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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [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: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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2
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Eslami SM, Padhi C, Rahman IR, van der Donk WA. Expression and Subcellular Localization of Lanthipeptides in Human Cells. ACS Synth Biol 2024. [PMID: 38925629 DOI: 10.1021/acssynbio.4c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Cyclic peptides, such as most ribosomally synthesized and post-translationally modified peptides (RiPPs), represent a burgeoning area of interest in therapeutic and biotechnological research because of their conformational constraints and reduced susceptibility to proteolytic degradation compared to their linear counterparts. Herein, an expression system is reported that enables the production of structurally diverse lanthipeptides and derivatives in mammalian cells. Successful targeting of lanthipeptides to the nucleus, the endoplasmic reticulum, and the plasma membrane is demonstrated. In vivo expression and targeting of such peptides in mammalian cells may allow for screening of lanthipeptide-based cyclic peptide inhibitors of native, organelle-specific protein-protein interactions in mammalian systems.
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Affiliation(s)
- Sara M Eslami
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chandrashekhar Padhi
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Imran R Rahman
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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3
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Reuben RC, Torres C. Bacteriocins: potentials and prospects in health and agrifood systems. Arch Microbiol 2024; 206:233. [PMID: 38662051 PMCID: PMC11045635 DOI: 10.1007/s00203-024-03948-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024]
Abstract
Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.
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Affiliation(s)
- Rine Christopher Reuben
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
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4
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Daba GM, Elkhateeb WA. Ribosomally synthesized bacteriocins of lactic acid bacteria: Simplicity yet having wide potentials - A review. Int J Biol Macromol 2024; 256:128325. [PMID: 38007012 DOI: 10.1016/j.ijbiomac.2023.128325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/02/2023] [Accepted: 11/11/2023] [Indexed: 11/27/2023]
Abstract
Bacteriocins are ribosomally made bacterial peptides that have outstanding contributions in the field of food industry, as biopreservatives, and promising potentials in the medical field for improving human and animal health. Bacteriocins have many advantages over antibiotics such as being primary metabolites with relatively simpler biosynthetic mechanisms, which made their bioengineering for activity or specificity improving purposes much easier. Also, bacteriocins are degraded by proteolytic enzymes and do not stay in environment, which reduce chances of developing resistance. Bacteriocins can improve activity of some antibiotics, and some bacteriocins show potency against multidrug-resistant bacteria. Moreover, some potent bacteriocins have antiviral, antifungal, and antiprotozoal (antileishmanial) activities. On the other hand, bacteriocins have been introduced into the treatment of some ulcers and types of cancer. These potentials make bacteriocins attract extra attention as promising biotechnological tool. Hence, the history, characteristics, and classification of bacteriocins are described in this review. Furthermore, the main difference between bacteriocins and other antimicrobial peptides is clarified. Also, bacteriocins biosynthesis and identified modes of action are elucidated. Additionally, current and potential applications of bacteriocins in food and medical fields are highlighted. Finally, future perspectives concerning studying bacteriocins and their applications are discussed.
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Affiliation(s)
- Ghoson Mosbah Daba
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Researches Institute, National Research Centre, El Buhouth St., Egypt.
| | - Waill Ahmed Elkhateeb
- Chemistry of Natural and Microbial Products Department, Pharmaceutical Industries Researches Institute, National Research Centre, El Buhouth St., Egypt
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5
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Eslami SM, Rahman IR, van der Donk WA. Expression of Lanthipeptides in Human Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563208. [PMID: 37961259 PMCID: PMC10634679 DOI: 10.1101/2023.10.19.563208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cyclic peptides represent a burgeoning area of interest in therapeutic and biotechnological research. In opposition to their linear counterparts, cyclic peptides, such as certain ribosomally synthesized and post-translationally modified peptides (RiPPs), are more conformationally constrained and less susceptible to proteolytic degradation. The lanthipeptide RiPP cytolysin L forms a covalently enforced helical structure that may be used to disrupt helical interactions at protein-protein interfaces. Herein, an expression system is reported to produce lanthipeptides and structurally diverse cytolysin L derivatives in mammalian cells. Successful targeting of lanthipeptides to the nucleus is demonstrated. In vivo expression and targeting of such peptides in mammalian cells may allow for screening of lanthipeptide inhibitors of native protein-protein interactions.
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Affiliation(s)
- Sara M. Eslami
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Imran R. Rahman
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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6
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Guryanova SV. Immunomodulation, Bioavailability and Safety of Bacteriocins. Life (Basel) 2023; 13:1521. [PMID: 37511896 PMCID: PMC10381439 DOI: 10.3390/life13071521] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
The rise of antibiotic-resistant bacteria and the emergence of new pathogens have created a need for new strategies to fight against infectious diseases. One promising approach is the use of antimicrobial peptides produced by a certain species of bacteria, known as bacteriocins, which are active against other strains of the same or related species. Bacteriocins can help in the treatment and prevention of infectious diseases. Moreover, bacteriocins can be obtained in prokaryotic organisms, and contribute s to their widespread use. While the use of bacteriocins is currently limited to the food industry (for example, nisin is used as a preservative, E234), a large number of studies on their microbicidal properties suggest that their use in medicine may increase in the foreseeable future. However, for the successful use of bacteriocins in medicine, it is necessary to understand their effect on the immune system, especially in cases where immunity is weakened due to infectious processes, oncological, allergic, or autoimmune diseases. Studies on the immuno-modulatory activity of bacteriocins in animal models and human cells have revealed their ability to induce both pro-inflammatory and anti-inflammatory factors involved in the implementation of innate immunity. The influence of bacteriocins on acquired immunity is revealed by an increase in the number of T-lymphocytes with a simultaneous decrease in B-lymphocyte levels, which makes them attractive substances for reducing inflammation. The widespread use of bacteriocins in the food industry, their low toxicity, and their broad and narrow specificity are reasons for researchers to pay attention to their immunomodulatory properties and explore their medical applications. Inflammation regulation by bacteriocins can be used in the treatment of various pathologies. The aim of the review was to analyze scientific publications on the immunomodulatory activity, bioavailability, and safety of bacteriocins in order to use the data obtained to organize preclinical and clinical studies.
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Affiliation(s)
- Svetlana V Guryanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Medical Institute, Peoples' Friendship University of Russia (RUDN University) of the Ministry of Science and Higher Education of the Russian Federation, 117198 Moscow, Russia
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7
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Chaudhary S, Kishen S, Singh M, Jassal S, Pathania R, Bisht K, Sareen D. Phylogeny-guided genome mining of roseocin family lantibiotics to generate improved variants of roseocin. AMB Express 2023; 13:34. [PMID: 36940043 PMCID: PMC10027976 DOI: 10.1186/s13568-023-01536-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/04/2023] [Indexed: 03/21/2023] Open
Abstract
Roseocin, the two-peptide lantibiotic from Streptomyces roseosporus, carries extensive intramolecular (methyl)lanthionine bridging in the peptides and exhibits synergistic antibacterial activity against clinically relevant Gram-positive pathogens. Both peptides have a conserved leader but a diverse core region. The biosynthesis of roseocin involves post-translational modification of the two precursor peptides by a single promiscuous lanthipeptide synthetase, RosM, to install an indispensable disulfide bond in the Rosα core along with four and six thioether rings in Rosα and Rosβ cores, respectively. RosM homologs in the phylum actinobacteria were identified here to reveal twelve other members of the roseocin family which diverged into three types of biosynthetic gene clusters (BGCs). Further, the evolutionary rate among the BGC variants and analysis of variability within the core peptide versus leader peptide revealed a phylum-dependent lanthipeptide evolution. Analysis of horizontal gene transfer revealed its role in the generation of core peptide diversity. The naturally occurring diverse congeners of roseocin peptides identified from the mined novel BGCs were carefully aligned to identify the conserved sites and the substitutions in the core peptide region. These selected sites in the Rosα peptide were mutated for permitted substitutions, expressed heterologously in E. coli, and post-translationally modified by RosM in vivo. Despite a limited number of generated variants, two variants, RosαL8F and RosαL8W exhibited significantly improved inhibitory activity in a species-dependent manner compared to the wild-type roseocin. Our study proves that a natural repository of evolved variants of roseocin is present in nature and the key variations can be used to generate improved variants.
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Affiliation(s)
- Sandeep Chaudhary
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Shweta Kishen
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Sunanda Jassal
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Reeva Pathania
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Kalpana Bisht
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Dipti Sareen
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India.
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8
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Class II two-peptide lanthipeptide proteases: exploring LicTP for biotechnological applications. Appl Microbiol Biotechnol 2023; 107:1687-1696. [PMID: 36763118 PMCID: PMC10006061 DOI: 10.1007/s00253-023-12388-5] [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: 09/05/2022] [Revised: 12/23/2022] [Accepted: 01/15/2023] [Indexed: 02/11/2023]
Abstract
The enzymatic machinery involved in the biosynthesis of lantibiotic is an untapped source of proteases with different specificities. Lanthipeptide biosynthesis requires proteolysis of specific target sequences by known proteases, which are encoded by contiguous genes. Herein, the activity of lichenicidin A2 (LicA2) trimming proteases (LicP and LicT) was investigated in vivo. Firstly, the impact of some residues and the size of the peptide were evaluated. Then followed trials in which LicA2 leader was evaluated as a tag to direct production and secretion of other relevant peptides. Our results show that a negatively charged residue (preferably Glu) at cleavage site is important for LicP efficacy. Some mutations of the lichenicidin hexapeptide such as Val-4Ala, Asp-5Ala, Asn-6Ser, and the alteration of GG-motif to GA resulted in higher processing rates, indicating the possibility of improved lichenicidin production in Escherichia coli. More importantly, insulin A, amylin (non-lanthipeptides), and epidermin were produced and secreted to E. coli supernatant, when fused to the LicA2 leader peptide. This work aids in clarifying the activity of lantibiotic-related transporters and proteases and to evaluate their possible application in industrial processes of relevant compounds, taking advantage of the potential of microorganisms as biofactories. KEY POINTS: • LicM2 correct activity implies a negatively charged residue at position -1. • Hexapeptide mutations can increase the amount of fully processed Bliβ. • LicA2 leader peptide directs LicTP cleavage and secretion of other peptides.
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9
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Romero-Rodríguez A, Ruiz-Villafán B, Martínez-de la Peña CF, Sánchez S. Targeting the Impossible: A Review of New Strategies against Endospores. Antibiotics (Basel) 2023; 12:antibiotics12020248. [PMID: 36830159 PMCID: PMC9951900 DOI: 10.3390/antibiotics12020248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Endospore-forming bacteria are ubiquitous, and their endospores can be present in food, in domestic animals, and on contaminated surfaces. Many spore-forming bacteria have been used in biotechnological applications, while others are human pathogens responsible for a wide range of critical clinical infections. Due to their resistant properties, it is challenging to eliminate spores and avoid the reactivation of latent spores that may lead to active infections. Furthermore, endospores play an essential role in the survival, transmission, and pathogenesis of some harmful strains that put human and animal health at risk. Thus, different methods have been applied for their eradication. Nevertheless, natural products are still a significant source for discovering and developing new antibiotics. Moreover, targeting the spore for clinical pathogens such as Clostridioides difficile is essential to disease prevention and therapeutics. These strategies could directly aim at the structural components of the spore or their germination process. This work summarizes the current advances in upcoming strategies and the development of natural products against endospores. This review also intends to highlight future perspectives in research and applications.
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Affiliation(s)
- Alba Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
- Correspondence:
| | - Beatriz Ruiz-Villafán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Claudia Fabiola Martínez-de la Peña
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72592, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
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10
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Panina IS, Balandin SV, Tsarev AV, Chugunov AO, Tagaev AA, Finkina EI, Antoshina DV, Sheremeteva EV, Paramonov AS, Rickmeyer J, Bierbaum G, Efremov RG, Shenkarev ZO, Ovchinnikova TV. Specific Binding of the α-Component of the Lantibiotic Lichenicidin to the Peptidoglycan Precursor Lipid II Predetermines Its Antimicrobial Activity. Int J Mol Sci 2023; 24:ijms24021332. [PMID: 36674846 PMCID: PMC9863751 DOI: 10.3390/ijms24021332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/21/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
To date, a number of lantibiotics have been shown to use lipid II-a highly conserved peptidoglycan precursor in the cytoplasmic membrane of bacteria-as their molecular target. The α-component (Lchα) of the two-component lantibiotic lichenicidin, previously isolated from the Bacillus licheniformis VK21 strain, seems to contain two putative lipid II binding sites in its N-terminal and C-terminal domains. Using NMR spectroscopy in DPC micelles, we obtained convincing evidence that the C-terminal mersacidin-like site is involved in the interaction with lipid II. These data were confirmed by the MD simulations. The contact area of lipid II includes pyrophosphate and disaccharide residues along with the first isoprene units of bactoprenol. MD also showed the potential for the formation of a stable N-terminal nisin-like complex; however, the conditions necessary for its implementation in vitro remain unknown. Overall, our results clarify the picture of two component lantibiotics mechanism of antimicrobial action.
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Affiliation(s)
- Irina S. Panina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey V. Balandin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-495-335-0900
| | - Andrey V. Tsarev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Anton O. Chugunov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Andrey A. Tagaev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ekaterina I. Finkina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Daria V. Antoshina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elvira V. Sheremeteva
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexander S. Paramonov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Jasmin Rickmeyer
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53117 Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53117 Bonn, Germany
| | - Roman G. Efremov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Applied Mathematics, National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Zakhar O. Shenkarev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Bioorganic Chemistry, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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11
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Guo E, Fu L, Fang X, Xie W, Li K, Zhang Z, Hong Z, Si T. Robotic Construction and Screening of Lanthipeptide Variant Libraries in Escherichia coli. ACS Synth Biol 2022; 11:3900-3911. [PMID: 36379012 DOI: 10.1021/acssynbio.2c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lanthipeptides are a major class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by thioether cross-links called lanthionine (Lan) and methyllanthionine (MeLan). Previously, we developed a method to produce mature lanthipeptides in recombinant Escherichia coli, but manual steps hinder large-scale analogue screening. Here we devised an automated workflow for creating and screening variant libraries of haloduracin, a two-component class II lanthipeptide. An integrated work cell of a synthetic biology foundry was programmed to robotically execute DNA library construction, host transformation, peptide production, mass spectrometry analysis, and activity screening by agar diffusion assay. For recombinantly produced Halα peptides, the sequence-activity relationship of 380 single-residue variants and >1300 triple-residue combinatorial variants were rapidly analyzed in microplates within weeks. The peptide expression levels in E. coli were also visualized via robotic creation and analysis of GFP-lanthipeptide fusions for select peptide mutants. Following shake-flask fermentation and purification, one Halα mutant was confirmed with enhanced specific antimicrobial activity relative to the wild-type peptide. Overall, this approach may be generally applicable for the high-throughput characterization and engineering of RiPP natural products.
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Affiliation(s)
- Erpeng Guo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - Lihao Fu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoting Fang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wenhao Xie
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Keyi Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhiyu Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhilai Hong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,BGI-Shenzhen, Shenzhen 518083, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Shenzhen 518055, China
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12
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Structure and Activity Relationships of the Two-Component Lantibiotic Bicereucin. ACS Infect Dis 2022; 8:2529-2539. [PMID: 36354217 DOI: 10.1021/acsinfecdis.2c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Identified from the pathogen Bacillus cereus SJ1, the two-component lantibiotic bicereucin is featured by the presence of a series of nonproteogenic amino acids and exhibits potent synergistic activity against a broad spectrum of Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci, as well as hemolytic activity against mammalian cells. In this study, we performed site-directed mutagenesis on the nonproteogenic amino acids as well as truncation of dehydrobutyrine-rich N-terminal residues and evaluated the effects on both biological activities. We identified that D-Ala21 and D-Ala26 of Bsjα and D-Ala23 and D-Ala28 of Bsjβ play an essential role in the antimicrobial activity, while the N-termini of both peptides are important for both activities. We also determined that the integrity of both subunits is essential for hemolytic activity. Finally, we obtained two variants BsjαtS17A+Bsjβ and BsjαS30A+BsjβT19A, which retained the antimicrobial activity and exhibited greatly decreased hemolytic toxicity. Overall, our results provide a comprehensive understanding of the structure-activity relationships of bicereucin and insights into the mechanism of action thereof, facilitating the further exploration of the molecular basis of the binding receptor of bicereucin and genome mining of potential novel two-component lantibiotics.
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13
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Bacteriocin Production by Bacillus Species: Isolation, Characterization, and Application. Probiotics Antimicrob Proteins 2022; 14:1151-1169. [PMID: 35881232 DOI: 10.1007/s12602-022-09966-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2022] [Indexed: 12/25/2022]
Abstract
Antibiotic resistance is a problem that has been increasing lately; therefore, it is important to find new alternatives to treat infections induced by pathogens that cannot be eliminated with available products. Small antimicrobial peptides (AMPs) known as bacteriocin could be an alternative to antibiotics because they have shown to be effective against a great number of multidrug-resistant microbes. In addition to its high specificity against microbial pathogens and its low cytotoxicity against human cells, most bacteriocin present tolerance to enzyme degradation and stability to temperature and pH alterations. Bacteriocins are small peptides with a great diversity of structures and functions; however, their mechanisms of action are still not well understood. In this review, bacteriocin produced by Bacillus species will be described, especially its mechanisms of action, culture conditions used to improve its production and state-of-the-art methodologies applied to identify them. Bacteriocin utilization as food preservatives and as new molecules to treat cancer also will be discussed.
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14
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Murugan R, Guru A, Haridevamuthu B, Sudhakaran G, Arshad A, Arockiaraj J. Lantibiotics: an antimicrobial asset in combating aquaculture diseases. AQUACULTURE INTERNATIONAL 2022; 30:2365-2387. [DOI: 10.1007/s10499-022-00908-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/20/2022] [Indexed: 10/16/2023]
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15
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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16
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Barbosa JC, Gonçalves S, Makowski M, Silva ÍC, Caetano T, Schneider T, Mösker E, Süssmuth RD, Santos NC, Mendo S. Insights into the mode of action of the two-peptide lantibiotic lichenicidin. Colloids Surf B Biointerfaces 2022; 211:112308. [PMID: 34973602 DOI: 10.1016/j.colsurfb.2021.112308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/30/2022]
Abstract
Lantibiotics are promising candidates to address the worldwide problem of antibiotic resistance. They belong to a class of natural compounds exhibiting strong activity against clinically relevant Gram-positive bacterial strains, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE). Lichenicidin is a class II two-peptide lantibiotic. The presence of the two mature peptides, Bliα and Bliβ, is necessary for full activity against target bacteria. This work aims at clarifying the synergistic activity of both peptides in their interaction with the target membranes. The effect of lichenicidin was tested against S. aureus cells and large unilamellar vesicles. Lichenicidin increases the net surface charge of S. aureus, as shown by zeta-potential measurements, without reaching electroneutralization. In addition, lichenicidin causes cell surface perturbations that culminate in the leakage of its internal contents, as observed by atomic force microscopy. Bliα seems to have low affinity for S. aureus, however, it contributes to increase the affinity of Bliβ, because together they present higher affinity than separately. In contrast, Bliα seems to provide an anchoring site for lichenicidin in lipid II-containing membranes. Interestingly, Bliβ alone can induce high levels of membrane leakage, but this effect appears to be faster in the presence of Bliα. Based on this information, we propose a mechanism of action of lichenicidin.
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Affiliation(s)
- Joana C Barbosa
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Marcin Makowski
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Ítala C Silva
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Tânia Caetano
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany.
| | - Eva Mösker
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany.
| | | | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Sónia Mendo
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
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17
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Bangar SP, Chaudhary V, Singh TP, Özogul F. Retrospecting the concept and industrial significance of LAB bacteriocins. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Antimicrobial Bacillus: Metabolites and Their Mode of Action. Antibiotics (Basel) 2022; 11:antibiotics11010088. [PMID: 35052965 PMCID: PMC8772736 DOI: 10.3390/antibiotics11010088] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/12/2022] Open
Abstract
The agricultural industry utilizes antibiotic growth promoters to promote livestock growth and health. However, the World Health Organization has raised concerns over the ongoing spread of antibiotic resistance transmission in the populace, leading to its subsequent ban in several countries, especially in the European Union. These restrictions have translated into an increase in pathogenic outbreaks in the agricultural industry, highlighting the need for an economically viable, non-toxic, and renewable alternative to antibiotics in livestock. Probiotics inhibit pathogen growth, promote a beneficial microbiota, regulate the immune response of its host, enhance feed conversion to nutrients, and form biofilms that block further infection. Commonly used lactic acid bacteria probiotics are vulnerable to the harsh conditions of the upper gastrointestinal system, leading to novel research using spore-forming bacteria from the genus Bacillus. However, the exact mechanisms behind Bacillus probiotics remain unexplored. This review tackles this issue, by reporting antimicrobial compounds produced from Bacillus strains, their proposed mechanisms of action, and any gaps in the mechanism studies of these compounds. Lastly, this paper explores omics approaches to clarify the mechanisms behind Bacillus probiotics.
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19
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Assessing the potential of the two-peptide lantibiotic lichenicidin as a new generation antimicrobial. World J Microbiol Biotechnol 2022; 38:18. [PMID: 34977979 DOI: 10.1007/s11274-021-03196-y] [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: 09/17/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
Abstract
Lantibiotics are a promising class of natural antimicrobial peptides. Lichenicidin is a two-peptide lantibiotic in which two mature peptides act synergistically to exhibit full bioactivity. Considering the two-peptide lantibiotics described so far, only cytolysin has been deeply characterized in terms of toxicity towards eukaryotic cells and it was found to be hemolytic and cytotoxic. This work aimed to improve the production of lichenicidin in vivo and characterize its antibacterial activity and toxicity against human cells. Peptides were purified and minimal inhibitory concentration (MIC) was determined against several strains; a time-kill assay was performed with Staphylococcus aureus. The hemolytic effect of lichenicidin was evaluated on blood samples from healthy donors and its toxicity towards human fibroblasts. The quantity of purified peptides was 1 mg/l Bliα and 0.4 mg/l Bliβ. MIC for methicillin-sensitive and resistant S. aureus (MSSA and MRSA) strains were 16-32 µg/ml and 64-128 µg/ml, respectively. At the MIC, lichenicidin took less than 3 h to eliminate MSSA, indicating a strong bactericidal effect. It induces cell lysis at the highest concentration, an effect that might be potentiated by Bliβ. Lichenicidin was not cytotoxic to human erythrocytes and fibroblasts. In this work, we evaluated the therapeutic potential of lichenicidin as a possible antimicrobial alternative.
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20
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Le T, Jeanne Dit Fouque K, Santos-Fernandez M, Navo CD, Jiménez-Osés G, Sarksian R, Fernandez-Lima FA, van der Donk WA. Substrate Sequence Controls Regioselectivity of Lanthionine Formation by ProcM. J Am Chem Soc 2021; 143:18733-18743. [PMID: 34724611 DOI: 10.1021/jacs.1c09370] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs). The (methyl)lanthionine cross-links characteristic to lanthipeptides are essential for their stability and bioactivities. In most bacteria, lanthipeptides are maturated from single precursor peptides encoded in the corresponding biosynthetic gene clusters. However, cyanobacteria engage in combinatorial biosynthesis and encode as many as 80 substrate peptides with highly diverse sequences that are modified by a single lanthionine synthetase into lanthipeptides of different lengths and ring patterns. It is puzzling how a single enzyme could exert control over the cyclization processes of such a wide range of substrates. Here, we used a library of ProcA3.3 precursor peptide variants and show that it is not the enzyme ProcM but rather its substrate sequences that determine the regioselectivity of lanthionine formation. We also demonstrate the utility of trapped ion mobility spectrometry-tandem mass spectrometry (TIMS-MS/MS) as a fast and convenient method to efficiently separate lanthipeptide constitutional isomers, particularly in cases where the isomers cannot be resolved by conventional liquid chromatography. Our data allowed identification of factors that are important for the cyclization outcome, but also showed that there are no easily identifiable predictive rules for all sequences. Our findings provide a platform for future deep learning approaches to allow such prediction of ring patterns of products of combinatorial biosynthesis.
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Affiliation(s)
- Tung Le
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Miguel Santos-Fernandez
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Raymond Sarksian
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Francisco Alberto Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
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21
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Lambo MT, Chang X, Liu D. The Recent Trend in the Use of Multistrain Probiotics in Livestock Production: An Overview. Animals (Basel) 2021; 11:2805. [PMID: 34679827 PMCID: PMC8532664 DOI: 10.3390/ani11102805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/09/2021] [Accepted: 09/23/2021] [Indexed: 01/16/2023] Open
Abstract
It has been established that introducing feed additives to livestock, either nutritional or non-nutritional, is beneficial in manipulating the microbial ecosystem to maintain a balance in the gut microbes and thereby improving nutrient utilization, productivity, and health status of animals. Probiotic use has gained popularity in the livestock industry, especially since antimicrobial growth promoter's use has been restricted due to the challenge of antibiotic resistance in both animals and consumers of animal products. Their usage has been linked to intestinal microbial balance and improved performance in administered animals. Even though monostrain probiotics could be beneficial, multistrain probiotics containing two or more species or strains have gained considerable attention. Combining different strains has presumably achieved several health benefits over single strains due to individual isolates' addition and positive synergistic adhesion effects on animal health and performance. However, there has been inconsistency in the effects of the probiotic complexes in literature. This review discusses multistrain probiotics, summarizes selected literature on their effects on ruminants, poultry, and swine productivity and the various modes by which they function.
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Affiliation(s)
- Modinat Tolani Lambo
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (M.T.L.); (X.C.)
| | - Xiaofeng Chang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (M.T.L.); (X.C.)
| | - Dasen Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (M.T.L.); (X.C.)
- College of Science, Northeast Agricultural University, Harbin 150030, China
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22
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Anumudu C, Hart A, Miri T, Onyeaka H. Recent Advances in the Application of the Antimicrobial Peptide Nisin in the Inactivation of Spore-Forming Bacteria in Foods. Molecules 2021; 26:5552. [PMID: 34577022 PMCID: PMC8469619 DOI: 10.3390/molecules26185552] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/01/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022] Open
Abstract
Conventional thermal and chemical treatments used in food preservation have come under scrutiny by consumers who demand minimally processed foods free from chemical agents but microbiologically safe. As a result, antimicrobial peptides (AMPs) such as bacteriocins and nisin that are ribosomally synthesised by bacteria, more prominently by the lactic acid bacteria (LAB) have appeared as a potent alternative due to their multiple biological activities. They represent a powerful strategy to prevent the development of spore-forming microorganisms in foods. Unlike thermal methods, they are natural without an adverse impact on food organoleptic and nutritional attributes. AMPs such as nisin and bacteriocins are generally effective in eliminating the vegetative forms of spore-forming bacteria compared to the more resilient spore forms. However, in combination with other non-thermal treatments, such as high pressure, supercritical carbon dioxide, electric pulses, a synergistic effect with AMPs such as nisin exists and has been proven to be effective in the inactivation of microbial spores through the disruption of the spore structure and prevention of spore outgrowth. The control of microbial spores in foods is essential in maintaining food safety and extension of shelf-life. Thus, exploration of the mechanisms of action of AMPs such as nisin is critical for their design and effective application in the food industry. This review harmonises information on the mechanisms of bacteria inactivation from published literature and the utilisation of AMPs in the control of microbial spores in food. It highlights future perspectives in research and application in food processing.
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Affiliation(s)
- Christian Anumudu
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (C.A.); (T.M.)
| | - Abarasi Hart
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK;
| | - Taghi Miri
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (C.A.); (T.M.)
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (C.A.); (T.M.)
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23
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Rahman IR, Sanchez A, Tang W, van der Donk WA. Structure-Activity Relationships of the Enterococcal Cytolysin. ACS Infect Dis 2021; 7:2445-2454. [PMID: 34265205 DOI: 10.1021/acsinfecdis.1c00197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enterococcal cytolysin is a hemolytic virulence factor linked to human disease and increased patient mortality. Produced by pathogenic strains of Enterococcus faecalis, cytolysin is made up of two small, post-translationally modified peptides called CylLL" and CylLS". They exhibit a unique toxicity profile where lytic activity is observed for both mammalian cells and Gram-positive bacteria that is dependent on the presence of both peptides. In this study, we performed alanine substitution of all residues in CylLL" and CylLS" and determined the effect on both activities. We identified key residues involved in overall activity and residues that dictate cell type specificity. All (methyl)lanthionines as well as a Gly-rich hinge region were critical for both activities. In addition, we investigated the binding of the two subunits to bacterial cells suggesting that the large subunit CylLL" has stronger affinity for the membrane or a target molecule therein. Genome mining identified other potential two-component lanthipeptides and provided insights into potential evolutionary origins.
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24
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C-protein α-antigen modulates the lantibiotic thusin resistance in Streptococcus agalactiae. Antonie van Leeuwenhoek 2021; 114:1595-1607. [PMID: 34319449 DOI: 10.1007/s10482-021-01626-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
Screening for producers of potent antimicrobial peptides, resulted in the isolation of Bacillus cereus BGNM1 with strong antimicrobial activity against Listeria monocytogenes. Genome sequence analysis revealed that BGNM1 contains the gene cluster associated with the production of the lantibiotic, thusin, previously identified in B. thuringiensis. Purification of the antimicrobial activity confirmed that strain BGMN1 produces thusin. Both thusin sensitive and resistant strains were detected among clinical isolates of Streptococcus agalactiae. Random mutagenesis of a thusin sensitive strain, S. agalactiae B782, was performed in an attempt to identify the receptor protein for thusin. Three independent thusin resistant mutants were selected and their complete genomes sequenced. Comparative sequence analysis of these mutants with the WT strain revealed that duplication of a region encoding a 79 amino acids repeat in a C-protein α-antigen was a common difference, suggesting it to be responsible for increased resistance to thusin. Since induced thusin resistant mutants showed higher level of resistance than the naturally resistant B761 strain, complete genome sequencing of strain B761 was performed to check the integrity of the C-protein α-antigen-encoding gene. This analysis revealed that this gene is deleted in B761, providing further evidence that this protein promotes interaction of the thusin with receptor.
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25
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Vaca J, Ortiz A, Sansinenea E. Bacillus sp. Bacteriocins: Natural Weapons against Bacterial Enemies. Curr Med Chem 2021; 29:2093-2108. [PMID: 34047258 DOI: 10.2174/0929867328666210527093041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Currently, antibiotic-resistant pathogenic bacteria are emerging as an important health problem worldwide. The search for new compounds with antibiotic characteristics is the most promising alternative. Bacteriocins are natural compounds that are inhibitory against pathogens, and Bacillus species are the major producers of these compounds, which have shown antimicrobial activity against clinically important bacteria. These peptides not only have potential in the pharmaceutical industry but also in food and agricultural sectors. OBJECTIVE We provide an overview of the recent bacteriocins isolated from different species of Bacillus including their applications and the older bacteriocins. RESULTS In this review, we have revised some works about the improvements carried out in the production of bacteriocins. CONCLUSION These applications make bacteriocins very promising compounds that need to study for industrial production.
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Affiliation(s)
- Jessica Vaca
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590 Puebla; Pue, Mexico
| | - Aurelio Ortiz
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590 Puebla; Pue, Mexico
| | - Estibaliz Sansinenea
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590 Puebla; Pue, Mexico
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26
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Identification and characterization of a novel circular bacteriocin, bacicyclicin XIN-1, from Bacillus sp. Xin1. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107696] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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27
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Soltani S, Hammami R, Cotter PD, Rebuffat S, Said LB, Gaudreau H, Bédard F, Biron E, Drider D, Fliss I. Bacteriocins as a new generation of antimicrobials: toxicity aspects and regulations. FEMS Microbiol Rev 2021; 45:fuaa039. [PMID: 32876664 PMCID: PMC7794045 DOI: 10.1093/femsre/fuaa039] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
In recent decades, bacteriocins have received substantial attention as antimicrobial compounds. Although bacteriocins have been predominantly exploited as food preservatives, they are now receiving increased attention as potential clinical antimicrobials and as possible immune-modulating agents. Infections caused by antibiotic-resistant bacteria have been declared as a global threat to public health. Bacteriocins represent a potential solution to this worldwide threat due to their broad- or narrow-spectrum activity against antibiotic-resistant bacteria. Notably, despite their role in food safety as natural alternatives to chemical preservatives, nisin remains the only bacteriocin legally approved by regulatory agencies as a food preservative. Moreover, insufficient data on the safety and toxicity of bacteriocins represent a barrier against the more widespread use of bacteriocins by the food and medical industry. Here, we focus on the most recent trends relating to the application of bacteriocins, their toxicity and impacts.
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Affiliation(s)
- Samira Soltani
- Food Science Department, Faculty of Agriculture and Food Sciences, Université Laval, G1V 0A6 Québec, Canada
| | - Riadh Hammami
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON K1N 6N5, Canada
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996 Ireland
- APC Microbiome Ireland, Institute and school of Microbiology, University College Cork, Western Road, Cork, T12 YN60, Ireland
| | - Sylvie Rebuffat
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM), UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Laila Ben Said
- Food Science Department, Faculty of Agriculture and Food Sciences, Université Laval, G1V 0A6 Québec, Canada
| | - Hélène Gaudreau
- Food Science Department, Faculty of Agriculture and Food Sciences, Université Laval, G1V 0A6 Québec, Canada
| | - François Bédard
- Faculty of Pharmacy and Centre de Recherche en Endocrinologie Moléculaire et Oncologique et Génomique Humaine, Université Laval, 2705 Boulevard Laurier, Quebec G1V 4G2, Canada
| | - Eric Biron
- Faculty of Pharmacy and Centre de Recherche en Endocrinologie Moléculaire et Oncologique et Génomique Humaine, Université Laval, 2705 Boulevard Laurier, Quebec G1V 4G2, Canada
| | - Djamel Drider
- Institut Charles Viollette, Université de Lille, EA 7394, 53955 Villeneuve d'Ascq, France
| | - Ismail Fliss
- Food Science Department, Faculty of Agriculture and Food Sciences, Université Laval, G1V 0A6 Québec, Canada
- Institute of Nutrition and Functional Foods, Université Laval, 2440 Boulevard Hochelaga, Québec G1V 0A6, Canada
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28
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Pipiya SO, Terekhov SS, Mokrushina YA, Knorre VD, Smirnov IV, Gabibov AG. Engineering Artificial Biodiversity of Lantibiotics to Expand Chemical Space of DNA-Encoded Antibiotics. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:1319-1334. [PMID: 33280576 DOI: 10.1134/s0006297920110048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The discovery of antibiotics was one of the fundamental stages in the development of humanity, leading to a dramatic increase in the life expectancy of millions of people all over the world. The uncontrolled use of antibiotics resulted in the selection of resistant strains of bacteria, limiting the effectiveness of antimicrobial therapy nowadays. Antimicrobial peptides (AMPs) were considered promising candidates for next-generation antibiotics for a long time. However, the practical application of AMPs is restricted by their low therapeutic indices, impaired pharmacokinetics, and pharmacodynamics, which is predetermined by their peptide structure. Nevertheless, the DNA-encoded nature of AMPs enables creating broad repertoires of artificial biodiversity of antibiotics, making them versatile templates for the directed evolution of antibiotic activity. Lantibiotics are a unique class of AMPs with an expanded chemical space. A variety of post-translational modifications, mechanisms of action on bacterial membranes, and DNA-encoded nature make them a convenient molecular template for creating highly representative libraries of antimicrobial compounds. Isolation of new drug candidates from this synthetic biodiversity is extremely attractive but requires high-throughput screening of antibiotic activity. The combination of synthetic biology and ultrahigh-throughput microfluidics allows implementing the concept of directed evolution of lantibiotics for accelerated creation of new promising drug candidates.
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Affiliation(s)
- S O Pipiya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - S S Terekhov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yu A Mokrushina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - V D Knorre
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - I V Smirnov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A G Gabibov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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Liu R, Zhang Y, Zhai G, Fu S, Xia Y, Hu B, Cai X, Zhang Y, Li Y, Deng Z, Liu T. A Cell-Free Platform Based on Nisin Biosynthesis for Discovering Novel Lanthipeptides and Guiding their Overproduction In Vivo. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001616. [PMID: 32995136 PMCID: PMC7507342 DOI: 10.1002/advs.202001616] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/10/2020] [Indexed: 05/12/2023]
Abstract
Lanthipeptides have extensive therapeutic and industrial applications. However, because many are bactericidal, traditional in vivo platforms are limited in their capacity to discover and mass produce novel lanthipeptides as bacterial organisms are often critical components in these systems. Herein, the development of a cell-free protein synthesis (CFPS) platform that enables rapid genome mining, screening, and guided overproduction of lanthipeptides in vivo is described. For proof-of-concept studies, a type I lanthipeptide, nisin, is selected. Four novel lanthipeptides with antibacterial activity are identified among all nisin analogs in the National Center for Biotechnology Information (NCBI) database in a single day. Further, the CFPS platform is coupled with a screening assay for anti-gram-negative bacteria growth, resulting in the identification of a potent nisin mutant, M5. The titers of nisin and the nisin analog are found to be improved with CFPS platform guidance. Owing to the similarities in biosynthesis, the CFPS platform is broadly applicable to other lanthipeptides, thereby providing a universal method for lanthipeptide discovery and overproduction.
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Affiliation(s)
- Ran Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Yuchen Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Guoqing Zhai
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Shuai Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Yao Xia
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Ben Hu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Xuan Cai
- Department of Clinical Laboratory Renmin Hospital of Wuhan University Wuhan 430060 China
| | - Yan Zhang
- Department of Clinical Laboratory Renmin Hospital of Wuhan University Wuhan 430060 China
| | - Yan Li
- Department of Clinical Laboratory Renmin Hospital of Wuhan University Wuhan 430060 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
- Hubei Engineering Laboratory for Synthetic Microbiology Wuhan Institute of Biotechnology Wuhan 430075 China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
- Hubei Engineering Laboratory for Synthetic Microbiology Wuhan Institute of Biotechnology Wuhan 430075 China
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Bobeica SC, Zhu L, Acedo JZ, Tang W, van der Donk WA. Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways. Chem Sci 2020; 11:12854-12870. [PMID: 34094481 PMCID: PMC8163290 DOI: 10.1039/d0sc01651a] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Lanthipeptides are characterized by thioether crosslinks formed by post-translational modifications. The cyclization process that favors a single ring pattern over many other possible ring patterns has been the topic of much speculation. Recent studies suggest that for some systems the cyclization pattern and stereochemistry is determined not by the enzyme, but by the sequence of the precursor peptide. However, the factors that govern the outcome of the cyclization process are not understood. This study presents the three-dimensional structures of seven lanthipeptides determined by nuclear magnetic resonance spectroscopy, including five prochlorosins and the two peptides that make up cytolysin, a virulence factor produced by Enterococcus faecalis that is directly linked to human disease. These peptides were chosen because their substrate sequence determines either the ring pattern (prochlorosins) or the stereochemistry of cyclization (cytolysins). We present the structures of prochlorosins 1.1, 2.1, 2.8, 2.10 and 2.11, the first three-dimensional structures of prochlorosins. Our findings provide insights into the molecular determinants of cyclization as well as why some prochlorosins may be better starting points for library generation than others. The structures of the large and small subunits of the enterococcal cytolysin show that these peptides have long helical stretches, a rare observation for lanthipeptides characterized to date. These helices may explain their pore forming activity and suggest that the small subunit may recognize a molecular target followed by recruitment of the large subunit to span the membrane.
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Affiliation(s)
- Silvia C Bobeica
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana Illinois 61801 USA +1-217-244-8533 +1-217-244-5360
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana-Champaign 505 South Mathews Avenue Urbana Illinois 61801 USA
| | - Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana Illinois 61801 USA +1-217-244-8533 +1-217-244-5360
| | - Weixin Tang
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana Illinois 61801 USA +1-217-244-8533 +1-217-244-5360
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana Illinois 61801 USA +1-217-244-8533 +1-217-244-5360
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In Silico Analysis Highlights the Diversity and Novelty of Circular Bacteriocins in Sequenced Microbial Genomes. mSystems 2020; 5:5/3/e00047-20. [PMID: 32487738 PMCID: PMC8534725 DOI: 10.1128/msystems.00047-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Consumer demand for “fresh food” with no chemical preservatives has prompted researchers to pay more attention to natural antimicrobial peptides such as bacteriocins. Nisin is currently the most widely used food biopreservative among the bacteriocins; however, its applications are restricted due to its low stability at neutral and alkaline pH values. Circular bacteriocins have potent antimicrobial activity against foodborne pathogens, show exceptional stability, and have great potential to be developed as biopreservatives. Here, we take advantage of the precursor peptides of 15 reported circular bacteriocins to devise an in silico approach to identify potential circular bacteriocins in sequenced microbial genomes. A total of nearly 7,000 putative precursor peptides were identified from 86 species of bacteria and further classified into 28 groups based on their amino acid similarity. Among the groups, 19 showed low similarity (less than 50%) to any known precursor peptide of circular bacteriocins. One novel circular bacteriocin in group 11, cerecyclin, showed the highest identity (34%) to the known circular bacteriocin enterocin NKR-5-3B and was selected for verification. Cerecyclin showed antimicrobial activity against several Gram-positive bacteria, inhibited the outgrowth of Bacillus cereus spores, and did not exhibit hemolysis activity. Moreover, it showed 4-fold- to 8-fold-higher antimicrobial activity against B. cereus and Listeria monocytogenes than nisin A. Cerecyclin also had increased stability compared to nisin A under neutral or alkaline conditions. This work not only identified a promising food biopreservative but also provided a rich source for novel circular bacteriocins. IMPORTANCE Circular bacteriocins are promising biopreservatives, and it is important to identify more novel circular bacteriocins to enhance the current arsenal of antimicrobials. In this study, we used an in silico approach to identify a large number of novel circular bacteriocins and classified these bacteriocins into 28 groups rather than the 2 groups that were described in previous studies. Nineteen groups were novel and had low similarity (less than 50%) to any known precursor peptides of circular bacteriocins; this finding greatly expands the awareness of the novelty and diversity of circular bacteriocins. A novel circular bacteriocin which we named cerecyclin was identified in the B. cereus group; this circular bacteriocin had great antimicrobial activity against some foodborne pathogens and showed extreme stability. This study not only identified a promising food biopreservative but also provided a rich source for the identification of novel circular bacteriocins and the development of new biopreservatives.
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An Engineered Double Lipid II Binding Motifs-Containing Lantibiotic Displays Potent and Selective Antimicrobial Activity against Enterococcus faecium. Antimicrob Agents Chemother 2020; 64:AAC.02050-19. [PMID: 32179527 PMCID: PMC7269505 DOI: 10.1128/aac.02050-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/22/2020] [Indexed: 12/23/2022] Open
Abstract
Lipid II is an essential precursor for bacterial cell wall biosynthesis and thereby an important target for various antibiotics. Several lanthionine-containing peptide antibiotics target lipid II with lanthionine-stabilized lipid II binding motifs. Here, we used the biosynthesis system of the lantibiotic nisin to synthesize a two-lipid II binding motifs-containing lantibiotic, termed TL19, which contains the N-terminal lipid II binding motif of nisin and the distinct C-terminal lipid II binding motif of one peptide of the two-component haloduracin (i. Lipid II is an essential precursor for bacterial cell wall biosynthesis and thereby an important target for various antibiotics. Several lanthionine-containing peptide antibiotics target lipid II with lanthionine-stabilized lipid II binding motifs. Here, we used the biosynthesis system of the lantibiotic nisin to synthesize a two-lipid II binding motifs-containing lantibiotic, termed TL19, which contains the N-terminal lipid II binding motif of nisin and the distinct C-terminal lipid II binding motif of one peptide of the two-component haloduracin (i.e., HalA1). Further characterization demonstrated that (i) TL19 exerts 64-fold stronger antimicrobial activity against Enterococcus faecium than nisin(1-22), which has only one lipid II binding site, and (ii) both the N- and C-terminal domains are essential for the potent antimicrobial activity of TL19, as evidenced by mutagenesis of each single and the double domains. These results show the feasibility of a new approach to synthesize potent lantibiotics with two different lipid II binding motifs to treat specific antibiotic-resistant pathogens.
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Wang X, Gu Q, Breukink E. Non-lipid II targeting lantibiotics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183244. [PMID: 32126235 DOI: 10.1016/j.bbamem.2020.183244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, China
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands.
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Miljkovic M, Jovanovic S, O’Connor PM, Mirkovic N, Jovcic B, Filipic B, Dinic M, Studholme DJ, Fira D, Cotter PD, Kojic M. Brevibacillus laterosporus strains BGSP7, BGSP9 and BGSP11 isolated from silage produce broad spectrum multi-antimicrobials. PLoS One 2019; 14:e0216773. [PMID: 31075157 PMCID: PMC6510442 DOI: 10.1371/journal.pone.0216773] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022] Open
Abstract
Bacteria active against multi-drug resistant pathogens, isolated by direct selection of colonies from clover silage samples, produce zones of inhibition against two Gram-negative (Klebsiella pneumoniae Ni9 and Pseudomonas aeruginosa MMA83) and two Gram-positive (Staphylococcus aureus ATCC25923 and Listeria monocytogenes ATCC19111) pathogens. Isolates BGSP7, BGSP9, BGSP11 and BGSP12 produced the largest zones of inhibition against all four pathogens when grown in LB broth with aeration at 37°C. Isolates BGSP7, BGSP9, BGSP11 and BGSP12 were identified as Brevibacillus laterosporus and pulsed field gel electrophoresis and extracellular protein profiles showed that three different strains (BGSP7, BGSP9 and BGSP11) were isolated. A semi-native SDS-PAGE (sodium dodecyl sulphate-polyacrylamide gel electrophoresis) gel overlay assay showed that BGSP7 and BGSP9 produce small antimicrobial molecules of about 1.5 kDa, while BGSP11 produces antimicrobial molecules of 1.5 and 6 kDa active against S. aureus ATCC25923. Amino acid analysis of two antimicrobial molecules (1583.73 Da; from BGSP7 and 1556.31 Da; from BGSP11) revealed that they have a similar composition and differ only by virtue of the presence of a methionine which is present only in BGSP11 molecule. Genome sequencing of the three isolates revealed the presence of gene clusters associated with the production of non-ribosomally synthesized peptides (brevibacillin, bogorol, gramicidin S, plipastatin and tyrocin) and bacteriocins (laterosporulin, a lactococcin 972-like bacteriocin, as well as putative linocin M18, sactipeptide, UviB and lantipeptide-like molecules). Ultimately, the purification of a number of antimicrobial molecules from each isolate suggests that they can be considered as potent biocontrol strains that produce an arsenal of antimicrobial molecules active against Gram-positive and Gram-negative multi-resistant pathogens, fungi and insects.
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Affiliation(s)
- Marija Miljkovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sofija Jovanovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Paula M. O’Connor
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Nemanja Mirkovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Branko Jovcic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Brankica Filipic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Miroslav Dinic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - David John Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Djordje Fira
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Milan Kojic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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35
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Acedo JZ, Chiorean S, Vederas JC, van Belkum MJ. The expanding structural variety among bacteriocins from Gram-positive bacteria. FEMS Microbiol Rev 2019; 42:805-828. [PMID: 30085042 DOI: 10.1093/femsre/fuy033] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteria use various strategies to compete in an ecological niche, including the production of bacteriocins. Bacteriocins are ribosomally synthesized antibacterial peptides, and it has been postulated that the majority of Gram-positive bacteria produce one or more of these natural products. Bacteriocins can be used in food preservation and are also considered as potential alternatives to antibiotics. The majority of bacteriocins from Gram-positive bacteria had been traditionally divided into two major classes, namely lantibiotics, which are post-translationally modified bacteriocins, and unmodified bacteriocins. The last decade has seen an expanding number of ribosomally synthesized and post-translationally modified peptides (RiPPs) in Gram-positive bacteria that have antibacterial activity. These include linear azol(in)e-containing peptides, thiopeptides, bottromycins, glycocins, lasso peptides and lipolanthines. In addition, the three-dimensional (3D) structures of a number of modified and unmodified bacteriocins have been elucidated in recent years. This review gives an overview on the structural variety of bacteriocins from Gram-positive bacteria. It will focus on the chemical and 3D structures of these peptides, and their interactions with receptors and membranes, structure-function relationships and possible modes of action.
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Affiliation(s)
- Jeella Z Acedo
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - Sorina Chiorean
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
| | - Marco J van Belkum
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, T6G 2G2, Canada
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Olishevska S, Nickzad A, Déziel E. Bacillus and Paenibacillus secreted polyketides and peptides involved in controlling human and plant pathogens. Appl Microbiol Biotechnol 2019; 103:1189-1215. [DOI: 10.1007/s00253-018-9541-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/25/2022]
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Si T, Tian Q, Min Y, Zhang L, Sweedler JV, van der Donk WA, Zhao H. Rapid Screening of Lanthipeptide Analogs via In-Colony Removal of Leader Peptides in Escherichia coli. J Am Chem Soc 2018; 140:11884-11888. [PMID: 30183279 DOI: 10.1021/jacs.8b05544] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Most native producers of ribosomally synthesized and post-translationally modified peptides (RiPPs) utilize N-terminal leader peptides to avoid potential cytotoxicity of mature products to the hosts. Unfortunately, the native machinery of leader peptide removal is often difficult to reconstitute in heterologous hosts. Here we devised a general method to produce bioactive lanthipeptides, a major class of RiPP molecules, in Escherichia coli colonies using synthetic biology principles, where leader peptide removal is programmed temporally by protease compartmentalization and inducible cell autolysis. We demonstrated the method for producing two lantibiotics, haloduracin and lacticin 481, and performed analog screening for haloduracin. This method enables facile, high throughput discovery, characterization, and engineering of RiPPs.
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Affiliation(s)
- Tong Si
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Qiqi Tian
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yuhao Min
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Linzixuan Zhang
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Jonathan V Sweedler
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,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
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Chemical and Biomolecular Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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Kers JA, Sharp RE, Muley S, Mayo M, Colbeck J, Zhu Y, DeFusco AW, Park JH, Handfield M. Blueprints for the rational design of therapeutic mutacin 1140 variants. Chem Biol Drug Des 2018; 92:1940-1953. [DOI: 10.1111/cbdd.13365] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/12/2018] [Accepted: 07/09/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Johan A. Kers
- Intrexon Corp.; Industrial Products Division; South San Francisco California
| | - R. Eryl Sharp
- Intrexon Corp.; Industrial Products Division; South San Francisco California
| | - Sheela Muley
- Intrexon Corp.; Industrial Products Division; South San Francisco California
| | - Melissa Mayo
- Intrexon Corp.; Industrial Products Division; South San Francisco California
| | - Jeffrey Colbeck
- Intrexon Corp.; Industrial Products Division; South San Francisco California
| | - Yihui Zhu
- Intrexon Corp.; Industrial Products Division; South San Francisco California
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CerR, a Single-Domain Regulatory Protein of the LuxR Family, Promotes Cerecidin Production and Immunity in Bacillus cereus. Appl Environ Microbiol 2018; 84:AEM.02245-17. [PMID: 29247062 DOI: 10.1128/aem.02245-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/12/2017] [Indexed: 12/14/2022] Open
Abstract
Cerecidins are small lantibiotics from Bacillus cereus that were obtained using a semi-in vitro biosynthesis strategy and showed prominent antimicrobial activities against certain Gram-positive bacteria. However, the parental strain B. cereus As 1.1846 is incapable of producing cerecidins, most probably due to the transcriptional repression of the cerecidin gene cluster. Located in the cerecidin gene cluster, cerR encodes a putative response regulator protein that belongs to the LuxR family transcriptional regulators. CerR (84 amino acids) contains only a conserved DNA binding domain and lacks a conventional phosphorylation domain, which is rarely found in lantibiotic gene clusters. To investigate its function in cerecidin biosynthesis, cerR was constitutively expressed in B. cereus As 1.1846. Surprisingly, Constitutive expression of cerR enabled the production of cerecidins and enhanced self-immunity of B. cereus toward cerecidins. Reverse transcription-PCR analysis and electrophoresis mobility shift assays indicated, respectively, that the cer cluster was transcribed in two transcripts (cerAM and cerRTPFE) and that CerR regulated the cerecidin gene cluster directly by binding to the two predicted promoter regions of cerA and cerR DNase I footprinting experiments further confirmed that CerR specifically bound to the two promoter regions at a conserved inverted repeat sequence that was designated a CerR binding motif (cerR box). The present study demonstrated that CerR, as the first single-domain LuxR family transcriptional regulator, serves as a transcriptional activator in cerecidin biosynthesis and activates the cerecidin gene cluster, which was otherwise cryptic in B. cereusIMPORTANCE Lantibiotics with intriguing and prominent bioactivities are potential peptide antibiotics that could be applied in many areas, including food and pharmaceutical industries. The biosynthesis of lantibiotics is generally controlled by two-component regulatory systems consisting of histidine kinases and response regulators, while some unique and interesting regulatory systems are also revealed with the ever-increasing discovery of lantibiotic gene clusters among diverse microorganisms. Dissection of diverse lantibiotic regulation machineries would permit deep understanding of the biological functions of lantibiotics in different niches and even enable genetic activation of lantibiotic gene clusters that are otherwise cryptic. The significance of our study is to illuminate the regulatory mechanism of a special single-domain protein, CerR, in regulating cerecidin biosynthesis in Bacillus cereus, providing a possible novel approach to activate cryptic lantibiotic clusters.
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Bakhtiary A, Cochrane SA, Mercier P, McKay RT, Miskolzie M, Sit CS, Vederas JC. Insights into the Mechanism of Action of the Two-Peptide Lantibiotic Lacticin 3147. J Am Chem Soc 2017; 139:17803-17810. [PMID: 29164875 DOI: 10.1021/jacs.7b04728] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lacticin 3147 is a two peptide lantibiotc (LtnA1 and LtnA2) that displays nanomolar activity against many Gram-positive bacteria. Lacticin 3147 may exert its antimicrobial effect by several mechanisms. Isothermal titration calorimetry experiments show that only LtnA1 binds to the peptidoglycan precursor lipid II, which could inhibit peptidoglycan biosynthesis. An experimentally supported model of the resulting complex suggests that the key binding partners are the C-terminus of LtnA1 and pyrophosphate of lipid II. A combination of in vivo and in vitro assays indicates that LtnA1 and LtnA2 can induce rapid membrane lysis without the need for lipid II binding. However, the presence of lipid II substantially increases the activity of lacticin 3147. Furthermore, studies with synthetic LtnA2 analogues containing either desmethyl- or oxa-lanthionine rings confirm that the precise geometry of these rings is essential for this synergistic activity.
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Affiliation(s)
- Alireza Bakhtiary
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queens University Belfast , Belfast BT9 5AG, United Kingdom
| | - Pascal Mercier
- National High Field NMR Centre, University of Alberta , Edmonton, Alberta T6G 2E1, Canada
| | - Ryan T McKay
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Mark Miskolzie
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Clarissa S Sit
- Department of Chemistry, Saint Mary's University , Halifax, Nova Scotia B3H 3C3, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
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Müller A, Klöckner A, Schneider T. Targeting a cell wall biosynthesis hot spot. Nat Prod Rep 2017; 34:909-932. [PMID: 28675405 DOI: 10.1039/c7np00012j] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: up to 2017History points to the bacterial cell wall biosynthetic network as a very effective target for antibiotic intervention, and numerous natural product inhibitors have been discovered. In addition to the inhibition of enzymes involved in the multistep synthesis of the macromolecular layer, in particular, interference with membrane-bound substrates and intermediates essential for the biosynthetic reactions has proven a valuable antibacterial strategy. A prominent target within the peptidoglycan biosynthetic pathway is lipid II, which represents a particular "Achilles' heel" for antibiotic attack, as it is readily accessible on the outside of the cytoplasmic membrane. Lipid II is a unique non-protein target that is one of the structurally most conserved molecules in bacterial cells. Notably, lipid II is more than just a target molecule, since sequestration of the cell wall precursor may be combined with additional antibiotic activities, such as the disruption of membrane integrity or disintegration of membrane-bound multi-enzyme machineries. Within the membrane bilayer lipid II is likely organized in specific anionic phospholipid patches that form a particular "landing platform" for antibiotics. Nature has invented a variety of different "lipid II binders" of at least 5 chemical classes, and their antibiotic activities can vary substantially depending on the compounds' physicochemical properties, such as amphiphilicity and charge, and thus trigger diverse cellular effects that are decisive for antibiotic activity.
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Affiliation(s)
- Anna Müller
- Institute of Pharmaceutical Microbiology, University of Bonn, Bonn, Germany.
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42
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Repka LM, Chekan JR, Nair SK, van der Donk WA. Mechanistic Understanding of Lanthipeptide Biosynthetic Enzymes. Chem Rev 2017; 117:5457-5520. [PMID: 28135077 PMCID: PMC5408752 DOI: 10.1021/acs.chemrev.6b00591] [Citation(s) in RCA: 317] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Lanthipeptides
are ribosomally synthesized and post-translationally
modified peptides (RiPPs) that display a wide variety of biological
activities, from antimicrobial to antiallodynic. Lanthipeptides that
display antimicrobial activity are called lantibiotics. The post-translational
modification reactions of lanthipeptides include dehydration of Ser
and Thr residues to dehydroalanine and dehydrobutyrine, a transformation
that is carried out in three unique ways in different classes of lanthipeptides.
In a cyclization process, Cys residues then attack the dehydrated
residues to generate the lanthionine and methyllanthionine thioether
cross-linked amino acids from which lanthipeptides derive their name.
The resulting polycyclic peptides have constrained conformations that
confer their biological activities. After installation of the characteristic
thioether cross-links, tailoring enzymes introduce additional post-translational
modifications that are unique to each lanthipeptide and that fine-tune
their activities and/or stability. This review focuses on studies
published over the past decade that have provided much insight into
the mechanisms of the enzymes that carry out the post-translational
modifications.
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Affiliation(s)
- Lindsay M Repka
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jonathan R Chekan
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Satish K Nair
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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Ahmad V, Khan MS, Jamal QMS, Alzohairy MA, Al Karaawi MA, Siddiqui MU. Antimicrobial potential of bacteriocins: in therapy, agriculture and food preservation. Int J Antimicrob Agents 2017; 49:1-11. [DOI: 10.1016/j.ijantimicag.2016.08.016] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 07/10/2016] [Accepted: 08/08/2016] [Indexed: 10/20/2022]
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44
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Synergistic effect of haloduracin and chloramphenicol against clinically important Gram-positive bacteria. ACTA ACUST UNITED AC 2016; 13:37-41. [PMID: 28352561 PMCID: PMC5361133 DOI: 10.1016/j.btre.2016.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 11/20/2016] [Accepted: 12/25/2016] [Indexed: 12/31/2022]
Abstract
Haloduracin and chloramphenicol exhibited synergistic effect against pathogens. The synergy indicates possibility of reducing the effective dose of chloramphenicol. Reduction of chloramphenicol dose minimizes its negative side effects. This shows a new window of using antibiotics and bacteriocins in combination therapy.
The emergence of drug-resistant pathogens has triggered the search for more efficient antimicrobial agents and formulations for treatment of infections. In recent years, combination therapy has become one of the effective clinical practices in treating infections. The present study deals with the effect of haloduracin, a lantibiotic bateriocin and chloramphenicol against clinically important bacteria. The combined use of haloduracin and chloramphenicol resulted in remarkable synergy against a spectrum of microorganisms including strains of Staphylococcus aureus, Enterococcus faecium, Enterococcus faecalis and different groups of Streptococcus. The synergy allowed using these antimicrobial agents at substantially reduced concentrations without compromising their efficiency. Use of lower doses of chloramphenicol can avoid the severity of its side effects. In addition to minimizing undesirable side effects of some drugs, this approach brings the possibility of using antibiotics that are no longer effective due to drug resistance. Furthermore, the observed synergy between haloduracin and chloramphenicol opens a new window of using bacteriocins and antibiotics in combination therapy of infections.
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45
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Towards Biocontained Cell Factories: An Evolutionarily Adapted Escherichia coli Strain Produces a New-to-nature Bioactive Lantibiotic Containing Thienopyrrole-Alanine. Sci Rep 2016; 6:33447. [PMID: 27634138 PMCID: PMC5025777 DOI: 10.1038/srep33447] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/25/2016] [Indexed: 11/08/2022] Open
Abstract
Genetic code engineering that enables reassignment of genetic codons to non-canonical amino acids (ncAAs) is a powerful strategy for enhancing ribosomally synthesized peptides and proteins with functions not commonly found in Nature. Here we report the expression of a ribosomally synthesized and post-translationally modified peptide (RiPP), the 32-mer lantibiotic lichenicidin with a canonical tryptophan (Trp) residue replaced by the ncAA L-β-(thieno[3,2-b]pyrrolyl)alanine ([3,2]Tpa) which does not sustain cell growth in the culture. We have demonstrated that cellular toxicity of [3,2]Tpa for the production of the new-to-nature bioactive congener of lichenicidin in the host Escherichia coli can be alleviated by using an evolutionarily adapted host strain MT21 which not only tolerates [3,2]Tpa but also uses it as a proteome-wide synthetic building block. This work underscores the feasibility of the biocontainment concept and establishes a general framework for design and large scale production of RiPPs with evolutionarily adapted host strains.
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Xin B, Zheng J, Liu H, Li J, Ruan L, Peng D, Sajid M, Sun M. Thusin, a Novel Two-Component Lantibiotic with Potent Antimicrobial Activity against Several Gram-Positive Pathogens. Front Microbiol 2016; 7:1115. [PMID: 27486447 PMCID: PMC4949975 DOI: 10.3389/fmicb.2016.01115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/04/2016] [Indexed: 12/28/2022] Open
Abstract
Due to the rapidly increasing prevalence of multidrug-resistant bacterial strains, the need for new antimicrobial drugs to treat infections has become urgent. Bacteriocins, which are antimicrobial peptides of bacterial origin, are considered potential alternatives to conventional antibiotics and have attracted widespread attention in recent years. Among these bacteriocins, lantibiotics, especially two-component lantibiotics, exhibit potent antimicrobial activity against some clinically relevant Gram-positive pathogens and have potential applications in the pharmaceutical industry. In this study, we characterized a novel two-component lantibiotic termed thusin that consists of Thsα, Thsβ, and Thsβ' (mutation of Thsβ, A14G) and that was isolated from a B. thuringiensis strain BGSC 4BT1. Thsα and Thsβ (or Thsβ') exhibit optimal antimicrobial activity at a 1:1 ratio and act sequentially to affect target cells, and they are all highly thermostable (100°C for 30 min) and pH tolerant (pH 2.0 to 9.0). Thusin shows remarkable efficacy against all tested Gram-positive bacteria and greater activities than two known lantibiotics thuricin 4A-4 and ticin A4, and one antibiotic vancomycin against various bacterial pathogens (Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus (MRSA), Staphylococcus sciuri, Enterococcus faecalis, and Streptococcus pneumoniae). Moreover, thusin is also able to inhibit the outgrowth of B. cereus spores. The potent antimicrobial activity of thusin against some Gram-positive pathogens indicates that it has potential for the development of new drugs.
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Affiliation(s)
- Bingyue Xin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Hualin Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Junhua Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Muhammad Sajid
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University Wuhan, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University Wuhan, China
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47
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Efficacy of Lantibiotic Treatment of Staphylococcus aureus-Induced Skin Infections, Monitored by In Vivo Bioluminescent Imaging. Antimicrob Agents Chemother 2016; 60:3948-55. [PMID: 27067340 DOI: 10.1128/aac.02938-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/08/2016] [Indexed: 02/02/2023] Open
Abstract
Staphylococcus aureus is a bacterial pathogen responsible for the majority of skin and soft tissue infections. Antibiotics are losing their efficacy as treatment for skin and soft tissue infections as a result of increased resistance in a variety of pathogens, including S. aureus It is thus imperative to explore alternative antimicrobial treatments to ensure future treatment options for skin and soft tissue infections. A select few lantibiotics, a group of natural defense peptides produced by bacteria, inhibit the growth of numerous clinical S. aureus isolates, including methicillin-resistant strains. In this study, the antimicrobial activities of nisin, clausin, and amyloliquecidin, separately administered, were compared to that of a mupirocin-based ointment, which is commonly used as treatment for S. aureus-induced skin infections. Full-thickness excisional wounds, generated on the dorsal surfaces of mice, were infected with a bioluminescent strain of S. aureus (strain Xen 36). The infections were monitored in real time using in vivo bioluminescent imaging. Lantibiotic treatments significantly reduced the bioluminescence of S. aureus Xen 36 to a level similar to that recorded with mupirocin treatment. Wound closure, however, was more pronounced during lantibiotic treatment. Lantibiotics thus have the potential to be used as an alternative treatment option for S. aureus-induced skin infections.
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48
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Huo L, van der Donk WA. Discovery and Characterization of Bicereucin, an Unusual d-Amino Acid-Containing Mixed Two-Component Lantibiotic. J Am Chem Soc 2016; 138:5254-7. [PMID: 27074593 PMCID: PMC4851115 DOI: 10.1021/jacs.6b02513] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Lantibiotics are a group of ribosomally synthesized and post-translationally modified peptides (RiPPs) exhibiting antimicrobial activity. They are characterized by the presence of the thioether-containing bisamino acids lanthionine and methyllanthionine. Here, we report a two-component lantibiotic from Bacillus cereus SJ1 with unusual structural features that we named bicereucin. Unlike all previous two-component lantibiotics, only one of the two peptides of bicereucin contains a lanthionine. The second peptide lacks any cysteines but contains several d-amino acids. These are installed by the dehydrogenase BsjJB, the activity of which was successfully reconstituted in vitro. The proteolytic removal of the leader peptide was also performed in vitro. Bicereucin displayed synergistic antimicrobial activities against Gram-positive strains including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci as well as hemolytic activity. To illustrate the utility of the enzymes, an analog of the d-amino acid containing opioid dermorphin was successfully produced in E. coli by employing the dehydratase BsjM and the dehydrogenase NpnJA.
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Affiliation(s)
- Liujie Huo
- Howard Hughes Medical Institute and Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign , 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign , 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
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49
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Kong W, Kapuganti VS, Lu T. A gene network engineering platform for lactic acid bacteria. Nucleic Acids Res 2016; 44:e37. [PMID: 26503255 PMCID: PMC4770204 DOI: 10.1093/nar/gkv1093] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 11/28/2022] Open
Abstract
Recent developments in synthetic biology have positioned lactic acid bacteria (LAB) as a major class of cellular chassis for applications. To achieve the full potential of LAB, one fundamental prerequisite is the capacity for rapid engineering of complex gene networks, such as natural biosynthetic pathways and multicomponent synthetic circuits, into which cellular functions are encoded. Here, we present a synthetic biology platform for rapid construction and optimization of large-scale gene networks in LAB. The platform involves a copy-controlled shuttle for hosting target networks and two associated strategies that enable efficient genetic editing and phenotypic validation. By using a nisin biosynthesis pathway and its variants as examples, we demonstrated multiplex, continuous editing of small DNA parts, such as ribosome-binding sites, as well as efficient manipulation of large building blocks such as genes and operons. To showcase the platform, we applied it to expand the phenotypic diversity of the nisin pathway by quickly generating a library of 63 pathway variants. We further demonstrated its utility by altering the regulatory topology of the nisin pathway for constitutive bacteriocin biosynthesis. This work demonstrates the feasibility of rapid and advanced engineering of gene networks in LAB, fostering their applications in biomedicine and other areas.
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Affiliation(s)
- Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Venkata S Kapuganti
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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50
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Zhao X, van der Donk WA. Structural Characterization and Bioactivity Analysis of the Two-Component Lantibiotic Flv System from a Ruminant Bacterium. Cell Chem Biol 2016; 23:246-256. [PMID: 27028884 PMCID: PMC4814930 DOI: 10.1016/j.chembiol.2015.11.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/10/2015] [Accepted: 11/20/2015] [Indexed: 12/17/2022]
Abstract
The discovery of new ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) has greatly benefitted from the influx of genomic information. The lanthipeptides are a subset of this class of compounds. Adopting the genome-mining approach revealed a novel lanthipeptide gene cluster encoded in the genome of Ruminococcus flavefaciens FD-1, an anaerobic bacterium that is an important member of the rumen microbiota of livestock. The post-translationally modified peptides were produced via heterologous expression in Escherichia coli. Subsequent structural characterization and assessment of their bioactivity revealed features reminiscent of and distinct from previously reported lanthipeptides. The lanthipeptides of R. flavefaciens FD-1 represent a unique example within two-component lanthipeptides, consisting of a highly conserved α-peptide and a diverse set of eight β-peptides.
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Affiliation(s)
- Xiling Zhao
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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