Molecular insight into RNA polymerase I promoter recognition and promoter melting

Nat Commun. 2019 Dec 5;10(1):5543. doi: 10.1038/s41467-019-13510-w.

Abstract

RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I initiation complexes from 2.7 to 3.7 Å resolution to visualize Pol I promoter melting and to structurally and biochemically characterize the recognition mechanism of Pol I promoter DNA. In the closed complex, double-stranded DNA runs outside the DNA-binding cleft. Rotation of CF and upstream DNA with respect to Pol I and Rrn3 results in the spontaneous loading and opening of the promoter followed by cleft closure and positioning of the Pol I A49 tandem winged helix domain (tWH) onto DNA. Conformational rearrangement of A49 tWH leads to a clash with Rrn3 to initiate complex disassembly and promoter escape. Comprehensive insight into the Pol I transcription initiation cycle allows comparisons with promoter opening by Pol II and Pol III.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites / genetics
  • Cryoelectron Microscopy
  • DNA, Fungal / chemistry
  • DNA, Fungal / genetics*
  • DNA, Fungal / metabolism
  • Models, Molecular
  • Nucleic Acid Conformation
  • Promoter Regions, Genetic / genetics*
  • Protein Binding
  • Protein Domains
  • RNA Polymerase I / chemistry
  • RNA Polymerase I / genetics*
  • RNA Polymerase I / metabolism
  • RNA Polymerase II / chemistry
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae / ultrastructure
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Transcription Initiation, Genetic
  • Transcription, Genetic*

Substances

  • DNA, Fungal
  • Saccharomyces cerevisiae Proteins
  • RNA Polymerase II
  • RNA Polymerase I