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Morandini L, Caulier S, Bragard C, Mahillon J. Bacillus cereus sensu lato antimicrobial arsenal: An overview. Microbiol Res 2024; 283:127697. [PMID: 38522411 DOI: 10.1016/j.micres.2024.127697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/25/2024] [Accepted: 03/16/2024] [Indexed: 03/26/2024]
Abstract
The Bacillus cereus group contains genetically closed bacteria displaying a variety of phenotypic features and lifestyles. The group is mainly known through the properties of three major species: the entomopathogen Bacillus thuringiensis, the animal and human pathogen Bacillus anthracis and the foodborne opportunistic strains of B. cereus sensu stricto. Yet, the actual diversity of the group is far broader and includes multiple lifestyles. Another less-appreciated aspect of B. cereus members lies within their antimicrobial potential which deserves consideration in the context of growing emergence of resistance to antibiotics and pesticides, and makes it crucial to find new sources of antimicrobial molecules. This review presents the state of knowledge on the known antimicrobial compounds of the B. cereus group members, which are grouped according to their chemical features and biosynthetic pathways. The objective is to provide a comprehensive review of the antimicrobial range exhibited by this group of bacteria, underscoring the interest in its potent biocontrol arsenal and encouraging further research in this regard.
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Affiliation(s)
| | - Simon Caulier
- Laboratory of Plant Health, Earth and Life Institute, UCLouvain, Louvain-la-Neuve B-1348, Belgium
| | - Claude Bragard
- Laboratory of Plant Health, Earth and Life Institute, UCLouvain, Louvain-la-Neuve B-1348, Belgium
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Zhang J, Zhao L, Tang W, Li J, Tang T, Sun X, Qiao X, He Z. Characterization of a novel circular bacteriocin from Bacillus velezensis 1-3, and its mode of action against Listeria monocytogenes. Heliyon 2024; 10:e29701. [PMID: 38726204 PMCID: PMC11078769 DOI: 10.1016/j.heliyon.2024.e29701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 05/12/2024] Open
Abstract
In this study, isolate Bacillus velezensis1-3 was selected out for its anti- Listeria potency, from which a novel circular bacteriocin, velezin, was purified out of the fermentate, and then characterized. Facilitated with a broad antibacterial spectrum, velezin has demonstrated decent inhibitive activity against of foodborne pathogen L. monocytogenes ATCC 19115. It exerted the antibacterial activity through damaging the membrane integrity of targeted cell and causing leakage of vital elements, including K+ ion. It was noteworthy that velezin also inhibited the biofilm formation by L. monocytogenes ATCC 19115. At the challenge of velezin, L. monocytogenes ATCC 19115 up-regulated expression of genes associated with membrane, ion transporters, stressing-related proteins as well as the genes responsible for the synthesis of small molecule. Taken together, velezin may have potential to be a candidate as natural additive used in food/feed in the future.
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Affiliation(s)
- Jun Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Bioantai Biotechnology Co., Ltd., Qingdao, 266071, China
| | - Lihong Zhao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Wei Tang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Marine Biomedical Research Institute of Qingdao, Qingdao, 266000, China
| | - Jiaxin Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Tao Tang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Marine Biomedical Research Institute of Qingdao, Qingdao, 266000, China
| | - Xiaowen Sun
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Bioantai Biotechnology Co., Ltd., Qingdao, 266071, China
| | - Xiaoni Qiao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Bioantai Biotechnology Co., Ltd., Qingdao, 266071, China
| | - Zengguo He
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Bioantai Biotechnology Co., Ltd., Qingdao, 266071, China
- Marine Biomedical Research Institute of Qingdao, Qingdao, 266000, China
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3
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Zhao X, Wang W, Zeng X, Xu R, Yuan B, Yu W, Wang M, Jia R, Chen S, Zhu D, Liu M, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Sun D, Cheng A. Klebicin E, a pore-forming bacteriocin of Klebsiella pneumoniae, exploits the porin OmpC and the Ton system for translocation. J Biol Chem 2024; 300:105694. [PMID: 38301890 PMCID: PMC10906532 DOI: 10.1016/j.jbc.2024.105694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriocins, which have narrow-spectrum activity and limited adverse effects, are promising alternatives to antibiotics. In this study, we identified klebicin E (KlebE), a small bacteriocin derived from Klebsiella pneumoniae. KlebE exhibited strong efficacy against multidrug-resistant K. pneumoniae isolates and conferred a significant growth advantage to the producing strain during intraspecies competition. A giant unilamellar vesicle leakage assay demonstrated the unique membrane permeabilization effect of KlebE, suggesting that it is a pore-forming toxin. In addition to a C-terminal toxic domain, KlebE also has a disordered N-terminal domain and a globular central domain. Pulldown assays and soft agar overlay experiments revealed the essential role of the outer membrane porin OmpC and the Ton system in KlebE recognition and cytotoxicity. Strong binding between KlebE and both OmpC and TonB was observed. The TonB-box, a crucial component of the toxin-TonB interaction, was identified as the 7-amino acid sequence (E3ETLTVV9) located in the N-terminal region. Further studies showed that a region near the bottom of the central domain of KlebE plays a primary role in recognizing OmpC, with eight residues surrounding this region identified as essential for KlebE toxicity. Finally, based on the discrepancies in OmpC sequences between the KlebE-resistant and sensitive strains, it was found that the 91st residue of OmpC, an aspartic acid residue, is a key determinant of KlebE toxicity. The identification and characterization of this toxin will facilitate the development of bacteriocin-based therapies targeting multidrug-resistant K. pneumoniae infections.
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Affiliation(s)
- Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Wenyu Wang
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Zeng
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Rong Xu
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Wenyao Yu
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China.
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Lafuente I, Sevillano E, Peña N, Cuartero A, Hernández PE, Cintas LM, Muñoz-Atienza E, Borrero J. Production of Pumilarin and a Novel Circular Bacteriocin, Altitudin A, by Bacillus altitudinis ECC22, a Soil-Derived Bacteriocin Producer. Int J Mol Sci 2024; 25:2020. [PMID: 38396696 PMCID: PMC10888436 DOI: 10.3390/ijms25042020] [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: 01/09/2024] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The rise of antimicrobial resistance poses a significant global health threat, necessitating urgent efforts to identify novel antimicrobial agents. In this study, we undertook a thorough screening of soil-derived bacterial isolates to identify candidates showing antimicrobial activity against Gram-positive bacteria. A highly active antagonistic isolate was initially identified as Bacillus altitudinis ECC22, being further subjected to whole genome sequencing. A bioinformatic analysis of the B. altitudinis ECC22 genome revealed the presence of two gene clusters responsible for synthesizing two circular bacteriocins: pumilarin and a novel circular bacteriocin named altitudin A, alongside a closticin 574-like bacteriocin (CLB) structural gene. The synthesis and antimicrobial activity of the bacteriocins, pumilarin and altitudin A, were evaluated and validated using an in vitro cell-free protein synthesis (IV-CFPS) protocol coupled to a split-intein-mediated ligation procedure, as well as through their in vivo production by recombinant E. coli cells. However, the IV-CFPS of CLB showed no antimicrobial activity against the bacterial indicators tested. The purification of the bacteriocins produced by B. altitudinis ECC22, and their evaluation by MALDI-TOF MS analysis and LC-MS/MS-derived targeted proteomics identification combined with massive peptide analysis, confirmed the production and circular conformation of pumilarin and altitudin A. Both bacteriocins exhibited a spectrum of activity primarily directed against other Bacillus spp. strains. Structural three-dimensional predictions revealed that pumilarin and altitudin A may adopt a circular conformation with five- and four-α-helices, respectively.
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Affiliation(s)
- Irene Lafuente
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Ester Sevillano
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Nuria Peña
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Alicia Cuartero
- Centro de Educación Infantil, Primaria y Secundaria Obligatoria (CEIPSO) El Cantizal, Avenida Atenas s/n, 28232 Las Rozas, Madrid, Spain;
| | - Pablo E. Hernández
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Luis M. Cintas
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Estefanía Muñoz-Atienza
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Juan Borrero
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
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5
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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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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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Liu F, van Heel AJ, Kuipers OP. Leader- and Terminal Residue Requirements for Circularin A Biosynthesis Probed by Systematic Mutational Analyses. ACS Synth Biol 2023; 12:852-862. [PMID: 36857413 PMCID: PMC10028692 DOI: 10.1021/acssynbio.2c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Circularin A is a circular bacteriocin belonging to a subgroup of the ribosomally synthesized and post-translationally modified peptide (RiPP) superfamily. The post-translational biosynthesis of circular bacteriocins primarily consists of leader cleavage, core peptide circularization, and bacteriocin secretion. However, none of these processes have been fully elucidated due to the complex biosynthesis of such bacteriocins and the lack of homology to the functions of other known biosynthetic enzymes. In this study, we investigated the leader- and terminal residue requirements for the biosynthesis of circularin A by systematic mutational analyses, including the mutational effects of variable leader lengths, as well as site-directed substitutions of residues at positions near the leader cleavage site and the circularization site. Results show that the leader with only one Met residue, the shortest leader possible, is sufficient to produce mature circularin A; helix-forming short-sidechain hydrophobic residues are required at positions Val1 and Ala2 of the N-terminus to form active peptide derivatives, indicating the possible steric hindrance effect at these two positions; and an aromatic residue is required at the C-terminal Tyr69 position to produce a mature circular derivative. However, the requirements for residues at position Ala68 are much more relaxed relative to the positions of Val1 and Ala2, since even substitution with the largest possible residue, i.e., tryptophan, still allows the generation of an active Ala68Trp derivative. Our findings provide new perspectives for the biosynthesis of this short-leader circular bacteriocin, which enables the application of circular bacteriocin biosynthesis in rational modified peptide engineering.
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Affiliation(s)
- Fangfang Liu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Auke J van Heel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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8
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Zhong G, Wang ZJ, Yan F, Zhang Y, Huo L. Recent Advances in Discovery, Bioengineering, and Bioactivity-Evaluation of Ribosomally Synthesized and Post-translationally Modified Peptides. ACS BIO & MED CHEM AU 2023; 3:1-31. [PMID: 37101606 PMCID: PMC10125368 DOI: 10.1021/acsbiomedchemau.2c00062] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 04/28/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are of increasing interest in natural products as well as drug discovery. This empowers not only the unique chemical structures and topologies in natural products but also the excellent bioactivities such as antibacteria, antifungi, antiviruses, and so on. Advances in genomics, bioinformatics, and chemical analytics have promoted the exponential increase of RiPPs as well as the evaluation of biological activities thereof. Furthermore, benefiting from their relatively simple and conserved biosynthetic logic, RiPPs are prone to be engineered to obtain diverse analogues that exhibit distinct physiological activities and are difficult to synthesize. This Review aims to systematically address the variety of biological activities and/or the mode of mechanisms of novel RiPPs discovered in the past decade, albeit the characteristics of selective structures and biosynthetic mechanisms are briefly covered as well. Almost one-half of the cases are involved in anti-Gram-positive bacteria. Meanwhile, an increasing number of RiPPs related to anti-Gram-negative bacteria, antitumor, antivirus, etc., are also discussed in detail. Last but not least, we sum up some disciplines of the RiPPs' biological activities to guide genome mining as well as drug discovery and optimization in the future.
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Affiliation(s)
- Guannan Zhong
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
| | - Zong-Jie Wang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fu Yan
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- CAS
Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liujie Huo
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
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9
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Incorporation of Non-Canonical Amino Acids into Antimicrobial Peptides: Advances, Challenges, and Perspectives. Appl Environ Microbiol 2022; 88:e0161722. [PMID: 36416555 PMCID: PMC9746297 DOI: 10.1128/aem.01617-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The emergence of antimicrobial resistance is a global health concern and calls for the development of novel antibiotic agents. Antimicrobial peptides seem to be promising candidates due to their diverse sources, mechanisms of action, and physicochemical characteristics, as well as the relatively low emergence of resistance. The incorporation of noncanonical amino acids into antimicrobial peptides could effectively improve their physicochemical and pharmacological diversity. Recently, various antimicrobial peptides variants with improved or novel properties have been produced by the incorporation of single and multiple distinct noncanonical amino acids. In this review, we summarize strategies for the incorporation of noncanonical amino acids into antimicrobial peptides, as well as their features and suitabilities. Recent applications of noncanonical amino acid incorporation into antimicrobial peptides are also presented. Finally, we discuss the related challenges and prospects.
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10
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Liu F, van Heel AJ, Chen J, Kuipers OP. Functional production of clostridial circularin A in Lactococcus lactis NZ9000 and mutational analysis of its aromatic and cationic residues. Front Microbiol 2022; 13:1026290. [PMID: 36504829 PMCID: PMC9726714 DOI: 10.3389/fmicb.2022.1026290] [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: 08/23/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
Circular bacteriocins, also known as bacterial head-to-tail cyclized peptides, are a subgroup of ribosomally synthesized and post-translationally modified peptides (RiPPs). Compared with their conventional linear counterparts, circular bacteriocins are highly stable over a broad temperature and pH range, and circularization decreases proteolytic degradation by exopeptidases. These features render them great potential as scaffold candidates to withstand strident conditions in food- and pharmaceutical applications. However, the biosynthesis and bioactivity of circular bacteriocins still remain largely unknown. To investigate and gain more insights into the biosynthesis of circular bacteriocins and to achieve efficient production and characterization of bacteriocin variants, we developed an efficient cloning and heterologous expression system for clostridial circularin A and successfully produced this circular peptide in Lactococcus lactis NZ9000. We report three system formats with single plasmid or plasmid combinations to achieve successful cloning and functional production of circularin A in L. lactis. These systematic varieties enabled us to choose the appropriate method to efficiently obtain various constructs with desired properties. With the established heterologous systems in L. lactis, we performed several mutagenesis studies in the precursor peptide to study its structure/function relationships. The overlay activity assay revealed that these mutant variants had variable effects on different indicator strains: lysine substitution for certain glutamine residue(s) greatly decreased its bioactivity against Clostridium perfringens and L. lactis NZ9000, and alanine replacement for the cationic residues significantly reduced the activity against Lactobacillus sake ATCC 15521, whereas alanine substitution for the aromatic residues decreased its bioactivity against all three testing strains dramatically. Moreover, the conditions for bacteriocin production were optimized. Results show that supplementing the minimal medium with extra glucose (or sucrose) and immediate nisin-induction improved the peptide yield significantly. Briefly, we developed an excellent system for the production of circularin A and a wide range of variant peptides in a convenient host, as well as a method for fast detection of peptide production and activity. This system facilitated our mutagenesis studies which provided valuable insights into the effects of mutating specific residues on its biosynthesis and bioactivity, and will eventually enable more complex research into the biosynthesis of circularin A.
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11
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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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12
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Liu S, Deng S, Liu H, Tang L, Wang M, Xin B, Li F. Four Novel Leaderless Bacteriocins, Bacin A1, A2, A3, and A4 Exhibit Potent Antimicrobial and Antibiofilm Activities against Methicillin-Resistant Staphylococcus aureus. Microbiol Spectr 2022; 10:e0094522. [PMID: 36000904 PMCID: PMC9602277 DOI: 10.1128/spectrum.00945-22] [Citation(s) in RCA: 4] [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: 03/21/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a major bacterial pathogen that causes hospital- and community-acquired infections. Owing to its multidrug resistance, it is imperative to develop new antimicrobial agents to treat MRSA infections. In this study, using genome mining analysis and a culture-based screening method to detect bacteriocin activity, we screened a strain, Bacillus sp. TL12, which harbored a putative leaderless bacteriocin gene cluster (bac gene cluster) and exhibited potent anti-MRSA activity. The antimicrobial agents, products of the bac gene cluster, were purified and identified as four novel leaderless bacteriocins: bacin A1, A2, A3, and A4. Bacin A2 was evaluated as a representative antimicrobial agent and showed remarkable antimicrobial activity against S. aureus, MRSA, and the foodborne pathogens Listeria monocytogenes and Bacillus cereus. Mechanistic experiments revealed that bacin A2 damaged cell membranes and exhibited bactericidal activity against MRSA. Bacin A2 effectively inhibited the formation of S. aureus and MRSA biofilms (>0.5× MIC) and killed the cells in their established biofilms (>4× MIC). The hemolytic and NIH/3T3 cytotoxicity assay results for bacin A2 confirmed its biosafety. Thus, bacins have potential as alternative antimicrobial agents for treating MRSA infections. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a major human pathogen that is difficult to treat because of its resistance to several widely used antibiotics. The present study aimed to identify novel anti-MRSA bacteriocins in a prominent producer of bacteriocins, Bacillus cereus group. Four novel leaderless bacteriocins, bacin A1, A2, A3, and A4, which show potent bactericidal effect against S. aureus and MRSA, were identified in Bacillus sp. TL12. Moreover, bacins inhibited biofilm formation and killed cells in the established biofilms of S. aureus and MRSA. These findings suggest that bacins are promising alternatives to treat MRSA infections.
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Affiliation(s)
- Shu Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
| | - Shulin Deng
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
| | - Hualin Liu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Liang Tang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
| | - Mengqi Wang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
| | - Bingyue Xin
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
| | - Feng Li
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
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13
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Three novel leaderless bacteriocins have antimicrobial activity against gram-positive bacteria to serve as promising food biopreservative. Microb Cell Fact 2022; 21:194. [PMID: 36123739 PMCID: PMC9484092 DOI: 10.1186/s12934-022-01912-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Due to the detrimental effects of chemical preservatives, there has been an increasing demand for safer, healthier and natural bio-preservatives. Bacteriocins have attracted increasing interest because of their potential as natural bio-preservatives. RESULTS We screened a large number of Bacillus thuringiensis strains and isolated one strain (B. thuringiensis P86) with antimicrobial activity against several foodborne pathogens. Three novel leaderless bacteriocins, including thucin A1, thucin A2 and thucin A3, were purified and identified from the culture supernatant of B. thuringiensis P86, whose molecular masses were 5552.02, 5578.07 and 5609.06 Da, respectively. Thucin A1 was then selected as a representative to be tested, and it exhibited potent inhibitory activity against all tested gram-positive bacteria. More importantly, thucin A1 showed stronger antimicrobial activity than nisin A against two important foodborne pathogens Bacillus cereus and Listeria monocytogenes. In addition, thucin A1 exhibited strong acid-base adaptability (pH 2-11), high endurance to heat, good stability to trypsin and pepsin, no hemolysis activity and cytotoxicity, and could effectively inhibit or eliminate Bacillus cereus and Listeria monocytogenes in skim milk. CONCLUSIONS Our findings indicate that these novel leaderless bacteriocins are potentially promising food biopreservatives.
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14
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Kita K, Yoshida S, Ishikawa S, Yoshida KI. Functional analysis of a gene cluster for putative bacteriocin deduced from the genome sequence of Aeribacillus pallidus PI8. J GEN APPL MICROBIOL 2022; 68:87-94. [PMID: 35418540 DOI: 10.2323/jgam.2021.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacteriocins are a large family of peptides synthesized ribosomally by a variety of bacterial species. The genome of one of the thermophilic Gram-positive bacteria, Aeribacillus pallidus PI8, was found to possess an operon comprising five genes possibly involved in the production of a putative bacteriocin that was named pcnABCDE for the production of "pallidocyclicin." This study investigated the function of the pcn operon experimentally. The heterologous expression of the entire pcn operon from the plasmid was toxic to Escherichia coli but not to Bacillus subtilis. However, when the entire pcn operon was expressed constitutively, even the growth of B. subtilis was impaired, and at least pcnA was implied to serve as the precursor of pallidocyclicin. In addition, a strain of B. subtilis expressing the entire pcn operon from the plasmid showed toxicity to another thermophilic species, Geobacillus kaustophilus, at elevated temperatures, whereas another strain lacking pcnE alone from the pcn operon lost the toxicity, suggesting that pcnE might be involved in the biosynthesis of pallidocyclicin when it is produced in B. subtilis.
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Affiliation(s)
- Kyosuke Kita
- Department of Science, Technology and Innovation, Kobe University
| | | | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University.,Department of Agrobioscience, Kobe University
| | - Ken-Ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University.,Department of Agrobioscience, Kobe University
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15
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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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16
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Heilbronner S, Krismer B, Brötz-Oesterhelt H, Peschel A. The microbiome-shaping roles of bacteriocins. Nat Rev Microbiol 2021; 19:726-739. [PMID: 34075213 DOI: 10.1038/s41579-021-00569-w] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.
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Affiliation(s)
- Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, Department of Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
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17
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Romero-Severson J, Moran TE, Shrader DG, Fields FR, Pandey-Joshi S, Thomas CL, Palmer EC, Shrout JD, Pfrender ME, Lee SW. A Seed-Endophytic Bacillus safensis Strain With Antimicrobial Activity Has Genes for Novel Bacteriocin-Like Antimicrobial Peptides. Front Microbiol 2021; 12:734216. [PMID: 34646254 PMCID: PMC8503640 DOI: 10.3389/fmicb.2021.734216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/20/2021] [Indexed: 12/04/2022] Open
Abstract
Bacteriocins are a highly diverse group of antimicrobial peptides that have been identified in a wide range of commensal and probiotic organisms, especially those resident in host microbiomes. Rising antibiotic resistance have fueled renewed research into new drug scaffolds such as antimicrobial peptides for use in therapeutics. In this investigation, we examined mung bean seeds for endophytes possessing activity against human and plant pathogens. We isolated a novel strain of Bacillus safensis, from the contents of surface-sterilized mung bean seed, which we termed B. safensis C3. Genome sequencing of C3 identified three distinct biosynthetic systems that produce bacteriocin-based peptides. C3 exhibited antibacterial activity against Escherichia coli, Xanthomonas axonopodis, and Pseudomonas syringae. Robust antimicrobial activity of B. safensis C3 was observed when C3 was co-cultured with Bacillus subtilis. Using the cell-free supernatant of C3 and cation exchange chromatography, we enriched a product that retained antimicrobial activity against B. subtilis. The peptide was found to be approximately 3.3 kDa in size by mass spectrometry, and resistant to proteolysis by Carboxypeptidase Y and Endoproteinase GluC, suggesting that it is a modified variant of an AS-48 like bacteriocin. Our findings open new avenues into further development of novel bacteriocin-based scaffolds for therapeutic development, as well as further investigations into how our discoveries of bacteriocin-producing plant commensal microorganisms may have the potential for an immediate impact on the safety of food supplies.
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Affiliation(s)
- Jeanne Romero-Severson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Thomas E Moran
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Donna G Shrader
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Francisco R Fields
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Susan Pandey-Joshi
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Clayton L Thomas
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Emily C Palmer
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States.,Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Joshua D Shrout
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States.,Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
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18
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Hudson LK, Orellana LAG, Bryan DW, Moore A, Munafo JP, den Bakker HC, Denes TG. Phylogeny of the Bacillus altitudinis Complex and Characterization of a Newly Isolated Strain with Antilisterial Activity. J Food Prot 2021; 84:1321-1332. [PMID: 33793813 DOI: 10.4315/jfp-20-498] [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: 12/31/2020] [Accepted: 03/27/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Bacillus strain UTK D1-0055 was isolated from a laboratory environment and appeared to have antilisterial activity. The genome was sequenced, the strain was identified as Bacillus altitudinis, and a high-quality complete annotated genome was produced. The taxonomy was evaluated for this and related Bacillus species (B. aerophilus, B. pumilus, B. safensis, B. stratosphericus, and B. xiamenensis) because the taxonomy is unclear and contains errors in public databases such as NCBI. The included strains grouped into seven clusters based on average nucleotide identity. Strains designated as B. aerophilus, B. altitudinis, and B. stratosphericus grouped together in the cluster containing the B. altitudinis type strain, suggesting that these three species should be considered a single species, B. altitudinis. The antimicrobial activity of UTK D1-0055 was evaluated against a panel of 15 Listeria strains (nine Listeria monocytogenes serotypes, Listeria innocua, and Listeria marthii), other foodborne pathogens (six Salmonella enterica serotypes and Escherichia coli), and three representative fungi (Saccharomyces cerevisiae, Botrytis cinerea, and Hyperdermium pulvinatum). Antibacterial activity was observed against all Listeria strains, but no antibacterial effects were found against the other tested bacterial and fungal strains. Biosynthetic gene clusters were identified in silico that may be related to the observed antibacterial activity, and these clusters included genes that putatively encode bacteriocins and nonribosomally synthesized peptides. The B. altitudinis strain identified in this investigation had a broad range of antilisterial activity, suggesting that it and other related strains may be useful for biocontrol in the food industry. HIGHLIGHTS
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Affiliation(s)
- Lauren K Hudson
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Leticia A G Orellana
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA.,Zamorano Pan-American Agricultural School, San Antonio de Oriente, Francisco Morazán, Honduras
| | - Daniel W Bryan
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Andrew Moore
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - John P Munafo
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Henk C den Bakker
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, Griffin, Georgia 30602, USA
| | - Thomas G Denes
- Department of Food Science, University of Tennessee, Knoxville, Tennessee 37996, USA
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19
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Prichula J, Primon-Barros M, Luz RCZ, Castro ÍMS, Paim TGS, Tavares M, Ligabue-Braun R, d’Azevedo PA, Frazzon J, Frazzon APG, Seixas A, Gilmore MS. Genome Mining for Antimicrobial Compounds in Wild Marine Animals-Associated Enterococci. Mar Drugs 2021; 19:328. [PMID: 34204046 PMCID: PMC8229437 DOI: 10.3390/md19060328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/20/2022] Open
Abstract
New ecosystems are being actively mined for new bioactive compounds. Because of the large amount of unexplored biodiversity, bacteria from marine environments are especially promising. Further, host-associated microbes are of special interest because of their low toxicity and compatibility with host health. Here, we identified and characterized biosynthetic gene clusters encoding antimicrobial compounds in host-associated enterococci recovered from fecal samples of wild marine animals remote from human-affected ecosystems. Putative biosynthetic gene clusters in the genomes of 22 Enterococcus strains of marine origin were predicted using antiSMASH5 and Bagel4 bioinformatic software. At least one gene cluster encoding a putative bioactive compound precursor was identified in each genome. Collectively, 73 putative antimicrobial compounds were identified, including 61 bacteriocins (83.56%), 10 terpenes (13.70%), and 2 (2.74%) related to putative nonribosomal peptides (NRPs). Two of the species studied, Enterococcus avium and Enterococcus mundtti, are rare causes of human disease and were found to lack any known pathogenic determinants but yet possessed bacteriocin biosynthetic genes, suggesting possible additional utility as probiotics. Wild marine animal-associated enterococci from human-remote ecosystems provide a potentially rich source for new antimicrobial compounds of therapeutic and industrial value and potential probiotic application.
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Affiliation(s)
- Janira Prichula
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Muriel Primon-Barros
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Romeu C. Z. Luz
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Ícaro M. S. Castro
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Thiago G. S. Paim
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Maurício Tavares
- Centro de Estudos Costeiros, Limnológicos e Marinhos (CECLIMAR), Universidade Federal do Rio Grande do Sul (UFRGS), Campus Litoral Norte, Imbé 95625-000, RS, Brazil;
| | - Rodrigo Ligabue-Braun
- Department of Pharmacosciences, UFCSPA, Porto Alegre 90050-170, RS, Brazil; (R.L.-B.); (A.S.)
| | - Pedro A. d’Azevedo
- Gram-Positive Cocci Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre 90050-170, RS, Brazil; (J.P.); (M.P.-B.); (R.C.Z.L.); (Í.M.S.C.); (T.G.S.P.); (P.A.d.)
| | - Jeverson Frazzon
- Food Science Institute, UFRGS, Porto Alegre 90035-003, RS, Brazil;
| | - Ana P. G. Frazzon
- Department of Microbiology, Immunology and Parasitology, UFRGS, Porto Alegre 90050-170, RS, Brazil;
| | - Adriana Seixas
- Department of Pharmacosciences, UFCSPA, Porto Alegre 90050-170, RS, Brazil; (R.L.-B.); (A.S.)
| | - Michael S. Gilmore
- Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
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Toyoncin, a Novel Leaderless Bacteriocin That Is Produced by Bacillus toyonensis XIN-YC13 and Specifically Targets B. cereus and Listeria monocytogenes. Appl Environ Microbiol 2021; 87:e0018521. [PMID: 33811023 PMCID: PMC8174769 DOI: 10.1128/aem.00185-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bacteriocins have attracted increasing interest because of their potential as natural preservatives. Recent studies showed that the Bacillus cereus group is a prominent producer of bacteriocins. Using a laboratory-based screening strategy, we identified a strain in the B. cereus group, Bacillus toyonensis XIN-YC13, with antimicrobial activity against B. cereus. A novel, 70-amino-acid-long leaderless bacteriocin, toyoncin, was purified from the culture supernatant of strain XIN-YC13, and its molecular mass was found to be 7,817.1012 Da. Toyoncin shares no similarity with any other known bacteriocins, and its N-terminal amino acid is formylmethionine rather than methionine. Toyoncin shows good pH and heat stability and exhibits specific antimicrobial activity against two important foodborne pathogens, B. cereus and Listeria monocytogenes. Additionally, toyoncin exerts bactericidal activity and induces cell membrane damage. Toyoncin can also inhibit the outgrowth of B. cereus spores. Preservation assays showed that toyoncin effectively suppressed or eradicated B. cereus and L. monocytogenes in pasteurized skim milk. These results suggest that toyoncin can be used as a new biopreservative against B. cereus and L. monocytogenes in the food industry. IMPORTANCE We identified a novel leaderless bacteriocin, toyoncin, produced by B. toyonensis XIN-YC13. Toyoncin shows good pH and heat stability, and it has specific antimicrobial activity against B. cereus and L. monocytogenes (two important foodborne pathogens), likely by destroying their cell membrane integrity. Toyoncin inhibited the outgrowth of B. cereus spores and effectively inhibited or eliminated B. cereus and L. monocytogenes in a milk model system. These results indicate the potential of toyoncin as a food preservative.
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Identification and characterization of a novel circular bacteriocin, bacicyclicin XIN-1, from Bacillus sp. Xin1. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107696] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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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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Discovery and characterisation of circular bacteriocin plantacyclin B21AG from Lactiplantibacillus plantarum B21. Heliyon 2020; 6:e04715. [PMID: 32904251 PMCID: PMC7452424 DOI: 10.1016/j.heliyon.2020.e04715] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/22/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023] Open
Abstract
Lactiplantibacillus plantarum B21 isolated from Vietnamese sausage (nem chua) has previously displayed broad antimicrobial activity against Gram-positive bacteria including foodborne pathogens Listeria monocytogenes and Clostridium perfringens. This study successfully identified the antimicrobial agent as plantacyclin B21AG, a 5668 Da circular bacteriocin demonstrating high thermostability, resistance to a wide range of pH, proteolytic resistance and temporal stability. We report a reverse genetics approach to identify and characterise plantacyclin B21AG from first principles. The bacteriocin was purified from culture supernatant by a three-step process consisting of concentration, n-butanol extraction and cation exchange chromatography. A de novo peptide sequencing using LC-MS/MS techniques identified two putative peptide fragments which were mapped to the genome sequence of L. plantarum B21. This revealed an ORF corresponding to a putative circular bacteriocin with a 33-amino acid leader peptide and a 58-amino acid mature peptide encoded on a native plasmid pB21AG01. The bacteriocin is shown to be a small cationic predominantly α-helical protein (69%). The corresponding gene cluster, consisted of seven genes associated with post-translational circularisation, immunity and secretion. Whilst plantacyclin B21AG is 86% identical to the newly published plantaricyclin A it is more highly cationic having a net charge of +3 due to an additional basic residue in the putative membrane interaction region. This and other substitutions may well go some way to explaining functional differences. The robust nature of plantacyclin B21AG, its antimicrobial activity and associated machinery for cyclisation make it an interesting biotechnological target for development, both as a food-safe antimicrobial or potentially a platform technology for recombinant protein circularisation.
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