The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase

• Published in: Journal of molecular biology Vol. 431; no. 20; pp. 3975 - 4006
• Main Authors: Belogurov, Georgiy A., Artsimovitch, Irina
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 20.09.2019
• Subjects: proofreading; RNA polymerase; transcription elongation; translocation; trigger loop; translocation; BH; trigger loop; RNA polymerase; NTP; RNAP; THB; transcription elongation; ntDNA; CTD; TEC; TH; tDNA; MD; CRE; TL; proofreading; NTD
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2019.05.042

Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs, ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has to make each RNA product in just one try, even if it takes millions of successive nucleotide addition steps. During each step, RNA polymerase selects a correct substrate, adds it to a growing chain, and moves one nucleotide forward before repeating the cycle. However, RNA synthesis is anything but monotonous: RNA polymerase frequently pauses upon encountering mechanical, chemical and torsional barriers, sometimes stepping back and cleaving off nucleotides from the growing RNA chain. A picture in which these intermittent dynamics enable processive, accurate, and controllable RNA synthesis is emerging from complementary structural, biochemical, computational, and single-molecule studies. Here, we summarize our current understanding of the mechanism and regulation of the on-pathway transcription elongation. We review the details of substrate selection, catalysis, proofreading, and translocation, focusing on rate-limiting steps, structural elements that modulate them, and accessory proteins that appear to control RNA polymerase translocation. [Display omitted] •RNA chain elongation is processive yet intermittent.•The trigger loop positions reactive groups for catalysis.•Translocation is controlled by nucleic acids energetics and trigger loop dynamics.•Error frequency and fast synthesis are counterbalanced.