Lysogeny

Abstract Lysogeny is the harbouring of a dormant bacteriophage (phage) genome in a growing bacterial host. The well‐studied coliphage lambda system provided the paradigm for the role of regulatory proteins in determining the fate of the infected cell (lysis vs lysogeny) as well as the role of environmental signals that influence this decision. Studies of lambda also led to the classic models for site‐specific integration of phage DNA into the bacterial chromosome and for prophage induction during the SOS response by RecA‐mediated repressor cleavage. Beyond a common requirement for a phage‐encoded repressor to maintain lysogeny, phages other than lambda exhibit substantial diversity in the mechanisms underlying regulation of the lysis/lysogeny decision, integration, and prophage induction. Lysogeny has profound consequences on bacterial evolution, leading to acquisition of new traits, enhanced bacterial fitness, gene disruption and/or genomic rearrangements. Phages that are capable of lysogeny provide a reservoir of genetic diversity for their hosts. Key Concepts Lysogeny is widespread; prophages are present in ∼1/2 of all sequenced bacterial chromosomes, and many strains carry multiple prophages. Regulation of the phage lysis/lysogeny decision is an example of a bistable gene expression circuit. DNA looping occurs when protein molecules which bind to noncontiguous DNA sites also bind to each other, bringing together DNA sites that are normally some distance apart. Some temperate phages can perpetuate their genomes without integration into the chromosome by plasmid formation, where phage genomes replicate autonomously to keep pace with cell division. Prophage induction is the activation of a prophage to enter the lytic cycle, either spontaneously or by treating lysogenic cells with various agents. Specialised recombination protein machineries are required to establish phage integration. These can be host or phage encoded and bind to dsDNA sequences to catalyse recombination. Site‐specific recombination, which entails breakage and joining of DNA at specific sequences, is used by phages and plasmids and facilitates separation of daughter chromosomes in bacterial cell division. In transposition, some DNA elements, including phage genomes, move from one site to another by action of transposases encoded by the element. Temperate phages provide a mobile genetic reservoir that allows bacteria to adapt to new environments. Prophage‐encoded accessory genes provide new traits that can enhance bacterial fitness or virulence. Lysogeny is transient, allowing bacteria plasticity in their responses to environmental challenges.