Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum

Abstract

Plasmids drive genomic diversity in bacteria via horizontal gene transfer [1, 2]; nevertheless, explaining their survival in bacterial populations is challenging [3]. Theory predicts that irrespective of their net fitness effects, plasmids should be lost: when parasitic (costs outweigh benefits), plasmids should decline due to purifying selection [4-6], yet under mutualism (benefits outweigh costs), selection favors the capture of beneficial accessory genes by the chromosome and loss of the costly plasmid backbone [4]. While compensatory evolution can enhance plasmid stability within populations [7-15], the propensity for this to occur across the parasitism-mutualism continuum is unknown. We experimentally evolved Pseudomonas fluorescens and its mercury resistance mega-plasmid, pQBR103 [16], across an environment-mediated parasitism-mutualism continuum. Compensatory evolution stabilized plasmids by rapidly ameliorating the cost of plasmid carriage in all environments. Genomic analysis revealed that, in both parasitic and mutualistic treatments, evolution repeatedly targeted the gacA/gacS bacterial two-component global regulatory system while leaving the plasmid sequence intact. Deletion of either gacA or gacS was sufficient to completely ameliorate the cost of plasmid carriage. Mutation of gacA/gacS downregulated the expression of ∼17% of chromosomal and plasmid genes and appears to have relieved the translational demand imposed by the plasmid. Chromosomal capture of mercury resistance accompanied by plasmid loss occurred throughout the experiment but very rarely invaded to high frequency, suggesting that rapid compensatory evolution can limit this process. Compensatory evolution can explain the widespread occurrence of plasmids and allows bacteria to retain horizontally acquired plasmids even in environments where their accessory genes are not immediately useful.

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

“…35). However, high conjugation rate is not essential for a plasmid source: hosts that achieve long-term plasmid stability through other routes, such as compensatory evolution (9,36), could also become sources, provided they retain some degree of interspecific conjugation.…”

“…Detailed molecular and genetic studies of plasmid-host adaptation are revealing the mechanisms behind plasmid stability (7,9,35,38,39). However, these studies have primarily been conducted in one-plasmid/one-host systems, which are not reflective of natural microbial populations containing many different bacterial species (40) and mobile genetic elements (21,41).…”

“…Compensatory evolution can ameliorate plasmid cost, thereby weakening selection against the plasmid (7)(8)(9). However, this process is unlikely to stabilize highly unstable plasmids or maintain plasmids in small populations where the rate of plasmid loss is likely to exceed the rate of compensatory evolution.…”

Fitness Costs of Plasmids: a Limit to Plasmid Transmission

“…The centrality of translation as the main plasmid fitness cost is exemplified by a recent study of pQBR103 (25). This mega plasmid from Pseudomonas fluorescens produces a major burden for the host cell due to the increased transcriptional demand imposed by the plasmidencoded genes.…”

“…The idea underlying this hypothesis is that even if plasmids produce a cost when they first arrive in a new bacterial host, this cost could be alleviated over time through compensatory mutations in the plasmid and/or the host chromosome (20). In recent years, several studies have analyzed the molecular basis of the cost and compensation of plasmids in bacterial populations (21)(22)(23)(24)(25)(26)(27)(28), generating new models of the existence conditions of plasmids (22,24). These studies evaluate a number of selection, transfer, and compensation regimes that could explain plasmid survival in bacterial populations, and have revealed new evidence about the molecular mechanisms underlying the cost of and adaptation to plasmids.…”