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

Abstract

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.

Evolution of the Stx2-Encoding Prophage in Persistent Bovine Escherichia coli O157:H7 Strains

“…The mixture was incubated at 4°C overnight and then centrifuged at 10,000 ϫ g for 1 h to pellet the phage particles. The pellets were suspended in SM buffer (0.58% NaCl, 0.25 MgSO 4 ·7H 2 O, 1 M Tris-Cl [pH 7.5], 0.01% gelatin) (35) and stored at 4°C.…”

Escherichia coli Serotype O55:H7 Diversity Supports Parallel Acquisition of Bacteriophage at Shiga Toxin Phage Insertion Sites during Evolution of the O157:H7 Lineage

“…In the O157:H7 Sakai strain, most phage boundaries excluded the attL, allowing the sequence of preceding tRNA or other genes to remain intact (26). However, att core regions were subsequently redefined for some Sakai prophages (2). In most cases, the original Sakai att regions were used to define phage boundaries in strain RM12579 (see Table S1 in the supplemental material).…”

Within-host competition determines reproductive success of temperate bacteriophages

“…Bacteria are susceptible to many phages, which can integrate into the same host genome if they use different insertion sites (Campbell, 2003). Consequently, polylysogens, cells harboring several different prophages, are found in a variety of bacterial species (Reynolds et al, 1988;Espeland et al, 2004;Asadulghani et al, 2009). Finally, phages contain a vast amount of genetic diversity, to which recombination has contributed an important part, indicating that multiple infections have always played a role in phage biology (Hendrix, 2002).…”