Nguyen Taylor H, Wang Benjamin X, Diaz Oscar R, Rajendram Manohary, McKenna Joy A, Butler Daniel S C, Hokamp Karsten, Hinton Jay C D, Monack Denise M, Huang Kerwyn Casey
Department of Bioengineering, Stanford University, Stanford, CA, USA.
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
Nat Microbiol. 2025 Apr;10(4):1006-1023. doi: 10.1038/s41564-025-01953-5. Epub 2025 Apr 2.
Salmonella enterica serovar Typhimurium must adapt to rapid environmental shifts, including those encountered upon entry and during replication to survive within macrophages during pathogenesis. Despite extensive RNA-seq-based investigations, questions remain regarding the range, timing and magnitude of response dynamics. Here we constructed a comprehensive GFP-reporter strain library representing 2,901 computationally identified Salmonella promoter regions to study time-resolved Salmonella transcriptional responses. Promoter activity was measured during in vitro growth and during intracellular infection of RAW 264.7 macrophages. Using bulk measurements and single-cell imaging, we uncovered condition-specific transcriptional regulation and population-level heterogeneity in SPI2-related promoter activity. We also discovered previously unidentified transcriptional activity from 234 promoters. These analyses revealed metabolic shifts including requirements for mntS expression to support manganese homeostasis and expression of Entner-Doudoroff pathway-associated genes to support growth within macrophages. Our library and datasets, made available through the online tool SalComKinetics, provide resources for systems-level interrogation of Salmonella transcriptional dynamics.
肠炎沙门氏菌鼠伤寒血清型必须适应快速的环境变化，包括在发病过程中进入巨噬细胞以及在巨噬细胞内复制期间所遇到的环境变化，才能存活。尽管基于RNA测序进行了广泛的研究，但关于反应动力学的范围、时间和幅度仍存在问题。在这里，我们构建了一个包含2901个经计算鉴定的沙门氏菌启动子区域的综合绿色荧光蛋白报告菌株文库，以研究时间分辨的沙门氏菌转录反应。在体外生长以及RAW 264.7巨噬细胞的细胞内感染过程中测量启动子活性。通过大量测量和单细胞成像，我们发现了SPI2相关启动子活性中条件特异性的转录调控和群体水平的异质性。我们还发现了234个启动子以前未被识别的转录活性。这些分析揭示了代谢变化，包括支持锰稳态所需的mntS表达以及支持巨噬细胞内生长的Entner-Doudoroff途径相关基因的表达。我们通过在线工具SalComKinetics提供的文库和数据集为沙门氏菌转录动力学的系统水平研究提供了资源。
