Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivanus, and Lactobacillus casei

Marco Ventura, Carlos Canchaya, Valentina Bernini, Eric Altermann, Rodolphe Barrangou, Stephen McGrath, Marcus J. Claesson, Yin Li, Sinead Leahy, Carey D. Walker, Ralf Zink, Erasmo Neviani, Jim Steele, Jeff Broadbent, Todd R. Klaenhammer, Gerald F. Fitzgerald, Paul W. O'Toole, Douwe Van Sinderen

Research output: Contribution to journalArticlepeer-review

57 Scopus citations

Abstract

Lactobacillus gasseri ATCC 33323, Lactobacillus salivarius subsp. salivarius UCC 118, and Lactobacillus casei ATCC 334 contain one (Lga1), four (Sal1, Sal2, Sal3, Sal4), and one (Lca1) distinguishable prophage sequences, respectively. Sequence analysis revealed that LgaI, Lca1, Sal1, and Sal2 prophages belong to the group of Sfi11-like pac site and cos site Siphoviridae, respectively. Phylogenetic investigation of these newly described prophage sequences revealed that they have not followed an evolutionary development similar to that of their bacterial hosts and that they show a high degree of diversity, even within a species. The attachment sites were determined for all these prophage elements; LgaI as well as Sal1 integrates in tRNA genes, while prophage Sal2 integrates in a predicted arginino-succinate lyase-encoding gene. In contrast, Lca1 and the Sal3 and Sal4 prophage remnants are integrated in noncoding regions in the L. casei ATCC 334 and L. salivarius UCC 118 genomes. Northern analysis showed that large parts of the prophage genomes are transcriptionally silent and that transcription is limited to genome segments located near the attachment site. Finally, pulsed-field gel electrophoresis followed by Southern blot hybridization with specific prophage probes indicates that these prophage sequences are narrowly distributed within lactobacilli.

Original languageEnglish (US)
Pages (from-to)3130-3146
Number of pages17
JournalApplied and environmental microbiology
Volume72
Issue number5
DOIs
StatePublished - May 2006

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

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