Lytic cascade in lambda (λ) phage

Notes on Lambda Phage DNA, Genes Involved in its Life Cycle, and the Lytic-
Lysogenic Switch

Structure of Phage DNA: The lambda (λ) bacteriophage has a linear DNA molecule with
early genes located centrally and late genes at both ends. Upon infection, this linear DNA
circularizes, bringing the late genes together to form a transcription unit. This circular DNA
structure is essential for the lambda phage to decide whether to enter the lytic or lysogenic
life cycle.
Genes Involved in the Life Cycle:

1. Immediate Early Genes (cro and N):

o cro: Controls the suppression of the repressor gene cI, which is necessary for
initiating the lytic cycle. Additionally, cro represses its own transcription and
that of other early genes when no longer needed.
o N: Produces an antiterminator protein that allows the transcription of delayed
early genes, bypassing the need for new promoters or operators.
2. Delayed Early Genes (cII, cIII, and Q):
o cII and cIII: Regulate the synthesis of the repressor encoded by cI, pushing
the phage towards lysogeny.
o Q: Acts as an antiterminator, promoting the transcription of late genes, which
are necessary for lysis.
3. Late Genes:
o Include structural components necessary for assembling new phage particles
and enzymes for host cell lysis.

Lytic and Lysogenic Cycles: The lambda phage can follow two alternative pathways:

 Lytic Cycle: Initiated if the late genes are expressed early in the infection. This
results in the production of new phage particles and the eventual lysis of the host cell.
 Lysogenic Cycle: Occurs if the repressor gene cI is expressed, leading to the
inhibition of late genes and integration of phage DNA into the host genome as a
prophage.

Switching Between Lytic and Lysogenic Cycles:

 The decision between lytic and lysogenic pathways hinges on the expression of the cI
gene. If cI is active, it produces a repressor that inhibits the lytic cycle and maintains
lysogeny. Conversely, if the repressor is inactivated (e.g., by environmental stress or
mutations), the phage exits lysogeny and enters the lytic cycle.
  The cro gene product antagonizes the repressor, favoring the lytic cycle, while cII
and cIII promote the expression of cI, thus favoring lysogeny.

Steps of Gene Expression in the Lambda (λ) Phage: Lytic vs. Lysogenic Life Cycle

A. Lysogenic Life Cycle:

1. Infection and Circularization of Phage DNA:

o After the phage injects its DNA into the host cell, the DNA circularizes, which
is necessary for regulating gene expression efficiently.

2. Early Gene Expression from Promoters PL and PR:

o PL (Left Promoter) initiates the transcription of the N gene on the left side of
the DNA.
o PR (Right Promoter) initiates the transcription of the cro gene to produce cro
protein an antirepressor, on the right side of the DNA.
o The N protein, an antiterminator, allows transcription to proceed beyond the
early termination sites into delayed early genes.
 o

3. Expression of Delayed Early Genes (cII and cIII):

o cII and cIII genes are transcribed. These proteins are critical for the lysogenic
pathway as they activate the PRE promoter (Promoter for repression
establishment for lysogeny).
o CII binding to PRE is highly unstable as bacterial HflA (high frequency
of lysogeny protein produced by the bacteria) protein degrades CII
protein.
o cII and cIII work together to stabilize CII and activate PRE

4. Activation of PRE and Synthesis of Repressor protein (cI):

o PRE initiates the transcription of the cI gene, which encodes the repressor
protein.
o The gene cI (regulator gene coding for repressor) lies in between-P R/OR and
PL/OL control regions and when active, it not only inhibits the expression of
cro and N but also promotes its own expression, so that the repressor has a
dual function and also works as an activator for its own autogenous expression
and regulation.
o The repressor binds to operators OL (associated with PL) and OR in a
sequential order, blocking further transcription from these promoters,
effectively shutting down the lytic genes.

5. Binding of CI Repressor to Operators:

o The cI repressor binds to three operator sites on each side of the phage DNA:
 OL1, OL2, OL3 (associated with PL)
 OR1, OR2, OR3 (associated with PR)
o OR1 and OL1 are the highest affinity binding sites, and the binding of the
repressor here strongly inhibits transcription from PR and PL, respectively.
Thus, there will be no expression of N and cro proteins
o The low cro level leads to the prevention of lytic cycle.
o Blocking of PL also prevents the transcription of N proteins, thus stops the
transcription of CII and CIII.
o At this point binding of CI repressor to OR2 helps to activate transcription
from PRM (Promoter for Maintenance of Repressor), ensuring continued
synthesis of the repressor.
o When the repressor binds to OR3 and OL3, it shuts down PRM as well,
creating a feedback loop that can fine-tune the repressor levels.
o High levels of the CI protein will therefore, lead to the decrease in its own
production, ensuring that it does not accumulate excessively.

6. Maintenance of Lysogeny through Promoter PRM:

o PRM ensures continued low-level transcription of the cI gene, maintaining
lysogeny.
 7. Integration of Phage DNA:
o The phage DNA integrates into the host’s chromosome as a prophage using
intrigrace enzyme, where it remains dormant until conditions change,
potentially switching to the lytic cycle.

B. Lytic Life Cycle:

1. Excision and Induction:

If the host cell experiences stress the lysogenic phage can induce to excise itself from
the host genome and enter into lytic cycle.

The xis gene encodes an excisionase enzyme that works with integrase to reverse the
integration process and this help to excise the viral DNA from the host genome.

2. Early Gene Expression from Promoters PL and PR:

o PL and PR drive the transcription of the N and cro genes, respectively.
o cro plays a crucial role in suppressing cI expression, which is necessary for
the lytic cycle.

3. Action of Cro Protein:

o The cro protein competes with the cI repressor for binding to OR and OL
sites.
o Cro has a higher affinity for OR3 and OL3, and binding here represses PRM,
preventing the synthesis of cI repressor, thereby promoting the lytic cycle.

4. Expression of Delayed Early Genes (cII, cIII, and Q):

o The Q gene is transcribed from PR’ (a promoter downstream of PR). Q acts
as an antiterminator, allowing the transcription of late genes necessary for the
lytic cycle.

5. Activation of Late Gene Transcription by Q:

o The Q an antiterminator protein enables the transcription of late genes from
PR’, which include genes responsible for phage particle assembly and lysis of
the host cell.

6. Assembly and Lysis:

o Late genes code for the structural components of the phage and lytic enzymes.
o The phage assembles, and the host cell is lysed, releasing new phage particles
to infect other cells.
Switch Between Lysogenic and Lytic Cycle:

 The decision between lysogeny and lysis hinges on the balance between cI (repressor)
and cro. If cII levels are high enough, it activates PE, leading to cI production and
lysogeny. However, cII is highly susceptible to degradation by the host bacterial
protein HflA (FtsH), which is an ATP-dependent protease.
 HflA/FtsH degrades cII, lowering the chances of establishing lysogeny, particularly
under conditions where the bacterial cell is healthy and growing rapidly.
 If cII is degraded and fails to activate PE, cro will dominate, repressing cI production
and driving the phage into the lytic cycle.