Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655
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DOI：
10.1093/nar/gky752
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发表时间：
2018-11-16
影响因子：
14.9
通讯作者：
Palsson, Bernhard O.
中科院分区：
文献类型：
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作者：
Gao, Ye;Yurkovich, James T.;Palsson, Bernhard O.
转录调节使细胞能够对环境变化做出反应。大肠杆菌 K-12 MG1655 中估计有 304 个候选转录因子 (TF)，其中 185 个已通过实验鉴定，但使用 ChIP 方法完全表征的只有几十个。识别这些剩余的 TF 是提高我们对大肠杆菌转录调控网络 (TRN) 的了解的关键。在这里，我们开发了一个集成的工作流程，使用一套全基因组实验对 TF 进行计算预测和综合实验验证。我们应用此工作流程来 (i) 从 100 多个未表征的基因中识别 16 个候选 TF； (ii) 捕获 10 个候选 TF 的总共 255 个 DNA 结合峰，从而产生 6 个高置信度结合基序； (iii) 通过确定删除每个 TF 后的基因表达变化来重建这 10 个 TF 的调节子，(iv) 确定三个 TF（YiaJ、YdcI 和 YeiE）分别作为 L-抗坏血酸利用、质子转移和乙酸代谢以及铁限制条件下铁稳态调节剂的调节作用。这些结果共同证明了如何使用该工作流程来并行发现、表征和阐明未表征的 TF 的调控功能。
Transcriptional regulation enables cells to respond to environmental changes. Of the estimated 304 candidate transcription factors (TFs) in Escherichia coli K-12 MG1655, 185 have been experimentally identified, but ChIP methods have been used to fully characterize only a few dozen. Identifying these remaining TFs is key to improving our knowledge of the E. coli transcriptional regulatory network (TRN). Here, we developed an integrated workflow for the computational prediction and comprehensive experimental validation of TFs using a suite of genome-wide experiments. We applied this workflow to (i) identify 16 candidate TFs from over a hundred uncharacterized genes; (ii) capture a total of 255 DNA binding peaks for ten candidate TFs resulting in six high-confidence binding motifs; (iii) reconstruct the regulons of these ten TFs by determining gene expression changes upon deletion of each TF and (iv) identify the regulatory roles of three TFs (YiaJ, YdcI, and YeiE) as regulators of L-ascorbate utilization, proton transfer and acetate metabolism, and iron homeostasis under iron-limited conditions, respectively. Together, these results demonstrate how this workflow can be used to discover, characterize, and elucidate regulatory functions of uncharacterized TFs in parallel.