Bacteriophage N4 virion RNA polymerase interaction with its promoter DNA hairpin

Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7033-8. doi: 10.1073/pnas.0610627104. Epub 2007 Apr 16.

Abstract

Bacteriophage N4 minivirion RNA polymerase (mini-vRNAP), the RNA polymerase (RNAP) domain of vRNAP, is a member of the T7-like RNAP family. Mini-vRNAP recognizes promoters that comprise conserved sequences and a 3-base loop-5-base pair (bp) stem DNA hairpin structure on single-stranded templates. Here, we defined the DNA structural and sequence requirements for mini-vRNAP promoter recognition. Mini-vRNAP binds a 20-nucleotide (nt) N4 P2 promoter deoxyoligonucleotide with high affinity (K(d) = 2 nM) to form a salt-resistant complex. We show that mini-vRNAP interacts specifically with the central base of the hairpin loop (-11G) and a base at the stem (-8G) and that the guanine 6-keto and 7-imino groups at both positions are essential for binding and complex salt resistance. The major determinant (-11G), which must be presented to mini-vRNAP in the context of a hairpin loop, appears to interact with mini-vRNAP Trp-129. This interaction requires template single-strandedness at positions -2 and -1. Contacts with the promoter are disrupted when the RNA product becomes 11-12 nt long. This detailed description of vRNAP interaction with its promoter hairpin provides insights into RNAP-promoter interactions and explains how the injected vRNAP, which is present in one or two copies, recognizes its promoters on a single copy of the injected genome.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacteriophage N4 / enzymology*
  • Base Sequence
  • DNA, Viral / chemistry*
  • DNA, Viral / genetics*
  • DNA-Directed RNA Polymerases / metabolism*
  • Guanine
  • Hydrogen Bonding / drug effects
  • Molecular Sequence Data
  • Nucleic Acid Conformation* / drug effects
  • Nucleotides
  • Promoter Regions, Genetic / genetics*
  • Protein Binding / drug effects
  • Salts / pharmacology
  • Templates, Genetic
  • Transcription, Genetic / drug effects
  • Tryptophan
  • Virion / enzymology*

Substances

  • DNA, Viral
  • Nucleotides
  • Salts
  • Guanine
  • Tryptophan
  • DNA-Directed RNA Polymerases