Transcriptome signature of E. coli under a prolonged starvation environment
Transcriptome signature of E. coli under a prolonged starvation environment
复制标题
长期饥饿环境下大肠杆菌的转录组特征
DOI：
10.1101/2020.05.11.085241
复制
发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Saburo Tsuru
中科院分区：
文献类型：
--
作者：
Sotaro Takano;H. Takahashi;Yoshie Yama;Ryo Miyazaki;Saburo Tsuru
研究背景“非生长型”微生物是自然界中的一种优势生命形式，可利用的营养物质和资源极其有限。然而，与生长细胞相比，微生物抵抗营养缺乏的方式的知识仍然是基本的。在实验室培养中，大肠杆菌可以在饥饿条件下存活数年，称为长期稳定期（LSP），其中一小部分细胞通过回收从饥饿的非活细胞释放的资源而存活，并构成理解长期饥饿下生存机制的模型系统。虽然LSP中的活细胞适应长期饥饿的生理学非常感兴趣，但它们的全基因组响应尚未完全理解。结果为了了解LSP环境中活细胞的生理状态，我们分析了暴露于LSP培养上清液的细胞的转录谱。我们发现，高表达的转运蛋白基因和低表达的生物合成基因的LSP上清液中的细胞相比，生长中的细胞，表现出类似的反应，从指数生长期进入稳定期的细胞的主要反应。我们还揭示了一些特定的转录反应在LSP上清，如更高的表达的应力响应基因和更低的表达的抑制相关基因，相比其他非生长条件。这表明LSP中的细胞在饥饿条件下的细胞存活和维持功能方面是高效的。我们还发现了LSP中种群密度依赖的基因表达谱，这也为了解细菌种群的生存机制提供了信息。结论我们目前对E.大肠杆菌细胞提供了对长期饥饿环境的全基因组响应的概述。我们在短期和长期稳定期培养物之间的主要转录变化中检测到共同和独特的反应，这可以为了解饥饿环境中生存能力的可能分子机制提供线索。
Background “Non-growing” is a dominant life form of microorganisms in nature, where available nutrients and resources are extremely limited. However, the knowledge of the manner in which microorganisms resist nutrient deficiency is still rudimentary compared to those of the growing cells. In laboratory culture, Escherichia coli can survive for several years under starvation, denoted as long-term stationary phase (LSP), where a small fraction of the cells survive by recycling resources released from the starved nonviable cells and constitute a model system for understanding survival mechanisms under long-term starvation. Although the physiology by which viable cells in LSP adapt to long-term starvation is of great interest, their genome-wide response has not yet been fully understood. Results To understand the physiological state of viable cells in the LSP environment, we analyzed the transcriptional profiles of cells exposed to the supernatant of LSP culture. We found that high expression of transporter genes and low expression of biosynthesis genes are the primary responses of the cells in the LSP supernatant compared to growing cells, which display similar responses to cells entering the stationary phase from the exponential growth phase. We also revealed some specific transcriptional responses in the LSP supernatant, such as higher expression of stress-response genes and lower expression of translation-related genes, compared to other non-growing conditions. This suggests that cells in LSP are highly efficient in terms of cellular survival and maintenance functions under starvation conditions. We also found population-density-dependent gene expression profiles in LSP, which are also informative to understand the survival mechanism of bacterial population. Conclusion Our current comprehensive analysis of the transcriptome of E. coli cells provides an overview of the genome-wide response to the long-term starvation environment. We detected both common and distinctive responses in the primary transcriptional changes between the short- and long-term stationary phase cultures, which could provide clues to understand the possible molecular mechanisms underlying survivability in the starved environment.
影响因子：
56.9
作者：
Gaal, T;Bartlett, MS;Gourse, RL
通讯作者：
Gourse, RL
DOI：
10.1073/pnas.91.6.2191
发表时间：
1994-03-15
影响因子：
11.1
作者：
WEINER, L;MODEL, P
通讯作者：
MODEL, P