Open AccessProphage-Like Elements in Bifidobacteria: Insights from Genomics, Transcription, Integration, Distribution, and Phylogenetic Analysis
Author(s) -
Marco Ventura,
Ju-Hoon Lee,
Carlos Canchaya,
Ralf Zink,
Sinead C. Leahy,
Jose Antonio Moreno-Munoz,
Mary O’Connell Motherway,
Desmond G. Higgins,
Gerald F. Fitzgerald,
Daniel J. O’Sullivan,
Douwe van Sinderen
Publication year - 2005
Publication title -
applied and environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.552
H-Index - 324
eISSN - 1070-6291
pISSN - 0099-2240
DOI - 10.1128/aem.71.12.8692-8705.2005
Subject(s) - prophage , biology , genetics , genome , bifidobacterium breve , lysogenic cycle , temperateness , phylogenetic tree , bifidobacterium longum , gene , bifidobacterium , microbiology and biotechnology , bacteriophage , bacteria , escherichia coli , lactobacillus
So far, there is only fragmentary and unconfirmed information on bacteriophages infecting the genusBifidobacterium . In this report we analyzed three prophage-like elements that are present in the genomes ofBifidobacterium breve UCC 2003,Bifidobacterium longum NCC 2705, andBifidobacterium 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 tRNAMet gene, which appears to be reconstructed following phage integration. Analysis of the distribution of this integration site in many bifidobacterial species revealed that theattB sites are well conserved. The Blj-1 prophage is 36.9 kb long and was induced when aB. 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 amongB. 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.