Meiji University, School of Agriculture, Kawasaki, Kanagawa 214-8571, Japan.
Shinshu University, Research Center for Supports to Advanced Science, Division of Gene Research, Ueda, Nagano 386-8567, Japan.
Nucleic Acids Res. 2018 May 4;46(8):3921-3936. doi: 10.1093/nar/gky138.
The identification of regulatory targets of all TFs is critical for understanding the entire network of the genome regulation. The lac regulon of Escherichia coli K-12 W3110 is composed of the lacZYA operon and its repressor lacI gene, and has long been recognized as the seminal model of transcription regulation in bacteria with only one highly preferred target. After the Genomic SELEX screening in vitro of more than 200 transcription factors (TFs) from E. coli K-12, however, we found that most TFs regulate multiple target genes. With respect to the number of regulatory targets, a total of these 200 E. coli TFs form a hierarchy ranging from a single target to as many as 1000 targets. Here we focus a total of 13 single-target TFs, 9 known TFs (BetI, KdpE, LacI, MarR, NanR, RpiR, TorR, UlaR and UxuR) and 4 uncharacterized TFs (YagI, YbaO, YbiH and YeaM), altogether forming only a minor group of TFs in E. coli. These single-target TFs were classified into three groups based on their functional regulation.
鉴定所有 TF 的调控靶标对于理解基因组调控的整个网络至关重要。大肠杆菌 K-12 W3110 的 lac 调控子由 lacZYA 操纵子及其阻遏物 lacI 基因组成，长期以来一直被认为是细菌转录调控的开创性模型，只有一个高度首选的靶标。然而，在对大肠杆菌 K-12 中的 200 多个转录因子（TF）进行体外基因组 SELEX 筛选后，我们发现大多数 TF 调节多个靶基因。就调控靶标的数量而言，这 200 个大肠杆菌 TF 总共形成了一个从单个靶标到多达 1000 个靶标的层次结构。在这里，我们总共关注了 13 个单靶标 TF，其中 9 个是已知的 TF（BetI、KdpE、LacI、MarR、NanR、RpiR、TorR、UlaR 和 UxuR），4 个是未表征的 TF（YagI、YbaO、YbiH 和 YeaM），它们共同构成了大肠杆菌中少数 TF 群体。这些单靶标 TF 根据其功能调节被分为三组。
