SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom.
Centre for Synthetic and Systems Biology, Edinburgh, United Kingdom.
Antimicrob Agents Chemother. 2020 Aug 20;64(9). doi: 10.1128/AAC.02487-19.
Fluoroquinolones, antibiotics that cause DNA damage by inhibiting DNA topoisomerases, are clinically important, but their mechanism of action is not yet fully understood. In particular, the dynamical response of bacterial cells to fluoroquinolone exposure has hardly been investigated, although the SOS response, triggered by DNA damage, is often thought to play a key role. Here, we investigated the growth inhibition of the bacterium by the fluoroquinolone ciprofloxacin at low concentrations. We measured the long-term and short-term dynamical response of the growth rate and DNA production rate to ciprofloxacin at both the population and single-cell levels. We show that, despite the molecular complexity of DNA metabolism, a simple roadblock-and-kill model focusing on replication fork blockage and DNA damage by ciprofloxacin-poisoned DNA topoisomerase II (gyrase) quantitatively reproduces long-term growth rates in the presence of ciprofloxacin. The model also predicts dynamical changes in the DNA production rate in wild-type and in a recombination-deficient mutant following a step-up of ciprofloxacin. Our work highlights that bacterial cells show a delayed growth rate response following fluoroquinolone exposure. Most importantly, our model explains why the response is delayed: it takes many doubling times to fragment the DNA sufficiently to inhibit gene expression. We also show that the dynamical response is controlled by the timescale of DNA replication and gyrase binding/unbinding to the DNA rather than by the SOS response, challenging the accepted view. Our work highlights the importance of including detailed biophysical processes in biochemical-systems models to quantitatively predict the bacterial response to antibiotics.
氟喹诺酮类药物是通过抑制 DNA 拓扑异构酶来导致 DNA 损伤的抗生素，在临床上具有重要意义，但它们的作用机制尚未完全阐明。特别是，尽管 SOS 反应（由 DNA 损伤引发）通常被认为起着关键作用，但细菌细胞对氟喹诺酮类药物暴露的动态反应几乎没有被研究过。在这里，我们研究了氟喹诺酮类药物环丙沙星在低浓度下对细菌的生长抑制作用。我们在群体和单细胞水平上测量了细菌对环丙沙星的生长率和 DNA 产生率的长期和短期动态响应。我们表明，尽管 DNA 代谢的分子复杂性很高，但一个简单的路障-杀伤模型，专注于复制叉阻塞和被环丙沙星毒害的 DNA 拓扑异构酶 II（回旋酶）的 DNA 损伤，能够定量再现环丙沙星存在时的长期生长速率。该模型还预测了野生型和重组缺陷突变体在环丙沙星浓度上升后 DNA 产生率的动态变化。我们的工作强调了细菌细胞在氟喹诺酮类药物暴露后会表现出延迟的生长速率响应。最重要的是，我们的模型解释了为什么这种反应会延迟：需要多个倍增时间才能使 DNA 片段化到足以抑制基因表达的程度。我们还表明，动态响应由 DNA 复制的时间尺度和回旋酶与 DNA 的结合/解结合控制，而不是由 SOS 反应控制，这挑战了公认的观点。我们的工作强调了在生化系统模型中包含详细的生物物理过程对于定量预测细菌对抗生素的反应的重要性。
