Positive selection inhibits plasmid coexistence in bacterial genomes

Abstract

Plasmids play an important role in bacterial evolution by transferring niche adaptive functional genes between lineages, thus driving genomic diversification. Bacterial genomes commonly contain multiple, coexisting plasmid replicons (i.e., plasmid coinfection), which could fuel adaptation by increasing the range of gene functions available to selection and allowing their recombination. However, plasmid coinfection is difficult to explain because the acquisition of plasmids typically incurs high fitness costs for the host cell. Here, we show that plasmid coinfection was stably maintained without positive selection for plasmid-encoded gene functions and was associated with compensatory evolution to reduce fitness costs. By contrast, with positive selection, plasmid coinfection was unstable despite compensatory evolution. Positive selection discriminated between differential fitness benefits of functionally redundant plasmid replicons, retaining only the more beneficial plasmid. These data suggest that while the efficiency of negative selection against plasmid fitness costs declines over time due to compensatory evolution, positive selection to maximise plasmid-derived fitness benefits remains efficient. Our findings help to explain the forces structuring bacterial genomes: Coexistence of multiple plasmids in a genome is likely to require either rare positive selection in nature or non-redundancy of accessory gene functions among coinfecting plasmids.

Plasmid fitness costs are caused by specific genetic conflicts

“…Consistent with our hypothesis, we detected a significant effect of mutation on the fitness costs of plasmid carriage (linear mixed-effects model (LMM), plasmid:host interaction likelihood ratio test (LRT) ߯ ଶ = 37.3, p < 1e-6). Each plasmid levied a significant cost in the wild-type background, corresponding with previous studies [37,45]: for pQBR57, 17.8% (t = 4.8, p = 0.003); for pQBR103, 52% (t = 10.2, p < 0.001). Mutation of PFLU4242 resulted in substantial amelioration such that we did not detect a significant fitness cost of either plasmid (post-hoc contrasts with multivariate t ('mvt') adjustment pQBR57 t = 0.87, p = 0.99; pQBR103 t = 1.19, p = 0.95).…”

“…Previous evolution experiments with P. fluorescens SBW25 and megaplasmids pQBR103, pQBR57, or pQBR55, have identified four key genes implicated in plasmid compensatory evolution in this strain [29,33,37,39,51] (Fig. 1, full details and discussion in Supplementary Text): the gacA/S two-component signalling pathway, which has repeatedly been associated with pQBR103 and pQBR55 carriage; PFLU4242, a chromosomal gene that has been mutated…”

“…Mutation of PFLU4242 resulted in substantial amelioration such that we did not detect a significant fitness cost of either plasmid (post-hoc contrasts with multivariate t ('mvt') adjustment pQBR57 t = 0.87, p = 0.99; pQBR103 t = 1.19, p = 0.95). Mutation to gacS was more equivocal, with more effective compensation of pQBR103 than of pQBR57 [37]. Neither the ∆ gacS nor the ∆ PFLU4242 mutants had a detectable fitness difference from wild-type (gacS t = -0.24, p = 1; PFLU4242 t = 0.27, p = 1), indicating that the effects of mutation were due to interaction with the plasmid rather than providing a direct fitness benefit.…”

“…Here, we take advantage of a plasmid-host system where multiple genetic pathways of compensatory evolution exist, to investigate the mechanistic bases of plasmid fitness costs and their amelioration. We have previously described two pathways of chromosomal compensatory mutation in Pseudomonas fluorescens SBW25, targeting the gacA/S global regulatory system or the hypothetical protein PFLU4242, which individually ameliorate the fitness costs of megaplasmids pQBR103 (425 kb), pQBR57 (307 kb), or pQBR55 (157 kb) [29,37]. In this study, we describe an additional plasmid-borne compensatory locus, the lambda-repressor-like protein PQBR57_0059, that ameliorates the cost of pQBR57.…”

“…without de novo compensation [29]), we focused on identifying the basis of fitness cost and amelioration in the the two larger megaplasmids, pQBR57 and pQBR103. Harrison et al [33]; Hall et al [29,39,52] and Carrilero et al [37]. Symbols indicate the location of the mutation in the nucleic acid sequence.…”