Transcription activation by a sliding clamp

Nat Commun. 2021 Feb 18;12(1):1131. doi: 10.1038/s41467-021-21392-0.

Abstract

Transcription activation of bacteriophage T4 late genes is accomplished by a transcription activation complex containing RNA polymerase (RNAP), the promoter specificity factor gp55, the coactivator gp33, and a universal component of cellular DNA replication, the sliding clamp gp45. Although genetic and biochemical studies have elucidated many aspects of T4 late gene transcription, no precise structure of the transcription machinery in the process is available. Here, we report the cryo-EM structures of a gp55-dependent RNAP-promoter open complex and an intact gp45-dependent transcription activation complex. The structures reveal the interactions between gp55 and the promoter DNA that mediate the recognition of T4 late promoters. In addition to the σR2 homology domain, gp55 has a helix-loop-helix motif that chaperons the template-strand single-stranded DNA of the transcription bubble. Gp33 contacts both RNAP and the upstream double-stranded DNA. Gp45 encircles the DNA and tethers RNAP to it, supporting the idea that gp45 switches the promoter search from three-dimensional diffusion mode to one-dimensional scanning mode.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Base Sequence
  • DNA Polymerase III / chemistry
  • DNA Polymerase III / metabolism*
  • DNA Polymerase III / ultrastructure
  • DNA, Single-Stranded / metabolism
  • DNA, Viral / metabolism
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics*
  • Models, Genetic
  • Models, Molecular
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Domains
  • Sigma Factor / chemistry
  • Sigma Factor / ultrastructure
  • Transcription, Genetic
  • Transcriptional Activation / genetics*
  • Viral Proteins / chemistry
  • Viral Proteins / ultrastructure

Substances

  • DNA, Single-Stranded
  • DNA, Viral
  • Sigma Factor
  • Viral Proteins
  • gene 33 protein, Enterobacteria phage T4
  • gene 55 protein, Enterobacteria phage T4
  • beta subunit, DNA polymerase III
  • DNA-Directed RNA Polymerases
  • DNA Polymerase III