Molecular Anatomy of RNA Polymerase : Identification of Transcription Factor Contact Sites

大肠杆菌RNA聚合酶全酶由α_2betabeta‘亚基结构的核心酶和七种不同分子亚基之一的Sigma亚基组成，每个亚基识别一个不同的启动子序列。RNA聚合酶的启动子选择性在与100多种不同种类的反式作用蛋白和核苷酸因子相互作用后被进一步调节，这些反式作用蛋白和核苷酸因子通常被称为转录因子，具有转录病毒的调节活性。RNA聚合酶的活性也受到顺式作用的调控DNA信号的调节，这些信号通常位于启动子的上游。已经确定了30多种转录调节蛋白或核苷酸因子在RNA聚合酶亚基上的接触位点。根据接触部位，我们建议将转录因子分为四类：CLSS-I(α接触)、II(西格玛接触)、III(β接触)和VI(β‘接触)。用一种新的化学试剂Fe-Babe证实了突变研究中估计的接触位点，该工具具有接触依赖的DNA和蛋白质的切割活性。由于RNA聚合酶核心酶的总数固定在一个低而恒定的水平上，这是细胞生长速度的特征，所以全酶和EZCH RNA聚合酶-转录因子复合体中的每个浓度都会随着每个sigma亚基和每个转录因子浓度的生长变化而波动。分析了大肠杆菌从指数生长期向稳定期生长转变过程中转录装置分子构型的变化。因此，大肠杆菌染色体上大约4000个基因中的基因转录的种类和顺序会随着细胞生长条件的不同而变化。

The RNA polymerase holoezyme of Escherichia coli is composed of core enzyme with the subunit structure of alpha_2betabeta' and one of seven different molecular species of sigma subunits, each recognizing a different promoter sequence. The promoter selectivity of RNA polymerase is further modulated after interaction with one or two of more than 100 different species of trans-acting protein and nucleotide factors, generally designated as transcription factors, with the regulatory activities of transcriprion. The RNA polymerase activity is also modulated by cis-acting regulatory DNA signals generally located upstream of promoters. The contact sites on RNA polymerase subunits have been determined for more than 30 transcription regulatory protein or nucleotide factors. Based on the contact sites, we proposed to classify the transcription factors into four groups : clss-I(alpha contact), II(sigma contact), III(beta contact) and VI(beta' contact) factors. The contact sites estimated from mutant studies have been confirmed using a new tool of chemical reagent, Fe-BABE,with contact-dependent cleavage activity of DNA and proteins.Since the total number of RNA polymerase core enzyme is fixed at a low and constant level characteristic of the rate of cell growth, the concentrations of each from holoenzyme and ezch RNA polymerase-transcription factor complex are subject to fluctuation depending on growth-dependent variations in the concentrations of each sigma subunit and each transcription factor. Variation in the molecular arhitecture of transcription apparatus was analyzed during growth transition of E.coli from exponentially growing to stationary phase. Accordingly, the species and order of gene transcription among about 4,000 genes on the E.coli chromosome change depending on the cell growth conditions.