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Horizontal transfer of bacteriocin biosynthesis genes requires metabolic adaptation to improve compound production and cellular fitness

ABSTRACT: Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread amongst bacterial isolates and are important genetic determinants of competitive fitness among bacterial lineages within a given habitat. Staphylococci produce a tremendous diversity of compounds and the corresponding gene clusters (Staphylococcal Antibiosis Islands - SAbIs) are frequently associated with mobile genetic elements, suggesting acquisition and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenged by the lack of optimal precursor supplies. Accordingly, many recipients produce low compound amounts or show reduced growth rates. To assess whether transfer of SAbIs between closely related S. aureus strains has similar effects, we used as model the SAbI encoding the ribosomally synthesized and post-translationally modified peptide (RiPP) Micrococcin P1 (MP1). We found that acquisition of the SAbI by S. aureus RN4220 did allow immediate MP1 production but also imposed a metabolic burden. Adaptive evolution selected for strains with increased TCA-cycle activity, which enhanced metabolic fitness and levels of compound production. Metabolome analysis showed that the adaptive mutation increased the levels of central metabolites including citrate and α-ketoglutarate, and the increased availability of citrate turned out to be essential to overcome SAbI associated growth defects. Our results indicate that acquisition of SAbIs represents a blessing for the recipient strain as long as its genetic and metabolic predispositions allow integration of bacteriocin production into the cellular metabolism. This in turn may be crucial to ensure the competitive fitness of SAbI recipients within natural bacterial communities.

ORGANISM(S): Staphylococcus aureus subsp. aureus RN4220

PROVIDER: GSE208001 | GEO | 2022/11/21

REPOSITORIES: GEO

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Project description: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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Horizontal transfer of bacteriocin biosynthesis genes requires metabolic adaptation to improve compound production and cellular fitness

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