Structural Basis for NusA Stabilized Transcriptional Pausing

Mol Cell. 2018 Mar 1;69(5):816-827.e4. doi: 10.1016/j.molcel.2018.02.008.


Transcriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial transcription factor NusA stimulates both pausing and termination of transcription, thus playing a central role. Here, we report single-particle electron cryo-microscopy reconstructions of NusA bound to paused E. coli RNAP elongation complexes with and without a pause-enhancing hairpin in the RNA exit channel. The structures reveal four interactions between NusA and RNAP that suggest how NusA stimulates RNA folding, pausing, and termination. An asymmetric translocation intermediate of RNA and DNA converts the active site of the enzyme into an inactive state, providing a structural explanation for the inhibition of catalysis. Comparing RNAP at different stages of pausing provides insights on the dynamic nature of the process and the role of NusA as a regulatory factor.

Keywords: NusA; RNA polymerase structure; cryo-EM; his-pause; transcription; transcriptional pausing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism
  • DNA-Directed RNA Polymerases* / chemistry
  • DNA-Directed RNA Polymerases* / metabolism
  • Escherichia coli Proteins* / chemistry
  • Escherichia coli Proteins* / metabolism
  • Escherichia coli* / chemistry
  • Escherichia coli* / metabolism
  • RNA Folding*
  • RNA, Bacterial* / biosynthesis
  • RNA, Bacterial* / chemistry
  • Transcription Termination, Genetic*
  • Transcriptional Elongation Factors* / chemistry
  • Transcriptional Elongation Factors* / metabolism


  • DNA, Bacterial
  • Escherichia coli Proteins
  • RNA, Bacterial
  • Transcriptional Elongation Factors
  • nusA protein, E coli
  • DNA-Directed RNA Polymerases