Profiling Salmonella transcriptional dynamics during macrophage infection using a comprehensive reporter library

IF 20.5 1区 生物学 Q1 MICROBIOLOGY
Taylor H. Nguyen, Benjamin X. Wang, Oscar R. Diaz, Manohary Rajendram, Joy A. McKenna, Daniel S. C. Butler, Karsten Hokamp, Jay C. D. Hinton, Denise M. Monack, Kerwyn Casey Huang
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Abstract

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. Construction and analysis of 2,901 promoter–GFP fusions in Salmonella reveal dynamic, heterogeneous transcriptional activity, including roles for manganese homeostasis and Entner–Doudoroff carbon metabolism in promoting intramacrophage growth and survival of bacteria.

Abstract Image

Abstract Image

利用综合报告文库分析巨噬细胞感染期间沙门氏菌转录动力学
肠炎沙门氏菌血清型鼠伤寒沙门氏菌必须适应快速的环境变化,包括在进入和复制过程中遇到的环境变化,以便在发病过程中在巨噬细胞内存活。尽管广泛的基于rna序列的研究,关于反应动力学的范围、时间和大小的问题仍然存在。在这里,我们构建了一个综合的gfp报告菌株文库,包含2,901个计算鉴定的沙门氏菌启动子区域,以研究时间分辨沙门氏菌的转录反应。在体外生长和细胞内感染RAW 264.7巨噬细胞期间测定启动子活性。通过大量测量和单细胞成像,我们发现了spi2相关启动子活性的条件特异性转录调控和群体水平异质性。我们还从234个启动子中发现了以前未确定的转录活性。这些分析揭示了代谢变化,包括支持锰稳态的mntS表达需求和支持巨噬细胞生长的enterner - doudoroff通路相关基因的表达需求。我们的数据库和数据集,通过在线工具SalComKinetics提供,为沙门氏菌转录动力学的系统级查询提供资源。
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来源期刊
Nature Microbiology
Nature Microbiology Immunology and Microbiology-Microbiology
CiteScore
44.40
自引率
1.10%
发文量
226
期刊介绍: Nature Microbiology aims to cover a comprehensive range of topics related to microorganisms. This includes: Evolution: The journal is interested in exploring the evolutionary aspects of microorganisms. This may include research on their genetic diversity, adaptation, and speciation over time. Physiology and cell biology: Nature Microbiology seeks to understand the functions and characteristics of microorganisms at the cellular and physiological levels. This may involve studying their metabolism, growth patterns, and cellular processes. Interactions: The journal focuses on the interactions microorganisms have with each other, as well as their interactions with hosts or the environment. This encompasses investigations into microbial communities, symbiotic relationships, and microbial responses to different environments. Societal significance: Nature Microbiology recognizes the societal impact of microorganisms and welcomes studies that explore their practical applications. This may include research on microbial diseases, biotechnology, or environmental remediation. In summary, Nature Microbiology is interested in research related to the evolution, physiology and cell biology of microorganisms, their interactions, and their societal relevance.
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