FN - Bacteriophages II Flashcards
How does a temperate phage genome decide between the lytic and lysogenic cycles? (2)
- Individual decisions and voting – e.g. phage lambda
- Group decision – e.g. phage phi3T
What are the roles of the CI and CII proteins in phage lambda life cycle? (4)
- Crucial regulators in the lifecycle of temperate bacteriophages
- Promote lysogeny
- CI protein - is both a repressor and activator of transcription
- CII protein- primary role is to initiate the repressor establishment cascade
How does phage lambda make the lytic vs. lysogenic decision? (5)
- Once inside the cell, phage lambda initiates early protein synthesis, including regulatory protein CII
- The decision is influenced by the relative levels of CI and Cro proteins:
- High CI levels → Favors lysogenic cycle (represses Cro, maintains prophage state)
- High Cro levels → Favors lytic cycle (represses CI, activates phage replication & lysis)
- CII protein plays a crucial role in promoting lysogeny by activating CI expression
What is Multiplicity of Infection (MOI)?
- The average number of phages per bacterial cell
Calculated as:
- MOI = (phage added) ÷ (bacteria added)
Examples:
- MOI 1 → One phage per bacterial cell
- MOI 2 → Two phages per bacterial cell
How does MOI affect the lytic vs. lysogenic decision? (2)
- Higher MOI → More CII protein → More probability of lysogeny
- Low phage concentration → More likely to go lytic (to replicate)
How does the metabolic state of the host affect the phage decision? (2)
- Starving cells are smaller, leading to higher CII concentration → favors lysogeny
- Poor nutrient conditions can trigger lytic cycle for phages to escape a dying host
Dependent on degree of starvation and what is more favourable
How is the lytic vs. lysogenic decision influenced when multiple phages infect a single cell? (3)
- The decision is integrated within the cell.
- Only a unanimous vote for lysogeny by all phages leads to a lysogenized bacterium.
- If even one phage follows the lytic cycle, the cell will be lysed, regardless of the others.
Still Individual decisions and voting
How do some phages (e.g. phi3T) make a group decision? (6)
- Phages communicate between infected cells using the Arbitrium system
During infection:
- Phages produce AimP protein, which is cleaved into Arbitrium peptide
- Arbitrium is exported from the bacterial cell
- Neighboring cells uptake Arbitrium via OPP transporter
- Low Arbitrium levels → More likely to go lytic
- High Arbitrium levels → More likely to go lysogenic
Different phages use different arbitriums, thus communicating only with phages of their own kind
What is the molecular mechanism behind phage communication and the lytic vs. lysogenic decision? (5)
- Early genes aimR and aimP are expressed immediately upon infection.
- AimR activates AimX expression, which inhibits lysogeny and directs the phage to a lytic cycle.
- AimP is also expressed, secreted, and processed to produce Arbitrium.
- Arbitrium is internalized into other bacteria via the OPP transporter.
- When a phage infects a bacterium with high Arbitrium levels, AimR binds Arbitrium and cannot activate AimX, leading to a lysogeny preference.
What is the chronic life cycle of filamentous phages (e.g. f1 phage)? (7)
- Filamentous phages have a ssDNA genome inside a long cylindrical protein coat
- When they enter the cell, the capsid disassembles
Replication:
- Host proteins convert ssDNA → dsDNA for transcription
- f1 also produces ssDNA-binding proteins to protect the genome
Exit:
- New phages leave the cell intact via a secretion channel
- f1encodes a secretion channel of its own (g4p secretin).
- Does not kill the host → allows continuous replication
When the f1 genome enters the cell, it does not leave the capsid outside, nor does it bring the capsid along with it into the cell - the capsid disassembles, depositing the proteins in the cell membrane for reuse later to coat progeny as they exit.
What tasks must a phage accomplish in the lytic cycle? (7)
Outside host cell:
- Capsid must protect the genome from environmental danagers e.g. UV
- Recognize and irreversibly bind to a host receptor
- Inject genome into the host
Inside host cell:
- Evade host defenses
- Redirect metabolism to produce progeny phages
- Replicate genome & synthesize capsid proteins
- Assemble & release new phages through host lysis
What are minimal phage genomes, and how do they function efficiently? (6)
- Some phages have tiny genomes optimized for replication
Example: Leviviridae Qβ
- ssRNA genome (4,212 nucleotides)
4 genes:
- 1 gene for replication: Replicase
- 2 genes for structural proteins: capsid assembly
- 1 gene for multifactoral protein: maturation protein
- Efficiently overlaps genes to maximize coding potential
DNA synthesis unnecessary for this phage
What is the role of the maturation protein? (3)
- Lyses the host cell so the assembled virions can exit
- Protects the encapsidated genome from RNases
- Recognizes and adsorbs to the receptor on its host
What is an example of a small DNA phage? (5)
Microviridae φX174
- Circular ssDNA genome (5,386 nucleotides)
- Encodes 11 genes, some overlapping
- Complex capsid assembly (6 genes)
- 2 genes are non-essential in lab conditions
What is the benefit of a larger genome? (5)
More genes = more capabilites
- Structural complexity (capsid, tail fibers)
- Countering host defenses
- Competing with other phages
- Acquiring nutrients for replication
- Expanding host range
E.g. T4 uses a 169 kbp genome that encodes about 300 genes.
Largest known phage has a genome of 735 kbp
How do phages evolve? (3)
- Accumulating mutations over generations
- Recombination events with other phages in which they exchange genetic material with other phages.
Creates a mosaic structure: Nearly identical sequences alternate with sequences that are merely similar or even completely divergent
How do temperate phages benefit bacteria? (6)
- Horizontal gene transfer → provides new bacterial traits
Possible benefits include:
- Superinfection exclusion (prevents infection by other phages)
- Virulence factors (e.g. extracellular toxins)
- Antimicrobial resistance genes
- Biofilm formation aid
- Suppressing mammalian immunity against the bacterium
How do phages contribute to biofilm formation? (4)
Example: Pseudomonas aeruginosa Pf phages
Pf phages stabilize biofilms by:
- Lysing a few cells, releasing DNA into the biofilm matrix (provides structural integrity)
- Aligning in the biofilm to provide liquid crystalline properties
- Enhances adhesion
- Protects from desiccation & antibiotics
Pseudomonas aeruginosa is a major cause of chronic lung infections in cystic fibrosis (CF)
How do phages influence mammalian immunity?
- Without phages: Bacteria trigger immune response (TNF production, phagocytosis)
-
With Pf phages:
- Pf phage is taken up by mammalian cells → inhibits TNF production
- Suppresses immune response to bacteria, making bacterial clearance harder
