Bacterial immunity Flashcards
Explain the different phage states
V - vegetative state
P - prophage
^ infection
B - Before release
D - during release
^ Viron maturation
F - free phage
^Free phage
Different types of phages and how the progress the different phage states
I :
V - Intact cell membrane, phage genome and capsid/ structural protein inside
—> B - lysed cell phage fully formed –> F free phage is obligatory,professionally, strictly lytic, or virulent
II:
V - Intact cell membrane, phage genome and structural protein inside
D - Genome and structural protein combine, membrane still intact, leaves cell
F - phage is chronic, non-temperate
III:
V - intact cell membrane, phage genome and capsid/ structural protein inside
OR
P - host DNA with prophage
B - Lysed cell
F - Phage is lytic, temperate
IV:
V - Intact cell membrane, phage genome and structural protein inside
OR
P - host DNA with prophage
D - Genome and structural protein combine, membrane still intact, leaves cell
F - Phage is chronic, temperate
Explain the terminology of phage type and how it relates to increasing genetic distance
1Temperate Phage: Genetically able to display lysogenic cycles as well as productive cycles
2Virulent mutant: Phage that is one or just a few genetic changes separate from a temperate phage ancestor
3Professionally lytic: Phage that is unrelated or extremely distantly related to temperate phages
Virulent/profesh are “obligatory” or “strictly” lytic phages
123 increasing genetic distance
Explain the diversity of anti-virus systems
prevent infection – block entry
prevent replication – cleave or block DNA and RNA
prevent spreading – dormancy and suicide
To prevent infection by phage and mobile genetic elements (MGEs)…
bacteria evolved myriad defence mechanisms, ranging from nucleic acid targeting to chemical warfare and self-inflicted cell death.
On the other side, phages have also evolved counter-defences to overcome these bacterial defences.
What proportions of bacterial genomes are R-M systems present in
3/4
What to R-M systems do?
Cleave phage DNA while modifying the bacterial DNA to prevent self cleavage
What are the two distinct functions of R-M systems
A DNA methyltransferase (Mod) that modifies DNA, at the target site to protect endogenous DNA
A restriction endonuclease (Res) that cleaves foreign DNA at unmethylated target sites
SAM serves as the methyl donor
Groups of RM systems
three major groups, types I, II, and III, on the basis of subunit composition, cleavage position, sequence-specificity, and cofactor requirements
Type 1 R-M system
- heteroligomeric enzymes
- Require ATP hydrolysis for restriction
- cut DNA at sites remote from the recognition sequence
- DEAD-box proteins
e.g. EcoK1
Type II R-M system
- ENase and MTase seperate enzymes
- Cut DNA within recognition sequence
e.g. EcoR1
Type III(R-M)
- Hetero-oligomeric ENase
- ATP required for restriction
- Cut DNA close to recognition sequence
- DEAD-box proteins
e.g. StyLTI
Explain the complexes ect. of the different types of R-M systems
Type I: Methylation of recognition site/motif, invasion of methylation site by restrictiom subunit, leading to cleavage after the recognitiom site (at variable distances)
Type II: Methyl transferase works with SAM, don’t need a complex, re4strictiom enzyme alone has cleavage function, cleaves at the recognition site
Type III: Usually a complex of methyl transferases, complex forms with restruction subitits, cleavage at close diastance to the site (usually 25bp before)
Usually require ATP and are palendromic sequences (apart from type 3)
What are the most common forms of DNA methylation in bacteria
N4-methylcytosine (4mC)
5-methylcytosine (5mC)
N6-mthyladenine (6mA)
In each instance, a methyltransferase (MTase) transfers a methyl group (CH3) from S-adenosyl-L-methionine (SAM) to the unmodified nucleotide, producing a methylated nucleotide and S-adenosyl-homocysteine (SAH)
Describe type IV R-M systems
have no methyltransferase, and are composed only of a restriction endonuclease that cleaves methylated foreign DNA
- methylation dependant REase cleave at variable distance from recognition site
- cleave m6A m5C hm5C and/or other modified DNA
- many different types
cleaves only modified bases
R-M systems can be found in plasmids, these tend to propagate as…
selfish genetic elements to promote their own survival
How do R-M systems in plasmids propogate as selfish genetic elements to promote their own survival
The R-M system expresses both REase and MTase: the REase restricts the foreign DNA, and the MTase protects the host genome against cleavage by the cognate REase.
The post-segregational loss of the R-M gene complex results in the loss of methylation. The REase, owing to its higher level of stability, attacks the unmodified host genome, resulting in cell death.
The R-M gene complex thus propagates in the clonal population, resulting in the addiction of the host cell.
Explain the process of a plasmid containing an R-M system infecting a bacterial cell
Bacterial cell -> infected with plasmid (containinhg R-M system) -> cell splits with MTase and REase in both-> one cell = cell death and other is addicted cell (with plasmid still present)
if theres not enough methyl transferases to modify the entire genome of the bacteria then…
cell death occurs
is all DNA methylation in bacterial pathogens associated with R-M system activities?
NO - Many pathogenic bacterial species also contain DNA methyltransferases
that are not associated with a restriction enzyme activitytargeting the same recognition sit
solitary (or orphan) methyltransferases include:
a 5-cytosine DNA methyltransferases called Dcm, which methylates cytosines in specific DNA motifs, and an N6-methyladenine DNA methyltransferase(Dam), which methylates theadenines in specific target sequences.
manyE. coliandSalmonella enterica serovar Typhimurium strains harbour…
specific genomic loci rich in R-M systems, termed “immigration control regions”.
In prokaryotes, REases, by the restriction of foreign DNA, function in…
DNA immigration control. Such a barrier would also serve the function of the maintenance of species in bacteria.
R-M systems facilitate…
genetic isolation, which is required for the acquisition of new biological properties. Genetic isolation is provided by controlling the uptake of DNA from the environment.
The methylation pattern provides…
a specific identity to that particular strain distinct from those of other closely related species and thus distinguishes self from nonself.
What is a biotype
the presence of different recognition specificities in various strains of the same species further divides the species into different variant strains of bacteria, termed “biotypes.” These variant strains would not exchange genetic material among each other due to differences in methylation patterns.
