title: Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution, and phylogenetic analysis.
abstract: So far, there is only fragmentary and unconfirmed information on bacteriophages infecting the genus Bifidobacterium. In this report we analyzed three prophage-like elements that are present in the genomes of Bifidobacterium breve UCC 2003, Bifidobacterium longum NCC 2705, and Bifidobacterium longum DJO10A, designated Bbr-1, Bl-1, and Blj-1, respectively. These prophagelike elements exhibit homology with genes of double-stranded DNA bacteriophages spanning a broad phylogenetic range of host bacteria and are surprisingly closely related to bacteriophages infecting low-G+C bacteria. All three prophage-like elements are integrated in a tRNA(Met) gene, which appears to be reconstructed following phage integration. Analysis of the distribution of this integration site in many bifidobacterial species revealed that the attB sites are well conserved. The Blj-1 prophage is 36.9 kb long and was induced when a B. longum DJO10A culture was exposed to mitomycin C or hydrogen peroxide. The Bbr-1 prophage-like element appears to consist of a noninducible 28.5-kb chimeric DNA fragment composed of a composite mobile element inserted into prophage-like sequences, which do not appear to be widely distributed among B. breve strains. Northern blot analysis of the Bbr-1 prophage-like element showed that large parts of its genome are transcriptionally silent. Interestingly, a gene predicted to encode an extracellular beta-glucosidase carried within the Bbr-1 prophage-like element was shown to be transcribed.
authors.affiliation: Alimentary Pharmabiotic Centre and Department of Microbiology, Biosciences Institute, National University of Ireland, Western Road, Cork, Ireland. marco.ventura@unipr.it
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
authors.forename: Ju-Hoon
authors.initials: JH
authors.lastname: Lee
authors.forename: Carlos
authors.initials: C
authors.lastname: Canchaya
authors.forename: Ralf
authors.initials: R
authors.lastname: Zink
authors.forename: S
authors.initials: S
authors.lastname: Leahy
authors.forename: J A
authors.initials: JA
authors.lastname: Moreno-Munoz
authors.forename: M
authors.initials: M
authors.lastname: O'Connell-Motherway
authors.forename: D
authors.initials: D
authors.lastname: Higgins
authors.forename: Gerald F
authors.initials: GF
authors.lastname: Fitzgerald
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: O'Sullivan
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
mesh_terms: D001483:Base Sequence; D001644:Bifidobacterium / Q000235:genetics / Q000821:virology*; D017931:DNA Primers; D004279:DNA, Viral / Q000235:genetics; D005784:Gene Amplification; D016680:Genome, Bacterial; D016679:Genome, Viral; D023281:Genomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D039002:Prophages / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D014158:Transcription, Genetic; D016662:Virus Integration / Q000235:genetics*
chemical_list: D017931:DNA Primers; D004279:DNA, Viral