title: Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4.
abstract: Five newly isolated mycobacteriophages--Angelica, CrimD, Adephagia, Anaya, and Pixie--have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them--with the exception of TM4--form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species.
authors: Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.
authors: Welkin H
authors: WH
authors: Pope
authors: Christina M
authors: CM
authors: Ferreira
authors: Deborah
authors: D
authors: Jacobs-Sera
authors: Robert C
authors: RC
authors: Benjamin
authors: Ariangela J
authors: AJ
authors: Davis
authors: Randall J
authors: RJ
authors: DeJong
authors: Sarah C R
authors: SC
authors: Elgin
authors: Forrest R
authors: FR
authors: Guilfoile
authors: Mark H
authors: MH
authors: Forsyth
authors: Alexander D
authors: AD
authors: Harris
authors: Samuel E
authors: SE
authors: Harvey
authors: Lee E
authors: LE
authors: Hughes
authors: Peter M
authors: PM
authors: Hynes
authors: Arrykka S
authors: AS
authors: Jackson
authors: Marilyn D
authors: MD
authors: Jalal
authors: Elizabeth A
authors: EA
authors: MacMurray
authors: Coreen M
authors: CM
authors: Manley
authors: Molly J
authors: MJ
authors: McDonough
authors: Jordan L
authors: JL
authors: Mosier
authors: Larissa J
authors: LJ
authors: Osterbann
authors: Hannah S
authors: HS
authors: Rabinowitz
authors: Corwin N
authors: CN
authors: Rhyan
authors: Daniel A
authors: DA
authors: Russell
authors: Margaret S
authors: MS
authors: Saha
authors: Christopher D
authors: CD
authors: Shaffer
authors: Stephanie E
authors: SE
authors: Simon
authors: Erika F
authors: EF
authors: Sims
authors: Isabel G
authors: IG
authors: Tovar
authors: Emilie G
authors: EG
authors: Weisser
authors: John T
authors: JT
authors: Wertz
authors: Kathleen A
authors: KA
authors: Weston-Hafer
authors: Kurt E
authors: KE
authors: Williamson
authors: Bo
authors: B
authors: Zhang
authors: Steven G
authors: SG
authors: Cresawn
authors: Paras
authors: P
authors: Jain
authors: Mariana
authors: M
authors: Piuri
authors: William R
authors: WR
authors: Jacobs
authors: Roger W
authors: RW
authors: Hendrix
authors: Graham F
authors: GF
authors: Hatfull
mesh_terms: D001287:Attachment Sites, Microbiological; D001483:Base Sequence; D002874:Chromosome Mapping; D016000:Cluster Analysis; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D017353:Gene Deletion; D016679:Genome, Viral / Q000235:genetics; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D009154:Mutation / Q000235:genetics; D009160:Mycobacteriophages / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification / Q000648:ultrastructure; D017422:Sequence Analysis, DNA; D013696:Temperature; D014764:Viral Proteins / Q000235:genetics; D014771:Virion / Q000235:genetics / Q000648:ultrastructure; D016662:Virus Integration / Q000235:genetics; D014779:Virus Replication / Q000502:physiology
chemical_list: D014764:Viral Proteins