Epistasis between antibiotic resistance mutations and genetic background shape the fitness effect of resistance across species of Pseudomonas

Antibiotic resistance often evolves by mutations at conserved sites in essential genes, resulting in parallel molecular evolution between divergent bacterial strains and species. Whether these resistance mutations are having parallel effects on fitness across bacterial taxa, however, is unclear. This is an important point to address, because the fitness effects of resistance mutations play a key role in the spread and maintenance of resistance in pathogen populations. We address this idea by measuring the fitness effect of a collection of rifampicin resistance mutations in the β subunit of RNA polymerase (rpoB) across 8 strains that span the diversity of the genus Pseudomonas. We find that almost 50% of rpoB mutations have background-dependent fitness costs, demonstrating that epistatic interactions between rpoB and the rest of the genome are common. Moreover, epistasis is typically strong, and it is the dominant genetic determinant of the cost of resistance mutations. To investigate the functional basis of epistasis, and because rpoB plays a central role in transcription, we measured the effects of common rpoB mutations on transcriptional efficiency across 3 strains of Pseudomonas. Transcriptional efficiency correlates strongly to fitness across strains, and epistasis arises because individual rpoB mutations have differential effects on transcriptional efficiency in different genetic backgrounds.

抗生素耐药性通常通过必需基因保守位点的突变演化而来，可在分歧的细菌菌株与物种之间引发平行分子进化。然而，这类耐药突变对不同细菌类群的适合度是否存在平行影响，目前仍不明确。这一问题具有重要研究价值，因为耐药突变的适合度效应在病原菌种群耐药性的传播与维持过程中发挥关键作用。为此，我们选取了覆盖假单胞菌属（Pseudomonas）全部多样性类群的8株菌株，对其RNA聚合酶β亚基（rpoB）上一系列利福平耐药突变的适合度效应进行了测定。研究发现，近50%的rpoB突变存在遗传背景依赖的适合度代价，表明rpoB与基因组其余区域之间的上位性互作十分普遍。此外，上位性效应通常较强，且是耐药突变代价的主导性遗传决定因素。鉴于rpoB在转录过程中发挥核心作用，为进一步探究上位性效应的功能基础，我们又选取了3株假单胞菌，测定了常见rpoB突变对其转录效率的影响。结果显示，不同菌株的转录效率与适合度紧密相关，而上位性效应的产生则是由于单个rpoB突变在不同遗传背景下对转录效率的影响存在差异。