Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12.
Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12.
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大肠杆菌 K-12 对不同 RpoS 水平的全基因组转录反应。
DOI：
10.1128/jb.00755-16
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发表时间：
2017
影响因子：
3.2
通讯作者：
Stoebel,DanielM
中科院分区：
文献类型：
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作者：
Wong,GarrettT;Bonocora,RichardP;Schep,AliciaN;Beeler,SuzannahM;LeeFong,AnnaJ;Shull,LaurenM;Batachari,LakshmiE;Dillon,Moira;Evans,Ciaran;Becker,CarlaJ;Bush,EliotC;Hardin,Johanna;Wade,JosephT;Stoebel,DanielM
替代σ因子RpoS是大肠杆菌中许多应激反应的中心调节因子。功能性RpoS的水平取决于压力。这些不同浓度的RpoS对整体转录反应的影响仍不清楚。我们研究了RpoS浓度对富培养基中稳定期期间转录组的影响。我们发现在E.大肠杆菌基因组受RpoS调控，我们鉴定了许多RpoS转录的基因和启动子。我们观察到调节子中的基因对RpoS的三种不同类型的反应：表达随着RpoS水平的增加而线性变化的基因，表达随着仅产生少量RpoS而发生显着变化的基因（“敏感”基因），以及表达的基因随着少量RpoS的产生而变化很小（“不敏感”）。我们发现，核心启动子区域以外的序列决定了Rpos调控基因是敏感还是不敏感。此外，我们发现，敏感和不敏感的基因富集特定的功能类和RpoS的基因的敏感性对应于诱导细胞进入稳定期的时间。因此，启动子RpoS的敏感性是一种机制，以协调特定的细胞过程与生长阶段，也可能有助于由RpoS.IMPORTANCEThe sigma因子RpoS的压力反应的多样性是一个全球性的调节器，控制许多应力在大肠杆菌。不同的压力导致不同水平的RpoS生产，但这种变化的后果是未知的。我们描述了如何改变RpoS的水平并不影响所有的RpoS调控基因平等。这种变异的原因可能是结合基因启动子的转录因子的作用。我们发现，一个基因的RpoS水平的敏感性解释了表达的时间，因为细胞进入稳定期，并具有不同的RpoS敏感性的基因富集特定的功能组。因此，启动子对RpoS的敏感性是一种协调特定细胞过程响应应激的机制。
The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli. The level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in the E. coli genome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS (“sensitive” genes), and genes whose expression changes very little with the production of a little RpoS (“insensitive”). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS.IMPORTANCEThe sigma factor RpoS is a global regulator that controls the response to many stresses in Escherichia coli. Different stresses result in different levels of RpoS production, but the consequences of this variation are unknown. We describe how changing the level of RpoS does not influence all RpoS-regulated genes equally. The cause of this variation is likely the action of transcription factors that bind the promoters of the genes. We show that the sensitivity of a gene to RpoS levels explains the timing of expression as cells enter stationary phase and that genes with different RpoS sensitivities are enriched for specific functional groups. Thus, promoter sensitivity to RpoS is a mechanism that coordinates specific cellular processes in response to stresses.