Transcription elongation

Abstract

This review is focused on recent progress in understanding how Escherichia coli RNAP polymerase translocates along the DNA template and the factors that affect this movement. We discuss the fundamental aspects of RNAP translocation, template signals that influence forward or backward movement, and host or phage factors that modulate translocation. Mechanism of transcription elongationTernary elongation complex (TEC) assembled by DNA template, RNA polymerase and emerging RNA product is the principal intermediate of transcription (Fig. 1). During the elongation step of RNA synthesis, the RNA product remains transiently base-paired to the template DNA strand, forming 9-10 bp RNA: DNA hybrid, 1 whereas the other DNA strand is separated from the template (Fig. 1). The resulting melted DNA region of 10-12 nt 2,3 is called the "transcription bubble." The crucial nucleic acid-protein interactions in TEC involve three principal functionally and structurally defined elements. 4 One of these, the downstream DNA binding site, encloses downstream DNA duplex and acts as a sliding clamp, whereas the two other sites resemble zip locks operationally. The rear zip lock clasps the upstream edge of the RNA:DNA hybrid and ensures displacement of RNA product from template during elongation, whereas the front zip lock, which coincides with RNAP active center, secludes the downstream boundary of the hybrid and also enables peeling of RNA from DNA upon backtracking RNAP. 1,5,6 Both front and rear zip locks accommodate the RNA:DNA hybrid in the hybrid binding site and maintain through topological contacts alone a constant configuration of nucleic acid scaffold upon RNAP lateral movement. Most interactions between the nucleic acid scaffold and RNAP in TEC are not sequence-specific. Some preference to dG residues has been demonstrated in the "core recognition element, CRE" of the b subunit (see below). However, these interactions do not seem to significantly affect TEC reactions, only in rare occasions contributing to RNAP escape from pausing. In X-ray structures of TEC, 7,8 the downstream DNA binding site is seen as a deep cleft formed by the b and b 0 subunits (Fig. 1). The RNA:DNA hybrid is accommodated in the main channel at the interface of the same subunits between the b 0 Bridge helix, b Fork loop II and the active center at its downstream end and the b 0 Rudder and b 0 Lid loops at its upstream end, which correspond to the front and rear zip locks respectively. After peeling from the DNA, the synthesized RNA transcript is channeled into an extended narrow cavity formed by the b 0 Lid and b 0 Zn-finger subdomains as well as the "Flap," which is a long flexible b subunit loop.Each individual step of RNA extension by RNA polymerase produces TEC in which the RNA 3 0 end occupies the iC1 site of the enzyme active center

Effects of DNA Topology on Transcription from rRNA Promoters in Bacillus subtilis

“…At this stage, initiating nucleoside triphosphates NTPs (iNTPs) can enter the active site and transcription can begin. RNAP then leaves the promoter and enters the elongation phase of transcription [ 7 ].…”

Efficiency of the synthetic self‐splicing RiboJ ribozyme is robust to cis‐ and trans‐changes in genetic background

“…The SNP may create a binding site causing a polymerase or transcription factor to pause during its linear search on the DNA strand for functional binding sites, thus inhibiting transcription. Processes such as transcriptional pausing and attenuation have been previously described in bacteria (Bailey et al, 2021 ; Blainey et al, 2006 ; Mustaev et al, 2017 ; Naville & Gautheret, 2009 ). These provide a more plausible explanation for the effect we see.…”

Understanding transcription across scales: From base pairs to chromosomes

“…The resulting 12-to 15-bp DNA bubble is then used to initiate transcription from the transcription start site (TSS) (Bae et al, 2015;Glyde et al, 2018;He et al, 2016;Plaschka et al, 2016). When RNA polymerase begins to synthesize RNA and escapes the promoter region, RNA polymerase enters the elongation phase of transcription (reviewed in Jonkers and Lis, 2015;Mustaev et al, 2017). At completion of gene synthesis, transcription is terminated when RNA polymerase is removed from the DNA template (reviewed in Peters et al, 2011;Porrua et al, 2016).…”