title: Cluster J mycobacteriophages: intron splicing in capsid and tail genes.
abstract: Bacteriophages isolated on Mycobacterium smegmatis mc(2)155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution.
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America .
authors.forename: Welkin H
authors.initials: WH
authors.lastname: Pope
authors.forename: Deborah
authors.initials: D
authors.lastname: Jacobs-Sera
authors.forename: Aaron A
authors.initials: AA
authors.lastname: Best
authors.forename: Gregory W
authors.initials: GW
authors.lastname: Broussard
authors.forename: Pamela L
authors.initials: PL
authors.lastname: Connerly
authors.forename: Rebekah M
authors.initials: RM
authors.lastname: Dedrick
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Kremer
authors.forename: Susan
authors.initials: S
authors.lastname: Offner
authors.forename: Amenawon H
authors.initials: AH
authors.lastname: Ogiefo
authors.forename: Marie C
authors.initials: MC
authors.lastname: Pizzorno
authors.forename: Kate
authors.initials: K
authors.lastname: Rockenbach
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Russell
authors.forename: Emily L
authors.initials: EL
authors.lastname: Stowe
authors.forename: Joseph
authors.initials: J
authors.lastname: Stukey
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Thibault
authors.forename: James F
authors.initials: JF
authors.lastname: Conway
authors.forename: Roger W
authors.initials: RW
authors.lastname: Hendrix
authors.forename: Graham F
authors.initials: GF
authors.lastname: Hatfull
mesh_terms: D000595:Amino Acid Sequence; D001433:Bacteriolysis / Q000235:genetics; D001482:Base Composition; D001483:Base Sequence; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics*; D016000:Cluster Analysis; D004251:DNA Transposable Elements; D023061:Gene Order; D059646:Genome Size; D016679:Genome, Viral; D007438:Introns; D008969:Molecular Sequence Data; D009160:Mycobacteriophages / Q000145:classification* / Q000235:genetics* / Q000648:ultrastructure; D016366:Open Reading Frames; D010802:Phylogeny; D012326:RNA Splicing; D017376:Viral Tail Proteins / Q000737:chemistry / Q000235:genetics*; D014771:Virion / Q000648:ultrastructure; D016662:Virus Integration / Q000235:genetics
chemical_list: D036022:Capsid Proteins; D004251:DNA Transposable Elements; D017376:Viral Tail Proteins