Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
Nucleic Acids Res. 2023 Feb 22;51(3):1208-1228. doi: 10.1093/nar/gkac1223.
Bacterial persisters are rare phenotypic variants that are suspected to be culprits of recurrent infections. Fluoroquinolones (FQs) are a class of antibiotics that facilitate bacterial killing by stabilizing bacterial type II topoisomerases when they are in a complex with cleaved DNA. In Escherichia coli, DNA gyrase is the primary FQ target, and previous work has demonstrated that persisters are not spared from FQ-induced DNA damage. Since DNA gyrase cleavage sites (GCSs) largely govern the sites of DNA damage from FQ treatment, we hypothesized that GCS characteristics (e.g. number, strength, location) may influence persistence. To test this hypothesis, we measured genome-wide GCS distributions after treatment with a panel of FQs in stationary-phase cultures. We found drug-specific effects on the GCS distribution and discovered a strong negative correlation between the genomic cleavage strength and FQ persister levels. Further experiments and analyses suggested that persistence was unlikely to be governed by cleavage to individual sites, but rather survival was a function of the genomic GCS distribution. Together, these findings demonstrate FQ-specific differences in GCS distribution that correlate with persister levels and suggest that FQs that better stabilize DNA gyrase in cleaved complexes with DNA will lead to lower levels of persistence.
细菌持久体是罕见的表型变异体，被怀疑是反复感染的罪魁祸首。氟喹诺酮类（FQs）是一类抗生素，通过稳定与断裂 DNA 结合的细菌 II 型拓扑异构酶，促进细菌的杀伤。在大肠杆菌中，DNA 回旋酶是 FQ 的主要靶标，先前的工作表明，持久体并没有免受 FQ 诱导的 DNA 损伤的影响。由于 DNA 回旋酶切割位点（GCS）在很大程度上决定了 FQ 处理后的 DNA 损伤部位，因此我们假设 GCS 特征（例如数量、强度、位置）可能会影响持久性。为了验证这一假设，我们在静止期培养物中用一组 FQs 处理后测量了全基因组 GCS 分布。我们发现药物对 GCS 分布有特定的影响，并发现基因组切割强度与 FQ 持久体水平之间存在强烈的负相关。进一步的实验和分析表明，持久性不太可能由单个位点的切割来控制，而是生存是基因组 GCS 分布的函数。总之，这些发现表明 FQ 在 GCS 分布上存在特异性差异，与持久体水平相关，并表明与 DNA 结合的 DNA 回旋酶更好稳定的 FQ 将导致更低水平的持久性。
