Binsfeld Christoph, Olayo-Alarcon Roberto, Pérez Jiménez Lucía, Wartel Morgane, Stadler Mara, Mateus André, Müller Christian, Brochado Ana Rita
Department of Microbiology, Biocenter, University of Würzburg, Würzburg, Germany.
Department of Statistics, Ludwig-Maximilians-Universität München, München, Germany.
PLoS Biol. 2025 Jul 22;23(7):e3003260. doi: 10.1371/journal.pbio.3003260. eCollection 2025 Jul.
In Gram-negative bacteria, the uptake and export of a wide range of molecules, including antibiotics, is facilitated by porins and efflux pumps. Because of their role in regulating small molecule permeability of the outer and inner membrane, these transport machineries are tightly regulated at the transcriptional and post-transcriptional levels. However, regulation of transport by external chemical cues remains poorly understood. Here we investigated transcriptional regulation of three prominent transporter genes in Escherichia coli across 94 defined chemical cues, and simultaneously mapped the contributions of the key regulators MarA, SoxS and Rob to promoter activity. One third of all tested compounds triggered transcriptional changes, the majority of which were previously unknown. Importantly, we exposed main drivers of transport control in E. coli, e.g., bacteriostatic but not bactericidal antibiotics trigger the expression of efflux pumps, and Rob contributes to ~1/3 of all measured transcriptional changes, thereby emerging as a more prominent regulator of transport than previously thought. We showcase the potential of our resource by elucidating the molecular mechanism of antibiotic antagonisms with widely consumed caffeine in E. coli. Altogether, our analysis provides a quantitative overview of how different regulators orchestrate the transcriptional response of major transport determinants to environmental chemical cues.
在革兰氏阴性菌中，包括抗生素在内的多种分子的摄取和输出由孔蛋白和外排泵介导。由于它们在调节外膜和内膜小分子通透性方面的作用，这些转运机制在转录和转录后水平受到严格调控。然而，外界化学信号对转运的调控仍知之甚少。在此，我们研究了大肠杆菌中三个重要转运蛋白基因在94种特定化学信号下的转录调控，并同时绘制了关键调控因子MarA、SoxS和Rob对启动子活性的贡献。所有测试化合物中有三分之一引发了转录变化，其中大多数变化此前未知。重要的是，我们揭示了大肠杆菌中转运控制的主要驱动因素，例如抑菌而非杀菌抗生素会触发外排泵的表达，并且Rob促成了所有测量到的转录变化的约三分之一，从而成为比之前认为的更为重要的转运调控因子。我们通过阐明大肠杆菌中广泛使用的咖啡因对抗生素拮抗作用的分子机制，展示了我们这一资源的潜力。总之，我们的分析提供了一个定量概述，说明了不同调控因子如何协调主要转运决定因素对环境化学信号的转录反应。
