Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival
Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival
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DOI：
10.1128/msystems.00364-20
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发表时间：
2020-07-01
期刊：
影响因子：
6.4
通讯作者：
Finkel, Steven E.
中科院分区：
文献类型：
--
作者：
Kram, Karin E.;Henderson, Autumn L.;Finkel, Steven E.
微生物生活在复杂和不断变化的环境中，但很难在实验室中复制这一点。多年来，大肠杆菌一直被用作实验进化研究的模式生物；具体来说，我们和其他人已经使用它来研究复杂环境下的进化，通过将细胞培养到富介质中的长期固定期（LTSP）。在LTSP中，细胞经历各种压力和变化的条件。虽然我们假设这个实验系统比其他一些实验室条件更类似于自然环境，但我们还不知道细胞如何从生物化学或生理上对这种环境做出反应。在这项研究中，我们开始通过表征细胞在LTSP期间的转录组来揭示细胞对这种环境的反应。我们发现LTSP中的细胞有一个独特的转录程序，几个基因在这个阶段被上调或下调。此外，我们确定了两个基因，cspB和cspI，它们在LTSP中表达最高，尽管这些基因主要被认为对冷休克有反应。通过与野生型细胞竞争缺乏这些基因的细胞，我们发现这些基因对LTSP期间的存活也很重要。这些数据可以帮助鉴定在这种复杂环境中可能在生存中发挥作用的基因产物，并导致鉴定蛋白质的新功能。实验进化研究已经阐明了进化过程，但通常是在化学定义明确和/或恒定的环境中。利用复杂的环境来开始理解进化如何在自然环境中发生是很重要的，比如土壤或宿主内部。然而，描述细胞在这些复杂环境中所经历的压力是具有挑战性的。解决这一问题的一种方法是确定细胞如何在生物化学上适应异质环境。在这项研究中，我们开始通过分析细胞在动态复杂环境中的转录组来表征生理变化。通过描述细胞在长期固定期、异质性和压力环境中的转录谱，我们可以开始了解细胞在生理和生化上如何对实验室环境做出反应，以及如何将其与更自然的条件进行比较。
Microbes live in complex and constantly changing environments, but it is difficult to replicate this in the laboratory. Escherichia coli has been used as a model organism in experimental evolution studies for years; specifically, we and others have used it to study evolution in complex environments by incubating the cells into long-term stationary phase (LTSP) in rich media. In LTSP, cells experience a variety of stresses and changing conditions. While we have hypothesized that this experimental system is more similar to natural environments than some other lab conditions, we do not yet know how cells respond to this environment biochemically or physiologically. In this study, we began to unravel the cells' responses to this environment by characterizing the transcriptome of cells during LTSP. We found that cells in LTSP have a unique transcriptional program and that several genes are uniquely upregulated or downregulated in this phase. Further, we identified two genes, cspB and cspI, which are most highly expressed in LTSP, even though these genes are primarily known to respond to cold shock. By competing cells lacking these genes with wild-type cells, we show that these genes are also important for survival during LTSP. These data can help identify gene products that may play a role in survival in this complex environment and lead to identification of novel functions of proteins.IMPORTANCE Experimental evolution studies have elucidated evolutionary processes, but usually in chemically well-defined and/or constant environments. Using complex environments is important to begin to understand how evolution may occur in natural environments, such as soils or within a host. However, characterizing the stresses that cells experience in these complex environments can be challenging. One way to approach this is by determining how cells biochemically acclimate to heterogenous environments. In this study, we began to characterize physiological changes by analyzing the transcriptome of cells in a dynamic complex environment. By characterizing the transcriptional profile of cells in long-term stationary phase, a heterogenous and stressful environment, we can begin to understand how cells physiologically and biochemically react to the laboratory environment, and how this compares to more-natural conditions.