Structure-Based Mechanisms of a Molecular RNA Polymerase/Chaperone Machine Required for Ribosome Biosynthesis

Mol Cell. 2020 Sep 17;79(6):1024-1036.e5. doi: 10.1016/j.molcel.2020.08.010. Epub 2020 Aug 31.


Bacterial ribosomal RNAs are synthesized by a dedicated, conserved transcription-elongation complex that transcribes at high rates, shields RNA polymerase from premature termination, and supports co-transcriptional RNA folding, modification, processing, and ribosomal subunit assembly by presently unknown mechanisms. We have determined cryo-electron microscopy structures of complete Escherichia coli ribosomal RNA transcription elongation complexes, comprising RNA polymerase; DNA; RNA bearing an N-utilization-site-like anti-termination element; Nus factors A, B, E, and G; inositol mono-phosphatase SuhB; and ribosomal protein S4. Our structures and structure-informed functional analyses show that fast transcription and anti-termination involve suppression of NusA-stabilized pausing, enhancement of NusG-mediated anti-backtracking, sequestration of the NusG C-terminal domain from termination factor ρ, and the ρ blockade. Strikingly, the factors form a composite RNA chaperone around the RNA polymerase RNA-exit tunnel, which supports co-transcriptional RNA folding and annealing of distal RNA regions. Our work reveals a polymerase/chaperone machine required for biosynthesis of functional ribosomes.

Keywords: Nus factors; RNA polymerase pausing and backtracking, RNA chaperone; co-transcriptional RNA folding and processing; ribosomal RNA transcription; single-particle cryo-electron microscopy; structural biology; transcription (anti-)termination; transcription regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites / genetics
  • Cryoelectron Microscopy
  • DNA-Directed RNA Polymerases / genetics*
  • Escherichia coli / genetics
  • Escherichia coli / ultrastructure
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / ultrastructure
  • Molecular Chaperones / genetics*
  • Phosphoric Monoester Hydrolases / genetics
  • Phosphoric Monoester Hydrolases / ultrastructure
  • Protein Biosynthesis / genetics
  • RNA Folding / genetics
  • RNA, Ribosomal / genetics
  • RNA, Ribosomal / ultrastructure
  • Ribosomal Proteins / genetics*
  • Ribosomal Proteins / ultrastructure
  • Ribosomes / genetics*
  • Ribosomes / ultrastructure
  • Transcriptional Elongation Factors / chemistry
  • Transcriptional Elongation Factors / genetics
  • Transcriptional Elongation Factors / ultrastructure


  • Escherichia coli Proteins
  • Molecular Chaperones
  • RNA, Ribosomal
  • Ribosomal Proteins
  • Transcriptional Elongation Factors
  • nusA protein, E coli
  • ribosomal protein S4
  • DNA-Directed RNA Polymerases
  • Phosphoric Monoester Hydrolases
  • SuhB protein, E coli