title: Characterization of the genome, proteome, and structure of yersiniophage ϕR1-37.
abstract: The bacteriophage vB_YecM-ϕR1-37 (ϕR1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed phage has deoxyuridine (dU) instead of thymidine in its DNA. In this study, we determined the genomic sequence of phage ϕR1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. The 262,391-bp genome of ϕR1-37 is one of the largest sequenced phage genomes, and it contains 367 putative open reading frames (ORFs) and 5 tRNA genes. Mass-spectrometric analysis identified 69 phage particle structural proteins with the genes scattered throughout the genome. A total of 269 of the ORFs (73%) lack homologues in sequence databases. Based on terminator and promoter sequences identified from the intergenic regions, the phage genome was predicted to consist of 40 to 60 transcriptional units. Image reconstruction revealed that the ϕR1-37 capsid consists of hexameric capsomers arranged on a T=27 lattice similar to the bacteriophage ϕKZ. The tail of ϕR1-37 has a contractile sheath. We conclude that phage ϕR1-37 is a representative of a novel phage type that carries the dU-containing genome in a ϕKZ-like head.
authors.affiliation: Department of Bacteriology and Immunology, Infection Biology Research Programme, Haartman Institute, University of Helsinki, Helsinki, Finland. mikael.skurnik@helsinki.fi
authors.forename: Mikael
authors.initials: M
authors.lastname: Skurnik
authors.forename: Heidi J
authors.initials: HJ
authors.lastname: Hyytiäinen
authors.forename: Lotta J
authors.initials: LJ
authors.lastname: Happonen
authors.forename: Saija
authors.initials: S
authors.lastname: Kiljunen
authors.forename: Neeta
authors.initials: N
authors.lastname: Datta
authors.forename: Laura
authors.initials: L
authors.lastname: Mattinen
authors.forename: Kirsty
authors.initials: K
authors.lastname: Williamson
authors.forename: Paula
authors.initials: P
authors.lastname: Kristo
authors.forename: Magdalena
authors.initials: M
authors.lastname: Szeliga
authors.forename: Laura
authors.initials: L
authors.lastname: Kalin-Mänttäri
authors.forename: Elina
authors.initials: E
authors.lastname: Ahola-Iivarinen
authors.forename: Nisse
authors.initials: N
authors.lastname: Kalkkinen
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Butcher
mesh_terms: D001435:Bacteriophages / Q000737:chemistry* / Q000235:genetics*; D001483:Base Sequence; D015152:Blotting, Northern; D015139:Blotting, Southern; D019295:Computational Biology; D020285:Cryoelectron Microscopy; D017931:DNA Primers / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics*; D007091:Image Processing, Computer-Assisted; D013058:Mass Spectrometry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020543:Proteome / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014771:Virion / Q000737:chemistry*; D015008:Yersinia enterocolitica / Q000821:virology*
chemical_list: D017931:DNA Primers; D020543:Proteome