Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways

Abstract

The acquisition of plasmids is often accompanied by fitness costs such that compensatory evolution is required to allow plasmid survival, but it is unclear whether compensatory evolution can be extensive or rapid enough to maintain plasmids when they are very costly. The mercury-resistance plasmid pQBR55 drastically reduced the growth of its host, Pseudomonas fluorescens SBW25, immediately after acquisition, causing a small colony phenotype. However, within 48 h of growth on agar plates we observed restoration of the ancestral large colony morphology, suggesting that compensatory mutations had occurred. Relative fitness of these evolved strains, in lab media and in soil microcosms, varied between replicates, indicating different mutational mechanisms. Using genome sequencing we identified that restoration was associated with chromosomal mutations in either a hypothetical DNA-binding protein PFLU4242, RNA polymerase or the GacA/S two-component system. Targeted deletions in PFLU4242, gacA or gacS recapitulated the ameliorated phenotype upon plasmid acquisition, indicating three distinct mutational pathways to compensation. Our data shows that plasmid compensatory evolution is fast enough to allow survival of a plasmid despite it imposing very high fitness costs upon its host, and indeed may regularly occur during the process of isolating and selecting individual plasmid-containing clones.

Positive selection inhibits plasmid coexistence in bacterial genomes

“…We observed mutations in three loci previously associated with compensatory evolution for pQBR plasmids. Specifically, mutations to either of the genes encoding the GacAS twocomponent global regulatory system [17,18], or the gene PFLU4242 of unknown function [17], were sufficient to ameliorate the fitness costs associated with coinfection by both pQBR103 and pQBR57. Similarly, deletion of either locus could completely ameliorate the cost of pQBR103, whereas amelioration of pQBR57 was more complete via deletion of PFLU4242 than gacS.…”

Piggybacking on niche-adaptation reduces the cost of multidrug resistance plasmids

“…Our study is not without limitations. We acknowledge that the pleiotropic effects on plasmid costs reported here may be specific to a single environment as others have reported that both fitness costs [32, 54] and compensatory evolution [55] are highly media-dependent. Consequently, the specific mutations reported here may be media-dependent, but the processes targeted (i.e.…”

Plasmid Interactions Can Improve Plasmid Persistence in Bacterial Populations

“…Additionally, our simulations encompass long times but consider static features, such that the entities are immutable (neither plasmids nor bacteria change by mutation or by recombination). Therefore, we neglect compensatory mutations that could mitigate the fitness cost of one ( San Millan et al, 2015 ) or several plasmids ( Loftie-Eaton et al, 2017 ; Hall et al, 2020 ; Jordt et al, 2020 ) and recombination events between plasmids allowing acquisition of addiction systems that alter loss rates ( Loftie-Eaton et al, 2016 ; Stalder et al, 2017 ), pleiotropic effects between mutations ( Jordt et al, 2020 ) or even the formation of co-integrates. The latter is especially important from a clinical point of view, in particular upon a fusion of plasmids encoding different resistance mechanisms thus creating multidrug-resistance plasmids ( Garcia et al, 2007 ; Desmet et al, 2018 ), or even between resistance and virulence plasmids ( Dong et al, 2018 ), that could explain the positive correlation between the diversity of resistance and virulence genes across metagenomes ( Escudeiro et al, 2019 ).…”