Probing the Role of Region 2 of Escherichia coli σ70 in Nucleation and Maintenance of the Single-Stranded DNA Bubble in RNA Polymerase-Promoter Open Complexes

Abstract

Publisher Summary This chapter reviews the bacterial RNA polymerase (RNAP), referred to as the “holoenzyme,” or “Eσ,” is a complex of the “core enzyme” (E) and sigma factor (σ), a type of bacterial initiation factor. The multisubunit core enzyme shows similarities in both sequence and structure to the multisubunit eukaryotic RNAP. The role of the sigma factor is to recognize promoter DNA and to initiate the process of RNAP-induced strand separation to form the transcription-competent open promoter complex. The chapter discusses the major advances in the understanding of transcriptional apparatus achieved with the determination of the structure of the bacterial sigma factor, core enzyme, holoenzyme, and a cocomplex of holoenzyme, with a forked DNA encompassing most of the sequence recognized by RNAP. Relevant features of these structures include: (1) the large total area of contact between core and σ 70 , (2) DNA-binding groups of sigma factor that stick out from the body of the holoenzyme, and (3) the existence of separate tunnels for each strand of promoter DNA. This leads the template strand deep in the hydrophobic core of the RNAP to the active site of the enzyme while keeping the nontemplate strand much closer to the surface.