RNA Synthesis Essay

Transcription in prokaryotes requires the formation of the holoenzyme RNA polymerase (holoRNAP), which consists of a core enzyme and a σ subunit. The core enzyme consists of 5 subunits: 2 copies of α, which assemble the enzyme and bind regulatory factors; one copy of β, which has polymerase activity of RNA chain initiation and elongation; one copy of β’, which binds nonspecifically to DNA; and omega. An active center where RNA synthesis occurs is located within the DNA binding channel formed by the β subunits. Several flexible domains stem from the β and β’ subunits (e.g. β’ jaw, β’ downstream clamp, etc.) that surround the DNA binding channel and stabilize DNA binding interactions. The core enzyme can bind DNA nonspecifically, but it requires the binding of the dissociable RNAP factor σ to form the holoenzyme RNAP. σ is capable of recognizing and binding promoters, so once it binds to RNAP, it increases RNAP specificity for certain promoter regions. Promoters are located upstream of transcription start sites of genes and contain short consensus sequences, in bacteria, those are found at -10 (TATAAT) and -35 (TTGACA) positions relative to the transcription start site. Specifically, the σ1 region …show more content…
1B, 1C, 2A) that TAP and σR4 contact the -35 promoter from different faces of the DNA double stranded helix. An important observation here is that TAP binding the -35 region distorts the DNA so that it’s turned 20° away from σR4 when compared to RPo without TAP. Thus, only 2 instead of 3 σR4 residues contact the -35 promoter, and this leads to 2 instead of 4 DNA bases contacted. This corroborates the observation that the recognition specificity of -35 region DNA sequences is smaller than in transcription lacking activators. Fig 2A shows the σR4 resitues that contact the -35 promoter DNA, and we can see that site-directed mutagenesis of these two residues to alanine (σR584A and σE585A) decreases RPo complex formation