1. Chapter 27 Phage Strategies

2. 27.1 Introduction bacteriophage (or phage) – A bacterial virus.
lytic infection – Infection of a bacterium by a phage that ends in the destruction of the bacterium with release of progeny phage.
lysis – The death of bacteria at the end of a phage infective cycle when they burst open to release the progeny of an infecting phage (because phage enzymes disrupt the bacterium’s cytoplasmic membrane or cell wall).

3. FIGURE 01: A phage may follow the lytic or lysogenic pathway
27.1 Introduction
FIGURE 01: A phage may follow the lytic or lysogenic pathway

4. 27.1 Introduction
virulent phage – A bacteriophage that can only follow the lytic cycle.
prophage – A phage genome covalently integrated as a linear part of the bacterial chromosome.
lysogeny – The ability of a phage to survive in a bacterium as a stable prophage component of the bacterial genome.

5. 27.1 Introduction
temperate phage – A bacteriophage that can follow the lytic or lysogenic pathway.
integration – Insertion of a viral or another DNA sequence into a host genome as a region covalently linked on either side to the host sequences.
excision – Release of phage from the host chromosome as an autonomous DNA molecule.

6. 27.1 Introduction
induction of phage – A phage’s entry into the lytic (infective) cycle as a result of destruction of the lysogenic repressor, which leads to excision of free phage DNA from the bacterial chromosome.
plasmid – Circular, extrachromosomal DNA. It is autonomous and can replicate itself.
episome – A plasmid able to integrate into bacterial DNA.

7. 27.2 Lytic Development Is Divided into Two Periods
A phage infective cycle is divided into the early period (before replication) and the late period (after the onset of replication).
A phage infection generates a pool of progeny phage genomes that replicate and recombine.
FIGURE 02: Phages reproduce in lytic development

8. 27.3 Lytic Development Is Controlled by a Cascade
cascade – A sequence of events, each of which is stimulated by the previous one.
Transcriptional regulation is divided into stages, and at each stage one of the genes that is expressed encodes a regulator needed to express the genes of the next stage.
FIGURE 03: Lytic development is a regulatory cascade

9. 27.3 Lytic Development Is Controlled by a Cascade
The early (or immediate early) genes transcribed by host RNA polymerase following infection include, or comprise, regulators required for expression of the middle (or delayed early) set of phage genes.
The middle group of genes includes regulators to transcribe the late genes.
This results in the ordered expression of groups of genes during phage infection.

10. 27.4 Two Types of Regulatory Events Control the Lytic Cascade
Regulator proteins used in phage cascades may sponsor initiation at new (phage) promoters or cause the host polymerase to read through transcription terminators.
FIGURE 06: RNA polymerase controls promoter recognition.

11. 27.5 The Phage T7 and T4 Genomes Show Functional Clustering
Genes concerned with related functions are often clustered.
FIGURE 08: T4 genes show functional clustering

12. 27.5 The Phage T7 and T4 Genomes Show Functional Clustering
Phages T7 and T4 are examples of regulatory cascades in which phage infection is divided into three periods.
FIGURE 09: T4 genes fall into two general groups

13. 27.6 Lambda Immediate Early and Delayed Early Genes Are Needed for Both Lysogeny and the Lytic Cycle
Lambda has two immediate early genes, N and cro, which are transcribed by host RNA polymerase.
The N gene is required to express the delayed early genes.
Three of the delayed early genes are regulators.

14. FIGURE 10: Lambda has two lifestyles
27.6 Lambda Immediate Early and Delayed Early Genes Are Needed for Both Lysogeny and the Lytic Cycle
Lysogeny requires the delayed early genes cII-cIII.
The lytic cycle requires the immediate early gene cro and the delayed early gene Q.
FIGURE 10: Lambda has two lifestyles

15. 27.7 The Lytic Cycle Depends on Antitermination by pN
pN is an antitermination factor that allows RNA polymerase to continue transcription past the ends of the two immediate early genes.
pQ is the product of a delayed early gene and is an antiterminator that allows RNA polymerase to transcribe the late genes.
FIGURE 12: Similar controls apply to left and right transcription

16. 27.7 The Lytic Cycle Depends on Antitermination by pN
Lambda DNA circularizes after infection; as a result, the late genes form a single transcription unit.
FIGURE 13: Lambda has three stages of development

17. 27.8 Lysogeny Is Maintained by the Lambda Repressor Protein
The lambda repressor, encoded by the cI gene, is required to maintain lysogeny.
The lambda repressor acts at the OL and OR operators to block transcription of the immediate early genes.
The immediate early genes trigger a regulatory cascade; as a result, their repression prevents the lytic cycle from proceeding.
FIGURE 15: Repressor maintains lysogeny

18. 27.9 The Lambda Repressor and Its Operators Define the Immunity Region
immunity – In phages, the ability of a prophage to prevent another phage of the same type from infecting a cell.
virulent mutations – Phage mutants that are unable to establish lysogeny.

19. 27.9 The Lambda Repressor and Its Operators Define the Immunity Region
Several lambdoid phages have different immunity regions.
A lysogenic phage confers immunity to further infection by any other phage with the same immunity region.
FIGURE 16: RNA polymerase initiates at Pl and Pr but not at Prm during the lytic cycle.

20. 27.10 The DNA-Binding Form of the Lambda Repressor Is a Dimer
A repressor monomer has two distinct domains.
The N-terminal domain contains the DNA-binding site.
The C-terminal domain dimerizes.
Binding to the operator requires the dimeric form so that two DNA-binding domains can contact the operator simultaneously.

21. 27.10 The DNA-Binding Form of the Lambda Repressor Is a Dimer
Cleavage of the repressor between the two domains reduces the affinity for the operator and induces a lytic cycle.
FIGURE 18: Repressor cleavage induces lytic cycle

22. 27.11 Lambda Repressor Uses a Helix-Turn-Helix Motif to Bind DNA
Each DNA-binding region in the repressor contacts a half-site in the DNA.
The DNA-binding site of the repressor includes two short α-helical regions that fit into the successive turns of the major groove of DNA (helix-turn-helix).
A DNA-binding site is a (partially) palindromic sequence of 17 bp.
FIGURE 19: The operator is a palindrome

23. 27.11 Lambda Repressor Uses a Helix-Turn-Helix Motif to Bind DNA
The amino acid sequence of the recognition helix makes contacts with particular bases in the operator sequence that it recognizes.
FIGURE 22: Helix-3 determines DNA-binding specificity

24. 27.12 Lambda Repressor Dimers Bind Cooperatively to the Operator
Repressor binding to one operator increases the affinity for binding a second repressor dimer to the adjacent operator.
The affinity is 10× greater for OL1 and OR1 than other operators, so they are bound first.
Cooperativity allows repressor to bind the OL2/OR2 sites at lower concentrations.
FIGURE 25: Lambda repressors bind DNA cooperatively

25. 27.13 Lambda Repressor Maintains an Autoregulatory Circuit
The DNA-binding region of repressor at OR2 contacts RNA polymerase and stabilizes its binding to PRM.
This is the basis for the autoregulatory control of repressor maintenance.
Repressor binding at OL blocks transcription of gene N from PL.
FIGURE 26: Repressor maintains lysogeny but is absent during the lytic cycle

26. 27.13 Lambda Repressor Maintains an Autoregulatory Circuit
Repressor binding at OR blocks transcription of cro, but also is required for transcription of cI.
Repressor binding to the operators therefore simultaneously blocks entry to the lytic cycle and promotes its own synthesis.
FIGURE 27: Helix-2 interacts with DNA polymerase

27. 27.14 Cooperative Interactions Increase the Sensitivity of Regulation
Repressor dimers bound at OL1 and OL2 interact with dimers bound at OR1 and OR2 to form octamers.
These cooperative interactions increase the sensitivity of regulation.
FIGURE 29: Repressors to bind to OL3 and OR3 at higher concentrations

28. 27.15 The cII and cIII Genes Are Needed to Establish Lysogeny
The delayed early gene products cII and cIII are necessary for RNA polymerase to initiate transcription at the promoter PRE.
cII acts directly at the promoter and cIII protects cII from degradation.
Transcription from PRE leads to synthesis of repressor and also blocks the transcription of cro.
FIGURE 30: Repressor establishment uses a special promoter

29. 27.16 A Poor Promoter Requires cII Protein
PRE has atypical sequences at –10 and –35.
RNA polymerase binds the promoter only in the presence of cII.
cII binds to sequences close to the –35 region.
FIGURE 31: cII enables RNA polymerase to bind to PRE

30. 27.17 Lysogeny Requires Several Events
cII and cIII cause repressor synthesis to be established and also trigger inhibition of late gene transcription.
Establishment of repressor turns off immediate and delayed early gene expression.
Repressor turns on the maintenance circuit for its own synthesis.
Lambda DNA is integrated into the bacterial genome at the final stage in establishing lysogeny.

31. 27.17 Lysogeny Requires Several Events
FIGURE 33: The lysogenic pathway leads to repressor synthesis

32. 27.18 The Cro Repressor Is Needed for Lytic Infection
Cro binds to the same operators as the lambda repressor, but with different affinities.
When Cro binds to OR3, it prevents RNA polymerase from binding to PRM and blocks the maintenance of repressor promoter.

33. 27.18 The Cro Repressor Is Needed for Lytic Infection
When Cro binds to other operators at OR or OL, it prevents RNA polymerase from expressing immediate early genes, which (indirectly) blocks repressor establishment.
FIGURE 34: The lytic pathway leads to expression of cro and late genes

34. 27.19 What Determines the Balance between Lysogeny and the Lytic Cycle?
The delayed early stage when both Cro and repressor are being expressed is common to lysogeny and the lytic cycle.
The critical event is whether cII causes sufficient synthesis of repressor to overcome the action of Cro.

35. 27.19 What Determines the Balance between Lysogeny and the Lytic Cycle?
FIGURE 35: Repressor determines lysogeny, and Cro determines the lytic cycle