title: The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases.
abstract: 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.
authors.affiliation: Institute of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia. Electronic address: daria.lavysh@img.ras.ru.
authors.forename: Daria
authors.initials: D
authors.lastname: Lavysh
authors.affiliation: Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia. Electronic address: maria.sokolova@skolkovotech.ru.
authors.forename: Maria
authors.initials: M
authors.lastname: Sokolova
authors.affiliation: Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ, USA. Electronic address: minakhin@waksman.rutgers.edu.
authors.forename: Leonid
authors.initials: L
authors.lastname: Minakhin
authors.affiliation: Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia. Electronic address: yakuninam@gmail.com.
authors.forename: Maria
authors.initials: M
authors.lastname: Yakunina
authors.affiliation: Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia. Electronic address: artamonova@nanobio.spbstu.ru.
authors.forename: Tatjana
authors.initials: T
authors.lastname: Artamonova
authors.affiliation: Fidelity Systems, Inc., Gaithersburg, MD 20879, USA. Electronic address: serg@fidelitysystems.com.
authors.forename: Sergei
authors.initials: S
authors.lastname: Kozyavkin
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. Electronic address: makarova@ncbi.nlm.nih.gov.
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. Electronic address: koonin@ncbi.nlm.nih.gov.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
authors.affiliation: Institute of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia; Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Russia; Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ, USA. Electronic address: severik@waksman.rutgers.edu.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Severinov
mesh_terms: D017103:Bacillus Phages / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D016384:Consensus Sequence; D004261:DNA Replication; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D023061:Gene Order; D016679:Genome, Viral; D007438:Introns; D016366:Open Reading Frames; D010802:Phylogeny; D056510:Position-Specific Scoring Matrices; D011401:Promoter Regions, Genetic; D021122:Protein Subunits / Q000235:genetics* / Q000378:metabolism; D012326:RNA Splicing; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D021122:Protein Subunits; D014764:Viral Proteins; D012321:DNA-Directed RNA Polymerases
keywords: Bacillus subtilis; Bacteriophage; Evolution; Genome; Introns; RNA polymerase; Transcription