Temporal Hierarchy of Gene Expression Mediated by Transcription Factor Binding Affinity and Activation Dynamics
Temporal Hierarchy of Gene Expression Mediated by Transcription Factor Binding Affinity and Activation Dynamics
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DOI：
10.1128/mbio.00686-15
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发表时间：
2015-05-01
期刊：
影响因子：
6.4
通讯作者：
Stock, Ann M.
中科院分区：
文献类型：
--
作者：
Gao, Rong;Stock, Ann M.
了解细胞对环境刺激的反应不仅需要了解特定的调控成分，还需要对调控事件的幅度和时间进行定量表征。双组分系统是主要的原核信号传导方案之一，也是信号动力学定量建模和研究广泛关注的焦点。在这里，我们报告了 PhoB 双组分反应调节器 (RR) 与目标启动子的结合亲和力如何影响 PhoB 调节基因的表达水平和时间。信息内容通常用于评估转录因子 (TF) 结合位点的保守程度。我们表明，增加设计的 phoA 启动子中 PhoB 结合位点的信息含量会增加结合亲和力，并且磷酸化 PhoB（PhoB 类似于 P）的结合亲和力和浓度共同决定 phoA 启动子变体的表达水平和时间。对于具有不同启动子结构的各种 PhoB 调节的启动子，表达水平似乎与 TF 结合亲和力不相关，这与直觉和过于简单化的假设相反，即对 TF 具有较高亲和力的启动子往往具有较高的表达水平。然而，PhoB 调控基因的核心组的表达时间与类似于 P 的 PhoB 与各个启动子的结合亲和力密切相关，并且基因表达的时间层次似乎与磷酸盐饥饿反应期间基因产物的功能相关。调节 TF 结合位点的信息内容和结合亲和力可能是 RR 调节基因表达谱的时间编程的常见策略。 重要性 单个 TF 通常会协调多个基因的表达以响应环境刺激。目前尚不清楚调节子内不同的 TF 结合位点如何决定表达谱。我们对大肠杆菌 PhoB 的研究表明，PhoB 调节基因的表达水平受到复杂的控制，并且不遵循与类似于 P 的 PhoB 与单个启动子的结合亲和力的简单相关性。然而，表达时间与 PhoB 结合亲和力和基因功能相关。参与磷直接吸收的基因含有高亲和力位点，并且比参与磷清除的基因转录更早。这说明了时间编程基因表达的复杂机制，即使对于非发育途径也是如此。
Understanding cellular responses to environmental stimuli requires not only the knowledge of specific regulatory components but also the quantitative characterization of the magnitude and timing of regulatory events. The two-component system is one of the major prokaryotic signaling schemes and is the focus of extensive interest in quantitative modeling and investigation of signaling dynamics. Here we report how the binding affinity of the PhoB two-component response regulator (RR) to target promoters impacts the level and timing of expression of PhoB-regulated genes. Information content has often been used to assess the degree of conservation for transcription factor (TF)-binding sites. We show that increasing the information content of PhoB-binding sites in designed phoA promoters increased the binding affinity and that the binding affinity and concentration of phosphorylated PhoB (PhoB similar to P) together dictate the level and timing of expression of phoA promoter variants. For various PhoB-regulated promoters with distinct promoter architectures, expression levels appear not to be correlated with TF-binding affinities, in contrast to the intuitive and oversimplified assumption that promoters with higher affinity for a TF tend to have higher expression levels. However, the expression timing of the core set of PhoB-regulated genes correlates well with the binding affinity of PhoB similar to P to individual promoters and the temporal hierarchy of gene expression appears to be related to the function of gene products during the phosphate starvation response. Modulation of the information content and binding affinity of TF-binding sites may be a common strategy for temporal programming of the expression profile of RR-regulated genes.IMPORTANCE A single TF often orchestrates the expression of multiple genes in response to environmental stimuli. It is not clear how different TF-binding sites within the regulon dictate the expression profile. Our studies of Escherichia coli PhoB, a response regulator that controls expression of a core set of phosphate assimilation genes in response to phosphate starvation, showed that expression levels of PhoB-regulated genes are under sophisticated control and do not follow a simple correlation with the binding affinity of PhoB similar to P to individual promoters. However, the expression timing correlates with the PhoB-binding affinity and gene functions. Genes involved in direct Pi uptake contain high-affinity sites and are transcribed earlier than genes involved in phosphorus scavenging. This illustrates an elaborate mechanism of temporally programmed gene expression, even for nondevelopmental pathways.