title: Functional requirements for bacteriophage growth: gene essentiality and expression in mycobacteriophage Giles.
abstract: Bacteriophages represent a majority of all life forms, and the vast, dynamic population with early origins is reflected in their enormous genetic diversity. A large number of bacteriophage genomes have been sequenced. They are replete with novel genes without known relatives. We know little about their functions, which genes are required for lytic growth, and how they are expressed. Furthermore, the diversity is such that even genes with required functions - such as virion proteins and repressors - cannot always be recognized. Here we describe a functional genomic dissection of mycobacteriophage Giles, in which the virion proteins are identified, genes required for lytic growth are determined, the repressor is identified, and the transcription patterns determined. We find that although all of the predicted phage genes are expressed either in lysogeny or in lytic growth, 45% of the predicted genes are non-essential for lytic growth. We also describe genes required for DNA replication, show that recombination is required for lytic growth, and that Giles encodes a novel repressor. RNAseq analysis reveals abundant expression of a small non-coding RNA in a lysogen and in late lytic growth, although it is non-essential for lytic growth and does not alter lysogeny.
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
authors.forename: Rebekah M
authors.initials: RM
authors.lastname: Dedrick
authors.forename: Laura J
authors.initials: LJ
authors.lastname: Marinelli
authors.forename: Gerald L
authors.initials: GL
authors.lastname: Newton
authors.forename: Kit
authors.initials: K
authors.lastname: Pogliano
authors.forename: Joseph
authors.initials: J
authors.lastname: Pogliano
authors.forename: Graham F
authors.initials: GF
authors.lastname: Hatfull
mesh_terms: D002853:Chromatography, Liquid; D004261:DNA Replication; D017353:Gene Deletion; D015967:Gene Expression Regulation, Viral; D020043:Genes, Essential; D016679:Genome, Viral; D008242:Lysogeny; D009160:Mycobacteriophages / Q000235:genetics* / Q000502:physiology; D020102:Mycobacterium smegmatis / Q000821:virology; D011401:Promoter Regions, Genetic; D058727:RNA, Small Untranslated / Q000235:genetics; D012097:Repressor Proteins; D053719:Tandem Mass Spectrometry; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000235:genetics; D014779:Virus Replication
chemical_list: D058727:RNA, Small Untranslated; D012097:Repressor Proteins; D014764:Viral Proteins
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