Lysis‐lysogeny coexistence: prophage integration during lytic development

Abstract

The infection of Escherichia coli cells by bacteriophage lambda results in bifurcated means of propagation, where the phage decides between the lytic and lysogenic pathways. Although traditionally thought to be mutually exclusive, increasing evidence suggests that this lysis‐lysogeny decision is more complex than once believed, but exploring its intricacies requires an improved resolution of study. Here, with a newly developed fluorescent reporter system labeling single phage and E. coli DNAs, these two distinct pathways can be visualized by following the DNA movements in vivo. Surprisingly, we frequently observed an interesting “lyso‐lysis” phenomenon in lytic cells, where phage integrates its DNA into the host, a characteristic event of the lysogenic pathway, followed by cell lysis. Furthermore, the frequency of lyso‐lysis increases with the number of infecting phages, and specifically, with CII activity. Moreover, in lytic cells, the integration site attB on the E. coli genome migrates toward the polar region over time, leading to more spatial overlap with the phage DNA and frequent colocalization/collision of attB and phage DNA, possibly contributing to a higher chance for DNA integration.

High-resolution studies of lysis–lysogeny decision-making in bacteriophage lambda

“…Using the ParB/parS system, researchers observed that in lysogenic cells, the bacterial attB locus migrated toward the largely stationary phage DNA over time to possibly facilitate integration (62). A similar behavior was observed using the SeqA-FP system to label lambda DNA and a tetO/TetR system to label bacterial attB in lysogenic cells (37). Even in lytic cells, attB generally converges with lambda DNA-rich regions in an integrase-independent manner, leading to more co-localization of attB and lambda DNA (37).…”

“…Methylated phage DNA was tracked by the binding of SeqA-FP, and E. coli DNA was labeled at the attB (the lambda DNA integration site) locus with an inserted tetO array being bound by TetR-FP. Combined with cell-fate reporter systems, lambda DNA integration indicative of the lysogenic pathway was observed for lytic cells (37). This suggests that subcellular phage entities show a degree of individuality and can behave differently from each other.…”

“…This idea marked a profound shift in our preconceptions about viruses, where we were now required to think about the hidden complexity of viral behaviors. Following this perspective, it was reported that both lytic and lysogenic choices could proceed simultaneously during infections, resulting in "lyso-lysis," where prophages were integrated into cells prior to lysis (37). In this study, phage behav-iors were dissected at the single-DNA level using fluorescent reporters tracking phage and E. coli DNA in vivo in real time.…”

Pelagiphages in the Podoviridiae family integrate into host genomes

“…It is possible that prophage is not able to stably integrate during the infection, the prophage-SAR11 genome coexistence is temporary in order to keep host genome streamlined. Recently, a “lyso-lysis” phenomenon was observed in bacteriophage lambda, where phage integration was followed by a lytic life cycle (61) and the frequency of lyso-lysis increases with the number of infecting phages. Even this bacteria-phage genome coexistence is likely temporary, still provides a window for evolution of mutually benefical functions (62).…”

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

“…When environmental conditions are favorable, e.g., abundant host cells living in copiotrophic conditions, the lytic cycle is preferred, but when hosts are scarce, the infecting phages may decide for the lysogenic cycle (Oppenheim et al, 2005;Zeng et al, 2010;Koskella and Brockhurst, 2014;Obeng et al, 2016). If phage concentration inside the cell is high enough phages will decide for the lysogenic cycle (Zeng et al, 2010;Shao et al, 2017). As shown recently (Erez et al, 2017), phages may have sophisticated mechanisms for sensing host abundance.…”