Partial Diversity Generates Effector Immunity Specificity of the Bac41-Like Bacteriocins of Enterococcus faecalis Clinical Strains

Abstract

Bacteriocin 41 (Bac41) is the plasmid-encoded bacteriocin produced by the opportunistic pathogen Enterococcus faecalis. Its genetic determinant consists of bacL 1 (effector), bacL 2 (regulator), bacA (effector), and bacI (immunity). The secreted effectors BacL 1 and BacA coordinate to induce the lytic cell death of E. faecalis. Meanwhile, the immunity factor BacI provides self-resistance to the Bac41 producer, E. faecalis, against the action of BacL 1 and BacA. In this study, we demonstrated that more than half of the 327 clinical strains of E. faecalis screened had functional Bac41 genes. Analysis of the genetic structure of the Bac41 genes in the DNA sequences of the E. faecalis strains revealed that the Bac41-like genes consist of a relatively conserved region and a variable region located downstream from bacA. Based on similarities in the variable region, the Bac41-like genes could be classified into type I, type IIa, and type IIb. Interestingly, the distinct Bac41 types had specific immunity factors for self-resistance, BacI1 or BacI2, and did not show cross-immunity to the other type of effector. We also demonstrated experimentally that the specificity of the immunity was determined by the combination of the C-terminal region of BacA and the presence of the unique BacI1 or BacI2 factor. These observations suggested that Bac41-like bacteriocin genes are extensively disseminated among E. faecalis strains in the clinical environment and can be grouped into at least three types. It was also indicated that the partial diversity results in specificity of self-resistance which may offer these strains a competitive advantage. IMPORTANCEBacteriocins are antibacterial effectors produced by bacteria. In general, a bacteriocin-coding gene is accompanied by a cognate immunity gene that confers self-resistance on the bacteriocin-producing bacterium itself. We demonstrated that one of the bacteriocins, Bac41, is disseminated among E. faecalis clinical strains and the Bac41 subtypes with partial diversity. The Bac41-like bacteriocins were found to be classified into type I, type IIa, and type IIb by variation of the cognate immunity factors. The antibacterial activity of the respective effectors was specifically inhibited by the immunity factor from the same type of Bac41 but not the other types. This specificity of effector-immunity pairs suggests that bacteriocin genes might have evolved to change the immunity specificity to acquire an advantage in interbacterial competition. Enterococcus faecalis is a Gram-positive commensal bacterium present in the intestinal tract of healthy humans or animals, but it is also a causative agent of opportunistic infectious diseases, including urinary infectious disease, bacteremia, infective endocarditis, and others (1-4). As represented by the development of drug resistance, the acquisition of new genes via mobile genetic elements (MGEs), such as plasmids, raises the concern of increased severity of these enterococcal diseases (5). Enterococcal plasmids also encode various bact...

Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium

“…In line with the hypothesis of different routes of hospital adaptation, we observed some plasmidome population core genes that are only present as core in some plasmidome populations associated with hospitalized patients. We observed the presence of a bacteriocin with homology to BacA in populations 5, 7, and 8 and previously described as a plasmid-borne bacteriocin in E. faecalis (29). BacA can act as a more evolved toxin-antitoxin system in which not only daughter cells but also cells from the same generation not bearing the BacA plasmid are excluded.…”

“…BacA can act as a more evolved toxin-antitoxin system in which not only daughter cells but also cells from the same generation not bearing the BacA plasmid are excluded. Furthermore, it was demonstrated that plasmid dissemination was more prominent under conditions of fluctuations in the population of E. faecium, since BacA activity exclusively affects dividing cells (29). We also observed a complete phosphotransferase system putatively involved in mannose/fructose/sorbose utilization present in the plasmidome cores of populations 6 and 7.…”

Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species

“…These adaptations include the presence of CRISPR‐Cas in the chromosome (Palmer and Gilmore, ; Price et al ., ), restriction‐modification (RM) and anti‐RM systems, which would act against certain plasmids (e.g. pCF10); or lineage‐specific bacteriocins carried by pheromone‐responsive plasmids (Kurushima et al ., ) or conjugative transposons (Tn 916 ‐like elements) that might influence the transfer of genetic material within and between lineages (Manson et al ., ; Laverde Gomez et al ., ; León‐Sampedro et al ., ; Price et al ., ).…”

Genomes of a major nosocomial pathogenEnterococcus faeciumare shaped by adaptive evolution of the chromosome and plasmidome

“…Exploration of plasmid genes specifically present in each of the isolation sources revealed the presence of a widely-spread bacteriocin-like gene (bacA) in our set of hospitalized isolates that was rarely present in other isolation sources. As previously reported for E. faecalis, bacA can act as a sophisticated toxin-antitoxin system, in which not only daughter but also co-existing bacA plasmidfree cells are excluded from the population (Kurushima et al 2016). As such, this bacA gene may have contributed to the ecological dominance of the distinct subpopulation of E. faecium hospital isolates in patients.…”

“…Plasmidomes of hospitalized patient isolates were enriched (Specificity & Sensitivity > 80%) for a large pool of genes (n = 589, OR > 1) ( Supplementary Fig. S8) with a variety of functions, including a bacteriocin-like protein (bacA) previously described as plasmid-related in E. faecalis (Kurushima et al 2016) and antibiotic-resistance related genes such as aacA-aphD or efflux permease ABC transporters ( Supplementary Table S6). Poultry and pig isolates showed a pool of 155 and 100 enriched plasmid genes (OR > 1; Specificity & Sensitivity > 80%), respectively ( Supplementary Fig.…”