Impact of off-target integron activity on bacteria evolution

Integrons are mobile genetic elements that have played an important role in the dissemination of antibiotic resistance. Under stress, the integron can generate combinatorial variation in resistance cassette expression by cassette re-shuffling, accelerating the evolution of resistance. However, the flexibility of the integron integrase site recognition motif hints at potential off-target effects of the integrase on the rest of the genome that may have important evolutionary consequences. Here we test this hypothesis by selecting for increased piperacillin resistance populations of P.aeruginosa with a mobile integron containing a hard-to-mobilise beta-lactamase cassette to minimize the potential for adaptive cassette re-shuffling. We found that integron activity can both decrease overall survival rate but also improve the fitness of the surviving populations. Off-target inversions mediated by the integron accelerated plasmid adaptation by disrupting costly conjugative genes otherwise mutated in control populations lacking a functional integrase. Plasmids containing integron-mediated inversions were associated with lower plasmid costs and higher stability than plasmids carrying mutations, albeit at a cost of reduced conjugative ability. These findings highlight the potential for integrons to create structural variation that can drive bacterial evolution, and they provide an interesting example showing how antibiotic pressure can drive the loss of conjugative genes.

整合子（Integrons）是一类在抗生素耐药性传播中发挥关键作用的可移动遗传元件。在应激条件下，整合子可通过基因盒重排实现耐药基因盒表达的组合变异，进而加速耐药性的进化过程。然而，整合酶识别位点基序的灵活性，提示整合酶可能对基因组其余区域产生潜在脱靶效应，此类效应或具备重要的进化意义。本研究通过筛选携带难以移动的β-内酰胺酶基因盒的可移动整合子的铜绿假单胞菌（Pseudomonas aeruginosa，P.aeruginosa）种群，以提升其对哌拉西林的耐药性，从而最小化适应性基因盒重排的潜在可能，以此验证上述假说。研究结果显示，整合子的活性既可降低种群整体存活率，又可提升存活种群的适合度。由整合子介导的脱靶倒位，通过破坏对照种群（缺乏功能性整合酶）中通常会发生突变的代价高昂的接合基因，加速了质粒的适应性进化。相较于携带突变的质粒，携带整合子介导倒位的质粒具有更低的质粒代谢代价与更高的结构稳定性，尽管这是以降低接合能力为代价的。本研究结果凸显了整合子通过产生结构变异推动细菌进化的潜在可能，同时为阐明抗生素压力如何驱动接合基因丢失提供了一则极具启发性的实例。