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Applied and Environmental Microbiology, May 2006, p. 3130-3146, Vol. 72, No. 5
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.5.3130-3146.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Comparative Genomics and Transcriptional Analysis of Prophages Identified in the Genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei{dagger}

Marco Ventura,1,2* Carlos Canchaya,1 Valentina Bernini,2 Eric Altermann,3 Rodolphe Barrangou,3 Stephen McGrath,1 Marcus J. Claesson,1 Yin Li,1 Sinead Leahy,1 Carey D. Walker,4 Ralf Zink,5 Erasmo Neviani,2 Jim Steele,6 Jeff Broadbent,7 Todd R. Klaenhammer,3 Gerald F. Fitzgerald,1 Paul W. O'Toole,1 and Douwe van Sinderen1

Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland,1 Department of Genetics, Anthropology and Evolution, University of Parma, Parma, Italy,2 Genomic Sciences Program and Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, North Carolina,3 Chr. Hansen, Milwaukee, Wisconsin,4 Department of Nutrition and Health, Cognis, Dusseldorf, Germany,5 Department of Food Sciences, University of Wisconsin-Madison, Madison, Wisconsin,6 Department of Nutrition and Food Sciences, Utah State University, Logan, Utah7

Received 21 December 2005/ Accepted 16 February 2006

Lactobacillus gasseri ATCC 33323, Lactobacillus salivarius subsp. salivarius UCC 118, and Lactobacillus casei ATCC 334 contain one (LgaI), 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.

* Corresponding author. Mailing address: Department of Genetics, Anthropology and Evolution, University of Parma, Parco Area delle Scienze 11/a, 43100 Parma, Italy. Phone: 39 521 906236. Fax: 39 521 905604. E-mail: marco.ventura{at}unipr.it.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, May 2006, p. 3130-3146, Vol. 72, No. 5
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.5.3130-3146.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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Copyright © 2006 by the American Society for Microbiology. All rights reserved.