The Parameter-Fitness Landscape of lexA Autoregulation in Escherichia coli.
The Parameter-Fitness Landscape of lexA Autoregulation in Escherichia coli.
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DOI：
10.1128/msphere.00718-20
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发表时间：
2020-08-19
期刊：
影响因子：
4.8
通讯作者：
Culyba, Matthew J
中科院分区：
文献类型：
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作者：
Kozuch, Beverley C;Shaffer, Marla G;Culyba, Matthew J
反馈机制是控制生理反应的基础。基因调控中的一个重要例子，称为负性自动调节（NAR），发生在转录因子（TF）通过转录抑制抑制其自身产生时。这使得能够更快速地稳态控制基因表达。NAR回路的进化大概是为了限制无偿基因表达的适应性成本。NAR的关键生化反应可以使用启动子活性的数学模型进行参数化;然而，NAR的这种模型主要是在与TF的靶基因断开的合成NAR回路的背景下进行研究的。因此，目前还不清楚如何约束NAR参数是在一个原生电路的情况下，TF靶基因可以对细胞的健身效果。为了量化这些限制，我们创建了一个面板的大肠杆菌菌株与不同的lexA-NAR电路参数，并分析SOS响应函数和细菌的健身效果。使用NAR的数学模型，这些实验数据被用来计算NAR参数值，并推导出参数适应度景观。在没有反馈的情况下，由于高莱克萨浓度和较慢的SOS "开启"动力学，DNA损伤的存活率降低。然而，我们表明，即使在没有DNA损伤的情况下，莱克萨启动子也足够强，以至于在没有反馈的情况下，高水平的莱克萨表达会导致细胞的适应性成本。相反，超反馈可以模拟莱克萨缺失，这也是昂贵的。这项工作阐明了lexA-NAR参数值能够平衡细胞的快速SOS响应激活的要求，限制其toxicity.IMPORTANCE反馈机制是至关重要的控制生理反应。在基因调控中，一个重要的例子，称为负性自动调节（NAR），发生在转录因子（TF）抑制其自身产生时。NAR在生命树中很常见，能够快速稳态控制基因表达。NAR的行为可以根据其核心生化参数来描述，但这些参数如何受到进化的限制尚不清楚。在这里，我们描述了一个模型的遗传网络控制的NAR电路内的细菌大肠杆菌和阐明这些限制，通过实验改变一个关键参数，并测量其对电路的响应和健身的影响。这种分析产生了一个代表遗传网络的参数适应度景观，提供了一个窗口，了解什么样的基因环境条件有利于这种调控策略的进化。
Feedback mechanisms are fundamental to the control of physiological responses. One important example in gene regulation, termed negative autoregulation (NAR), occurs when a transcription factor (TF) inhibits its own production through transcriptional repression. This enables more-rapid homeostatic control of gene expression. NAR circuits presumably evolve to limit the fitness costs of gratuitous gene expression. The key biochemical reactions of NAR can be parameterized using a mathematical model of promoter activity; however, this model of NAR has been studied mostly in the context of synthetic NAR circuits that are disconnected from the target genes of the TFs. Thus, it remains unclear how constrained NAR parameters are in a native circuit context, where the TF target genes can have fitness effects on the cell. To quantify these constraints, we created a panel of Escherichia coli strains with different lexA-NAR circuit parameters and analyzed the effect on SOS response function and bacterial fitness. Using a mathematical model for NAR, these experimental data were used to calculate NAR parameter values and derive a parameter-fitness landscape. Without feedback, survival of DNA damage was decreased due to high LexA concentrations and slower SOS "turn-on" kinetics. However, we show that, even in the absence of DNA damage, the lexA promoter is strong enough that, without feedback, high levels of lexA expression result in a fitness cost to the cell. Conversely, hyperfeedback can mimic lexA deletion, which is also costly. This work elucidates the lexA-NAR parameter values capable of balancing the cell's requirement for rapid SOS response activation with limiting its toxicity.IMPORTANCE Feedback mechanisms are critical to control physiological responses. In gene regulation, one important example, termed negative autoregulation (NAR), occurs when a transcription factor (TF) inhibits its own production. NAR is common across the tree of life, enabling rapid homeostatic control of gene expression. NAR behavior can be described in accordance with its core biochemical parameters, but how constrained these parameters are by evolution is unclear. Here, we describe a model genetic network controlled by an NAR circuit within the bacterium Escherichia coli and elucidate these constraints by experimentally changing a key parameter and measuring its effect on circuit response and fitness. This analysis yielded a parameter-fitness landscape representing the genetic network, providing a window into what gene-environment conditions favor evolution of this regulatory strategy.