FN - Bacterial Immunity I Flashcards
(27 cards)
What are the 4 main types of bacteriophage life cycles and their key features?
I. Obligately Lytic:
- Phage replicates and lyses host to release progeny
- No prophage stage (no integration into host genome)
II. Chronic, Non-temperate:
- Phage released continuously without lysing the host
- No prophage stage; host remains alive
III. Lytic, Temperate:
- Phage can integrate into host genome as a prophage (lysogeny)
- Can switch to lytic cycle and lyse host
IV. Chronic, Temperate:
- Phage integrates as prophage or establishes chronic infection
- Phage particles continuously released without host lysis
Common stages across all types:
V = Vegetative | P = Prophage | B = Before release | D = During release | F = Free phage
How are phages classified based on genetic distance and life cycle strategy?
Temperate Phage:
- Can switch between lysogenic and productive (lytic) cycles
- Genetically equipped for integration into the host genome
Virulent Mutant:
- Closely related to temperate phages
- Lytic-only due to a few genetic changes
Professionally Lytic Phage:
- Genetically unrelated or distantly related to temperate phages
- Exclusively lytic with no lysogenic capability
Genetic distance increases from temperate → virulent mutant → professionally lytic.
What are 3 major ways prokaryotes defend against phages?
- Prevent infection – block entry
- Prevent replication – cleave or block phage DNA/RNA
- Prevent spreading – induce dormancy or suicide (abortive infection)
What are Restriction-Modification (R-M) systems and their two key components? (3)
- Bacterial defence systems present in about three quarters of bacterial genomes, and cleave phage DNA while modifying the bacterial DNA to prevent self-cleavage.
- DNA methyltransferase (Mod/MTase): methylates host DNA to protect it
- Restriction endonuclease (Res/REase): cleaves foreign (unmethylated) DNA
What are the 3 major types of Restriction-Modification (R-M) systems and how are they classified? (5)
- Type I, II, and III
Classification based on:
- Subunit composition
- Cleavage position relative to recognition site
- Sequence specificity
- Cofactor requirements (e.g., ATP)
What are the key features of all R-M systems? (3)
Use SAM (S-adenosyl-L-methionine) as a methyl donor
- Modification (M) subunit methylates host DNA at recognition motifs
- Restriction (R) subunit cleaves unmethylated foreign DNA at or near those motifs
What are the key features of Type I R-M systems? (6)
- Subunits: HsdR (R), HsdM (M), HsdS (S) – form a hetero-oligomeric complex
- Methylation: Uses SAM; recognizes bipartite motifs
- Cleavage: Cuts DNA far from the recognition site after translocation
- Cofactor: Requires ATP and contains DEAD-box proteins
- Example: EcoKI
- Recognition motif: Long bipartite (e.g., 5’-AAGN₆CTC-3’)
What are the key features of Type II R-M systems? (7)
- Subunits: Separate ENase (Res) and MTase (Mod)
- Methylation: Targets palindromic sequences using SAM
- Cleavage: Cuts within or directly adjacent to the recognition site (precise)
- Cofactor: Does not require ATP
- Most widely used in molecular cloning
- Examples: EcoRI (Res), EcoRIM (Mod)
- Recognition motif: Short palindromic (e.g., 5’-GATC-3’)
What are the key features of Type III R-M systems? (7)
- Subunits: Mod (M + sequence recognition), Res (R) – form a hetero-oligomer
- Methylation: Modifies one DNA strand using SAM
- Cleavage: Cuts ~25 bp downstream of recognition site
- Requires two inversely oriented recognition sites for cleavage
- Cofactor: Requires ATP for restriction, not methylation
- Example: StyLTI
- Recognition motif: Short, asymmetric (e.g., 5’-TCAG-3’)
What are the three most common DNA methylation types in bacteria?
- N4-methylcytosine (4mC)
- 5-methylcytosine (5mC)
- N6-methyladenine (6mA)
What is the Type IV R-M system and its features? (7)
- No methyltransferase (MTase) component
- Cleave methylated or modified foreign DNA (e.g., m⁶A, m⁵C, hm⁵C)
- Cleavage occurs at a variable distance from recognition site
- Function as methylation-dependent restriction enzymes
- Proteins are unrelated and structurally diverse
- Examples of associated genes: mcrA, mcrBC, mrr
- Broad diversity with many putative enzymes identified (e.g., 4822 in REBASE)
How do R-M systems act as selfish genetic elements? (4)
- REase is more stable than MTase
- Loss of the R-M gene complex → loss of methylation
- Stable REase cleaves host DNA → cell death
- Results in post-segregational killing and gene complex addiction
What is the role of R-M systems in genome evolution and speciation? (3)
- Restricts horizontal DNA transfer – acts as genetic immigration control
- Methylation patterns define strain-specific identity
- Prevents gene flow → emergence of biotypes, then new species
What are solitary (or orphan) methyltransferases, and how do they differ from R-M systems? (4)
- Not linked to a restriction enzyme
Examples:
- Dam (N6-methyladenine)
- Dcm (5-cytosine)
Often act as epigenetic regulators
How did R-M systems contribute to genome evolution in bacteria and phages? (4)
- Step A: Bacteria evolved RNA-dependent endonucleases to restrict RNA viruses
- Step B: Viruses evolved U-DNA genomes to evade RNA-targeting enzymes
- Step C: Bacteria evolved U-DNA-targeting R-M systems, pushing viruses to adopt T-DNA (thymidine-DNA) genomes
- Step D: An arms race began, leading to further evolution of both phages and bacteria using modified DNA bases and specialized R-M systems
What is the role of Type IV R-M systems in the evolutionary arms race? (2)
- Type IV systems evolved to target and restrict methylated or modified DNA
- These systems represent a late stage in the arms race between phage DNA modification and bacterial defence adaptation
What is the “guilt-by-association” principle in discovering new defence systems? (3)
- Genes located near known defence genes are more likely to have similar functions
- Used in gene function prediction and discovery of novel anti-phage defence systems
- Assumes genes with shared genomic context are functionally related
What is the BREX (Bacteriophage Exclusion) system, and how does it work? (7)
- Composed of 6 genes
- Blocks phage DNA replication without cleaving DNA
- Methylates host DNA for self vs. non-self recognition
- Lacks endonuclease – deletion of methylase gene is not lethal
- Complementary to Type IV R-M:
- BREX → protects against non-methylated phage DNA
- Type IV R-M (e.g. BrxU) → protects against methylated phage DNA
What is the DISARM (Defence Island System Associated with Restriction-Modification) system? (2)
- A widespread bacterial defence system
- Provides broad anti-phage activity
What are the two classes of DISARM and how do they differ?
- Class I: Contains drmD, drmMI, drmA, drmB, drmC
- drmMI = adenine methylase
- Class II: Contains drmE, drmA, drmB, drmC, drmMII
- drmMII = cytosine methylase
- Both classes use helicase, PLD, and methylation domains
How does DISARM protect against foreign DNA? (3)
- Methylases (e.g., drmMI or drmMII) methylate host DNA at specific motifs
- DISARM targets and restricts unmethylated foreign DNA, including plasmids and phage DNA
- Protection increases with the number of unmethylated motifs in incoming plasmid DNA
How is foreign DNA recognized by DISARM? (4)
- drmA and drmB form a complex with a trigger loop (TL)
- TL partially blocks the DNA-binding site, causing autoinhibition
- Binding to DNA with a 5’ overhang dislodges the TL
- This triggers a conformational change that activates the DrmAB complex
How does the DrmAB complex in the DISARM system detect and respond to phage infection? (4)
- In the absence of infection, DrmAB is autoinhibited by a trigger loop that blocks its DNA-binding site.
- Upon infection, DISARM binds to phage ssDNA with a 5’ overhang, which dislodges the trigger loop.
- This activates DrmAB through a conformational change.
- Once active, DISARM may:
– Block phage replication by binding DNA ends
– Or recruit nucleases (e.g., DrmC) to degrade the foreign DNA.
Why do prokaryotic genomes encode multiple defence systems? (3)
- To protect against a wide variety of phages.
- Some defences are phage-specific; overlapping systems help avoid phage resistance.
- Multiple systems can act against the same phage for robust protection.
