Prophage genomics reveals patterns in phage genome organization and replication

Han Suh Kang; Katelyn McNair; Daniel A. Cuevas; Barbara A. Bailey; Anca M. Segall; Robert A. Edwards

Phages are major drivers in global biogeochemical cycles through the control they exert on bacterial populations. Despite their abundance in the environment they are under-represented in sequence databases and knowledge-bases. Phages' two life cycles, the lytic and lysogenic cycles, provide a unique window into phage genomics. During the lysogenic cycle, temperate phages integrate their genomes into their host's genome in a non-lethal fashion to generate a region of DNA known as a prophage -either as a plasmid (1) or by directly recombining with the host's genome (2, 3) . The phage replicates in the host genome until external signals promote a transition to the lytic cycle, at which point the phage hijacks the host's cellular DNA replication machinery in order to replicate the phage genome, and adopts the host's protein synthesis machinery to create new phage particles. Eventually the phage lyse releases infective particles to find new hosts to attack.