title: The genome of the virulent phage Lc-Nu of probiotic Lactobacillus rhamnosus, and comparative genomics with Lactobacillus casei phages.
abstract: The complete 36,466-bp genome sequence of the virulent phage Lc-Nu of probiotic Lactobacillus rhamnosus was determined. The linear dsDNA with a GC-content of 44.2% contained 3' single-stranded cohesive ends of 12 nucleotides. A total of 51 putative open reading frames (orfs) were predicted. Lc-Nu showed to be evolutionary closely related to the temperate Lactobacillus casei phages phi AT3 and A2. High DNA homology with phi AT3 was shared over the late transcribed genes, and the highest homology with A2 was within the genetic switch region. The truncated cI-like repressor was the only lysogeny related gene left, which strongly suggested Lc-Nu to be recently evolved from a temperate origin. Three putative methylases and endonucleases were detected from the region of early-transcribed genes. The putative origin of replication within the putative gene orf34 homologous to replisome organizers resembled to that of lambdoid phages. The present study suggested Lc-Nu to be a new candidate for the proposed Sfi21-like species.
authors.affiliation: Department of Biology, University of Oulu, Oulu, Finland.
authors.forename: A
authors.initials: A
authors.lastname: Tuohimaa
authors.forename: K-A
authors.initials: KA
authors.lastname: Riipinen
authors.forename: K
authors.initials: K
authors.lastname: Brandt
authors.forename: T
authors.initials: T
authors.lastname: Alatossava
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics*; D004720:Endonucleases / Q000235:genetics; D019143:Evolution, Molecular; D023061:Gene Order; D016679:Genome, Viral; D007780:Lacticaseibacillus casei / Q000821:virology; D052201:Lacticaseibacillus rhamnosus / Q000821:virology*; D008780:Methyltransferases / Q000235:genetics; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D018741:Replication Origin / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D017906:Siphoviridae / Q000235:genetics*; D026801:Synteny
chemical_list: D004279:DNA, Viral; D012097:Repressor Proteins; D008780:Methyltransferases; D004720:Endonucleases