 plasmid indicated that Mcc activity was neutralized by two open reading frames (ORFs), each predicted to encode a domain of unknown function (DUF)-containing protein. In a germfree mouse model of infection, colonization with 0.1229 suppressed subsequent colonization by EHEC. Although Mcc1229 was produced in vivo, it was dispensable for colonization suppression. The regulation, import, and immunity determinants identified here are consistent with features of other Mccs, suggesting that Mcc1229 should be included in this class of small molecules.
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13
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Bin Hafeez A, Jiang X, Bergen PJ, Zhu Y. Antimicrobial Peptides: An Update on Classifications and Databases. Int J Mol Sci 2021; 22:11691. [PMID: 34769122 PMCID: PMC8583803 DOI: 10.3390/ijms222111691] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.
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Affiliation(s)
- Ahmer Bin Hafeez
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan;
| | - Xukai Jiang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Phillip J. Bergen
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
| | - Yan Zhu
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
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14
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Sibinelli-Sousa S, de Araújo-Silva AL, Hespanhol JT, Bayer-Santos E. Revisiting the steps of Salmonella gut infection with a focus on antagonistic interbacterial interactions. FEBS J 2021; 289:4192-4211. [PMID: 34546626 DOI: 10.1111/febs.16211] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/12/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022]
Abstract
A commensal microbial community is established in the mammalian gut during its development, and these organisms protect the host against pathogenic invaders. The hallmark of noninvasive Salmonella gut infection is the induction of inflammation via effector proteins secreted by the type III secretion system, which modulate host responses to create a new niche in which the pathogen can overcome the colonization resistance imposed by the microbiota. Several studies have shown that endogenous microbes are important to control Salmonella infection by competing for resources. However, there is limited information about antimicrobial mechanisms used by commensals and pathogens during these in vivo disputes for niche control. This review aims to revisit the steps that Salmonella needs to overcome during gut colonization-before and after the induction of inflammation-to achieve an effective infection. We focus on a series of reported and hypothetical antagonistic interbacterial interactions in which both contact-independent and contact-dependent mechanisms might define the outcome of the infection.
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Affiliation(s)
| | | | - Julia Takuno Hespanhol
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil
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15
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Ayala JA, Kolter R. The Spanish Society for Microbiology and Latin American microbiologists: seventy-five years of joint scientific ventures. Int Microbiol 2021; 24:657-664. [PMID: 34231086 PMCID: PMC8260328 DOI: 10.1007/s10123-021-00186-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/06/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
As part of this Special Issue of International Microbiology celebrating the 75th anniversary of the founding of the Spanish Society for Microbiology (SEM), Guest Editor Rafael Giraldo invited us to contribute an opinion article on the topic of 75 years of joint scientific ventures between Latin American microbiologists and Spanish microbiologists. Since the creation of SEM in 1945 (Pérez Prieto, NoticiaSEM 98:1, 2016) Latin American microbiologists have been participants, both as individuals and as members of the national associations that are currently integrated into the Latin American Association for Microbiology (ALAM). Thus, the histories of Spanish and Latin American microbiology (Chica and Skinner, Int Microbiol 13:159–164, 2010; Chica, Int Microbiol 11:221–225, 2008) have been closely linked over the last 75 years. In order to provide our perspective on the topic, we decided to provide answers to three questions: What are key aspects of the history of Spanish and Latin American Microbiology interactions? What have been some of our personal experiences in which these interactions shaped our careers? What is our outlook for the future of such interactions?
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Affiliation(s)
- Juan A Ayala
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa, CSIC-UAM, Madrid, Spain.
| | - Roberto Kolter
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
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16
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Dhingra H, Kaur K, Singh B. Engineering and characterization of human β-defensin-3 and its analogues and microcin J25 peptides against Mannheimia haemolytica and bovine neutrophils. Vet Res 2021; 52:83. [PMID: 34112244 PMCID: PMC8194028 DOI: 10.1186/s13567-021-00956-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 05/03/2021] [Indexed: 11/10/2022] Open
Abstract
Mannheimia haemolytica-induced bovine respiratory disease causes loss of millions of dollars to Canadian cattle industry. Current antimicrobials are proving to be ineffective and leave residues in meat. Antimicrobial peptides (AMPs) may be effective against M. haemolytica while minimizing the risk of drug residues. Cationic AMPs can kill bacteria through interactions with the anionic bacterial membrane. Human β-Defensin 3 (HBD3) and microcin J25 (MccJ25) are AMPs with potent activity against many Gram-negative bacteria. We tested the microbicidal activity of wild-type HBD3, three HBD3 peptide analogues (28 amino acid, 20AA, and 10AA) derived from the sequence of natural HBD3, and MccJ25 in vitro against M. haemolytica. Three C-terminal analogues of HBD3 with all cysteines replaced with valines were manually synthesized using solid phase peptide synthesis. Since AMPs can act as chemoattractant we tested the chemotactic effect of HBD3, 28AA, 20AA, and 10AA peptides on bovine neutrophils in Boyden chamber. Minimum bactericidal concentration (MBC) assay showed that M. haemolytica was intermediately sensitive to HBD3, 28AA and 20AA analogues with an MBC of 50 µg/mL. The 10AA analogue had MBC 6.3 µg/mL which is likely a result of lower final inoculum size. MccJ25 didn't have significant bactericidal effect below an MBC < 100 µg/mL. Bovine neutrophils showed chemotaxis towards HBD3 and 20AA peptides (P < 0.05) but not towards 28AA analogue. Co-incubation of neutrophils with any of the peptides did not affect their chemotaxis towards N-formyl-L-methionyl-L-leucyl-phenylalanine (fMLP). The data show that these peptides are effective against M. haemolytica and are chemotactic for neutrophils in vitro.
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Affiliation(s)
- Harpreet Dhingra
- Department of Veterinary Biomedical Science, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Kamaljit Kaur
- Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA, 92618-1908, USA
| | - Baljit Singh
- Department of Veterinary Biomedical Science, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada.
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17
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Shang L, Yu H, Liu H, Chen M, Zeng X, Qiao S. Recombinant antimicrobial peptide microcin J25 alleviates DSS-induced colitis via regulating intestinal barrier function and modifying gut microbiota. Biomed Pharmacother 2021; 139:111127. [PMID: 33819810 DOI: 10.1016/j.biopha.2020.111127] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is rising constantly all over the world. However, current medical treatments are not universally practical. Microcin J25 (MccJ25), a member of the lasso peptides class, has excellent antimicrobial activity both in vitro and in vivo. Here, we assessed the anti-inflammatory effects of MccJ25 through DSS-induced UC mouse model. MccJ25 significantly ameliorated the UC-associated parameters such as decreased body weight, increased disease activity index (DAI) and shortened colon length. MccJ25 also provides barrier protection by preserving structural integrity and reducing inflammatory infiltrates of colon epithelium. The underlying mechanism may be associated with gut microbiota. To test this uncertainty, co-housing experiment was performed, and results indicate homogenized microbiota could relief the inflammatory. Meanwhile, we also proved the prominent role of the possible targets of MccJ25, namely genus Lactobacillus, Bacteroides and Akkermansia (as well as the possible strains related to the important OTUs) in inflammation status through comprehensive analysis. In conclusion, MccJ25 effectively attenuates inflammation and improves disrupted barrier function, and the MccJ25-modified gut microbiota plays a central role in this process.
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Affiliation(s)
- Lijun Shang
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China.
| | - Haitao Yu
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China
| | - Hongbin Liu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518000, PR China
| | - Meixia Chen
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China.
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18
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Pang L, Weeks SD, Van Aerschot A. Aminoacyl-tRNA Synthetases as Valuable Targets for Antimicrobial Drug Discovery. Int J Mol Sci 2021; 22:1750. [PMID: 33578647 PMCID: PMC7916415 DOI: 10.3390/ijms22041750] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 12/20/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyze the esterification of tRNA with a cognate amino acid and are essential enzymes in all three kingdoms of life. Due to their important role in the translation of the genetic code, aaRSs have been recognized as suitable targets for the development of small molecule anti-infectives. In this review, following a concise discussion of aaRS catalytic and proof-reading activities, the various inhibitory mechanisms of reported natural and synthetic aaRS inhibitors are discussed. Using the expanding repository of ligand-bound X-ray crystal structures, we classified these compounds based on their binding sites, focusing on their ability to compete with the association of one, or more of the canonical aaRS substrates. In parallel, we examined the determinants of species-selectivity and discuss potential resistance mechanisms of some of the inhibitor classes. Combined, this structural perspective highlights the opportunities for further exploration of the aaRS enzyme family as antimicrobial targets.
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Affiliation(s)
- Luping Pang
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49–box 1041, 3000 Leuven, Belgium;
- KU Leuven, Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Herestraat 49–box 822, 3000 Leuven, Belgium
| | | | - Arthur Van Aerschot
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49–box 1041, 3000 Leuven, Belgium;
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19
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Telhig S, Ben Said L, Zirah S, Fliss I, Rebuffat S. Bacteriocins to Thwart Bacterial Resistance in Gram Negative Bacteria. Front Microbiol 2020; 11:586433. [PMID: 33240239 PMCID: PMC7680869 DOI: 10.3389/fmicb.2020.586433] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022] Open
Abstract
An overuse of antibiotics both in human and animal health and as growth promoters in farming practices has increased the prevalence of antibiotic resistance in bacteria. Antibiotic resistant and multi-resistant bacteria are now considered a major and increasing threat by national health agencies, making the need for novel strategies to fight bugs and super bugs a first priority. In particular, Gram-negative bacteria are responsible for a high proportion of nosocomial infections attributable for a large part to Enterobacteriaceae, such as pathogenic Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. To cope with their highly competitive environments, bacteria have evolved various adaptive strategies, among which the production of narrow spectrum antimicrobial peptides called bacteriocins and specifically microcins in Gram-negative bacteria. They are produced as precursor peptides that further undergo proteolytic cleavage and in many cases more or less complex posttranslational modifications, which contribute to improve their stability and efficiency. Many have a high stability in the gastrointestinal tract where they can target a single pathogen whilst only slightly perturbing the gut microbiota. Several microcins and antibiotics can bind to similar bacterial receptors and use similar pathways to cross the double-membrane of Gram-negative bacteria and reach their intracellular targets, which they also can share. Consequently, bacteria may use common mechanisms of resistance against microcins and antibiotics. This review describes both unmodified and modified microcins [lasso peptides, siderophore peptides, nucleotide peptides, linear azole(in)e-containing peptides], highlighting their potential as weapons to thwart bacterial resistance in Gram-negative pathogens and discusses the possibility of cross-resistance and co-resistance occurrence between antibiotics and microcins in Gram-negative bacteria.
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Affiliation(s)
- Soufiane Telhig
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Laila Ben Said
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Séverine Zirah
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Ismail Fliss
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
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20
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Bosák J, Hrala M, Micenková L, Šmajs D. Non-antibiotic antibacterial peptides and proteins of Escherichia coli: efficacy and potency of bacteriocins. Expert Rev Anti Infect Ther 2020; 19:309-322. [PMID: 32856960 DOI: 10.1080/14787210.2020.1816824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION The emergence and spread of antibiotic resistance among pathogenic bacteria drives the search for alternative antimicrobial therapies. Bacteriocins represent a potential alternative to antibiotic treatment. In contrast to antibiotics, bacteriocins are peptides or proteins that have relatively narrow spectra of antibacterial activities and are produced by a wide range of bacterial species. Bacteriocins of Escherichia coli are historically classified as microcins and colicins, and, until now, more than 30 different bacteriocin types have been identified and characterized. AREAS COVERED We performed bibliographical searches of online databases to review the literature regarding bacteriocins produced by E. coli with respect to their occurrence, bacteriocin role in bacterial colonization and pathogenicity, and application of their antimicrobial effect. EXPERT OPINION The potential use of bacteriocins for applications in human and animal medicine and the food industry includes (i) the use of bacteriocin-producing probiotic strains, (ii) recombinant production in plants and application in food, and (iii) application of purified bacteriocins.
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Affiliation(s)
- Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Matěj Hrala
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Micenková
- Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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21
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Luna B, Trebosc V, Lee B, Bakowski M, Ulhaq A, Yan J, Lu P, Cheng J, Nielsen T, Lim J, Ketphan W, Eoh H, McNamara C, Skandalis N, She R, Kemmer C, Lociuro S, Dale GE, Spellberg B. A nutrient-limited screen unmasks rifabutin hyperactivity for extensively drug-resistant Acinetobacter baumannii. Nat Microbiol 2020; 5:1134-1143. [PMID: 32514072 PMCID: PMC7483275 DOI: 10.1038/s41564-020-0737-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/10/2020] [Indexed: 11/09/2022]
Abstract
Industry screens of large chemical libraries have traditionally relied on rich media to ensure rapid bacterial growth in high-throughput testing. We used eukaryotic, nutrient-limited growth media in a compound screen that unmasked a previously unknown hyperactivity of the old antibiotic, rifabutin (RBT), against highly resistant Acinetobacter baumannii. In nutrient-limited, but not rich, media, RBT was 200-fold more potent than rifampin. RBT was also substantially more effective in vivo. The mechanism of enhanced efficacy was a Trojan horse-like import of RBT, but not rifampin, through fhuE, only in nutrient-limited conditions. These results are of fundamental importance to efforts to discover antibacterial agents.
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Affiliation(s)
- Brian Luna
- Department of Molecular Microbiology and Immunology, USC Keck School of Medicine, Los Angeles, CA, USA.
| | | | - Bosul Lee
- Department of Molecular Microbiology and Immunology, USC Keck School of Medicine, Los Angeles, CA, USA
| | | | - Amber Ulhaq
- Department of Molecular Microbiology and Immunology, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Jun Yan
- Department of Molecular Microbiology and Immunology, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Peggy Lu
- Department of Molecular Microbiology and Immunology, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Jiaqi Cheng
- Department of Molecular Microbiology and Immunology, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Travis Nielsen
- Department of Molecular Microbiology and Immunology, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Juhyeon Lim
- Department of Molecular Microbiology and Immunology, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Warisa Ketphan
- Department of Molecular Microbiology and Immunology, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Hyungjin Eoh
- Department of Molecular Microbiology and Immunology, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Case McNamara
- Calibr, Scripps Research Institute, La Jolla, CA, USA
| | - Nicholas Skandalis
- Department of Medicine, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Rosemary She
- Department of Pathology, USC Keck School of Medicine, Los Angeles, CA, USA
| | | | | | | | - Brad Spellberg
- Los Angeles County and University of Southern California Medical Center, Los Angeles, CA, USA.
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22
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Massip C, Oswald E. Siderophore-Microcins in Escherichia coli: Determinants of Digestive Colonization, the First Step Toward Virulence. Front Cell Infect Microbiol 2020; 10:381. [PMID: 32974212 PMCID: PMC7472721 DOI: 10.3389/fcimb.2020.00381] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Siderophore-microcins are antimicrobial peptides produced by enterobacteria, especially Escherichia coli and Klebsiella pneumoniae strains. The antibiotic peptide is post-translationally modified by the linkage of a siderophore moiety. Therefore, it can enter and kill phylogenetically related bacteria by a “Trojan Horse” stratagem, by mimicking the iron–siderophore complexes. Consequently, these antimicrobial peptides are key determinants of bacterial competition within the intestinal niche, which is the reservoir for pathogenic E. coli. The most frequent extraintestinal infections caused by E. coli are urinary tract infections. Uropathogenic E. coli (UPEC) can produce many virulence factors, including siderophore-microcins. Siderophore-microcins are chromosomally encoded by small genomic islands that exhibit conserved organization. In UPEC, the siderophore-microcin gene clusters and biosynthetic pathways differ from the “archetypal” models described in fecal strains. The gene cluster is shorter. Thus, active siderophore-microcin production requires proteins from two other genomic islands that also code for virulence factors. This functional and modular synergy confers a strong selective advantage for the domination of the colonic niche, which is the first step toward infection. This optimization of genetic resources might favor the selection of additional virulence factors, which are essential in the subsequent steps of pathogenesis in E. coli infection.
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Affiliation(s)
- Clémence Massip
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France.,Service de Bactériologie-Hygiène, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France.,Service de Bactériologie-Hygiène, Hôpital Purpan, CHU de Toulouse, Toulouse, France
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23
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Kim CS, Li JH, Barco B, Park HB, Gatsios A, Damania A, Wang R, Wyche TP, Piizzi G, Clay NK, Crawford JM. Cellular Stress Upregulates Indole Signaling Metabolites in Escherichia coli. Cell Chem Biol 2020; 27:698-707.e7. [PMID: 32243812 PMCID: PMC7306003 DOI: 10.1016/j.chembiol.2020.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/04/2020] [Accepted: 03/02/2020] [Indexed: 12/13/2022]
Abstract
Escherichia coli broadly colonize the intestinal tract of humans and produce a variety of small molecule signals. However, many of these small molecules remain unknown. Here, we describe a family of widely distributed bacterial metabolites termed the "indolokines." In E. coli, the indolokines are upregulated in response to a redox stressor via aspC and tyrB transaminases. Although indolokine 1 represents a previously unreported metabolite, four of the indolokines (2-5) were previously shown to be derived from indole-3-carbonyl nitrile (ICN) in the plant pathogen defense response. We show that the indolokines are produced in a convergent evolutionary manner relative to plants, enhance E. coli persister cell formation, outperform ICN protection in an Arabidopsis thaliana-Pseudomonas syringae infection model, trigger a hallmark plant innate immune response, and activate distinct immunological responses in primary human tissues. Our molecular studies link a family of cellular stress-induced metabolites to defensive responses across bacteria, plants, and humans.
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Affiliation(s)
- Chung Sub Kim
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jhe-Hao Li
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Brenden Barco
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Hyun Bong Park
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Alexandra Gatsios
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Ashiti Damania
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Rurun Wang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Thomas P Wyche
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Grazia Piizzi
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Nicole K Clay
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA.
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24
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Li Z, Chinnasamy S, Zhang Y, Wei DQ. Molecular dynamics simulation and binding free energy calculations of microcin J25 binding to the FhuA receptor. J Biomol Struct Dyn 2020; 39:2585-2594. [DOI: 10.1080/07391102.2020.1751293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Zhenhua Li
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yonghong Zhang
- Chongqing Research Center for Pharmaceutical Engineering, College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism and College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Center of Interdisciplinary Science-Computational Life Sciences, College of Food Science and Engineering, Henan University of Technology, Zhengzhou High-tech Industrial Development Zone, Zhengzhou, Henan, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, P.R China
- Ministry of Education, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, P.R China
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25
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Mhlongo JT, Brasil E, de la Torre BG, Albericio F. Naturally Occurring Oxazole-Containing Peptides. Mar Drugs 2020; 18:md18040203. [PMID: 32290087 PMCID: PMC7231064 DOI: 10.3390/md18040203] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/29/2022] Open
Abstract
Oxazole-containing peptides are mostly of marine origin and they form an intriguing family with a broad range of biological activities. Here we classify these peptides on the basis of their chemical structure and discuss a number of representatives of each class that reflect the extraordinary potential of this family as a source of new drugs.
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Affiliation(s)
- Jessica T. Mhlongo
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa; (J.T.M.); (E.B.)
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Edikarlos Brasil
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa; (J.T.M.); (E.B.)
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Beatriz G. de la Torre
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa; (J.T.M.); (E.B.)
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- Correspondence: (B.G.d.l.T.); (F.A.); Tel.: +27-614009144 (F.A.)
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa; (J.T.M.); (E.B.)
- CIBER-BBN (Networking Centre on Bioengineering, Biomaterials and Nanomedicine) and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
- Correspondence: (B.G.d.l.T.); (F.A.); Tel.: +27-614009144 (F.A.)
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26
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Wang N, Saidhareddy P, Jiang X. Construction of sulfur-containing moieties in the total synthesis of natural products. Nat Prod Rep 2020; 37:246-275. [DOI: 10.1039/c8np00093j] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This review surveys the total syntheses of sulfur-containing natural products where sulfur atoms are introduced with different sulfurization agents to construct related sulfur-containing moieties.
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Affiliation(s)
- Nengzhong Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- P. R. China
| | - Puli Saidhareddy
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- P. R. China
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
- P. R. China
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Baquero F, Lanza VF, Baquero MR, Del Campo R, Bravo-Vázquez DA. Microcins in Enterobacteriaceae: Peptide Antimicrobials in the Eco-Active Intestinal Chemosphere. Front Microbiol 2019; 10:2261. [PMID: 31649628 PMCID: PMC6795089 DOI: 10.3389/fmicb.2019.02261] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/17/2019] [Indexed: 12/31/2022] Open
Abstract
Microcins are low-molecular-weight, ribosomally produced, highly stable, bacterial-inhibitory molecules involved in competitive, and amensalistic interactions between Enterobacteriaceae in the intestine. These interactions take place in a highly complex chemical landscape, the intestinal eco-active chemosphere, composed of chemical substances that positively or negatively influence bacterial growth, including those originated from nutrient uptake, and those produced by the action of the human or animal host and the intestinal microbiome. The contribution of bacteria results from their effect on the host generated molecules, on food and digested food, and organic substances from microbial origin, including from bacterial degradation. Here, we comprehensively review the main chemical substances present in the human intestinal chemosphere, particularly of those having inhibitory effects on microorganisms. With this background, and focusing on Enterobacteriaceae, the most relevant human pathogens from the intestinal microbiota, the microcin’s history and classification, mechanisms of action, and mechanisms involved in microcin’s immunity (in microcin producers) and resistance (non-producers) are reviewed. Products from the chemosphere likely modulate the ecological effects of microcin activity. Several cross-resistance mechanisms are shared by microcins, colicins, bacteriophages, and some conventional antibiotics, which are expected to produce cross-effects. Double-microcin-producing strains (such as microcins MccM and MccH47) have been successfully used for decades in the control of pathogenic gut organisms. Microcins are associated with successful gut colonization, facilitating translocation and invasion, leading to bacteremia, and urinary tract infections. In fact, Escherichia coli strains from the more invasive phylogroups (e.g., B2) are frequently microcinogenic. A publicly accessible APD3 database http://aps.unmc.edu/AP/ shows particular genes encoding microcins in 34.1% of E. coli strains (mostly MccV, MccM, MccH47, and MccI47), and much less in Shigella and Salmonella (<2%). Some 4.65% of Klebsiella pneumoniae are microcinogenic (mostly with MccE492), and even less in Enterobacter or Citrobacter (mostly MccS). The high frequency and variety of microcins in some Enterobacteriaceae indicate key ecological functions, a notion supported by their dominance in the intestinal microbiota of biosynthetic gene clusters involved in the synthesis of post-translationally modified peptide microcins.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Val F Lanza
- Bioinformatics Unit, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Maria-Rosario Baquero
- Department of Microbiology, Alfonso X El Sabio University, Villanueva de la Cañada, Spain
| | - Rosa Del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Daniel A Bravo-Vázquez
- Department of Microbiology, Alfonso X El Sabio University, Villanueva de la Cañada, Spain
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Massip C, Branchu P, Bossuet-Greif N, Chagneau CV, Gaillard D, Martin P, Boury M, Sécher T, Dubois D, Nougayrède JP, Oswald E. Deciphering the interplay between the genotoxic and probiotic activities of Escherichia coli Nissle 1917. PLoS Pathog 2019; 15:e1008029. [PMID: 31545853 PMCID: PMC6776366 DOI: 10.1371/journal.ppat.1008029] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 10/03/2019] [Accepted: 08/14/2019] [Indexed: 12/28/2022] Open
Abstract
Although Escherichia coli Nissle 1917 (EcN) has been used therapeutically for over a century, the determinants of its probiotic properties remain elusive. EcN produces two siderophore-microcins (Mcc) responsible for an antagonistic activity against other Enterobacteriaceae. EcN also synthesizes the genotoxin colibactin encoded by the pks island. Colibactin is a virulence factor and a putative pro-carcinogenic compound. Therefore, we aimed to decouple the antagonistic activity of EcN from its genotoxic activity. We demonstrated that the pks-encoded ClbP, the peptidase that activates colibactin, is required for the antagonistic activity of EcN. The analysis of a series of ClbP mutants revealed that this activity is linked to the transmembrane helices of ClbP and not the periplasmic peptidase domain, indicating the transmembrane domain is involved in some aspect of Mcc biosynthesis or secretion. A single amino acid substitution in ClbP inactivates the genotoxic activity but maintains the antagonistic activity. In an in vivo salmonellosis model, this point mutant reduced the clinical signs and the fecal shedding of Salmonella similarly to the wild type strain, whereas the clbP deletion mutant could neither protect nor outcompete the pathogen. The ClbP-dependent antibacterial effect was also observed in vitro with other E. coli strains that carry both a truncated form of the Mcc gene cluster and the pks island. In such strains, siderophore-Mcc synthesis also required the glucosyltransferase IroB involved in salmochelin production. This interplay between colibactin, salmochelin, and siderophore-Mcc biosynthetic pathways suggests that these genomic islands were co-selected and played a role in the evolution of E. coli from phylogroup B2. This co-evolution observed in EcN illustrates the fine margin between pathogenicity and probiotic activity, and the need to address both the effectiveness and safety of probiotics. Decoupling the antagonistic from the genotoxic activity by specifically inactivating ClbP peptidase domain opens the way to the safe use of EcN.
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Affiliation(s)
- Clémence Massip
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | - Priscilla Branchu
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | | | | | - Déborah Gaillard
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Patricia Martin
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Michèle Boury
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Thomas Sécher
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Damien Dubois
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
| | | | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Service de Bactériologie-Hygiène, Toulouse, France
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Thiostrepton Hijacks Pyoverdine Receptors To Inhibit Growth of Pseudomonas aeruginosa. Antimicrob Agents Chemother 2019; 63:AAC.00472-19. [PMID: 31262758 DOI: 10.1128/aac.00472-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/23/2019] [Indexed: 12/24/2022] Open
Abstract
Pseudomonas aeruginosa is a biofilm-forming opportunistic pathogen and is intrinsically resistant to many antibiotics. In a high-throughput screen for molecules that modulate biofilm formation, we discovered that the thiopeptide antibiotic thiostrepton (TS), which is considered to be inactive against Gram-negative bacteria, stimulated P. aeruginosa biofilm formation in a dose-dependent manner. This phenotype is characteristic of exposure to antimicrobial compounds at subinhibitory concentrations, suggesting that TS was active against P. aeruginosa Supporting this observation, TS inhibited the growth of a panel of 96 multidrug-resistant (MDR) P. aeruginosa clinical isolates at low-micromolar concentrations. TS also had activity against Acinetobacter baumannii clinical isolates. The expression of Tsr, a 23S rRNA-modifying methyltransferase from TS producer Streptomyces azureus, in trans conferred TS resistance, confirming that the drug acted via its canonical mode of action, inhibition of ribosome function. The deletion of oligopeptide permease systems used by other peptide antibiotics for uptake failed to confer TS resistance. TS susceptibility was inversely proportional to iron availability, suggesting that TS exploits uptake pathways whose expression is increased under iron starvation. Consistent with this finding, TS activity against P. aeruginosa and A. baumannii was potentiated by the FDA-approved iron chelators deferiprone and deferasirox and by heat-inactivated serum. Screening of P. aeruginosa mutants for TS resistance revealed that it exploits pyoverdine receptors FpvA and FpvB to cross the outer membrane. We show that the biofilm stimulation phenotype can reveal cryptic subinhibitory antibiotic activity, and that TS has activity against select multidrug-resistant Gram-negative pathogens under iron-limited growth conditions, similar to those encountered at sites of infection.
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30
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Raffatellu M. Learning from bacterial competition in the host to develop antimicrobials. Nat Med 2018; 24:1097-1103. [DOI: 10.1038/s41591-018-0145-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 05/24/2018] [Accepted: 07/03/2018] [Indexed: 02/07/2023]
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31
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Garcia-Gutierrez E, Mayer MJ, Cotter PD, Narbad A. Gut microbiota as a source of novel antimicrobials. Gut Microbes 2018; 10:1-21. [PMID: 29584555 PMCID: PMC6363078 DOI: 10.1080/19490976.2018.1455790] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 02/08/2023] Open
Abstract
Bacteria, Archaea, Eukarya and viruses coexist in the human gut, and this coexistence is functionally balanced by symbiotic or antagonistic relationships. Antagonism is often characterized by the production of antimicrobials against other organisms occupying the same environmental niche. Indeed, close co-evolution in the gut has led to the development of specialized antimicrobials, which is attracting increased attention as these may serve as novel alternatives to antibiotics and thereby help to address the global problem of antimicrobial resistance. The gastrointestinal (GI) tract is especially suitable for finding novel antimicrobials due to the vast array of microbes that inhabit it, and a considerable number of antimicrobial producers of both wide and narrow spectrum have been described. In this review, we summarize some of the antimicrobial compounds that are produced by bacteria isolated from the gut environment, with a special focus on bacteriocins. We also evaluate the potential therapeutic application of these compounds to maintain homeostasis in the gut and the biocontrol of pathogenic bacteria.
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Affiliation(s)
- Enriqueta Garcia-Gutierrez
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
- Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
| | - Melinda J. Mayer
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
| | - Paul D. Cotter
- Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
- APC Microbiome, Ireland
| | - Arjan Narbad
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
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32
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Iyer SS, Gensollen T, Gandhi A, Oh SF, Neves JF, Collin F, Lavin R, Serra C, Glickman J, de Silva PSA, Sartor RB, Besra G, Hauser R, Maxwell A, Llebaria A, Blumberg RS. Dietary and Microbial Oxazoles Induce Intestinal Inflammation by Modulating Aryl Hydrocarbon Receptor Responses. Cell 2018; 173:1123-1134.e11. [PMID: 29775592 PMCID: PMC6119676 DOI: 10.1016/j.cell.2018.04.037] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 12/07/2017] [Accepted: 04/25/2018] [Indexed: 11/22/2022]
Abstract
Genome-wide association studies have identified risk loci associated with the development of inflammatory bowel disease, while epidemiological studies have emphasized that pathogenesis likely involves host interactions with environmental elements whose source and structure need to be defined. Here, we identify a class of compounds derived from dietary, microbial, and industrial sources that are characterized by the presence of a five-membered oxazole ring and induce CD1d-dependent intestinal inflammation. We observe that minimal oxazole structures modulate natural killer T cell-dependent inflammation by regulating lipid antigen presentation by CD1d on intestinal epithelial cells (IECs). CD1d-restricted production of interleukin 10 by IECs is limited through activity of the aryl hydrocarbon receptor (AhR) pathway in response to oxazole induction of tryptophan metabolites. As such, the depletion of the AhR in the intestinal epithelium abrogates oxazole-induced inflammation. In summary, we identify environmentally derived oxazoles as triggers of CD1d-dependent intestinal inflammatory responses that occur via activation of the AhR in the intestinal epithelium.
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MESH Headings
- Animals
- Antigens, CD1d/genetics
- Antigens, CD1d/metabolism
- Colitis/chemically induced
- Colitis/metabolism
- Colitis/pathology
- Diet
- Disease Models, Animal
- Epithelial Cells/cytology
- Epithelial Cells/drug effects
- Epithelial Cells/metabolism
- Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism
- Interleukin-10/metabolism
- Intestines/cytology
- Intestines/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Natural Killer T-Cells/immunology
- Oxazoles/pharmacology
- RNA Interference
- RNA, Small Interfering/metabolism
- Receptors, Aryl Hydrocarbon/antagonists & inhibitors
- Receptors, Aryl Hydrocarbon/genetics
- Receptors, Aryl Hydrocarbon/metabolism
- Signal Transduction/drug effects
- Tryptophan/metabolism
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Affiliation(s)
- Shankar S Iyer
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Thomas Gensollen
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amit Gandhi
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sungwhan F Oh
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joana F Neves
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Frederic Collin
- Inspiralis, Innovation Centre, Norwich Research Park, Colney Lane, Norwich NR4 7GJ, UK
| | - Richard Lavin
- Center for Clinical and Translational Metagenomics, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carme Serra
- Laboratory of Medicinal Chemistry, Department of Biomedicinal Chemistry, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain
| | - Jonathan Glickman
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Punyanganie S A de Silva
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - R Balfour Sartor
- Departments of Medicine, and Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Gurdyal Besra
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Russell Hauser
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Amadeu Llebaria
- Laboratory of Medicinal Chemistry, Department of Biomedicinal Chemistry, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain
| | - Richard S Blumberg
- Division of Gastroenterology, Hepatology, and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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33
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Danilovich ME, Sánchez LA, Acosta F, Delgado OD. Antarctic bioprospecting: in pursuit of microorganisms producing new antimicrobials and enzymes. Polar Biol 2018. [DOI: 10.1007/s00300-018-2295-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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34
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Marcoleta AE, Varas MA, Ortiz-Severín J, Vásquez L, Berríos-Pastén C, Sabag AV, Chávez FP, Allende ML, Santiviago CA, Monasterio O, Lagos R. Evaluating Different Virulence Traits of Klebsiella pneumoniae Using Dictyostelium discoideum and Zebrafish Larvae as Host Models. Front Cell Infect Microbiol 2018; 8:30. [PMID: 29479519 PMCID: PMC5811510 DOI: 10.3389/fcimb.2018.00030] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/23/2018] [Indexed: 01/26/2023] Open
Abstract
Multiresistant and invasive hypervirulent Klebsiella pneumoniae strains have become one of the most urgent bacterial pathogen threats. Recent analyses revealed a high genomic plasticity of this species, harboring a variety of mobile genetic elements associated with virulent strains, encoding proteins of unknown function whose possible role in pathogenesis have not been addressed. K. pneumoniae virulence has been studied mainly in animal models such as mice and pigs, however, practical, financial, ethical and methodological issues limit the use of mammal hosts. Consequently, the development of simple and cost-effective experimental approaches with alternative host models is needed. In this work we described the use of both, the social amoeba and professional phagocyte Dictyostelium discoideum and the fish Danio rerio (zebrafish) as surrogate host models to study K. pneumoniae virulence. We compared three K. pneumoniae clinical isolates evaluating their resistance to phagocytosis, intracellular survival, lethality, intestinal colonization, and innate immune cells recruitment. Optical transparency of both host models permitted studying the infective process in vivo, following the Klebsiella-host interactions through live-cell imaging. We demonstrated that K. pneumoniae RYC492, but not the multiresistant strains 700603 and BAA-1705, is virulent to both host models and elicits a strong immune response. Moreover, this strain showed a high resistance to phagocytosis by D. discoideum, an increased ability to form biofilms and a more prominent and irregular capsule. Besides, the strain 700603 showed the unique ability to replicate inside amoeba cells. Genomic comparison of the K. pneumoniae strains showed that the RYC492 strain has a higher overall content of virulence factors although no specific genes could be linked to its phagocytosis resistance, nor to the intracellular survival observed for the 700603 strain. Our results indicate that both zebrafish and D. discoideum are advantageous host models to study different traits of K. pneumoniae that are associated with virulence.
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Affiliation(s)
- Andrés E Marcoleta
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Macarena A Varas
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Javiera Ortiz-Severín
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Leonardo Vásquez
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Berríos-Pastén
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Andrea V Sabag
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Miguel L Allende
- Departamento de Biología, Facultad de Ciencias, Centro FONDAP de Regulación del Genoma, Universidad de Chile, Santiago, Chile
| | - Carlos A Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rosalba Lagos
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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35
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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36
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Microcin PDI regulation and proteolytic cleavage are unique among known microcins. Sci Rep 2017; 7:42529. [PMID: 28205647 PMCID: PMC5311971 DOI: 10.1038/srep42529] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/09/2017] [Indexed: 11/16/2022] Open
Abstract
Microcin PDI inhibits a diversity of pathogenic Escherichia coli through the action of an effector protein, McpM. In this study we demonstrated that expression of the inhibitory phenotype is induced under low osmolarity conditions and expression is primarily controlled by the EnvZ/OmpR two-component regulatory system. Functional, mutagenesis and complementation experiments were used to empirically demonstrate that EnvZ is required for the inhibitory phenotype and that regulation of mcpM is dependent on binding of the phosphorylated OmpR to the mcpM promoter region. The phosphorylated OmpR may recognize three different binding sites within this promoter region. Site-directed mutagenesis revealed that the McpM precursor peptide includes two leader peptides that undergo sequential cleavage at positions G17/G18 and G35/A36 during export through the type I secretion system. Competition assays showed that both cleaved products are required for the PDI phenotype although we could not distinguish loss of function from loss of secretion in these assays. McpM has four cysteines within the mature peptide and site-directed mutagenesis experiments demonstrated that the first two cysteines are necessary for McpM to inhibit susceptible cells. Together these data combined with previous work indicate that MccPDI is unique amongst the microcins that have been described to date.
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37
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Quereda JJ, Meza-Torres J, Cossart P, Pizarro-Cerdá J. Listeriolysin S: A bacteriocin from epidemic Listeria monocytogenes strains that targets the gut microbiota. Gut Microbes 2017; 8:384-391. [PMID: 28156183 PMCID: PMC5570420 DOI: 10.1080/19490976.2017.1290759] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Listeria monocytogenes is a Gram-positive food-borne pathogen that in humans may traverse the intestinal, placental and blood/brain barriers, causing gastroenteritis, abortions and meningitis. Crossing of these barriers is dependent on the bacterial ability to enter host cells, and several L. monocytogenes surface and secreted virulence factors are known to facilitate entry and the intracellular lifecycle. The study of L. monocytogenes strains associated to human listeriosis epidemics has revealed the presence of novel virulence factors. One such factor is Listeriolysin S, a thiazole/oxazole modified microcin that displays bactericidal activity and modifies the host microbiota during infection. Our recent results therefore highlight the interaction of L. monocytogenes with gut microbes as a crucial step in epidemic listeriosis. In this article, we will discuss novel implications for this family of toxins in the pathogenesis of diverse medically relevant microorganisms.
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Affiliation(s)
- Juan J. Quereda
- Institut Pasteur, Unité Des Interactions Bactéries-Cellules, Paris, France,INSERM, U604, Paris, France,INRA, USC2020, Paris, France
| | - Jazmín Meza-Torres
- Institut Pasteur, Unité Des Interactions Bactéries-Cellules, Paris, France,INSERM, U604, Paris, France,INRA, USC2020, Paris, France
| | - Pascale Cossart
- Institut Pasteur, Unité Des Interactions Bactéries-Cellules, Paris, France,INSERM, U604, Paris, France,INRA, USC2020, Paris, France
| | - Javier Pizarro-Cerdá
- Institut Pasteur, Unité Des Interactions Bactéries-Cellules, Paris, France,INSERM, U604, Paris, France,INRA, USC2020, Paris, France,CONTACT Javier Pizarro-Cerda Unité des Interactions Bactéries-Cellules, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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38
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Maxson T, Mitchell DA. Targeted Treatment for Bacterial Infections: Prospects for Pathogen-Specific Antibiotics Coupled with Rapid Diagnostics. Tetrahedron 2016; 72:3609-3624. [PMID: 27429480 PMCID: PMC4941824 DOI: 10.1016/j.tet.2015.09.069] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Antibiotics are a cornerstone of modern medicine and have significantly reduced the burden of infectious diseases. However, commonly used broad-spectrum antibiotics can cause major collateral damage to the human microbiome, causing complications ranging from antibiotic-associated colitis to the rapid spread of resistance. Employing narrower spectrum antibiotics targeting specific pathogens may alleviate this predicament as well as provide additional tools to expand an antibiotic repertoire threatened by the inevitability of resistance. Improvements in clinical diagnosis will be required to effectively utilize pathogen-specific antibiotics and new molecular diagnostics are poised to fulfill this need. Here we review recent trends and the future prospects of deploying narrower spectrum antibiotics coupled with rapid diagnostics. Further, we discuss the theoretical advantages and limitations of this emerging approach to controlling bacterial infectious diseases.
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Affiliation(s)
- Tucker Maxson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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39
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Marcoleta AE, Berríos-Pastén C, Nuñez G, Monasterio O, Lagos R. Klebsiella pneumoniae Asparagine tDNAs Are Integration Hotspots for Different Genomic Islands Encoding Microcin E492 Production Determinants and Other Putative Virulence Factors Present in Hypervirulent Strains. Front Microbiol 2016; 7:849. [PMID: 27375573 PMCID: PMC4891358 DOI: 10.3389/fmicb.2016.00849] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/23/2016] [Indexed: 01/09/2023] Open
Abstract
Due to the developing of multi-resistant and invasive hypervirulent strains, Klebsiella pneumoniae has become one of the most urgent bacterial pathogen threats in the last years. Genomic comparison of a growing number of sequenced isolates has allowed the identification of putative virulence factors, proposed to be acquirable mainly through horizontal gene transfer. In particular, those related with synthesizing the antibacterial peptide microcin E492 (MccE492) and salmochelin siderophores were found to be highly prevalent among hypervirulent strains. The determinants for the production of both molecules were first reported as part of a 13-kbp segment of K. pneumoniae RYC492 chromosome, and were cloned and characterized in E. coli. However, the genomic context of this segment in K. pneumoniae remained uncharacterized. In this work, we provided experimental and bioinformatics evidence indicating that the MccE492 cluster is part of a highly conserved 23-kbp genomic island (GI) named GIE492, that was integrated in a specific asparagine-tRNA gene (asn-tDNA) and was found in a high proportion of isolates from liver abscesses sampled around the world. This element resulted to be unstable and its excision frequency increased after treating bacteria with mitomycin C and upon the overexpression of the island-encoded integrase. Besides the MccE492 genetic cluster, it invariably included an integrase-coding gene, at least seven protein-coding genes of unknown function, and a putative transfer origin that possibly allows this GI to be mobilized through conjugation. In addition, we analyzed the asn-tDNA loci of all the available K. pneumoniae assembled chromosomes to evaluate them as GI-integration sites. Remarkably, 73% of the strains harbored at least one GI integrated in one of the four asn-tDNA present in this species, confirming them as integration hotspots. Each of these tDNAs was occupied with different frequencies, although they were 100% identical. Also, we identified a total of 47 asn-tDNA-associated GIs that were classified into 12 groups of homology differing in theencoded functionalities but sharing with GIE492 a conserved recombination module and potentially its mobility features. Most of these GIs encoded factors with proven or potential role in pathogenesis, constituting a major reservoir of virulence factors in this species.
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Affiliation(s)
- Andrés E Marcoleta
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Camilo Berríos-Pastén
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Gonzalo Nuñez
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Rosalba Lagos
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
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40
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Zukher I, Novikova M, Tikhonov A, Nesterchuk MV, Osterman IA, Djordjevic M, Sergiev PV, Sharma CM, Severinov K. Ribosome-controlled transcription termination is essential for the production of antibiotic microcin C. Nucleic Acids Res 2014; 42:11891-902. [PMID: 25274735 PMCID: PMC4231749 DOI: 10.1093/nar/gku880] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Microcin C (McC) is a peptide–nucleotide antibiotic produced by Escherichia coli cells harboring a plasmid-borne operon mccABCDE. The heptapeptide MccA is converted into McC by adenylation catalyzed by the MccB enzyme. Since MccA is a substrate for MccB, a mechanism that regulates the MccA/MccB ratio likely exists. Here, we show that transcription from a promoter located upstream of mccA directs the synthesis of two transcripts: a short highly abundant transcript containing the mccA ORF and a longer minor transcript containing mccA and downstream ORFs. The short transcript is generated when RNA polymerase terminates transcription at an intrinsic terminator located in the intergenic region between the mccA and mccB genes. The function of this terminator is strongly attenuated by upstream mcc sequences. Attenuation is relieved and transcription termination is induced when ribosome binds to the mccA ORF. Ribosome binding also makes the mccA RNA exceptionally stable. Together, these two effects—ribosome-induced transcription termination and stabilization of the message—account for very high abundance of the mccA transcript that is essential for McC production. The general scheme appears to be evolutionary conserved as ribosome-induced transcription termination also occurs in a homologous operon from Helicobacter pylori.
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Affiliation(s)
- Inna Zukher
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia Waksman Institute for Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA St. Petersburg State Polytechnical University, St. Petersburg, Russia
| | - Maria Novikova
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Anton Tikhonov
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, Russia
| | | | - Ilya A Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | - Petr V Sergiev
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Cynthia M Sharma
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg, Germany
| | - Konstantin Severinov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia Waksman Institute for Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA St. Petersburg State Polytechnical University, St. Petersburg, Russia Skolkovo Institute of Science and Technology, Skolkovo, Russia
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41
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Genomic and metabolomic insights into the natural product biosynthetic diversity of a feral-hog-associated Brevibacillus laterosporus strain. PLoS One 2014; 9:e90124. [PMID: 24595070 PMCID: PMC3940840 DOI: 10.1371/journal.pone.0090124] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/26/2014] [Indexed: 12/04/2022] Open
Abstract
Bacteria associated with mammals are a rich source of microbial biodiversity; however, little is known concerning the abilities of these microbes to generate secondary metabolites. This report focuses on a bacterium isolated from the ear of a feral hog from southwestern Oklahoma, USA. The bacterium was identified as a new strain (PE36) of Brevibacillus latersporus, which was shown via genomic analysis to contain a large number of gene clusters presumably involved in secondary metabolite biosynthesis. A scale-up culture of B. latersporus PE36 yielded three bioactive compounds that inhibited the growth of methicillin-resistant Staphylococcus aureus (basiliskamides A and B and 12-methyltetradecanoic acid). Further studies of the isolate's secondary metabolome provided both new (auripyrazine) and previously-described pyrazine-containing compounds. In addition, a new peptidic natural product (auriporcine) was purified that was determined to be composed of a polyketide unit, two L-proline residues, two D-leucine residues, one L-leucine residue, and a reduced L-phenylalanine (L-phenylalanol). An examination of the genome revealed two gene clusters that are likely responsible for generating the basiliskamides and auriporcine. These combined genomic and chemical studies confirm that new and unusual secondary metabolites can be obtained from the bacterial associates of wild mammals.
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42
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Thompson RE, Collin F, Maxwell A, Jolliffe KA, Payne RJ. Synthesis of full length and truncated microcin B17 analogues as DNA gyrase poisons. Org Biomol Chem 2014; 12:1570-8. [DOI: 10.1039/c3ob42516a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a combination of solid-phase peptide synthesis and fragment assembly strategies a library of full-length and truncated analogues of the antibacterial post-translationally modified peptide microcin B17 have been synthesised. Both antibacterial and DNA gyrase poisoning activities are also described for the synthetic analogues.
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Affiliation(s)
| | - Frédéric Collin
- Department of Biological Chemistry
- John Innes Centre
- Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry
- John Innes Centre
- Norwich NR4 7UH, UK
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43
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Structure of microcin B-like compounds produced by Pseudomonas syringae and species specificity of their antibacterial action. J Bacteriol 2013; 195:4129-37. [PMID: 23852863 DOI: 10.1128/jb.00665-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli microcin B (Ec-McB) is a posttranslationally modified antibacterial peptide containing multiple oxazole and thiazole heterocycles and targeting the DNA gyrase. We have found operons homologous to the Ec-McB biosynthesis-immunity operon mcb in recently sequenced genomes of several pathovars of the plant pathogen Pseudomonas syringae, and we produced two variants of P. syringae microcin B (Ps-McB) in E. coli by heterologous expression. Like Ec-McB, both versions of Ps-McB target the DNA gyrase, but unlike Ec-McB, they are active against various species of the Pseudomonas genus, including human pathogen P. aeruginosa. Through analysis of Ec-McB/Ps-McB chimeras, we demonstrate that three centrally located unmodified amino acids of Ps-McB are sufficient to determine activity against Pseudomonas, likely by allowing specific recognition by a transport system that remains to be identified. The results open the way for construction of McB-based antibacterial molecules with extended spectra of biological activity.
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44
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The role of bacterial membrane proteins in the internalization of microcin MccJ25 and MccB17. Biochem Soc Trans 2013; 40:1539-43. [PMID: 23176513 DOI: 10.1042/bst20120176] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Microcins are gene-encoded antibacterial peptides of low molecular mass (<10 kDa), produced by Enterobactericeae. They are produced and secreted under conditions of limited essential nutrients and are active against related species. Bacterial strains under starvation conditions can produce and release microcins that can kill microcin-sensitive cells and therefore have more nutrients for survival. The outer-membrane protein OmpF and FhuA TonB-dependent pathways facilitate the internalization of the MccB17 and MccJ25 microcins into the target cell respectively. The inner-membrane protein SbmA transports the microcins through the inner membrane to the cytoplasmic face. Inside the cell, MccB17 targets DNA gyrase, whereas MccJ25 inhibits the bacterial RNA polymerase.
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45
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Whole-Genome Sequence of the Microcin E492-Producing Strain Klebsiella pneumoniae RYC492. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00178-13. [PMID: 23661477 PMCID: PMC3650436 DOI: 10.1128/genomea.00178-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of the Gram-negative strain Klebsiella pneumoniae RYC492, which produces the amyloid-forming and antibacterial peptide microcin E492. The sequenced genome consists of a 5,095,761-bp assembled open chromosome where the gene cluster for microcin production is located in a putative 31-kb genomic island flanked by sequence repeats and containing a putative integrase-coding gene.
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46
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Collin F, Thompson RE, Jolliffe KA, Payne RJ, Maxwell A. Fragments of the bacterial toxin microcin B17 as gyrase poisons. PLoS One 2013; 8:e61459. [PMID: 23593482 PMCID: PMC3622597 DOI: 10.1371/journal.pone.0061459] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/09/2013] [Indexed: 11/18/2022] Open
Abstract
Fluoroquinolones are very important drugs in the clinical antibacterial arsenal; their success is principally due to their mode of action: the stabilisation of a gyrase-DNA intermediate (the cleavage complex), which triggers a chain of events leading to cell death. Microcin B17 (MccB17) is a modified peptide bacterial toxin that acts by a similar mode of action, but is unfortunately unsuitable as a therapeutic drug. However, its structure and mechanism could inspire the design of new antibacterial compounds that are needed to circumvent the rise in bacterial resistance to current antibiotics. Here we describe the investigation of the structural features responsible for MccB17 activity and the identification of fragments of the toxin that retain the ability to stabilise the cleavage complex.
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Affiliation(s)
- Frédéric Collin
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Robert E. Thompson
- School of Chemistry, The University of Sydney, New South Wales, Australia
| | | | - Richard J. Payne
- School of Chemistry, The University of Sydney, New South Wales, Australia
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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47
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Abstract
Solutions are urgently required for the growing number of infections caused by antibiotic-resistant bacteria. Bacteriocins, which are antimicrobial peptides produced by certain bacteria, might warrant serious consideration as alternatives to traditional antibiotics. These molecules exhibit significant potency against other bacteria (including antibiotic-resistant strains), are stable and can have narrow or broad activity spectra. Bacteriocins can even be produced in situ in the gut by probiotic bacteria to combat intestinal infections. Although the application of specific bacteriocins might be curtailed by the development of resistance, an understanding of the mechanisms by which such resistance could emerge will enable researchers to develop strategies to minimize this potential problem.
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Affiliation(s)
- Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
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48
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Characterization of a novel microcin that kills enterohemorrhagic Escherichia coli O157:H7 and O26. Appl Environ Microbiol 2012; 78:6592-9. [PMID: 22773653 DOI: 10.1128/aem.01067-12] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel phenotype was recently identified in which specific strains of Escherichia coli inhibit competing E. coli strains via a mechanism that was designated "proximity-dependent inhibition" (PDI). PDI-expressing (PDI(+)) E. coli is known to inhibit susceptible (PDI(-)) E. coli strains, including several enterohemorrhagic (EHEC) and enterotoxigenic (ETEC) E. coli strains. In this study, every strain from a genetically diverse panel of E. coli O157:H7 (n = 25) and additional strains of E. coli serovar O26 were susceptible to the PDI phenotype. LIVE/DEAD staining was consistent with inhibition by killing of susceptible cells. Comparative genome analysis identified the genetic component of PDI, which is composed of a plasmid-borne (Incl1) operon encoding a putative microcin and associated genes for transport, immunity, and microcin activation. Transfer of the plasmid to a PDI(-) strain resulted in transfer of the phenotype, and deletion of the genes within the operon resulted in loss of the inhibition phenotype. Deletion of chromosomally encoded tolC also resulted in loss of the inhibitory phenotype, and this confirmed that the putative microcin is most likely secreted via a type I secretion pathway. Deletion of an unrelated plasmid gene did not affect the PDI phenotype. Quantitative reverse transcription (RT)-PCR demonstrated that microcin expression is correlated with logarithmic-phase growth. The ability to inhibit a diversity of E. coli strains indicates that this microcin may influence gut community composition and could be useful for control of important enteric pathogens.
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Severinov K, Nair SK. Microcin C: biosynthesis and mechanisms of bacterial resistance. Future Microbiol 2012; 7:281-9. [PMID: 22324995 DOI: 10.2217/fmb.11.148] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nonhydrolyzable aminoacyl-adenylates that inhibit protein synthesis provide a promising route towards the development of novel antibiotics whose mechanism of action limits the appearance of bacterial drug resistance. The 'Trojan horse' antibiotic microcin C (McC) consists of a nonhydrolyzable aspartyl-adenylate that is efficiently imported into bacterial cells owing to a covalently attached peptide carrier. Once inside the cell, the carrier is removed by proteolytic processing to release a potent aspartyl tRNA synthetase inhibitor. The focus of this article is on the mechanism of biosynthesis of McC. We also examine the strategies utilized by McC-producing strains to overcome toxicity due to unwanted, premature processing of the drug. This article will discuss how McC biosynthesis can be systematically manipulated for the development of derivatives that will target the entire battery of aminoacyl tRNA synthetases in various bacteria.
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Affiliation(s)
- Konstantin Severinov
- Department of Molecular Biology & Biochemistry, Rutgers University Piscataway, NJ 08854, USA.
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50
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Zschüttig A, Zimmermann K, Blom J, Goesmann A, Pöhlmann C, Gunzer F. Identification and characterization of microcin S, a new antibacterial peptide produced by probiotic Escherichia coli G3/10. PLoS One 2012; 7:e33351. [PMID: 22479389 PMCID: PMC3316575 DOI: 10.1371/journal.pone.0033351] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 02/13/2012] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli G3/10 is a component of the probiotic drug Symbioflor 2. In an in vitro assay with human intestinal epithelial cells, E. coli G3/10 is capable of suppressing adherence of enteropathogenic E. coli E2348/69. In this study, we demonstrate that a completely novel class II microcin, produced by probiotic E. coli G3/10, is responsible for this behavior. We named this antibacterial peptide microcin S (MccS). Microcin S is coded on a 50.6 kb megaplasmid of E. coli G3/10, which we have completely sequenced and annotated. The microcin S operon is about 4.7 kb in size and is comprised of four genes. Subcloning of the genes and gene fragments followed by gene expression experiments enabled us to functionally characterize all members of this operon, and to clearly identify the nucleotide sequences encoding the microcin itself (mcsS), its transport apparatus and the gene mcsI conferring self immunity against microcin S. Overexpression of cloned mcsI antagonizes MccS activity, thus protecting indicator strain E. coli E2348/69 in the in vitro adherence assay. Moreover, growth of E. coli transformed with a plasmid containing mcsS under control of an araC PBAD activator-promoter is inhibited upon mcsS induction. Our data provide further mechanistic insight into the probiotic behavior of E. coli G3/10.
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Affiliation(s)
- Anke Zschüttig
- Institute of Medical Microbiology and Hygiene, TU Dresden, Dresden, Germany
| | | | - Jochen Blom
- CeBiTec, University of Bielefeld, Bielefeld, Germany
| | | | - Christoph Pöhlmann
- Abteilung für Labormedizin, Robert Bosch Krankenhaus, Stuttgart, Germany
| | - Florian Gunzer
- Institute of Medical Microbiology and Hygiene, TU Dresden, Dresden, Germany
- * E-mail:
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