Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli
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DOI：
10.1073/pnas.0807227105
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发表时间：
2008-12-09
影响因子：
11.1
通讯作者：
Palsson, Bernhard O.
中科院分区：
文献类型：
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作者：
Cho, Byung-Kwan;Barrett, Christian L.;Palsson, Bernhard O.
细菌形式调节中的广泛作用转录因子（TFS）。在这里，我们提出了一种四步方法，可以完全重建大肠杆菌K-12MG 1655中的亮氨酸反应蛋白（LRP）调节，从而调节氮代谢。步骤1包括在多个环境条件下获得LRP，RNA聚合酶和表达谱的高分辨率芯片数据。我们确定了138个独特且可重现的LRP结合区域，并在不同条件下对其结合状态进行了分类。在第二步中，对这些数据的分析揭示了单个ORF的6种不同的调节模式。在第三步中，我们使用调节ORF的功能分配来重建受相应基因产物影响的代谢产物周围的4种类型的调节网络基序。在第四步中，我们确定了亮氨酸作为信号分子如何改变特定代谢物的调节基序。出现的生理结构显示了不同氨基酸的调节基序落入氨基酸家族的传统分类中，从而阐明了LRP-Regulon的结构和生理功能。可以将相同的程序应用于其他广泛的TF，为细菌细胞中转录调节网络的完全自下而上的重建开辟了道路。
Broad-acting transcription factors (TFs) in bacteria form regulons. Here, we present a 4-step method to fully reconstruct the leucine-responsive protein (Lrp) regulon in Escherichia coli K-12MG 1655 that regulates nitrogen metabolism. Step 1 is composed of obtaining high-resolution ChIP-chip data for Lrp, the RNA polymerase and expression profiles under multiple environmental conditions. We identified 138 unique and reproducible Lrp-binding regions and classified their binding state under different conditions. In the second step, the analysis of these data revealed 6 distinct regulatory modes for individual ORFs. In the third step, we used the functional assignment of the regulated ORFs to reconstruct 4 types of regulatory network motifs around the metabolites that are affected by the corresponding gene products. In the fourth step, we determined how leucine, as a signaling molecule, shifts the regulatory motifs for particular metabolites. The physiological structure that emerges shows the regulatory motifs for different amino acid fall into the traditional classification of amino acid families, thus elucidating the structure and physiological functions of the Lrp-regulon. The same procedure can be applied to other broad-acting TFs, opening the way to full bottom-up reconstruction of the transcriptional regulatory network in bacterial cells.