Gene Regulation Strategy In Bacteriophage:

• Bacteriophage lambda (λ) is a temperate phage that infects the bacterium E.coli. After infecting host cells, lambda phage can follow one of two alternative cycles: lytic and lysogenic cycles.
• Lysogeny maintaintains long term relationship between host bacterium and parasitic bacteriophage, hence, Bacteriophage have evolved gene regulation strategy to offer tight regulation of lytic pathway gene.
• Lambda bacteriophage have evolved tight regulation of lysogeny. They takes lysogenic induction (termination of lysogeny to lytic cycle) only when there are damages in bacterial DNA because of mutagens (mainly caused by UV radiation).
• Bacteria have evolved Restriction Endonuclease to impart defense against bacteriophage to counter this defense, many bacteriophages have evolved restriction site methylation.

GENES OF LAMBDA PHAGE:

• There are three classes of genes in phage genome that regulates whether the lytic or lysogenic cycle will emerge- 

1. Immediate early gene - Cro, CII & N gene
2. Delayed early genes - replication gene O, P and Q
3. Late genes

• Genes that favour the lysogenic and lytic cycle are:

1. Genes favouring lysogenic Cycle - cI, cII, cIII, int and N gene.
2. Genes favouring lytic Cycle - cro, Q and xis.

GENE FAVOURING LYSOGENY:

1. cI gene : 'c' stands for 'clear' as in clear plaque mutant. It was reported that bacterial colonies in culture were cleary developed when bacteriophage have wild type cI gene.

• cI mutation formed lytic plaque in colony.
• cI codes for "λ repressor" protein.
• λ repressor acts as strong repressor and offers tight regulation to cro gene.
• λ repressor made up of 236 amino acid residues and folds into a structure ressembling a dumbbell, with two domains separated.The C-terminal domains associate to form dimers, the N-terminal domains bind DNA. The repressor exists primarily as a homodimer.

Fig: A repressor binds to three sites in the right operator

• λ repressor can bind at three operators and sequence of binding affinity is OR1 > OR2 > OR3.
• λ repressor has strong affinity to bind at OR1 which is the operator of cro gene. Large number of λ repressor binds at OR1 due to the feature of dimerization & tetramerization thus tight blocking of cro gene and leaving no chance of leaky expression.
• λ repressor also acts as autoactivator as it binds at OR2 with medium affinity and activates α- NTD (N- terminal domain) of RNA polymerase of PRM (Promoter Repressor Maintenance) thus, increases its own production.
• λ repressor also acts as autorepressor as it can bind with poor affinity at OR3, thus, blocking transcription of cI but it happens only when the concentration of λ repressor is lysogenized bacterial cell increases upto 20 fold over threshold.
• PRM is the weak promoter, hence, it requires activation. PRM is activated by cII.

Fig: In the lysogenic state, Repressor are bound to OR1 and OR2, but not to OR3 which allows RNA polymerase to binds to PRM and trancribe the cI gene

2. cII gene : Transcribed by PL promoter (Promoter Leftward), cII protein acts as activator of PRM and it prepares PRM for RNA polymerase binding but cII is highly unstable protein because bacteria 'Hfl' protein (High frequency of lysogeny) causes degradation of cII.

• Hfl is an evolution of bacterial cell to prevent lysogeny.
• cIII protein is evolved by bacteriophage to protects cII from Hfl mediated degradation.

3. cIII gene : Transcribed by RNA polymerase of PRE (Promoter Repressor Establishment) 

• cIII protects cII from Hfl mediated degradation.

4. N-gene : Transcribed with cII & forms N-protein. 

• N- protein prevents Rho dependent transcription termination of cI gene. Thus, N-protein is an antiterminator of cI.
• N-protein binds at Rho utilisation sites of cI mRNA thus, blocking the binding of Rho and no premature transcription termination.

EXPRESSION SEQUENCE OF LYSOGENIC GENES:

               cIII → cII → N→ cI

LYSOGENIC INDUCTION:

• Termination of Lysogeny to lytic cycle.
• Lambda bacteriophage shows lysogenic induction when the cytosolic level of Rec A protein is increased in bacterial cell.
• Rec A protein is synthesized by bacterium when the amount of single stranded DNA increases.
• Single stranded DNA increased in bacterial cell due to-

1. Paused DNA polymerases at pyrimidine dimers while helicase unwinding the DNA.
2. Pick up of DNA through transformation or conjugation mechanism.
3. Increase in temperature may causes generation of ssDNA.

• λ repressor of bacteriophage has an evolutionary novality as it takes autocleavage upon interaction with Rec A.

Fig: Activated RecA protein cleaves repressor which then cannot dimerize

GENES FAVOURING LYTIC CYCLE:

• Upon autocleavage of λ repressor, cro gene is switched on.
• cro (Control of Repressor) gene acts as negative regulator of cIII, cII & cI. Futher, cro gene induces the expression of xis gene &Q gene.
• xis gene codes for excisase enzyme which cuts to separate the phage DNA from bacterial DNA.
• Q gene coded Q-protein acts as antiterminator of cro gene.

The decision between lysis and lysogeny is, therefore, determined by the outcome of a race between cI and cro. If the cI repressor is synthesized more quickly than the cro repressor, the lysogeny follows. However, if cro wins the race, then the cro repressor block cI expression before enough cI repressor has been synthesized to silence the cro gene. As a result, the phage follows the lytic cycle. The decision appear to the random, depending on chance events that lead to either the cI or the cro repressor accumulating the quickest in the cell.