Prophages

A prophage is a phage genome that has integrated into a bacterial chromosome or exists as a plasmid-like element within the lysogenic cycle. It results from infection by a temperate bacteriophage and is maintained by phage-encoded repressors that suppress lytic genes. In a lysogen, the bacterial host is immune to superinfection by related phages due to the prophage-encoded repressor, and the prophage may contribute new traits to the host, a phenomenon known as lysogenic conversion.

Integration occurs by site-specific recombination between the phage attachment site (attP) and the bacterial attachment site (attB), typically mediated by an integrase enzyme. The integrated genome is flanked by attL and attR; upon induction, recombination reconstitutes attP and attB and triggers excision. Induction can be caused by DNA damage or stress, activating the host SOS response and RecA, which promotes cleavage of the phage repressor (e.g., cI). This leads to the lytic cycle, genome replication, assembly of phage particles, and host cell lysis.

Prophages can harbor genes that affect host phenotype, including toxins, virulence factors, and metabolic functions, contributing to bacterial ecology and evolution. Examples include CTXφ in Vibrio cholerae, which carries cholera toxin genes, and various lambda-like (lambdoid) prophages in Escherichia coli. Prophage genomes are frequently detected in bacterial genome analyses as prophage regions or genomic islands and are a major mechanism of horizontal gene transfer.