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Horizontal Transfer of Bacteriocin Biosynthesis Genes Requires Metabolic Adaptation To Improve Compound Production and Cellular Fitness. Microbiol Spectr 2023; 11:e0317622. [PMID: 36472430 PMCID: PMC9927498 DOI: 10.1128/spectrum.03176-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread among bacterial isolates and are important genetic determinants of competitive fitness within a given habitat. Staphylococci produce a tremendous diversity of compounds, and the corresponding BGCs are frequently associated with mobile genetic elements, suggesting gain and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenging, and many BGC recipients initially produce small amounts of compound or show reduced growth rates. To assess whether transfer of BGCs between closely related Staphylococcus aureus strains can be instantly effective or requires elaborate metabolic adaptation, we investigated the intraspecies transfer of a BGC encoding the ribosomally synthesized and posttranslationally modified peptide (RiPP) micrococcin P1 (MP1). We found that acquisition of the BGC by S. aureus RN4220 enabled immediate MP1 production but also imposed a metabolic burden, which was relieved after prolonged cultivation by adaptive mutation. We used a multiomics approach to study this phenomenon and found adaptive evolution to select for strains with increased activity of the tricarboxylic acid cycle (TCA), which enhanced metabolic fitness and levels of compound production. Metabolome analysis revealed increases of central metabolites, including citrate and α-ketoglutarate in the adapted strain, suggesting metabolic adaptation to overcome the BGC-associated growth defects. Our results indicate that BGC acquisition requires genetic and metabolic predispositions, allowing the integration of bacteriocin production into the cellular metabolism. Inappropriate metabolic characteristics of recipients can entail physiological burdens, negatively impacting the competitive fitness of recipients within natural bacterial communities. IMPORTANCE Human microbiomes are critically associated with human health and disease. Importantly, pathogenic bacteria can hide in human-associated communities and can cause disease when the composition of the community becomes unbalanced. Bacteriocin-producing commensals are able to displace pathogens from microbial communities, suggesting that their targeted introduction into human microbiomes might prevent pathogen colonization and infection. However, to develop probiotic approaches, strains are needed that produce high levels of bioactive compounds and retain cellular fitness within mixed bacterial communities. Our work offers insights into the metabolic burdens associated with the production of the bacteriocin micrococcin P1 and highlights evolutionary strategies that increase cellular fitness in the context of production. Metabolic adaptations are most likely broadly relevant for bacteriocin producers and need to be considered for the future development of effective microbiome editing strategies.
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Salustiano Marques-Bastos SL, Varella Coelho ML, Ceotto-Vigoder H, Carlin Fagundes P, Silva Almeida G, Brede DA, Nes IF, Vasconcelos de Paiva Brito MA, de Freire Bastos MDC. Molecular characterization of aureocin 4181: a natural N-formylated aureocin A70 variant with a broad spectrum of activity. Braz J Microbiol 2020; 51:1527-1538. [PMID: 32542423 DOI: 10.1007/s42770-020-00315-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/05/2020] [Indexed: 11/27/2022] Open
Abstract
Bacteriocins are ribosomally synthesized antimicrobial peptides produced by prokaryotes. Here, the molecular characterization of aureocin 4181, a bacteriocin produced by Staphylococcus aureus 4181, a strain involved in bovine mastitis, is presented. Aureocin 4181 gene cluster (aurRID1CBAT) was mined from scaffold 15 of the draft genome of its producer strain. Three (AurABC) out of the four structural peptides of aureocin 4181 are identical to those of aureocin A70, except for AurD1 of aureocin 4181, which showed a conservative substitution of Leu29 to Phe29 when compared to AurD of aureocin A70. According to molecular mass determination and peptide sequencing, combined with genome sequencing data, aureocin 4181 is an N-formylated variant of aureocin A70. The analysis of its antimicrobial spectrum was extended to include strains of the two major contagious pathogens involved in bovine mastitis, S. aureus and Streptococcus agalactiae. Aureocin 4181 exhibited a striking activity against S. aureus, inhibiting most strains tested. Besides having a broader spectrum of activity, aureocin 4181 exhibited a stronger bacteriolytic action against the target strains and proved to be from two- to fourfold more active than aureocin A70 against S. aureus. Aureocin 4181 has potential to become an alternative drug for prevention and control of mastitic staphylococci, a pathogen that imposes a huge economic burden to dairy industry worldwide. It also represents the third four-component bacteriocin described in the literature, the second in staphylococci.
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Affiliation(s)
| | - Marcus Lívio Varella Coelho
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,Instituto Nacional da Propriedade Industrial, Rio de Janeiro, RJ, Brazil
| | - Hilana Ceotto-Vigoder
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Patrícia Carlin Fagundes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gabriela Silva Almeida
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Dag A Brede
- Laboratory of Microbial Gene Technology, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Ingolf F Nes
- Laboratory of Microbial Gene Technology, Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Maria do Carmo de Freire Bastos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil. .,Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, UFRJ, Av. Carlos Chagas Filho, 373, CCS, Bloco I, room I-1-059, Cidade Universitária, Rio de Janeiro, RJ, 21941-902, Brazil.
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López-Cuellar MDR, Rodríguez-Hernández AI, Chavarría-Hernández N. LAB bacteriocin applications in the last decade. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1232605] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Ma. del Rocío López-Cuellar
- Agro-Food Biotechnology Research Group (CABA), Institute of Food and Agricultural Sciences (ICAp), Autonomous University of Hidalgo State (UAEH) , Tulancingo de Bravo, Hidalgo, Mexico
| | - Adriana-Inés Rodríguez-Hernández
- Agro-Food Biotechnology Research Group (CABA), Institute of Food and Agricultural Sciences (ICAp), Autonomous University of Hidalgo State (UAEH) , Tulancingo de Bravo, Hidalgo, Mexico
| | - Norberto Chavarría-Hernández
- Agro-Food Biotechnology Research Group (CABA), Institute of Food and Agricultural Sciences (ICAp), Autonomous University of Hidalgo State (UAEH) , Tulancingo de Bravo, Hidalgo, Mexico
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Novel Group of Leaderless Multipeptide Bacteriocins from Gram-Positive Bacteria. Appl Environ Microbiol 2016; 82:5216-24. [PMID: 27316965 DOI: 10.1128/aem.01094-16] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED From raw milk we found 10 Lactococcus garvieae isolates that produce a new broad-spectrum bacteriocin. Though the isolates were obtained from different farms, they turned out to possess identical inhibitory spectra, fermentation profiles of sugars, and repetitive sequence-based PCR (rep-PCR) DNA patterns, indicating that they produce the same bacteriocin. One of the isolates (L. garvieae KS1546) was chosen for further assessment. Purification and peptide sequencing combined with genome sequencing revealed that the antimicrobial activity was due to a bacteriocin unit composed of three similar peptides of 32 to 34 amino acids. The three peptides are produced without leader sequences, and their genes are located next to each other in an operon-like structure, adjacent to the genes normally involved in bacteriocin transport (ABC transporter) and self-immunity. The bacteriocin, termed garvicin KS (GarKS), showed sequence homology to four multipeptide bacteriocins in databases: the known staphylococcal aureocin A70, consisting of four peptides, and three unannotated putative multipeptide bacteriocins produced by Bacillus cereus All these multipeptide bacteriocin loci show conserved genetic organization, including being located adjacent to conserved genetic determinants (Cro/cI and integrase) which are normally associated with mobile genetic elements or genome rearrangements. The antimicrobial activity of all multipeptide bacteriocins was confirmed with synthetic peptides, and all were shown to have broad antimicrobial spectra, with GarKS being the most active of them. The inhibitory spectrum of GarKS includes important pathogens belonging to the genera Staphylococcus, Bacillus, Listeria, and Enterococcus IMPORTANCE Bacterial resistance to antibiotics is a very serious global problem. There are no new antibiotics with novel antimicrobial mechanisms in clinical trials. Bacteriocins use antimicrobial mechanisms different from those of antibiotics and can kill antibiotic-resistant bacteria, but the number of bacteriocins with very broad antimicrobial spectra is very small. In this study, we have found and purified a novel three-peptide bacteriocin, garvicin KS. By homology search, we were able to find one known and three novel sequence-related bacteriocins consisting of 3 or 4 peptides. None of the peptides has modified amino acids in its sequence. Thus, the activity of all bacteriocins was confirmed with chemically synthesized peptides. All of them, especially garvicin KS, have very broad antibacterial spectra, thus representing a great potential in antimicrobial applications in the food industry and medicine.
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Ceotto-Vigoder H, Marques S, Santos I, Alves M, Barrias E, Potter A, Alviano D, Bastos M. Nisin and lysostaphin activity against preformed biofilm of Staphylococcus aureus
involved in bovine mastitis. J Appl Microbiol 2016; 121:101-14. [DOI: 10.1111/jam.13136] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 12/24/2022]
Affiliation(s)
- H. Ceotto-Vigoder
- Departamento de Microbiologia Geral; Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro; Rio de Janeiro Brazil
| | - S.L.S. Marques
- Departamento de Microbiologia Geral; Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro; Rio de Janeiro Brazil
| | - I.N.S. Santos
- Departamento de Microbiologia Geral; Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro; Rio de Janeiro Brazil
| | - M.D.B. Alves
- Departamento de Microbiologia Geral; Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro; Rio de Janeiro Brazil
| | - E.S. Barrias
- Instituto Nacional de Metrologia, Qualidade e Tecnologia; Duque de Caxias; Brazil
| | - A. Potter
- Departamento de Microbiologia Geral; Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro; Rio de Janeiro Brazil
| | - D.S. Alviano
- Departamento de Microbiologia Geral; Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro; Rio de Janeiro Brazil
| | - M.C.F. Bastos
- Departamento de Microbiologia Geral; Instituto de Microbiologia Paulo de Góes; Universidade Federal do Rio de Janeiro; Rio de Janeiro Brazil
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Braem G, Stijlemans B, Van Haken W, De Vliegher S, De Vuyst L, Leroy F. Antibacterial activities of coagulase-negative staphylococci from bovine teat apex skin and their inhibitory effect on mastitis-related pathogens. J Appl Microbiol 2014; 116:1084-93. [PMID: 24443828 DOI: 10.1111/jam.12447] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/28/2013] [Accepted: 01/08/2014] [Indexed: 11/30/2022]
Abstract
AIMS To explore antibacterial activities of coagulase-negative staphylococci (CoNS) from teat apices of dairy cows towards mastitis-causing pathogens. METHODS AND RESULTS Of 254 CoNS, 38 displayed bacteriocin-like activity after a first screening. Seven of these strains displayed activity against at least one mastitis-related pathogen (Streptococcus uberis, Streptococcus dysgalactiae and Staphylococcus aureus). Staphylococcus chromogenes L217 displayed the strongest inhibitory effect, being active against all tested mastitis-related pathogens and most tested CoNS. Based on cation exchange and reversed-phase chromatography, in addition to N-terminal Edman degradation and PCR, the antibacterial peptide was identified as a nukacin-type bacteriocin and named nukacin L217. Although staphylococcal bacteriocins are generally found in the cell-free supernatants of liquid cultures, Staph. chromogenes L217 only led to detectable activity when grown on agar medium. CONCLUSIONS Bacteriocin-like activities are not uncommon among CoNS from teat apices and may inhibit mastitis-causing pathogens, as found for nukacin L217 production by Staph. chromogenes L217. SIGNIFICANCE AND IMPACT OF THE STUDY Nukacin L217 is the first identified bacteriocin of the species Staph. chromogenes and displays unusual production kinetics, that is, requiring surface growth of its producer. The fact that nukacins are produced by different CoNS species suggests a role in the teat skin ecosystem.
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Affiliation(s)
- G Braem
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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