Structural Basis for the Action of an All-Purpose Transcription Anti-termination Factor

Mol Cell. 2019 Apr 4;74(1):143-157.e5. doi: 10.1016/j.molcel.2019.01.016. Epub 2019 Feb 19.

Abstract

Bacteriophage λN protein, a model anti-termination factor, binds nascent RNA and host Nus factors, rendering RNA polymerase resistant to all pause and termination signals. A 3.7-Å-resolution cryo-electron microscopy structure and structure-informed functional analyses reveal a multi-pronged strategy by which the intrinsically unstructured λN directly modifies RNA polymerase interactions with the nucleic acids and subverts essential functions of NusA, NusE, and NusG to reprogram the transcriptional apparatus. λN repositions NusA and remodels the β subunit flap tip, which likely precludes folding of pause or termination RNA hairpins in the exit tunnel and disrupts termination-supporting interactions of the α subunit C-terminal domains. λN invades and traverses the RNA polymerase hybrid cavity, likely stabilizing the hybrid and impeding pause- or termination-related conformational changes of polymerase. λN also lines upstream DNA, seemingly reinforcing anti-backtracking and anti-swiveling by NusG. Moreover, λN-repositioned NusA and NusE sequester the NusG C-terminal domain, counteracting ρ-dependent termination. Other anti-terminators likely utilize similar mechanisms to enable processive transcription.

Keywords: N proteins of lambdoid phages; Nus factors; RNA polymerase regulation; intrinsic transcription termination; processive transcription anti-termination; single-particle cryo-electron microscopy; structural biology; transcription regulation; transcriptional pausing; ρ-dependent transcription termination.

Publication types

  • Research Support, Non-U.S. Gov't
  • Video-Audio Media

MeSH terms

  • Bacteriophage lambda / genetics
  • Bacteriophage lambda / metabolism*
  • Binding Sites
  • Cryoelectron Microscopy
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Escherichia coli / virology
  • Gene Expression Regulation, Bacterial
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Conformation
  • RNA, Bacterial / biosynthesis*
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / genetics
  • Structure-Activity Relationship
  • Transcription Factors / chemistry
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Transcription Termination, Genetic*
  • Viral Regulatory and Accessory Proteins / chemistry
  • Viral Regulatory and Accessory Proteins / genetics
  • Viral Regulatory and Accessory Proteins / metabolism*

Substances

  • N protein, Bacteriophage lambda
  • RNA, Bacterial
  • Transcription Factors
  • Viral Regulatory and Accessory Proteins
  • DNA-Directed RNA Polymerases