Data from: Linking system-wide impacts of RNA polymerase mutations to the fitness cost of rifampin resistance in Pseudomonas aeruginosa

Fitness costs play a key role in the evolutionary dynamics of antibiotic resistance in bacteria by generating selection against resistance in the absence of antibiotics. Although the genetic basis of antibiotic resistance is well understood, the precise molecular mechanisms linking the genetic basis of resistance to its fitness cost remain poorly characterized. Here, we examine how the system-wide impacts of mutations in the RNA polymerase (RNAP) gene rpoB shape the fitness cost of rifampin resistance in Pseudomonas aeruginosa. Rifampin resistance mutations reduce transcriptional efficiency, and this explains 76% of the variation in fitness among rpoB mutants. The pleiotropic consequence of rpoB mutations is that mutants show altered relative transcript levels of essential genes. We find no evidence that global transcriptional responses have an impact on the fitness cost of rifampin resistance as revealed by transcriptome sequencing (RNA-Seq). Global changes in the transcriptional profiles of rpoB mutants compared to the transcriptional profile of the rifampin-sensitive ancestral strain are subtle, demonstrating that the transcriptional regulatory network of P. aeruginosa is robust to the decreased transcriptional efficiency associated with rpoB mutations. On a smaller scale, we find that rifampin resistance mutations increase the expression of RNAP due to decreased termination at an attenuator upstream from rpoB, and we argue that this helps to minimize the cost of rifampin resistance by buffering against reduced RNAP activity. In summary, our study shows that it is possible to dissect the molecular mechanisms underpinning variation in the cost of rifampin resistance and highlights the importance of genome-wide buffering of relative transcript levels in providing robustness against resistance mutations.适应度成本在细菌抗生素抗性的进化动力学中发挥关键作用，其通过在无抗生素环境下产生针对抗性的选择压力。尽管抗生素抗性的遗传基础已得到充分阐明，但将抗性遗传基础与其适应度成本关联起来的精确分子机制，仍未得到充分表征。本研究探讨了铜绿假单胞菌（Pseudomonas aeruginosa）中，RNA聚合酶（RNA polymerase, RNAP）基因rpoB的突变所产生的全系统影响，如何塑造利福平抗性的适应度成本。利福平抗性突变会降低转录效率，这一现象可解释rpoB突变体中76%的适应度变异。rpoB突变具有多效性后果：突变体的必需基因相对转录水平发生改变。通过转录组测序（RNA-Seq）分析，我们未发现全局转录响应对利福平抗性的适应度成本存在影响的证据。相较于利福平敏感的祖先菌株，rpoB突变体的转录谱整体变化较为微弱，这表明铜绿假单胞菌的转录调控网络对rpoB突变相关的转录效率降低具有鲁棒性。在更小的尺度上，我们发现利福平抗性突变会通过削弱rpoB上游衰减子的终止作用，提升RNA聚合酶的表达量；我们认为，这一机制可通过缓冲RNA聚合酶活性降低的影响，帮助最小化利福平抗性的适应度成本。综上，本研究表明，我们可以解析支撑利福平抗性成本变异的分子机制，并强调了全基因组相对转录水平缓冲在为抗性突变提供鲁棒性方面的重要性。