Structural basis for promoter specificity switching of RNA polymerase by a phage factor

Shunsuke Tagami, Shun Ichi Sekine, Leonid Minakhin, Daria Esyunina, Ryogo Akasaka, Mikako Shirouzu, Andrey Kulbachinskiy, Konstantin Severinov, Shigeyuki Yokoyama

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


Transcription of DNA to RNA by DNA-dependent RNA polymerase (RNAP) is the first step of gene expression and a major regulation point. Bacteriophages hijack their host's transcription machinery and direct it to serve their needs. The gp39 protein encoded by Thermus thermophilus phage P23-45 binds the host's RNAP and inhibits transcription initiation from its major "-10/-35" class promoters. Phage promoters belonging to the minor "extended -10" class are minimally inhibited. We report the crystal structure of the T. thermophilus RNAP holoenzyme complexed with gp39, which explains the mechanism for RNAP promoter specificity switching. gp39 simultaneously binds to the RNAP β-flap domain and the C-terminal domain of the σ subunit (region 4 of the σ subunit [σ4]), thus relocating the β-flap tip and σ4. The ~45 Å displacement of σ4 is incompatible with its binding to the -35 promoter consensus element, thus accounting for the inhibition of transcription from -10/-35 class promoters. In contrast, this conformational change is compatible with the recognition of extended -10 class promoters. These results provide the structural bases for the conformational modulation of the host's RNAP promoter specificity to switch gene expression toward supporting phage development for gp39 and, potentially, other phage proteins, such as T4 AsiA.

Original languageEnglish (US)
Pages (from-to)521-531
Number of pages11
JournalGenes and Development
Issue number5
StatePublished - Mar 1 2014

All Science Journal Classification (ASJC) codes

  • Genetics
  • Developmental Biology


  • Bacteriophage
  • RNA polymerase
  • Transcription control
  • Transcription factor
  • X-ray crystallography


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