## 1 Early Research on the Structure of Bacterial RNA Polymerase  
The common core of multi-subunit RNAP in cellular organisms is composed of five subunits that are conserved in all three domains of life. Bacterial RNAP core enzyme is the simplest and best characterized form, consisting of \(\alpha\) (two copies), \(\beta\), \(\beta^{\prime}\), and \(\omega\) subunits (Figures 1 and 2a). The core enzyme is responsible for binding to template DNA to synthesize RNA, which is complemented by a \(\sigma\) factor to form a holoenzyme that recognizes the promoter sequence to begin promoter-specific transcription [1,2]. Structural study of bacterial RNAP by electron microscopy [3] began in the mid-1960s. Crystallization of RNAP isolated from _Thermusthermophilus_ was first reported in the late 1970s [4]; however, the X-ray crystal structure was not determined until the end of the millennium. Before determining the complete structure of RNAP, stable domains and subcomplexes within RNAP were targeted for structural studies (Table 1). These structures were important guides for building the entire structure of RNAP. The first atomic view of RNAP was obtained from the C-terminal domain of _Escherichia coli_ RNAP \(\alpha\) subunit (residues 250-329), also known as \(\alpha\)CTD (PDB: 1 COO) [5], which plays important roles in regulating transcription via interaction with many transcription factors (Figure 2a) and also binds to the upstream promoter DNA [6]. The structure of \(\alpha\)CTD was determined by NMR, which revealed its compact structure and distinct protein topology compared with other DNA binding proteins. The characterization of the structure of \(\alpha\)CTD was a springboard for a series of mutagenesis experiments that revealed communication of bacterial RNAP with numerous transcription factors during gene regulation. Figure 1: RNAP assembly and transcription cycle. The figure shows the general scheme for bacterial RNAP assembly and the transcription cycle. PDB codes of RNAP structures (in brackets) belonging to each phase of the transcription cycle. Figure 2: **(a)** Three-dimensional representation of the interaction between RNAP and transcription factors. The _E. coli_ RNAP holoenzyme is shown as a molecular surface representation (\(\alpha\) subunits: white; \(\beta\) subunit: cyan; \(\beta\)’ subunit: pink; \(\alpha\) subunit: gray; \(\sigma^{70}\): orange; \(\sigma\) region 1.1: red). Transcription factors binding sites are indicated in double quotation marks and PDB codes of structures are shown in brackets; **(b)** Three-dimensional representation of the interaction between \(\sigma\) and anti-\(\sigma\) factors. _E. coli_ RNAP holoenzyme is shown as a molecular surface representation, and only the core enzyme is partially transparent (\(\alpha\) subunits: white; \(\beta\) subunit: cyan; \(\beta\)’ subunit: pink; \(\omega\) subunit: gray; \(\sigma^{70}\): orange). Targets of anti-\(\sigma\) factors are indicated in double quotation marks and PDB codes of structures are shown in brackets. A subsequent study revealed the X-ray crystal structure of the \(\alpha\) subunit N-terminal domain (\(\alpha\)NTD) (PDB: 1 BDF) [7]. The structure showed the \(\alpha\) subunit homodimer, which is an essential platform for binding of the largest subunits, \(\beta\) and \(\beta\)' (Figure 1).