1
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Garrett SR, Palmer T. The role of proteinaceous toxins secreted by Staphylococcus aureus in interbacterial competition. FEMS MICROBES 2024; 5:xtae006. [PMID: 38495077 PMCID: PMC10941976 DOI: 10.1093/femsmc/xtae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/17/2024] [Accepted: 02/27/2024] [Indexed: 03/19/2024] Open
Abstract
Staphylococcus aureus is highly adapted to colonization of the mammalian host. In humans the primary site of colonization is the epithelium of the nasal cavity. A major barrier to colonization is the resident microbiota, which have mechanisms to exclude S. aureus. As such, S. aureus has evolved mechanisms to compete with other bacteria, one of which is through secretion of proteinaceous toxins. S. aureus strains collectively produce a number of well-characterized Class I, II, and IV bacteriocins as well as several bacteriocin-like substances, about which less is known. These bacteriocins have potent antibacterial activity against several Gram-positive organisms, with some also active against Gram-negative species. S. aureus bacteriocins characterized to date are sporadically produced, and often encoded on plasmids. More recently the type VII secretion system (T7SS) of S. aureus has also been shown to play a role in interbacterial competition. The T7SS is encoded by all S. aureus isolates and so may represent a more widespread mechanism of competition used by this species. T7SS antagonism is mediated by the secretion of large protein toxins, three of which have been characterized to date: a nuclease toxin, EsaD; a membrane depolarizing toxin, TspA; and a phospholipase toxin, TslA. Further study is required to decipher the role that these different types of secreted toxins play in interbacterial competition and colonization of the host.
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Affiliation(s)
- Stephen R Garrett
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Tracy Palmer
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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2
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Liu F, van Heel AJ, Kuipers OP. Engineering circular bacteriocins: structural and functional effects of α-helix exchanges and disulfide introductions in circularin A. Front Microbiol 2024; 15:1337647. [PMID: 38435696 PMCID: PMC10905743 DOI: 10.3389/fmicb.2024.1337647] [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: 11/13/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024] Open
Abstract
Circular bacteriocins form a distinct group of antimicrobial peptides (AMPs) characterized by their unique head-to-tail ligated circular structure and functional properties. They belong to the ribosomally synthesized and post-translationally modified peptide (RiPP) family. The ribosomal origin of these peptides facilitates rapid diversification through mutations in the precursor genes combined with specific modification enzymes. In this study, we primarily explored the bacteriocin engineering potential of circularin A, a circular bacteriocin produced by Clostridium beijerinckii ATCC 25752. Specifically, we employed strategies involving α-helix replacements and disulfide bond introductions to investigate their effects on both biosynthesis and bioactivity of the bacteriocin. The results show the feasibility of peptide engineering to introduce certain structural properties into circularin A through carefully designed approaches. The introduction of cysteines for potential disulfide bonds resulted in a substantial reduction in bacteriocin biosynthesis and/or bioactivity, indicating the importance of maintaining dynamic flexibility of α-helices in circularin A, while reduction of the potential disulfide in one case increased the activity. The 5 α-helices of circularin A were respectively replaced by corresponding helices from another circular peptide, enterocin AS-48, and modestly active peptides were obtained in a few cases. Overall, this study provides valuable insights into the engineering potential of circular bacteriocins as antimicrobial agents, including their structural and functional restrictions and their suitability as peptide engineering scaffolds. This helps to pave the way for the development of novel antimicrobial peptides with tailored properties based on circular bacteriocins.
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Affiliation(s)
- Fangfang Liu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Auke J. van Heel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
- Omnicin Therapeutics, Groningen, Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
- Omnicin Therapeutics, Groningen, Netherlands
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3
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Kita K, Yoshida S, Masuo S, Nakamura A, Ishikawa S, Yoshida KI. Genes encoding a novel thermostable bacteriocin in the thermophilic bacterium Aeribacillus pallidus PI8. J Appl Microbiol 2023; 134:lxad293. [PMID: 38040658 DOI: 10.1093/jambio/lxad293] [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: 06/13/2023] [Revised: 11/10/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023]
Abstract
AIM Aeribacillus pallidus PI8 is a Gram-positive thermophilic bacterium that produces thermostable antimicrobial substances against several bacterial species, including Geobacillus kaustophilus HTA426. In the present study, we sought to identify genes of PI8 with antibacterial activity. METHODS AND RESULTS We isolated, cloned, and characterized a thermostable bacteriocin from A. pallidus PI8 and named it pallidocyclin. Mass spectrometric analyses of pallidocyclin revealed that it had a circular peptide structure, and its precursor was encoded by pcynA in the PI8 genome. pcynA is the second gene within the pcynBACDEF operon. Expression of the full-length pcynBACDEF operon in Bacillus subtilis produced intact pallidocyclin, whereas expression of pcynF in G. kaustophilus HTA426 conferred resistance to pallidocyclin. CONCLUSION Aeribacillus pallidus PI8 possesses the pcynBACDEF operon to produce pallidocyclin. pcynA encodes the pallidocyclin precursor, and pcynF acts as an antagonist of pallidocyclin.
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Affiliation(s)
- Kyosuke Kita
- Department of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Sanako Yoshida
- Department of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572 Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572 Ibaraki, Japan
| | - Akira Nakamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572 Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572 Ibaraki, Japan
| | - Shu Ishikawa
- Department of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ken-Ichi Yoshida
- Department of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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4
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Teso-Pérez C, Martínez-Bueno M, Peralta Sánchez JM, Valdivia E, Fárez-Vidal ME, Martín-Platero AM. Circular and L50-like leaderless enterocins share a common ABC-transporter immunity gene. BMC Genomics 2023; 24:639. [PMID: 37875795 PMCID: PMC10598978 DOI: 10.1186/s12864-023-09750-2] [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: 07/07/2023] [Accepted: 10/18/2023] [Indexed: 10/26/2023] Open
Abstract
Microbes live within complex communities of interacting populations, either free-living in waters and soils or symbionts of animals and plants. Their interactions include the production of antimicrobial peptides (bacteriocins) to antagonize competitors, and these producers must carry their own immunity gene for self-protection. Whether other coexisting populations are sensitive or resistant to the bacteriocin producer will be key for the population dynamics within the microbial community. The immunity gene frequently consists of an ABC transporter to repel its own bacteriocin but rarely protects against a nonrelated bacteriocin. A case where this cross-resistance occurs mediated by a shared ABC transporter has been shown between enterocins MR10A/B and AS-48. The first is an L50-like leaderless enterocin, while AS-48 is a circular enterocin. In addition, L50-like enterocins such as MR10A/B have been found in E. faecalis and E. faecium, but AS-48 appears only in E. faecalis. Thus, using the ABC transporter of the enterocin MR10A/B gene cluster of Enterococcus faecalis MRR10-3 as a cross-resistance model, we aimed to unravel to what extent a particular ABC transporter can be shared across multiple bacteriocinogenic bacterial populations. To this end, we screened the MR10A/B-ABC transporters in available microbial genomes and analyzed their sequence homologies and distribution. Overall, our main findings are as follows: (i) the MR10A/B-ABC transporter is associated with multiple enterocin gene clusters; (ii) the different enterocins associated with this transporter have a saposin-like fold in common; (iii) the Mr10E component of the transporter is more conserved within its associated enterocin, while the Mr10FGH components are more conserved within the carrying species. This is the least known component of the transporter, but it has shown the greatest specificity to its corresponding enterocin. Bacteriocins are now being investigated as an alternative to antibiotics; hence, the wider or narrower distribution of the particular immunity gene should be taken into account for clinical applications to avoid the selection of resistant strains. Further research will be needed to investigate the mechanistic interactions between the Mr10E transporter component and the bacteriocin as well as the specific ecological and evolutionary mechanisms involved in the spread of the immunity transporter across multiple bacteriocins.
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Affiliation(s)
- Claudia Teso-Pérez
- Department of Microbiology, University of Granada, Avda. Fuentenueva, s/n, Granada, 18071, Spain
| | - Manuel Martínez-Bueno
- Department of Microbiology, University of Granada, Avda. Fuentenueva, s/n, Granada, 18071, Spain
| | - Juan Manuel Peralta Sánchez
- Department of Microbiology, University of Granada, Avda. Fuentenueva, s/n, Granada, 18071, Spain
- Department of Zoology, University of Seville, Avda. Reina Mercedes, 6, Seville, 41012, Spain
| | - Eva Valdivia
- Department of Microbiology, University of Granada, Avda. Fuentenueva, s/n, Granada, 18071, Spain
| | - María Esther Fárez-Vidal
- Department of Biochemistry and Molecular Biology III and Immunology, School of Medicine, University of Granada, Granada, 18016, Spain.
- Biomedical Research Institute of Granada, University Hospital Complex of Granada, University of Granada, Granada, 18071, Spain.
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5
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Fernández-Fernández R, Elsherbini AMA, Lozano C, Martínez A, de Toro M, Zarazaga M, Peschel A, Krismer B, Torres C. Genomic Analysis of Bacteriocin-Producing Staphylococci: High Prevalence of Lanthipeptides and the Micrococcin P1 Biosynthetic Gene Clusters. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10119-w. [PMID: 37632676 DOI: 10.1007/s12602-023-10119-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 08/28/2023]
Abstract
Bacteriocins are antimicrobial peptides produced by bacteria. This study aimed to in silico analyze the presence of bacteriocin gene clusters (BGCs) among the genomes of 22 commensal Staphylococcus isolates from different origins (environment/human/food/pet/wild animals) previously identified as bacteriocin producers. The resistome and plasmidome were studied in all isolates. Five types of BGC were detected in 18 genomes of the 22 bacteriocin-producing staphylococci included in this study: class I (Lanthipeptides), class II, circular bacteriocins, the non-ribosomal-peptide lugdunin and the thiopeptide micrococcin P1 (MP1). A high frequency of lanthipeptides was detected in this collection: BGC variants of BSA, bacCH91, and epilancin15X were identified in two Staphylococcus aureus and one Staphylococcus warneri isolates from food and wild animals. Moreover, two potentially new lanthipeptide-like BGCs with no identity to database entries were found in Staphylococcus epidermidis and Staphylococcus simulans from food and wild animal, respectively. Interestingly, four isolates (one S. aureus and one Staphylococcus hominis, environmental origin; two Staphylococcus sciuri, food) carried the MP1 BGC with differences to those previously described. On the other hand, seven of the 22 genomes (~32%) lacked known genes related with antibiotic or disinfectant-acquired resistance mechanisms. Moreover, the potential carriage of plasmids was evaluated, and several Rep-proteins were identified (~73% of strains). In conclusion, a wide variety of BGCs has been observed among the 22 genomes, and an interesting relationship between related Staphylococcus species and the type of bacteriocin has been revealed. Therefore, bacteriocin-producing Staphylococcus and especially coagulase-negative staphylococci (CoNS) can be considered good candidates as a source of novel bacteriocins.
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Affiliation(s)
- Rosa Fernández-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
| | - Ahmed M A Elsherbini
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
| | - Agustí Martínez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
| | - María de Toro
- Genomics and Bioinformatics Core Facility, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
| | - Andreas Peschel
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Bernhard Krismer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
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6
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Wang CK, Huang YH, Shabbir F, Pham HT, Lawrence N, Benfield AH, van der Donk W, Henriques ST, Turner MS, Craik DJ. The Circular Bacteriocin enterocin NKR-5-3B has an Improved Stability Profile over Nisin. Peptides 2023:171049. [PMID: 37390898 DOI: 10.1016/j.peptides.2023.171049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023]
Abstract
Bacteriocins are a large family of bacterial peptides that have antimicrobial activity and potential applications as clinical antibiotics or food preservatives. Circular bacteriocins are a unique class of these biomolecules distinguished by a seamless circular topology, and are widely assumed to be ultra-stable based on this constraining structural feature. However, without quantitative studies of their susceptibility to defined thermal, chemical, and enzymatic conditions, their stability characteristics remain poorly understood, limiting their translational development. Here, we produced the circular bacteriocin enterocin NKR-5-3B (Ent53B) in mg/L quantities using a heterologous Lactococcus expression system, and characterized its thermal stability by NMR, chemical stability by circular dichroism and analytical HPLC, and enzymatic stability by analytical HPLC. We demonstrate that Ent53B is ultra-stable, resistant to temperatures approaching boiling, acidic (pH 2.6) and alkaline (pH 9.0) conditions, the chaotropic agent 6M urea, and following incubation with a range of proteases (i.e., trypsin, chymotrypsin, pepsin, and papain), conditions under which most peptides and proteins degrade. Ent53B is stable across a broader range of pH conditions and proteases than nisin, the most widely used bacteriocin in food manufacturing. Antimicrobial assays showed that differences in stability correlated with differences in bactericidal activity. Overall, this study provides quantitative support for circular bacteriocins being an ultra-stable class of peptide molecules, suggesting easier handling and distribution options available to them in practical applications as antimicrobial agents.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science,.
| | - Yen-Hua Huang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
| | - Fatima Shabbir
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
| | - Huong T Pham
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
| | - Aurélie H Benfield
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Wilfred van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sónia T Henriques
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Mark S Turner
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science
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7
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Fernández-Fernández R, Lozano C, Reuben RC, Ruiz-Ripa L, Zarazaga M, Torres C. Comprehensive Approaches for the Search and Characterization of Staphylococcins. Microorganisms 2023; 11:1329. [PMID: 37317303 DOI: 10.3390/microorganisms11051329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
Novel and sustainable approaches are required to curb the increasing threat of antimicrobial resistance (AMR). Within the last decades, antimicrobial peptides, especially bacteriocins, have received increased attention and are being explored as suitable alternatives to antibiotics. Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria as a self-preservation method against competitors. Bacteriocins produced by Staphylococcus, also referred to as staphylococcins, have steadily shown great antimicrobial potential and are currently being considered promising candidates to mitigate the AMR menace. Moreover, several bacteriocin-producing Staphylococcus isolates of different species, especially coagulase-negative staphylococci (CoNS), have been described and are being targeted as a good alternative. This revision aims to help researchers in the search and characterization of staphylococcins, so we provide an up-to-date list of bacteriocin produced by Staphylococcus. Moreover, a universal nucleotide and amino acid-based phylogeny system of the well-characterized staphylococcins is proposed that could be of interest in the classification and search for these promising antimicrobials. Finally, we discuss the state of art of the staphylococcin applications and an overview of the emerging concerns.
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Affiliation(s)
- Rosa Fernández-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain
| | - Rine Christopher Reuben
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain
| | - Laura Ruiz-Ripa
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain
| | - Myriam Zarazaga
- 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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8
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Nanomedicine for drug resistant pathogens and COVID-19 using mushroom nanocomposite inspired with bacteriocin – A Review. INORG CHEM COMMUN 2023; 152:110682. [PMID: 37041990 PMCID: PMC10067464 DOI: 10.1016/j.inoche.2023.110682] [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: 12/30/2022] [Revised: 03/25/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
Multidrug resistant (MDR) pathogens have become a major global health challenge and have severely threatened the health of society. Current conditions have gotten worse as a result of the COVID-19 pandemic, and infection rates in the future will rise. It is necessary to design, respond effectively, and take action to address these challenges by investigating new avenues. In this regard, the fabrication of metal NPs utilized by various methods, including green synthesis using mushroom, is highly versatile, cost-effective, eco-compatible, and superior. In contrast, biofabrication of metal NPs can be employed as a powerful weapon against MDR pathogens and have immense biomedical applications. In addition, the advancement in nanotechnology has made possible to modify the nanomaterials and enhance their activities. Metal NPs with biomolecules composite to prevents their microbial adhesion and kills the microbial pathogens through biofilm formation. Bacteriocin is an excellent antimicrobial peptide that works well as an augmentation substance to boost the antimicrobial effects. As a result, we concentrate on the creation of new, eco-compatible mycosynthesized metal NPs with bacteriocin nanocomposite via electrostatic, covalent, or non-covalent bindings. The synergistic benefits of metal NPs with bacteriocin to combat MDR pathogens and COVID-19, as well as other biomedical applications, are discussed in this review. Moreover, the importance of the adverse outcome pathway (AOP) in risk analysis of manufactured metal nanocomposite nanomaterial and their future possibilities also discussed.
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9
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Ishida K, Nakamura A, Kojima S. Crystal structure of the AlbEF complex involved in subtilosin A biosynthesis. Structure 2022; 30:1637-1646.e3. [DOI: 10.1016/j.str.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/12/2022] [Accepted: 09/30/2022] [Indexed: 12/05/2022]
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10
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Peña N, Bland MJ, Sevillano E, Muñoz-Atienza E, Lafuente I, Bakkoury ME, Cintas LM, Hernández PE, Gabant P, Borrero J. In vitro and in vivo production and split-intein mediated ligation (SIML) of circular bacteriocins. Front Microbiol 2022; 13:1052686. [DOI: 10.3389/fmicb.2022.1052686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Circular bacteriocins are antimicrobial peptides produced by bacteria that after synthesis undergo a head-to-tail circularization. Compared to their linear counterparts, circular bacteriocins are, in general, very stable to temperature and pH changes and more resistant to proteolytic enzymes, being considered as one of the most promising groups of antimicrobial peptides for their potential biotechnological applications. Up to now, only a reduced number of circular bacteriocins have been identified and fully characterized, although many operons potentially coding for new circular bacteriocins have been recently found in the genomes of different bacterial species. The production of these peptides is very complex and depends on the expression of different genes involved in their synthesis, circularization, and secretion. This complexity has greatly limited the identification and characterization of these bacteriocins, as well as their production in heterologous microbial hosts. In this work, we have evaluated a synthetic biology approach for the in vitro and in vivo production combined with a split-intein mediated ligation (SIML) of the circular bacteriocin garvicin ML (GarML). The expression of one single gene is enough to produce a protein that after intein splicing, circularizes in an active peptide with the exact molecular mass and amino acid sequence as native GarML. In vitro production coupled with SIML has been validated with other, well described and not yet characterized, circular bacteriocins. The results obtained suggest that this synthetic biology tool holds great potential for production, engineering, improving and testing the antimicrobial activity of circular bacteriocins.
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11
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Dini I, De Biasi MG, Mancusi A. An Overview of the Potentialities of Antimicrobial Peptides Derived from Natural Sources. Antibiotics (Basel) 2022; 11:1483. [PMID: 36358138 PMCID: PMC9686932 DOI: 10.3390/antibiotics11111483] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial peptides (AMPs) are constituents of the innate immune system in every kind of living organism. They can act by disrupting the microbial membrane or without affecting membrane stability. Interest in these small peptides stems from the fear of antibiotics and the emergence of microorganisms resistant to antibiotics. Through membrane or metabolic disruption, they defend an organism against invading bacteria, viruses, protozoa, and fungi. High efficacy and specificity, low drug interaction and toxicity, thermostability, solubility in water, and biological diversity suggest their applications in food, medicine, agriculture, animal husbandry, and aquaculture. Nanocarriers can be used to protect, deliver, and improve their bioavailability effectiveness. High cost of production could limit their use. This review summarizes the natural sources, structures, modes of action, and applications of microbial peptides in the food and pharmaceutical industries. Any restrictions on AMPs' large-scale production are also taken into consideration.
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Affiliation(s)
- Irene Dini
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | | | - Andrea Mancusi
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy
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12
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Yaghoubi A, Ghazvini K, Hasanian SM, Avan A, Soleimanpour S, Khazaei M. Bacterial Peptides and Bacteriocins as a Promising Therapy for Solid Tumor. Curr Pharm Des 2022; 28:3105-3113. [PMID: 36154595 DOI: 10.2174/1381612828666220921150037] [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: 03/03/2022] [Accepted: 05/24/2022] [Indexed: 01/28/2023]
Abstract
The conventional treatment is faced with limitations in treating solid tumors due to their specific pathophysiology. Several novel therapeutics have been introduced in recent decades to treat solid tumors. Among these new methods, tumor therapy using bacterial products like bacteriocins and peptides has been of great interest due to their unique characteristics and advantages of them in comparison to the conventional treatment, including that they can precisely target tumor cells, selective toxicity for tumor cells, low side effect on normal cells, toxicity activity for MDR cancer cells, used as the target delivery vehicles and enhancing drug delivery. Moreover, their small size and low molecular weight have made them easy to synthesize and modify. Furthermore, in recent years, genetic engineering has expanded the therapeutic ability of peptides to treat solid tumors, which results in overcoming the peptide drawbacks. The present review mainly focuses on the new advances in applying bacterial peptides and bacteriocins in treating human solid tumors.
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Affiliation(s)
- Atieh Yaghoubi
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hasanian
- Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical, Sciences, Mashhad, Iran
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saman Soleimanpour
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Department of Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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13
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Yaghoubi A, Khazaei M, Ghazvini K, Hasanian SM, Avan A, Soleimanpour S. Bacterial Peptide and Bacteriocins in Treating Gynecological Cancers. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10411-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Basi-Chipalu S, Sthapit P, Dhital S. A review on characterization, applications and structure-activity relationships of Bacillus species-produced bacteriocins. Drug Discov Ther 2022; 16:55-62. [PMID: 35466124 DOI: 10.5582/ddt.2021.01087] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Antimicrobial peptides (AMPs) are inherently occurring proteins that are produced by microorganisms as secondary metabolites. Members of genus Bacillus produce many types of AMPs by ribosomal (bacteriocins) and non-ribosomal (polymyxins and iturins) mechanisms. Bacteriocins are ribosomally synthesized peptides that inhibit the growth of closely related bacterial strains. Moreover, bacteriocins produced by Bacillus species have been widely used in pharmaceutical, food industry, fishery, livestock as well as in agriculture sector. The objective of this review is to assess the characterization of the Bacillus-derived bacteriocins, their potential use in different sectors and structure-activity relationships.
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Affiliation(s)
- Shradha Basi-Chipalu
- Department of Microbiology, Tri-Chandra Multiple Campus, Ghantaghar, Kathmandu, Nepal
| | - Pallavi Sthapit
- Department of Microbiology, Tri-Chandra Multiple Campus, Ghantaghar, Kathmandu, Nepal
| | - Saphala Dhital
- Department of Bioengineering, Clemson University, SC, USA
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15
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Tiwari SK. Bacteriocin-Producing Probiotic Lactic Acid Bacteria in Controlling Dysbiosis of the Gut Microbiota. Front Cell Infect Microbiol 2022; 12:851140. [PMID: 35651753 PMCID: PMC9149203 DOI: 10.3389/fcimb.2022.851140] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 03/16/2022] [Indexed: 11/20/2022] Open
Abstract
Several strains of lactic acid bacteria are potent probiotics and can cure a variety of diseases using different modes of actions. These bacteria produce antimicrobial peptides, bacteriocins, which inhibit or kill generally closely related bacterial strains and other pathogenic bacteria such as Listeria, Clostridium, and Salmonella. Bacteriocins are cationic peptides that kill the target cells by pore formation and the dissipation of cytosolic contents, leading to cell death. Bacteriocins are also known to modulate native microbiota and host immunity, affecting several health-promoting functions of the host. In this review, we have discussed the ability of bacteriocin-producing probiotic lactic acid bacteria in the modulation of gut microbiota correcting dysbiosis and treatment/maintenance of a few important human disorders such as chronic infections, inflammatory bowel diseases, obesity, and cancer.
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16
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Biosynthesis and Production of Class II Bacteriocins of Food-Associated Lactic Acid Bacteria. FERMENTATION 2022. [DOI: 10.3390/fermentation8050217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacteriocins are ribosomally synthesized peptides made by bacteria that inhibit the growth of similar or closely related bacterial strains. Class II bacteriocins are a class of bacteriocins that are heat-resistant and do not undergo extensive posttranslational modification. In lactic acid bacteria (LAB), class II bacteriocins are widely distributed, and some of them have been successfully applied as food preservatives or antibiotic alternatives. Class II bacteriocins can be further divided into four subcategories. In the same subcategory, variations were observed in terms of amino acid identity, peptide length, pI, etc. The production of class II bacteriocin is controlled by a dedicated gene cluster located in the plasmid or chromosome. Besides the pre-bacteriocin encoding gene, the gene cluster generally includes various combinations of immunity, transportation, and regulatory genes. Among class II bacteriocin-producing LAB, some strains/species showed low yield. A multitude of fermentation factors including medium composition, temperature, and pH have a strong influence on bacteriocin production which is usually strain-specific. Consequently, scientists are motivated to develop high-yielding strains through the genetic engineering approach. Thus, this review aims to present and discuss the distribution, sequence characteristics, as well as biosynthesis of class II bacteriocins of LAB. Moreover, the integration of modern biotechnology and genetics with conventional fermentation technology to improve bacteriocin production will also be discussed in this review.
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17
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Current status and potentiality of class II bacteriocins from lactic acid bacteria: structure, mode of action and applications in the food industry. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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18
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Major D, Flanzbaum L, Lussier L, Davies C, Caldo KMP, Acedo JZ. Transporter Protein-Guided Genome Mining for Head-to-Tail Cyclized Bacteriocins. Molecules 2021; 26:7218. [PMID: 34885800 PMCID: PMC8659200 DOI: 10.3390/molecules26237218] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/02/2022] Open
Abstract
Head-to-tail cyclized bacteriocins are ribosomally synthesized antimicrobial peptides that are defined by peptide backbone cyclization involving the N- and C- terminal amino acids. Their cyclic nature and overall three-dimensional fold confer superior stability against extreme pH and temperature conditions, and protease degradation. Most of the characterized head-to-tail cyclized bacteriocins were discovered through a traditional approach that involved the screening of bacterial isolates for antimicrobial activity and subsequent isolation and characterization of the active molecule. In this study, we performed genome mining using transporter protein sequences associated with experimentally validated head-to-tail cyclized bacteriocins as driver sequences to search for novel bacteriocins. Biosynthetic gene cluster analysis was then performed to select the high probability functional gene clusters. A total of 387 producer strains that encode putative head-to-tail cyclized bacteriocins were identified. Sequence and phylogenetic analyses revealed that this class of bacteriocins is more diverse than previously thought. Furthermore, our genome mining strategy captured hits that were not identified in precursor-based bioprospecting, showcasing the utility of this approach to expanding the repertoire of head-to-tail cyclized bacteriocins. This work sets the stage for future isolation of novel head-to-tail cyclized bacteriocins to serve as possible alternatives to traditional antibiotics and potentially help address the increasing threat posed by resistant pathogens.
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Affiliation(s)
- Daniel Major
- Department of Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada; (D.M.); (L.F.); (C.D.)
| | - Lara Flanzbaum
- Department of Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada; (D.M.); (L.F.); (C.D.)
| | - Leah Lussier
- Department of Chemistry and Physics, Mount Royal University, Calgary, AB T3E 6K6, Canada;
| | - Carly Davies
- Department of Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada; (D.M.); (L.F.); (C.D.)
| | - Kristian Mark P. Caldo
- Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Jeella Z. Acedo
- Department of Chemistry and Physics, Mount Royal University, Calgary, AB T3E 6K6, Canada;
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19
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Bin Hafeez A, Jiang X, Bergen PJ, Zhu Y. Antimicrobial Peptides: An Update on Classifications and Databases. Int J Mol Sci 2021; 22:11691. [PMID: 34769122 PMCID: PMC8583803 DOI: 10.3390/ijms222111691] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.
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Affiliation(s)
- Ahmer Bin Hafeez
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan;
| | - Xukai Jiang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Phillip J. Bergen
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
| | - Yan Zhu
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
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20
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Pérez-Ramos A, Madi-Moussa D, Coucheney F, Drider D. Current Knowledge of the Mode of Action and Immunity Mechanisms of LAB-Bacteriocins. Microorganisms 2021; 9:2107. [PMID: 34683428 PMCID: PMC8538875 DOI: 10.3390/microorganisms9102107] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteriocins produced by lactic acid bacteria (LAB-bacteriocins) may serve as alternatives for aging antibiotics. LAB-bacteriocins can be used alone, or in some cases as potentiating agents to treat bacterial infections. This approach could meet the different calls and politics, which aim to reduce the use of traditional antibiotics and develop novel therapeutic options. Considering the clinical applications of LAB-bacteriocins as a reasonable and desirable therapeutic approach, it is therefore important to assess the advances achieved in understanding their modes of action, and the resistance mechanisms developed by the producing bacteria to their own bacteriocins. Most LAB-bacteriocins act by disturbing the cytoplasmic membrane through forming pores, or by cell wall degradation. Nevertheless, some of these peptides still have unknown modes of action, especially those that are active against Gram-negative bacteria. Regarding immunity, most bacteriocin-producing strains have an immunity mechanism involving an immunity protein and a dedicated ABC transporter system. However, these immunity mechanisms vary from one bacteriocin to another.
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Affiliation(s)
| | | | | | - Djamel Drider
- UMR Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV—Institut Charles Viollette, F-59000 Lille, France; (A.P.-R.); (D.M.-M.); (F.C.)
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21
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Biswas S, Wu C, van der Donk WA. The Antimicrobial Activity of the Glycocin Sublancin Is Dependent on an Active Phosphoenolpyruvate-Sugar Phosphotransferase System. ACS Infect Dis 2021; 7:2402-2412. [PMID: 34242010 DOI: 10.1021/acsinfecdis.1c00157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Antimicrobial resistance is a global challenge that is compounded by the limited number of available targets. Glycocins are antimicrobial glycopeptides that are believed to have novel targets. Previous studies have shown that the mechanism of action of the glycocin sublancin 168 involves the glucose uptake system. The phosphoenolpyruvate:sugar phosphotransferase system (PTS) phosphorylates the C6 hydroxyl group on glucose during import. Since sublancin carries a glucose on a Cys on an exposed loop, we investigated whether phosphorylation of this glucose might be involved in its mechanism of action by replacement with xylose. Surprisingly, the xylose analog was more active than wild-type sublancin and still required the glucose PTS for activity. Overexpression of the individual components of the PTS rendered cells more sensitive to sublancin, and their resistance frequency was considerably decreased. These observations suggest that sublancin is activated in some form by the glucose PTS or that sublancin imparts a deleterious gain-of-function on the PTS. Superresolution microscopy studies with fluorescent sublancin and fluorescently labeled PTS proteins revealed localization of both at the poles of cells. Resistant mutants raised under conditions that would minimize mutation of the PTS revealed mutations in FliQ, a protein involved in the flagellar protein export process. Overexpression of FliQ lead to decreased sensitivity of cells to sublancin. Collectively, these findings enforce a model in which the PTS is required for sublancin activity, either by inducing a deleterious gain-of-function or by activating or transporting sublancin.
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22
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Peterson SB, Bertolli SK, Mougous JD. The Central Role of Interbacterial Antagonism in Bacterial Life. Curr Biol 2021; 30:R1203-R1214. [PMID: 33022265 DOI: 10.1016/j.cub.2020.06.103] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of bacteria interacting with their environment has historically centered on strategies for obtaining nutrients and resisting abiotic stresses. We argue this focus has deemphasized a third facet of bacterial life that is equally central to their existence: namely, the threat to survival posed by antagonizing bacteria. The diversity and ubiquity of interbacterial antagonism pathways is becoming increasingly apparent, and the insidious manner by which interbacterial toxins disarm their targets emphasizes the highly evolved nature of these processes. Studies examining the role of antagonism in natural communities reveal it can serve many functions, from facilitating colonization of naïve habitats to maintaining bacterial community stability. The pervasiveness of antagonistic pathways is necessarily matched by an equally extensive array of defense strategies. These overlap with well characterized, central stress response pathways, highlighting the contribution of bacterial interactions to shaping cell physiology. In this review, we build the case for the ubiquity and importance of interbacterial antagonism.
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Affiliation(s)
- S Brook Peterson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Savannah K Bertolli
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA.
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23
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Parlindungan E, Dekiwadia C, Jones OA. Factors that influence growth and bacteriocin production in Lactiplantibacillus plantarum B21. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Bacteriocins from Lactic Acid Bacteria. A Powerful Alternative as Antimicrobials, Probiotics, and Immunomodulators in Veterinary Medicine. Animals (Basel) 2021; 11:ani11040979. [PMID: 33915717 PMCID: PMC8067144 DOI: 10.3390/ani11040979] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/20/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
In the search for an alternative treatment to reduce antimicrobial resistance, bacteriocins shine a light on reducing this problem in public and animal health. Bacteriocins are peptides synthesized by bacteria that can inhibit the growth of other bacteria and fungi, parasites, and viruses. Lactic acid bacteria (LAB) are a group of bacteria that produce bacteriocins; their mechanism of action can replace antibiotics and prevent bacterial resistance. In veterinary medicine, LAB and bacteriocins have been used as antimicrobials and probiotics. However, another critical role of bacteriocins is their immunomodulatory effect. This review shows the advances in applying bacteriocins in animal production and veterinary medicine, highlighting their biological roles.
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25
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S S, S R. Cyclic peptide production from lactic acid bacteria (LAB) and their diverse applications. Crit Rev Food Sci Nutr 2020; 62:2909-2927. [PMID: 33356473 DOI: 10.1080/10408398.2020.1860900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, cyclic peptides gave gained increasing attention owing to their pH tolerance, heat stability and resistance to enzymatic actions. The increasing outbreaks of antibiotic resistant pathogens and food spoilage have prompted researchers to search for new approaches to combat them. The increasing number of reports on novel cyclic peptides from lactic acid bacteria (LAB) is considered as a breakthrough due to their potential applications. Although an extensive investigation is required to understand the mechanism of action and range of applications, LAB cyclic peptides can be considered as potential substitutes for commercially available antibiotics and bio preservatives. This review summarizes the current updates of LAB cyclic peptides with emphasis on their structure, mode of action and applications. Recent trends in cyclic peptide applications are also discussed.
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Affiliation(s)
- Silpa S
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankalathur, Tamilnadu, India
| | - Rupachandra S
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankalathur, Tamilnadu, India
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26
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Ishibashi N, Matsumoto N, Perez RH, Iwatani S, Sugino H, Zendo T, Wilaipun P, Leelawatcharamas V, Nakayama J, Sonomoto K. Molecular characterization of the possible regulation of multiple bacteriocin production through a three-component regulatory system in Enterococcus faecium NKR-5-3. J Biosci Bioeng 2020; 131:S1389-1723(20)30368-6. [PMID: 34756351 DOI: 10.1016/j.jbiosc.2020.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 09/19/2020] [Accepted: 09/28/2020] [Indexed: 01/01/2023]
Abstract
Enterococcus faecium NKR-5-3 produces multiple-bacteriocins, enterocins NKR-5-3A, B, C, D, and Z (Ent53A, Ent53B, Ent53C, Ent53D, and Ent53Z). However, the biosynthetic mechanisms on how their productions are regulated are yet to be fully understood. In silico analysis revealed putative promoters and terminators in the enterocin NKR-5-3ACDZ gene cluster, and the putative direct repeats (5'-ATTTTAGGATA-3') were conserved upstream of each promoter. Transcriptional analysis by quantitative real-time polymerase chain reaction (PCR) of the biosynthetic genes for the enterocins NKR-5-3 suggested that an inducing peptide (Ent53D) regulates the transcription of the structure genes and corresponding biosynthetic genes of enterocins NKR-5-3, except for Ent53B (a circular bacteriocin), thus consequently regulating their production. Moreover, transcriptional analysis of some knock-out mutants showed that the production of Ent53A, C, D and Z is controlled by a three-component regulatory system (TCS) consisting of Ent53D, EnkR (response regulator), and EnkK (histidine kinase). The production of the circular bacteriocin Ent53B appeared to be independent from this TCS. Nevertheless, disrupting the TCS by deletion of a single component (enkD, enkR and enkK) resulted in a slight increase of enkB transcription and consequently the production of Ent53B, presumably, as an indirect consequence of the increase of available energy to the strain NKR-5-3. Here, we demonstrate the regulatory control of the multiple bacteriocin production of strain NKR-5-3 likely through the TCS consisting of Ent53D, EnkR, and EnkK. The information of the sharing of the regulatory machinery between bacteriocins in strain NKR-5-3 can be useful in its future application such as designing strategies to effectively dispense its multiple bacteriocin arsenal.
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Affiliation(s)
- Naoki Ishibashi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Naho Matsumoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Rodney Honrada Perez
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan; National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños (UPLB), Los Baños, Laguna 4031, Philippines
| | - Shun Iwatani
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Haruki Sugino
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Takeshi Zendo
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan.
| | - Pongtep Wilaipun
- Department of Fishery Products, Faculty of Fisheries, Kasetsart University, 50 Paholyothin Rd., Chatuchak, Bangkok 10900, Thailand
| | - Vichien Leelawatcharamas
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, 50 Paholyothin Rd., Chatuchak, Bangkok 10900, Thailand
| | - Jiro Nakayama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Kenji Sonomoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
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27
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Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity. Sci Rep 2020; 10:17398. [PMID: 33060678 PMCID: PMC7562740 DOI: 10.1038/s41598-020-74332-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/21/2020] [Indexed: 12/02/2022] Open
Abstract
Plantacyclin B21AG is a circular bacteriocin produced by Lactiplantibacillus plantarum B21 which displays antimicrobial activity against various Gram-positive bacteria including foodborne pathogens, Listeria monocytogenes and Clostridium perfringens. It is a 58-amino acid cyclised antimicrobial peptide, with the N and C termini covalently linked together. The circular peptide backbone contributes to remarkable stability, conferring partial proteolytic resistance and structural integrity under a wide temperature and pH range. Here, we report the first crystal structure of a circular bacteriocin from a food grade Lactobacillus. The protein was crystallised using the hanging drop vapour diffusion method and the structure solved to a resolution of 1.8 Å. Sequence alignment against 18 previously characterised circular bacteriocins revealed the presence of conserved charged and aromatic residues. Alanine substitution mutagenesis validated the importance of these residues. Minimum inhibitory concentration analysis of these Ala mutants showed that Phe8Ala and Trp45Ala mutants displayed a 48- and 32-fold reduction in activity, compared to wild type. The Lys19Ala mutant displayed the weakest activity, with a 128-fold reduction. These experiments demonstrate the relative importance of aromatic and cationic residues for the antimicrobial activity of plantacyclin B21AG and by extension, other circular bacteriocins sharing these evolutionarily conserved residues.
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28
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Al-Madboly LA, El-Deeb NM, Kabbash A, Nael MA, Kenawy AM, Ragab AE. Purification, Characterization, Identification, and Anticancer Activity of a Circular Bacteriocin From Enterococcus thailandicus. Front Bioeng Biotechnol 2020; 8:450. [PMID: 32656185 PMCID: PMC7324803 DOI: 10.3389/fbioe.2020.00450] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/20/2020] [Indexed: 11/13/2022] Open
Abstract
New anticancer agents are continually needed because cancerous cells continue to evolve resistance to the currently available chemotherapeutic agents. The aim of the present study was to screen, purify and characterize a hepatotoxic bacteriocin from Enterococcus species. The production of bacteriocin from the Enterococcus isolates was achieved based on their antibacterial activity against indicator reference strains. Enterococcus isolates showed a broad spectrum of antibacterial activity by forming inhibition zones with diameters ranged between 12 and 29 mm. The most potent bacteriocin producing strain was molecularly identified as Enterococcus thailandicus. The crude extracted bacteriocin was purified by cation exchange and size exclusion chromatography that resulted in 83 fractions. Among them, 18 factions were considered as bacteriocins based on their positive antibacterial effects. The anticancer effects of the purified bacteriocins were tested against HepG2 cell line. The most promising enterocin (LNS18) showed the highest anticancer effects against HepG2 cells (with 75.24% cellular inhibition percentages), with IC50 value 15.643 μM and without any significant cytotoxic effects on normal fibroblast cells (BJ ATCC® CRL-2522™). The mode of anticancer action of enterocin LNS18 against HepG2 cells could be explained by its efficacy to induce cellular ROS, decrease HepG2 CD markers and arrest cells in G0 phase. Amino acid sequence of enterocin LNS18 was determined and the deduced peptide of the structural gene showed 86 amino acids that shared 94.7% identity with enterocin NKR-5-3B from E. faecium. Enterocin LNS18 consisted of 6 α-helices; 5 circular and one linear. Model-template alignment constructed between enterocin LNS18 and NKR-5-3B revealed 95.31% identity. The predicted 3D homology model of LNS18, after circularization and release of 22 amino acids, showed the formation of a bond between Leu23 and Trp86 amino acid residues at the site of circularization. Furthermore, areas of positive charges were due to the presence of 6 lysine residues resulting in a net positive charge of +4 on the bacteriocin surface. Based on the above mentioned results, our characterized bacteriocin is a promising agent to target liver cancer without any significant toxic effects on normal cell lines.
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Affiliation(s)
- Lamiaa A Al-Madboly
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Nehal M El-Deeb
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Amal Kabbash
- Department of Pharmacognosy, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Manal A Nael
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Ahmed M Kenawy
- Nucleic Acids Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Amany E Ragab
- Department of Pharmacognosy, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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Yaghoubi A, Khazaei M, Jalili S, Hasanian SM, Avan A, Soleimanpour S, Cho WC. Bacteria as a double-action sword in cancer. Biochim Biophys Acta Rev Cancer 2020; 1874:188388. [PMID: 32589907 DOI: 10.1016/j.bbcan.2020.188388] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/09/2020] [Accepted: 06/18/2020] [Indexed: 01/10/2023]
Abstract
Bacteria have long been known as one of the primary causative agents of cancer, however, recent studies suggest that they can be used as a promising agent in cancer therapy. Because of the limitations that conventional treatment faces due to the specific pathophysiology and the tumor environment, there is a great need for the new anticancer therapeutic agents. Bacteriotherapy utilizes live, attenuated strains or toxins, peptides, bacteriocins of the bacteria in the treatment of cancer. Moreover, they are widely used as a vector for delivering genes, peptides, or drugs to the tumor target. Interestingly, it was found that their combination with the conventional therapeutic approaches may enhance the treatment outcome. In the genome editing era, it is feasible to develop a novel generation of therapeutic bacteria with fewer side effects and more efficacy for cancer therapy. Here we review the current knowledge on the dual role of bacteria in the development of cancer as well as cancer therapy.
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Affiliation(s)
- Atieh Yaghoubi
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Department of Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saba Jalili
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hasanian
- Department of Medical Biochemistry, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saman Soleimanpour
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong, SAR, China.
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Hornung BVH, Kuijper EJ, Smits WK. An in silico survey of Clostridioides difficile extrachromosomal elements . Microb Genom 2020; 5. [PMID: 31526450 PMCID: PMC6807378 DOI: 10.1099/mgen.0.000296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Gram-positive enteropathogen Clostridioides difficile (Clostridium difficile) is the major cause of healthcare-associated diarrhoea and is also an important cause of community-acquired infectious diarrhoea. Considering the burden of the disease, many studies have employed whole-genome sequencing of bacterial isolates to identify factors that contribute to virulence and pathogenesis. Though extrachromosomal elements (ECEs) such as plasmids are important for these processes in other bacteria, the few characterized plasmids of C. difficile have no relevant functions assigned and no systematic identification of plasmids has been carried out to date. Here, we perform an in silico analysis of publicly available sequence data to show that ~13 % of all C. difficile strains contain ECEs, with 1–6 elements per strain. Our approach identifies known plasmids (e.g. pCD6, pCD630 and cloning plasmids) and six novel putative plasmid families. Our study shows that plasmids are abundant and may encode functions that are relevant for C. difficile physiology. The newly identified plasmids may also form the basis for the construction of novel cloning plasmids for C. difficile that are compatible with existing tools.
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Affiliation(s)
- Bastian V H Hornung
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Ed J Kuijper
- Netherlands Centre for One Health, The Netherlands.,Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Wiep Klaas Smits
- Netherlands Centre for One Health, The Netherlands.,Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden, The Netherlands
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Soleimanpour S, Hasanian SM, Avan A, Yaghoubi A, Khazaei M. Bacteriotherapy in gastrointestinal cancer. Life Sci 2020; 254:117754. [PMID: 32389833 DOI: 10.1016/j.lfs.2020.117754] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/27/2020] [Accepted: 05/04/2020] [Indexed: 01/13/2023]
Abstract
The most prevalent gastrointestinal (GI) cancers include colorectal cancer, stomach cancer, and liver cancer, known as the most common causes of cancer-related death in both men and women populations in the world. Traditional therapeutic approaches, including surgery, radiotherapy, and chemotherapy have failed in the effective treatment of cancer. Therefore, there is an urgent need for finding new effective anticancer agents. The available evidence and also the promising results of using bacteria as the anticancer agents on numerous cancer cell lines have attracted the attention of scientists for the therapeutic role of bacteria in the field of cancer therapy. Moreover, several studies on the bacteriotherapy agents have used genetic engineering to overcome the challenges and enhance the efficacy with the least drawbacks. Numerous bacterial species that can specifically target and internalize into the tumor cells are used live, attenuated, or genetically as compared to selectively consider the hypoxic condition of tumor, which results in the tumor suppression. The present study is a comprehensive review of the current literature on the use of bacteria and their substances such as bacteriocins and toxins in the treatment of different types of gastrointestinal cancers.
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Affiliation(s)
- Saman Soleimanpour
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hasanian
- Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atieh Yaghoubi
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majid Khazaei
- Department of Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Vezina B, Rehm BHA, Smith AT. Bioinformatic prospecting and phylogenetic analysis reveals 94 undescribed circular bacteriocins and key motifs. BMC Microbiol 2020; 20:77. [PMID: 32252629 PMCID: PMC7132975 DOI: 10.1186/s12866-020-01772-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/29/2020] [Indexed: 12/19/2022] Open
Abstract
Background Circular bacteriocins are antimicrobial peptides produced by bacteria with a N and C termini ligation. They have desirable properties such as activity at low concentrations along with thermal, pH and proteolytic resistance. There are twenty experimentally confirmed circular bacteriocins as part of bacteriocin gene clusters, with transport, membrane and immunity proteins. Traditionally, novel antimicrobials are found by testing large numbers of isolates against indicator strains, with no promise of corresponding novel sequence. Results Through bioprospecting publicly available sequence databases, we identified ninety-nine circular bacteriocins across a variety of bacteria bringing the total to 119. They were grouped into two families within class I modified bacteriocins (i and ii) and further divided into subfamilies based on similarity to experimentally confirmed circular bacteriocins. Within subfamilies, sequences overwhelmingly shared similar characteristics such as sequence length, presence of a polybasic region, conserved locations of aromatic residues, C and N termini, gene clusters similarity, translational coupling and hydrophobicity profiles. At least ninety were predicted to be putatively functional based on gene clusters. Furthermore, bacteriocins identified from Enterococcus, Staphylococcus and Streptococcus species may have activity against clinically relevant strains, due to the presence of putative immunity genes required for expression in a toxin-antitoxin system. Some strains such as Paenibacillus larvae subsp. pulvifaciens SAG 10367 contained multiple circular bacteriocin gene clusters from different subfamilies, while some strains such as Bacillus cereus BCE-01 contained clusters with multiple circular bacteriocin structural genes. Conclusions Sequence analysis provided rapid insight into identification of novel, putative circular bacteriocins, as well as conserved genes likely essential for circularisation. This represents an expanded library of putative antimicrobial proteins which are potentially active against human, plant and animal pathogens.
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Affiliation(s)
- Ben Vezina
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia
| | - Andrew T Smith
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia.
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Antimicrobial secondary metabolites from agriculturally important bacteria as next-generation pesticides. Appl Microbiol Biotechnol 2019; 104:1013-1034. [PMID: 31858191 DOI: 10.1007/s00253-019-10300-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
The whole organisms can be packaged as biopesticides, but secondary metabolites secreted by microorganisms can also have a wide range of biological activities that either protect the plant against pests and pathogens or act as plant growth promotors which can be beneficial for the agricultural crops. In this review, we have compiled information about the most important secondary metabolites of three important bacterial genera currently used in agriculture pest and disease management.
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Yaghoubi A, Khazaei M, Hasanian SM, Avan A, C. Cho W, Soleimanpour S. Bacteriotherapy in Breast Cancer. Int J Mol Sci 2019; 20:E5880. [PMID: 31771178 PMCID: PMC6928964 DOI: 10.3390/ijms20235880] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is the second most common cause of cancer-related mortality among women around the world. Conventional treatments in the fight against breast cancer, such as chemotherapy, are being challenged regarding their effectiveness. Thus, strategies for the treatment of breast cancer need to be continuously refined to achieve a better patient outcome. We know that a number of bacteria are pathogenic and some are even associated with tumor development, however, recent studies have demonstrated interesting results suggesting some bacteria may have potential for cancer therapy. Therefore, the therapeutic role of bacteria has aroused attention in medical and pharmaceutical studies. Furthermore, genetic engineering has been used in bacterial therapy and may led to greater efficacy with few side effects. Some genetically modified non-pathogenic bacterial species are more successful due to their selectivity for cancer cells but with low toxicity for normal cells. Some live, attenuated, or genetically modified bacterias are capable to multiply in tumors and inhibit their growth. This article aims to review the role of bacteria and their products including bacterial peptides, bacteriocins, and toxins for the treatment of breast cancer.
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Affiliation(s)
- Atieh Yaghoubi
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad 91387-35499, Iran;
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91387-35499, Iran
| | - Majid Khazaei
- Department of Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 9138735499, Iran;
| | - Seyed Mahdi Hasanian
- Department of Medical Biochemistry, Faculty of Medicine, Mashhad University of Medical, Sciences, Mashhad 91387-35499, Iran;
| | - Amir Avan
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad 91387-35499, Iran;
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Saman Soleimanpour
- Antimicrobial Resistance Research Center, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad 91387-35499, Iran;
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91387-35499, Iran
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Genome mining for ribosomally synthesised and post-translationally modified peptides (RiPPs) reveals undiscovered bioactive potentials of actinobacteria. Antonie van Leeuwenhoek 2019; 112:1477-1499. [DOI: 10.1007/s10482-019-01276-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/14/2019] [Indexed: 01/22/2023]
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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: 86] [Impact Index Per Article: 17.2] [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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37
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Fan B, Wang C, Song X, Ding X, Wu L, Wu H, Gao X, Borriss R. Bacillus velezensis FZB42 in 2018: The Gram-Positive Model Strain for Plant Growth Promotion and Biocontrol. Front Microbiol 2018; 9:2491. [PMID: 30386322 PMCID: PMC6198173 DOI: 10.3389/fmicb.2018.02491] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/28/2018] [Indexed: 12/31/2022] Open
Abstract
Bacillus velezensis FZB42, the model strain for Gram-positive plant-growth-promoting and biocontrol rhizobacteria, has been isolated in 1998 and sequenced in 2007. In order to celebrate these anniversaries, we summarize here the recent knowledge about FZB42. In last 20 years, more than 140 articles devoted to FZB42 have been published. At first, research was mainly focused on antimicrobial compounds, apparently responsible for biocontrol effects against plant pathogens, recent research is increasingly directed to expression of genes involved in bacteria–plant interaction, regulatory small RNAs (sRNAs), and on modification of enzymes involved in synthesis of antimicrobial compounds by processes such as acetylation and malonylation. Till now, 13 gene clusters involved in non-ribosomal and ribosomal synthesis of secondary metabolites with putative antimicrobial action have been identified within the genome of FZB42. These gene clusters cover around 10% of the whole genome. Antimicrobial compounds suppress not only growth of plant pathogenic bacteria and fungi, but could also stimulate induced systemic resistance (ISR) in plants. It has been found that besides secondary metabolites also volatile organic compounds are involved in the biocontrol effect exerted by FZB42 under biotic (plant pathogens) and abiotic stress conditions. In order to facilitate easy access to the genomic data, we have established an integrating data bank ‘AmyloWiki’ containing accumulated information about the genes present in FZB42, available mutant strains, and other aspects of FZB42 research, which is structured similar as the famous SubtiWiki data bank.
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Affiliation(s)
- Ben Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Cong Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Xiaolei Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liming Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Rainer Borriss
- Institut für Biologie, Humboldt Universität Berlin, Berlin, Germany.,Nord Reet UG, Greifswald, Germany
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Garcia-Gutierrez E, Mayer MJ, Cotter PD, Narbad A. Gut microbiota as a source of novel antimicrobials. Gut Microbes 2018; 10:1-21. [PMID: 29584555 PMCID: PMC6363078 DOI: 10.1080/19490976.2018.1455790] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 02/08/2023] Open
Abstract
Bacteria, Archaea, Eukarya and viruses coexist in the human gut, and this coexistence is functionally balanced by symbiotic or antagonistic relationships. Antagonism is often characterized by the production of antimicrobials against other organisms occupying the same environmental niche. Indeed, close co-evolution in the gut has led to the development of specialized antimicrobials, which is attracting increased attention as these may serve as novel alternatives to antibiotics and thereby help to address the global problem of antimicrobial resistance. The gastrointestinal (GI) tract is especially suitable for finding novel antimicrobials due to the vast array of microbes that inhabit it, and a considerable number of antimicrobial producers of both wide and narrow spectrum have been described. In this review, we summarize some of the antimicrobial compounds that are produced by bacteria isolated from the gut environment, with a special focus on bacteriocins. We also evaluate the potential therapeutic application of these compounds to maintain homeostasis in the gut and the biocontrol of pathogenic bacteria.
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Affiliation(s)
- Enriqueta Garcia-Gutierrez
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
- Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
| | - Melinda J. Mayer
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
| | - Paul D. Cotter
- Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
- APC Microbiome, Ireland
| | - Arjan Narbad
- Gut Health and Food Safety Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
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Balay DR, Gänzle MG, McMullen LM. The Effect of Carbohydrates and Bacteriocins on the Growth Kinetics and Resistance of Listeria monocytogenes. Front Microbiol 2018; 9:347. [PMID: 29545781 PMCID: PMC5838005 DOI: 10.3389/fmicb.2018.00347] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/13/2018] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to determine if different carbohydrates influence the growth of Listeria monocytogenes in the presence of carnocyclin A or leucocin A. Carnobacterium maltaromaticum ATCC PTA-5313 and Leuconostoc gelidum UAL187 were used to produce carnocyclin A and leucocin A, respectively. Growth curves were modeled for five strains of L. monocytogenes grown in basal medium supplemented with glucose, sucrose, fructose, mannose, or cellobiose, in the presence of carnocyclin A or leucocin A. The growth of L. monocytogenes to leucocin A or carnocyclin A was influenced by carbohydrate and/or strain. Carnocyclin A inhibited the growth of L. monocytogenes more than leucocin A. Growth in media containing glucose, mannose, and fructose increased the sensitivity of some strains of L. monocytogenes to bacteriocins, while growth in cellobiose and sucrose increased the resistance of L. monocytogenes to bacteriocins, as evidenced by a shorter lag phase. Strains of L. monocytogenes developed resistance to both leucocin A and carnocyclin A, but the time to develop resistance was longer when strains are treated with carnocyclin A. Carbohydrate influences the development of resistance of L. monocytogenes to the bacteriocins, but the ability of strains to develop resistance to leucocin A or carnocyclin A differs. Results of this study indicate that carbohydrates influence the ability of L. monocytogenes to grow in the presence of bacteriocins.
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Affiliation(s)
| | | | - Lynn M. McMullen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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40
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Plantaricyclin A, a Novel Circular Bacteriocin Produced by Lactobacillus plantarum NI326: Purification, Characterization, and Heterologous Production. Appl Environ Microbiol 2017; 84:AEM.01801-17. [PMID: 29030449 DOI: 10.1128/aem.01801-17] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/10/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteriocins from lactic acid bacteria (LAB) are of increasing interest in recent years due to their potential as natural preservatives against food and beverage spoilage microorganisms. In a screening study for LAB, we isolated from olives a strain, Lactobacillus plantarum NI326, with activity against the beverage-spoilage bacterium Alicyclobacillus acidoterrestris Genome sequencing of NI326 enabled the identification of a gene cluster (designated plc) encoding a putative circular bacteriocin and proteins involved in its modification, transport, and immunity. This novel bacteriocin, named plantaricyclin A (PlcA), was grouped into the circular bacteriocin subgroup II due to its high degree of similarity with other gassericin A-like bacteriocins. Purification of PlcA from the supernatant of Lb. plantarum NI326 resulted in an active peptide with a molecular mass of 5,570 Da, corresponding to that predicted from the (processed) PlcA amino acid sequence. The plc gene cluster was cloned and expressed in Lactococcus lactis NZ9000, resulting in the production of an active 5,570-Da bacteriocin in the supernatant. PlcA is believed to be produced as a 91-amino-acid precursor with a 33-amino-acid leader peptide, which is predicted to be removed, followed by joining of the N and C termini via a covalent linkage to form the mature 58-amino-acid circular bacteriocin PlcA. We report the characterization of a circular bacteriocin produced by Lb. plantarum The inhibition displayed against A. acidoterrestris highlights its potential use as a preservative in food and beverages.IMPORTANCE In this work, we describe the purification and characterization of an antimicrobial peptide, termed plantaricyclin A (PlcA), produced by a Lactobacillus plantarum strain isolated from olives. This peptide has a circular structure, and all genes involved in its production, circularization, and secretion were identified. PlcA shows antimicrobial activity against different strains, including Alicyclobacillus acidoterrestris, a common spoilage bacterium, which causes substantial economic losses in the beverage industry every year. In this study, we describe a circular antimicrobial peptide, PlcA, for a Lactobacillus plantarum strain.
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Gomes KM, Duarte RS, de Freire Bastos MDC. Lantibiotics produced by Actinobacteria and their potential applications (a review). MICROBIOLOGY-SGM 2017; 163:109-121. [PMID: 28270262 DOI: 10.1099/mic.0.000397] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The phylum Actinobacteria, which comprises a great variety of Gram-positive bacteria with a high G+C content in their genomes, is known for its large production of bioactive compounds, including those with antimicrobial activity. Among the antimicrobials, bacteriocins, ribosomally synthesized peptides, represent an important arsenal of potential new drugs to face the increasing prevalence of resistance to antibiotics among microbial pathogens. The actinobacterial bacteriocins form a heterogeneous group of substances that is difficult to adapt to most proposed classification schemes. However, recent updates have accommodated efficiently the diversity of bacteriocins produced by this phylum. Among the bacteriocins, the lantibiotics represent a source of new antimicrobials to control infections caused mainly by Gram-positive bacteria and with a low propensity for resistance development. Moreover, some of these compounds have additional biological properties, exhibiting activity against viruses and tumour cells and having also potential to be used in blood pressure or inflammation control and in pain relief. Thus, lantibiotics already described in Actinobacteria exhibit potential practical applications in medical settings, food industry and agriculture, with examples at different stages of pre-clinical and clinical trials.
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Affiliation(s)
- Karen Machado Gomes
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, UFRJ, Rio de Janeiro, Brazil
| | - Rafael Silva Duarte
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, UFRJ, Rio de Janeiro, Brazil
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van Heel AJ, Montalban-Lopez M, Oliveau Q, Kuipers OP. Genome-guided identification of novel head-to-tail cyclized antimicrobial peptides, exemplified by the discovery of pumilarin. Microb Genom 2017; 3:e000134. [PMID: 29177092 PMCID: PMC5695211 DOI: 10.1099/mgen.0.000134] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 09/01/2017] [Indexed: 11/18/2022] Open
Abstract
The need for novel antibiotics in an era where antimicrobial resistance is on the rise, and the number of new approved antimicrobial drugs reaching the market is declining, is evident. The underused potential of post-translationally modified peptides for clinical use makes this class of peptides interesting candidates. In this study, we made use of the vast amounts of available genomic data and screened all publicly available prokaryotic genomes (~3000) to identify 394 novel head-to-tail cyclized antimicrobial peptides. To verify these in silico results, we isolated and characterized a novel antimicrobial peptide from Bacillus pumilus that we named pumilarin. Pumilarin was demonstrated to have a circular structure and showed antimicrobial activity against several indicator strains, including pathogens.
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Affiliation(s)
- Auke J van Heel
- 1Molecular Genetics, University of Groningen, Groningen, Nijenborgh 7, NA 9747 AG, The Netherlands
| | - Manuel Montalban-Lopez
- 1Molecular Genetics, University of Groningen, Groningen, Nijenborgh 7, NA 9747 AG, The Netherlands.,2Department of Microbiology, University of Granada, Granada, Spain
| | - Quentin Oliveau
- 1Molecular Genetics, University of Groningen, Groningen, Nijenborgh 7, NA 9747 AG, The Netherlands
| | - Oscar P Kuipers
- 1Molecular Genetics, University of Groningen, Groningen, Nijenborgh 7, NA 9747 AG, The Netherlands
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Bartholomae M, Buivydas A, Viel JH, Montalbán-López M, Kuipers OP. Major gene-regulatory mechanisms operating in ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthesis. Mol Microbiol 2017; 106:186-206. [DOI: 10.1111/mmi.13764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Maike Bartholomae
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
| | - Andrius Buivydas
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
| | - Jakob H. Viel
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
| | - Manuel Montalbán-López
- Department of Microbiology; University of Granada, C. Fuentenueva s/n; 18071 Granada Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics; University of Groningen, Nijenborgh 7; 9747AG Groningen The Netherlands
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Duarte AFDS, Ceotto-Vigoder H, Barrias ES, Souto-Padrón TCBS, Nes IF, Bastos MDCDF. Hyicin 4244, the first sactibiotic described in staphylococci, exhibits an anti-staphylococcal biofilm activity. Int J Antimicrob Agents 2017; 51:349-356. [PMID: 28705677 DOI: 10.1016/j.ijantimicag.2017.06.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/13/2017] [Accepted: 06/24/2017] [Indexed: 11/19/2022]
Abstract
Hyicin 4244 is a small antimicrobial peptide with a broad spectrum of activity that was found in the culture supernatant of Staphylococcus hyicus 4244, the genome of which was then sequenced. The bacteriocin gene cluster (hyiSABCDEFG) was mined from its single chromosome and exhibited a genetic organization similar to that of subtilosin A. All genes involved in hyicin 4244 biosynthesis proved to be transcribed and encode proteins that share at least 42% similarity to proteins encoded by the subtilosin A gene cluster. Due to its resemblance to subtilosin A and the presence of three thioether bonds in its structure, hyicin 4244 is assumed to be a 35-amino acid circular sactibiotic, the first to be described in staphylococci. Hyicin 4244 inhibited 14 staphylococcal isolates from either human infections or bovine mastitis, all biofilm formers. Hyicin 4244 significantly reduced the number of colony-forming units (CFU) and the biofilm formation by two strong biofilm-forming strains randomly chosen as representatives of the strains involved in human infections and bovine mastitis. It also reduced the proliferation and viability of sessile cells in established biofilms. Therefore, hyicin 4244 proved not only to prevent biofilm formation by planktonic cells, but also to penetrate the biofilm matrix in vitro, exerting bactericidal activity against staphylococcal sessile cells. This bacteriocin has the potential to become an alternative antimicrobial for either prevention or treatment of biofilm-related infections caused by different staphylococcal species.
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Affiliation(s)
- Andreza Freitas de Souza Duarte
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Hilana Ceotto-Vigoder
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Emile Santos Barrias
- Instituto Nacional de Metrologia, Qualidade e Tecnologia, Duque de Caxias, Brazil
| | | | - Ingolf Figved Nes
- Laboratory of Microbial Gene Technology, Norwegian University of Life Science, Ås, Norway
| | - Maria do Carmo de Freire Bastos
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Collins FWJ, O'Connor PM, O'Sullivan O, Gómez-Sala B, Rea MC, Hill C, Ross RP. Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome. Sci Rep 2017; 7:3481. [PMID: 28615683 PMCID: PMC5471241 DOI: 10.1038/s41598-017-03339-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/20/2017] [Indexed: 11/09/2022] Open
Abstract
Lactobacilli constitute a large genus of Gram-positive lactic acid bacteria which have widespread roles ranging from gut commensals to starters in fermented foods. A combination of in silico and laboratory-based screening allowed us to determine the overall bacteriocin producing potential of representative strains of each species of the genus. The genomes of 175 lactobacilli and 38 associated species were screened for the presence of antimicrobial producing genes and combined with screening for antimicrobial activity against a range of indicators. There also appears to be a link between the strains' environment and bacteriocin production, with those from the animal and human microbiota encoding over twice as many bacteriocins as those from other sources. Five novel bacteriocins were identified belonging to differing bacteriocin classes, including two-peptide bacteriocins (muricidin and acidocin X) and circular bacteriocins (paracyclicin). In addition, there was a clear clustering of helveticin type bacteriolysins in the Lactobacillus acidophilus group of species. This combined in silico and in vitro approach to screening has demonstrated the true diversity and complexity of bacteriocins across the genus. It also highlights their biological importance in terms of communication and competition between closely related strains in diverse complex microbial environments.
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Affiliation(s)
- Fergus W J Collins
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Paula M O'Connor
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Mary C Rea
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland. .,APC Microbiome Institute, University College Cork, Cork, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
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Acedo JZ, Towle KM, Lohans CT, Miskolzie M, McKay RT, Doerksen TA, Vederas JC, Martin-Visscher LA. Identification and three-dimensional structure of carnobacteriocin XY, a class IIb bacteriocin produced by Carnobacteria. FEBS Lett 2017; 591:1349-1359. [PMID: 28391617 DOI: 10.1002/1873-3468.12648] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 11/10/2022]
Abstract
In this study, we report that CbnX (33 residues) and CbnY (29 residues) comprise a class IIb (two-component) bacteriocin in Carnobacteria. Individually, CbnX and CbnY are inactive, but together act synergistically to exert a narrow spectrum of activity. The structures of CbnX and CbnY in structure-inducing conditions were determined and strongly resemble other class IIb bacteriocins (i.e., LcnG, PlnEF, PlnJK). CbnX has an extended, amphipathic α-helix and a flexible C terminus. CbnY has two α-helices (one hydrophobic, one amphipathic) connected by a short loop and a cationic C terminus. CbnX and CbnY do not appear to interact directly and likely require a membrane-bound receptor to facilitate formation of the bacteriocin complex. This is the first class IIb bacteriocin reported for Carnobacteria.
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Affiliation(s)
- Jeella Z Acedo
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Kaitlyn M Towle
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | | | - Mark Miskolzie
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Ryan T McKay
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Thomas A Doerksen
- Department of Chemistry, The King's University, Edmonton, AB, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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47
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Ben Lagha A, Haas B, Gottschalk M, Grenier D. Antimicrobial potential of bacteriocins in poultry and swine production. Vet Res 2017; 48:22. [PMID: 28399941 PMCID: PMC5387282 DOI: 10.1186/s13567-017-0425-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/21/2017] [Indexed: 12/17/2022] Open
Abstract
The routine use of antibiotics in agriculture has contributed to an increase in drug-resistant bacterial pathogens in animals that can potentially be transmitted to humans. In 2000, the World Health Organization identified resistance to antibiotics as one of the most significant global threats to public health and recommended that the use of antibiotics as additives in animal feed be phased out or terminated, particularly those used to treat human infections. Research is currently being carried out to identify alternative antimicrobial compounds for use in animal production. A number of studies, mostly in vitro, have provided evidence indicating that bacteriocins, which are antimicrobial peptides of bacterial origin, may be promising alternatives to conventional antibiotics in poultry and swine production. This review provides an update on bacteriocins and their potential for use in the poultry and swine industries.
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Affiliation(s)
- Amel Ben Lagha
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada
| | - Bruno Haas
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses du Porc (GREMIP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.,Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Fonds de Recherche du Québec-Nature et Technologies (FQRNT), Saint-Hyacinthe, QC, Canada
| | - Daniel Grenier
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada. .,Centre de Recherche en Infectiologie Porcine et Avicole (CRIPA), Fonds de Recherche du Québec-Nature et Technologies (FQRNT), Saint-Hyacinthe, QC, Canada.
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48
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Perez RH, Sugino H, Ishibashi N, Zendo T, Wilaipun P, Leelawatcharamas V, Nakayama J, Sonomoto K. Mutations near the cleavage site of enterocin NKR-5-3B prepeptide reveal new insights into its biosynthesis. Microbiology (Reading) 2017; 163:431-441. [DOI: 10.1099/mic.0.000435] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rodney H Perez
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
- Present address: National Institute for Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, Laguna 4031, Philippines
| | - Haruki Sugino
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
| | - Naoki Ishibashi
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
| | - Takeshi Zendo
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
| | - Pongtep Wilaipun
- Department of Fishery Products, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Vichien Leelawatcharamas
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
- Laboratory of Functional Food Design, Department of Functional Metabolic Design, Bio-Architecture Center, Kyushu University, Fukuoka 812-8581, Japan
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Towle KM, Vederas JC. Structural features of many circular and leaderless bacteriocins are similar to those in saposins and saposin-like peptides. MEDCHEMCOMM 2017; 8:276-285. [PMID: 30108744 PMCID: PMC6072434 DOI: 10.1039/c6md00607h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/09/2016] [Indexed: 12/14/2022]
Abstract
Bacteriocins are potent antimicrobial peptides that are ribosomally produced and exported by bacteria, presumably to aid elimination of competing microorganisms. Many circular and linear leaderless bacteriocins have a recuring three dimensional structural motif known as a saposin-like fold. Although these bacteriocin sizes and sequences are often quite different, and their mechanisms of action vary, this conserved motif of multiple helices appears critical for activity and may enable peptide-lipid and peptide-receptor interactions in target bacterial cell membranes. Comparisons between electrostatic surfaces and hydrophobic surface maps of different bacteriocins are discussed emphasizing similarities and differences in the context of proposed modes of action.
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Affiliation(s)
- K M Towle
- Department of Chemistry , University of Alberta , Edmonton , Alberta , T6G 2G2 Canada .
| | - J C Vederas
- Department of Chemistry , University of Alberta , Edmonton , Alberta , T6G 2G2 Canada .
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50
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Liu L, Hao T, Xie Z, Horsman GP, Chen Y. Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans. Sci Rep 2016; 6:37479. [PMID: 27869143 PMCID: PMC5116633 DOI: 10.1038/srep37479] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/28/2016] [Indexed: 11/09/2022] Open
Abstract
Streptococcus mutans is a major pathogen causing human dental caries. As a Gram-positive bacterium with a small genome (about 2 Mb) it is considered a poor source of natural products. Due to a recent explosion in genomic data available for S. mutans strains, we were motivated to explore the natural product production potential of this organism. Bioinformatic characterization of 169 publically available genomes of S. mutans from human dental caries revealed a surprisingly rich source of natural product biosynthetic gene clusters. Anti-SMASH analysis identified one nonribosomal peptide synthetase (NRPS) gene cluster, seven polyketide synthase (PKS) gene clusters and 136 hybrid PKS/NRPS gene clusters. In addition, 211 ribosomally synthesized and post-translationally modified peptides (RiPPs) clusters and 615 bacteriocin precursors were identified by a combined analysis using BAGEL and anti-SMASH. S. mutans harbors a rich and diverse natural product genetic capacity, which underscores the importance of probing the human microbiome and revisiting species that have traditionally been overlooked as "poor" sources of natural products.
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Affiliation(s)
- Liwei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Hao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhoujie Xie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ON, N2L3C5, Canada
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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