The Genome of AR9, a Giant Transducing Bacillus Phage Encoding Two Multisubunit RNA Polymerases

Virology. 2016 Aug;495:185-96. doi: 10.1016/j.virol.2016.04.030. Epub 2016 May 26.


Bacteriophage AR9 and its close relative PBS1 have been extensively used to construct early Bacillus subtilis genetic maps. Here, we present the 251,042bp AR9 genome, a linear, terminally redundant double-stranded DNA containing deoxyuridine instead of thymine. Multiple AR9 genes are interrupted by non-coding sequences or sequences encoding putative endonucleases. We show that these sequences are group I and group II self-splicing introns. Eight AR9 proteins are homologous to fragments of bacterial RNA polymerase (RNAP) subunits β/β'. These proteins comprise two sets of paralogs of RNAP largest subunits, with each paralog encoded by two disjoint phage genes. Thus, AR9 is a phiKZ-related giant phage that relies on two multisubunit viral RNAPs to transcribe its genome independently of host transcription apparatus. Purification of one of PBS1/AR9 RNAPs has been reported previously, which makes AR9 a promising object for further studies of RNAP evolution, assembly and mechanism.

Keywords: Bacillus subtilis; Bacteriophage; Evolution; Genome; Introns; RNA polymerase; Transcription.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacillus Phages / classification
  • Bacillus Phages / genetics*
  • Bacillus Phages / metabolism
  • Base Sequence
  • Consensus Sequence
  • DNA Replication
  • DNA-Directed RNA Polymerases / chemistry
  • DNA-Directed RNA Polymerases / genetics*
  • DNA-Directed RNA Polymerases / metabolism
  • Gene Order
  • Genome, Viral*
  • Introns
  • Open Reading Frames
  • Phylogeny
  • Position-Specific Scoring Matrices
  • Promoter Regions, Genetic
  • Protein Subunits / genetics*
  • Protein Subunits / metabolism
  • RNA Splicing
  • Viral Proteins / genetics
  • Viral Proteins / metabolism


  • Protein Subunits
  • Viral Proteins
  • DNA-Directed RNA Polymerases