The Defective Prophage Pool of Escherichia coli O157: Prophage–Prophage Interactions Potentiate Horizontal Transfer of Virulence Determinants

et al. (2009) The Defective Prophage Pool of Escherichia coli O157: Prophage-Prophage Interactions Potentiate Horizontal Transfer of Virulence Determinants. PLoS Pathog 5(5): e1000408. doi:10.1371/journal.ppat.1000408 The Defective Prophage Pool of Escherichia coli O157: Prophage-Prophage Interactions Potentiate Horizontal Transfer of Virulence Determinants Md Asadulghani 0 Yoshitoshi Ogura 0 Tadasuke Ooka 0 Takehiko Itoh 0 Akira Sawaguchi 0 Atsushi 0 Iguchi 0 Keisuke Nakayama 0 Tetsuya Hayashi 0 Howard Ochman, University of Arizona, Tucson, United States of America 0 1 Division of Bioenvironmental Sciences, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan, 2 Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan, 3 Division of Microbiology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan, 4 Advanced Sciences Innovation Group, Mitsubishi Research Institute, Inc., Tokyo, Japan, 5 Bio-Frontier Research Center, Tokyo Institute of Technology , Kanagawa , Japan , 6 Department of Anatomy, Ultrastructural Cell Biology, Faculty of Medicine, University of Miyazaki , Miyazaki , Japan Bacteriophages are major genetic factors promoting horizontal gene transfer (HGT) between bacteria. Their roles in dynamic bacterial genome evolution have been increasingly highlighted by the fact that many sequenced bacterial genomes contain multiple prophages carrying a wide range of genes. Enterohemorrhagic Escherichia coli O157 is the most striking case. A sequenced strain (O157 Sakai) possesses 18 prophages (Sp1-Sp18) that encode numerous genes related to O157 virulence, including those for two potent cytotoxins, Shiga toxins (Stx) 1 and 2. However, most of these prophages appeared to contain multiple genetic defects. To understand whether these defective prophages have the potential to act as mobile genetic elements to spread virulence determinants, we looked closely at the Sp1-Sp18 sequences, defined the genetic defects of each Sp, and then systematically analyzed all Sps for their biological activities. We show that many of the defective prophages, including the Stx1 phage, are inducible and released from O157 cells as particulate DNA. In fact, some prophages can even be transferred to other E. coli strains. We also show that new Stx1 phages are generated by recombination between the Stx1 and Stx2 phage genomes. The results indicate that these defective prophages are not simply genetic remnants generated in the course of O157 evolution, but rather genetic elements with a high potential for disseminating virulence-related genes and other genetic traits to other bacteria. We speculate that recombination and various other types of inter-prophage interactions in the O157 prophage pool potentiate such activities. Our data provide new insights into the potential activities of the defective prophages embedded in bacterial genomes and lead to the formulation of a novel concept of inter-prophage interactions in defective prophage communities. - Funding: This work was supported by a Grant-in-Aid (17019058) for Scientific Research on Priority Areas in the area of Applied Genomics from the Ministry of Education, Science, and Technology of Japan to TH and by grants (ARLAB2007-95 and ARLAB2008-92) from the Yakult Foundation to TH. MA was supported by the Education and Research Project for Zoonosis of University of Miyazaki and by a research grant (P06244) from the Japan Society for the Promotion of Science (JSPS). Funding agencies had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Horizontal gene transfer (HGT) is a major mechanism involved in bacterial evolution. In HGT between bacteria, viruses known as bacteriophages (or phages) play particularly important roles as gene transfer vehicles [1,2]. Incoming temperate bacteriophages parasitize their hosts by integrating their genomes into the host genetic material. The additional genetic information that they provide to the host bacterium encodes various novel abilities, such as niche adaptation and the production of new virulence factors [2,3]. Although phage-mediated HGT was first described in the 1950s in the conversion of Corynebacterium diphtheriae strains that did not produce a toxin to strains that did [4], studies in recent decades have identified a number of virulence determinants carried by phages [13,57]. Furthermore, because numerous bacterial genomes have been sequenced, it has become increasingly clear that many bacterial genomes contain multiple prophages carrying a variety of genes [8]. However, the prophages identified from the genome sequences often contain genetic defects, such as deletions or disruptions of genes required for phage induction and propagation. Thus, such prophages are regarded simply as genetic remna (...truncated)