title: Transcription Profiling ofBacillus subtilisCells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases.
abstract: Bacteriophage AR9 is a recently sequenced jumbo phage that encodes two multisubunit RNA polymerases. Here we investigated the AR9 transcription strategy and the effect of AR9 infection on the transcription of its host,Bacillus subtilisAnalysis of whole-genome transcription revealed early, late, and continuously expressed AR9 genes. Alignment of sequences upstream of the 5' ends of AR9 transcripts revealed consensus sequences that define early and late phage promoters. Continuously expressed AR9 genes have both early and late promoters in front of them. Early AR9 transcription is independent of protein synthesis and must be determined by virion RNA polymerase injected together with viral DNA. During infection, the overall amount of host mRNAs is significantly decreased. Analysis of relative amounts of host transcripts revealed notable differences in the levels of some mRNAs. The physiological significance of up- or downregulation of host genes for AR9 phage infection remains to be established. AR9 infection is significantly affected by rifampin, an inhibitor of host RNA polymerase transcription. The effect is likely caused by the antibiotic-induced killing of host cells, while phage genome transcription is solely performed by viral RNA polymerases.IMPORTANCEPhages regulate the timing of the expression of their own genes to coordinate processes in the infected cell and maximize the release of viral progeny. Phages also alter the levels of host transcripts. Here we present the results of a temporal analysis of the host and viral transcriptomes ofBacillus subtilisinfected with a giant phage, AR9. We identify viral promoters recognized by two virus-encoded RNA polymerases that are a unique feature of the phiKZ-related group of phages to which AR9 belongs. Our results set the stage for future analyses of highly unusual RNA polymerases encoded by AR9 and other phiKZ-related phages.
authors.affiliation: Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.|Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia.
authors.forename: Daria
authors.initials: D
authors.lastname: Lavysh
authors.affiliation: Skolkovo Institute of Science and Technology, Skolkovo, Russia.|Peter the Great St.Petersburg Polytechnic University, Saint-Petersburg, Russia.
authors.forename: Maria
authors.identifier: 0000-0001-7251-6952
authors.initials: M
authors.lastname: Sokolova
authors.affiliation: Peter the Great St.Petersburg Polytechnic University, Saint-Petersburg, Russia.
authors.forename: Marina
authors.initials: M
authors.lastname: Slashcheva
authors.affiliation: Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany.
authors.forename: Konrad U
authors.initials: KU
authors.lastname: Förstner
authors.affiliation: Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia severik@waksman.rutgers.edu.|Skolkovo Institute of Science and Technology, Skolkovo, Russia.|Peter the Great St.Petersburg Polytechnic University, Saint-Petersburg, Russia.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Severinov
mesh_terms: D000904:Antibiotics, Antitubercular / Q000494:pharmacology; D017103:Bacillus Phages / Q000201:enzymology / Q000235:genetics / Q000502:physiology*; D001412:Bacillus subtilis / Q000187:drug effects / Q000235:genetics* / Q000821:virology*; D004279:DNA, Viral; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D054884:Host-Pathogen Interactions / Q000235:genetics; D011401:Promoter Regions, Genetic; D012293:Rifampin / Q000494:pharmacology; D016415:Sequence Alignment; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000378:metabolism
chemical_list: D000904:Antibiotics, Antitubercular; D004279:DNA, Viral; D014764:Viral Proteins; D012321:DNA-Directed RNA Polymerases; D012293:Rifampin