Instituto Gulbenkian de Ciência, Oeiras, Portugal.
Mol Biol Evol. 2021 Jul 29;38(8):3220-3234. doi: 10.1093/molbev/msab093.
Antibiotic resistance often generates defects in bacterial growth called fitness cost. Understanding the causes of this cost is of paramount importance, as it is one of the main determinants of the prevalence of resistances upon reducing antibiotics use. Here we show that the fitness costs of antibiotic resistance mutations that affect transcription and translation in Escherichia coli strongly correlate with DNA breaks, which are generated via transcription-translation uncoupling, increased formation of RNA-DNA hybrids (R-loops), and elevated replication-transcription conflicts. We also demonstrated that the mechanisms generating DNA breaks are repeatedly targeted by compensatory evolution, and that DNA breaks and the cost of resistance can be increased by targeting the RNase HI, which specifically degrades R-loops. We further show that the DNA damage and thus the fitness cost caused by lack of RNase HI function drive resistant clones to extinction in populations with high initial frequency of resistance, both in laboratory conditions and in a mouse model of gut colonization. Thus, RNase HI provides a target specific against resistant bacteria, which we validate using a repurposed drug. In summary, we revealed key mechanisms underlying the fitness cost of antibiotic resistance mutations that can be exploited to specifically eliminate resistant bacteria.
抗生素耐药性通常会导致细菌生长缺陷，称为适应性成本。了解这种成本的原因至关重要，因为它是减少抗生素使用后耐药性流行的主要决定因素之一。在这里，我们表明，影响大肠杆菌转录和翻译的抗生素耐药性突变的适应性成本与通过转录-翻译解偶联、增加 RNA-DNA 杂交（R 环）形成以及升高的复制-转录冲突而产生的 DNA 断裂强烈相关。我们还证明了产生 DNA 断裂的机制会被补偿性进化反复靶向，并且通过靶向专门降解 R 环的核糖核酸酶 HI，可以增加 DNA 断裂和耐药性的成本。我们进一步表明，缺乏核糖核酸酶 HI 功能引起的 DNA 损伤和因此导致的适应性成本会导致具有高初始耐药性频率的群体中的耐药克隆灭绝，无论是在实验室条件下还是在肠道定植的小鼠模型中。因此，核糖核酸酶 HI 提供了针对耐药细菌的特异性靶点，我们使用重新利用的药物对此进行了验证。总之，我们揭示了抗生素耐药性突变的适应性成本的关键机制，这些机制可以被利用来专门消除耐药细菌。
