Questions: Temperate Phages and Lysogenic Pathways

Question 1

A bacterium harboring a lambda prophage is exposed to UV radiation. Which outcome is most likely?

• A. Nothing happens — the CI repressor protects the phage DNA from UV-induced damage
• B. The prophage induces into the lytic cycle after RecA-mediated cleavage of the CI repressor
• C. The prophage excises but remains as a circular episome without replicating
• D. The bacterium immediately lyses because UV light directly activates lytic gene expression

Answer: (B)

UV damage activates the bacterial SOS response, which stimulates RecA protein. RecA then promotes autocatalytic cleavage of the CI repressor. With CI destroyed, lytic genes are derepressed, the prophage excises (via excisionase), and the phage enters the lytic cycle. The CI repressor maintains lysogeny under normal conditions but is deliberately designed to be destroyed when the host is under mortal threat.

Question 2

During stable lysogeny, what is the function of the CI repressor?

• A. It degrades phage structural proteins to prevent accidental particle assembly
• B. It catalyzes site-specific recombination to keep the prophage integrated in the chromosome
• C. It binds operator regions on the phage chromosome and silences lytic gene transcription
• D. It activates host restriction enzymes to destroy any re-infecting phage particles

Answer: (C)

The CI repressor (lambda repressor) binds to OL and OR operator sites on the phage DNA, blocking transcription of lytic cycle genes — including those encoding Cro protein, replication proteins, and structural components. Low-level continuous CI production maintains this silenced state through cell divisions. Integration is catalyzed by integrase, not CI, and CI does not degrade proteins or activate restriction systems.

Question 3

During lysogeny, the prophage DNA replicates along with the host chromosome every time the bacterium divides, and each daughter cell inherits a copy.

• T. True
• F. False

Answer: True

Once integrated, the prophage is indistinguishable from any chromosomal locus — it is replicated by the host's own DNA polymerase and partitioned into both daughter cells at division. No new phage particles are produced. This passive inheritance is why a single infection event can spread a prophage through an entire bacterial population over generations without any sign of lytic activity.

Question 4

When lambda phage first infects a bacterium, the lytic cycle automatically occurs because the CI repressor is not yet present at the start of infection.

• T. True
• F. False

Answer: False

The lytic vs. lysogenic decision is made during the initial infection, not after CI builds up. Both CI and Cro proteins are transcribed shortly after phage DNA injection, and their relative accumulation — shaped by multiplicity of infection, host nutritional state, and other signals — determines which pathway dominates. High multiplicity of infection favors lysogeny; well-fed, rapidly growing hosts favor lysis. The phage does not simply default to lysis because CI is initially absent.

Question 5

Why does severe DNA damage to the bacterial host cell trigger a dormant prophage to enter the lytic cycle?

Model answer: DNA damage activates the bacterial SOS response, which induces RecA protein to stimulate autocatalytic cleavage of the CI repressor. With CI destroyed, lytic genes are derepressed and the phage switches to replication — it escapes from a host that is likely doomed.

The CI repressor is the molecular switch maintaining lysogeny, and it is engineered to be destroyed precisely when host viability is threatened. The phage does not directly detect DNA damage; instead, it monitors host stress indirectly via RecA activity. This is adaptive: abandoning a doomed host and producing many progeny phage particles is far better than replicating passively with a cell that is about to die.