Evolutionary tuning of protein expression levels of a positively autoregulated two-component system.
Evolutionary tuning of protein expression levels of a positively autoregulated two-component system.
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DOI：
10.1371/journal.pgen.1003927
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发表时间：
2013-10
期刊：
影响因子：
4.5
通讯作者：
Stock AM
中科院分区：
文献类型：
--
作者：
Gao R;Stock AM
细胞适应依赖于制定适当的调控方案，以准确控制基因表达水平，以响应环境提示。由于成本增加或收益不足，过度表达或表达不足会导致细胞适合性降低。正向自动调节是一种常见的调节机制，它控制蛋白质的表达水平，并在不同的信号系统中产生基本特征，但它在细胞适应性中的作用却鲜为人知。在很大程度上还不清楚在特定的细胞外条件下，有多少蛋白质表达是最适合细胞健康的，以及动态环境如何塑造调控方案以达到适当的表达水平。在这里，我们研究了细胞适应性和输出响应与大肠杆菌PHOB/PHOR双组分系统(TCS)蛋白质表达水平的相关性。作为对磷(PI)耗竭的响应，PHOB/PHOR系统激活与磷同化相关的基因以及编码自身的基因，类似于许多其他正向自我调节的TCS。我们开发了一种在连续培养中的细菌竞争试验，并发现不同的PI条件对最佳细胞适应性的蛋白质表达水平的要求是相互冲突的。PI充足条件有利于PHOB/PHOR水平较低的细胞，而PI耗竭条件则选择PHOB/PHOR水平较高的细胞。这两个水平分别与野生型细胞在PI充足和耗尽条件下通过正自动调节获得的Phob/Phor浓度相匹配。适合度最优与野生型表达水平相关，超过这一水平，磷酸化输出达到饱和，因此进一步增加表达可能不会提供额外的好处。实验室进化实验进一步表明，具有非理想蛋白质水平的细胞可以通过不同的突变策略进化到最佳水平。我们的结果表明，TCS的自然蛋白质表达水平和反馈调节机制是为了匹配系统的磷酸化输出，这是由TCS蛋白质的内在活性决定的。不同的蛋白质在不同的水平上表达，这些蛋白质可能已经进化成在特定环境条件下的最佳适应性。此外，细胞调节蛋白质的表达水平，以响应环境的变化。对于其益处并不立即与其表达水平成正比的信号蛋白，人们对其表达水平是否优化以及蛋白质表达水平如何与其调节的输出反应相关的了解较少。我们开发了一种连续培养竞争试验来检测不同表达水平的大肠杆菌phb/phor系统的细胞适合性。PHOB/PHOR系统是广泛分布的原核生物二组分信号转导机制的原型，它诱导磷(PI)限制条件下磷同化相关基因的表达。野生型细胞在不同的PI条件下表达不同水平的PHOB/PHOR；这些水平在不同的条件下提供接近最大的适合度。在PI耗竭的条件下，Phob调节的基因表达对生存是重要的，最佳表达水平似乎与Phob/Phor系统的磷酸化输出相关。用表达不利水平的蛋白质挑战细胞会导致各种突变，这些突变都将蛋白质表达转移到最佳水平。我们的结果表明，PHOB/PHOR系统的自我调节方案和表达水平是进化而来的，以提供最佳适应性。
Cellular adaptation relies on the development of proper regulatory schemes for accurate control of gene expression levels in response to environmental cues. Over- or under-expression can lead to diminished cell fitness due to increased costs or insufficient benefits. Positive autoregulation is a common regulatory scheme that controls protein expression levels and gives rise to essential features in diverse signaling systems, yet its roles in cell fitness are less understood. It remains largely unknown how much protein expression is ‘appropriate’ for optimal cell fitness under specific extracellular conditions and how the dynamic environment shapes the regulatory scheme to reach appropriate expression levels. Here, we investigate the correlation of cell fitness and output response with protein expression levels of the E. coli PhoB/PhoR two-component system (TCS). In response to phosphate (Pi)-depletion, the PhoB/PhoR system activates genes involved in phosphorus assimilation as well as genes encoding themselves, similarly to many other positively autoregulated TCSs. We developed a bacteria competition assay in continuous cultures and discovered that different Pi conditions have conflicting requirements of protein expression levels for optimal cell fitness. Pi-replete conditions favored cells with low levels of PhoB/PhoR while Pi-deplete conditions selected for cells with high levels of PhoB/PhoR. These two levels matched PhoB/PhoR concentrations achieved via positive autoregulation in wild-type cells under Pi-replete and -deplete conditions, respectively. The fitness optimum correlates with the wild-type expression level, above which the phosphorylation output saturates, thus further increase in expression presumably provides no additional benefits. Laboratory evolution experiments further indicate that cells with non-ideal protein levels can evolve toward the optimal levels with diverse mutational strategies. Our results suggest that the natural protein expression levels and feedback regulatory schemes of TCSs are evolved to match the phosphorylation output of the system, which is determined by intrinsic activities of TCS proteins. Different proteins are expressed at different levels that may have evolved for optimal fitness under specific environmental conditions. Additionally, cells regulate protein expression levels in response to environmental changes. For signaling proteins whose benefits are not immediately proportional to their expression levels, it is less understood whether expression levels are optimized and how protein expression levels correlate with the output responses they regulate. We developed a continuous culture competition assay to examine cell fitness at different expression levels of the E. coli PhoB/PhoR system. The PhoB/PhoR system, which induces expression of genes for phosphate assimilation under phosphate (Pi)-limited conditions, represents an archetype of the widely distributed prokaryotic two-component signal transduction scheme. Wild-type cells express different levels of PhoB/PhoR under different Pi conditions; these levels provide near maximal fitness under respective conditions. Under Pi-deplete conditions where PhoB-regulated gene expression is important for survival, the optimal expression level appears to correlate with the phosphorylation output of the PhoB/PhoR system. Challenging cells with expression of unfavorable levels of proteins led to diverse mutations that all shifted protein expression towards optimal levels. Our results indicate that the autoregulatory scheme and expression levels of the PhoB/PhoR system are evolved to provide optimal fitness.
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影响因子：
64.8
作者：
Dekel, E;Alon, U
通讯作者：
Alon, U
影响因子：
56.9
作者：
Eames, Matt;Kortemme, Tanja
通讯作者：
Kortemme, Tanja
影响因子：
3.2
作者：
Haldimann, A;Daniels, LL;Wanner, BL
通讯作者：
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影响因子：
9.8
作者：
Levine JH;Fontes ME;Dworkin J;Elowitz MB
通讯作者：
Elowitz MB
DOI：
10.1073/pnas.120163297
发表时间：
2000-06-06
影响因子：
11.1
作者：
Datsenko, KA;Wanner, BL
通讯作者：
Wanner, BL