Once inside a cell, phage adopt one of two strategies. The first is to go through a straightforward round of replication, using their host’s machinery. The second is to stick around a while. To do that, the phage inserts its genome into that of its host, creating an addition called a “prophage” that will be propagated indefinitely through cell replication. At some point in the future, usually in response to a stress that threatens the host, the prophage uses special DNA sequences at its ends akin to an ejection seat to pop its genes back out of the host genome, and carry out a normal viral replication and release cycle. Prophage are not simply passengers, though. Some confer a beneficial function on the host; a filamentous inophage carries the human-disease-causing “cholera toxin” in the Vibrio cholerae genome. Prophage also offer a source of genetic diversity to their host. Mutations sometimes alter the ejection sequences, rendering a prophage a permanent part of the genome, or genetic recombination may shuffle some or part of the prophage into a different part of the genome. Further evolution may then put these pieces to new use. This may be how bacteria got the contractile weapons you saw in the last chapter, repurposing genes encoding phage tail components.
Whether the phage replicates immediately or waits a while as a prophage first, once the cycle of replication and release starts it is rapid. The virus hijacks the cell’s protein-making machinery to churn out packaging proteins like capsid, and its replication machinery to churn out copies of the genome. Genomes are quickly (and very densely) packed into new heads, tails attached if necessary, and the mature phage released. Not all phage lyse their hosts; some filamentous phage (which are commonly beneficial) use secretion machinery to exit without harm. Most, though, use proteins that self-assemble into ports in the inner membrane, allowing another phage-encoded protein to access and chew up the cell wall, causing the cell to lyse. Here you can see a snapshot of this process in a Vibrio cholerae cell infected by a phage that is not its virulence-enhancing friend. The phage is replicating, and has just lysed the cell to make its escape.