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Applied and Environmental Microbiology, August 2008, p. 4601-4609, Vol. 74, No. 15
0099-2240/08/$08.00+0     doi:10.1128/AEM.00010-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Genome Sequence and Characteristics of Lrm1, a Prophage from Industrial Lactobacillus rhamnosus Strain M1 ^,

Evelyn Durmaz,^1, Michael J. Miller,^1,, M. Andrea Azcarate-Peril,¹ Stephen P. Toon,³ and Todd R. Klaenhammer^1,2*

Departments of Food, Bioprocessing, and Nutrition Sciences,¹ Microbiology, North Carolina State University, Raleigh, North Carolina 27695,² Verenium Corporation, San Diego, California 92121³

Received 2 January 2008/ Accepted 2 May 2008

Prophage Lrm1 was induced with mitomycin C from an industrial Lactobacillus rhamnosus starter culture, M1. Electron microscopy of the lysate revealed relatively few intact bacteriophage particles among empty heads and disassociated tails. The defective Siphoviridae phage had an isometric head of approximately 55 nm and noncontractile tail of about 275 nm with a small baseplate. In repeated attempts, the prophage could not be cured from L. rhamnosus M1, nor could a sensitive host be identified. Sequencing of the phage Lrm1 DNA revealed a genome of 39,989 bp and a G+C content of 45.5%. A similar genomic organization and mosaic pattern of identities align Lrm1 among the closely related Lactobacillus casei temperate phages A2, AT3, and LcaI and with L. rhamnosus virulent phage Lu-Nu. Of the 54 open reading frames (ORFs) identified, all but 8 shared homology with other phages of this group. Five unknown ORFs were identified that had no homologies in the databases nor predicted functions. Notably, Lrm1 encodes a putative endonuclease and a putative DNA methylase with homology to a methylase in Lactococcus lactis phage Tuc2009. Possibly, the DNA methylase, endonuclease, or other Lrm1 genes provide a function crucial to L. rhamnosus M1 survival, resulting in the stability of the defective prophage in its lysogenic state. The presence of a defective prophage in an industrial strain could provide superinfection immunity to the host but could also contribute DNA in recombination events to produce new phages potentially infective for the host strain in a large-scale fermentation environment.

Published ahead of print on 6 June 2008.

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

E.D. and M.J.M. contributed equally to this study.

Present address: Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL 61801.