Bacterial Immunity Flashcards
2 types Chronic infection life cycles
Temperate
Non temperate
Can chronic cycle lead to cell death
Yes
But chronic infections don’t perceive the lysis of the cell
Increasing genetic distance
Temperate phage - phage that is genetically able to display lysogenic cycles as well as productive cycles
Virulent mutant - phage that is one or a few genetic changes separated from temperate phage ancestor
Professionally lytic - phage unrelated or distant to temperate Phages
Prokaryotic host virus arms race
Huge diversity of antivirus systems
Prevent infection - block entry
Prevent replication - cleave or block DNA and RNA
Prevent spreading - dormancy and suicide
What causes bacterial evolution
Phage infection
Pre 2018
Only 2 defence systems known
CRISPR cas
Restriction modification
Post 2018
201 defence systems known
Restriction modification (R-M) systems
Present in 3/4 bacterial genomes
Cleave phage DNA while modifying bacterial DNA to prevent self cleavage
DNA methyltransferase (Mod) modifies DNA at target site to protect endogenous DNA
restriction endonuclease (Res) cleaves foreign DNA at unmethylated target sites
R-M system type 1
Cuts without recognition (variable distance)
R-M system type 2
Cut DNA at site of recognition
Used for cloning
Palindromic sequence
R-M systems type 3
Cuts close to site of recognition
~25 bp from site
Requires ATP
How are R-M systems classified?
Subunit composition, cleavage position, sequence specificity and cofactor requirements
Most common forms of DNA methylation in bacteria
N4-methylcytosine (4mC)
5-methylcyticine (5mC)
N6-methyladinine (6mA)
How does DNA methylation in bacteria work?
Methyltransferase (MTase) transfers a methyl group (CH3) from s-adenosyl-L-methionine (SAM) to the unmodified nucleotide, producing a methylated bucleotide and a-adenosyl-homocytosije (SAH)
R-M system type 4
No methyltransferase
Composed of restriction endonuclease that cleaves methylated foreign DNA
Can cleave m6, m5c and hm5c and other modified DNA
Methylation dependent enzyme - cleaves modified DNA
Where can R-M restriction systems found?
In plasmids
“Selfish genetic elements” to promote own survival
Express both Erase (restricts foreign) and MTase (protects host genome)
Post segregational loss of R-M causes cell death
R-M gene complex replicated in clinal population resulting in the addiction of host cell
Why does the cell get addicted to the R-M plasmid?
Plasmid has the ability to modify genome upon entry
Loss of plasmid causes cell death
Addiction drives evolution as it also helps survival
DNA methyltransferases not associated with R-M system
3 solitary (or Logan) methyltransferases - Dcm, DAM
Epigenetic regulators of gene expression in many host adapted bacterial pathogens
What does DNA methylation in bacteria do?
Defence against foreign DNA
Chromosome replication and segregation
Mismatch repair
Conjugation, packaging of phage DNA
Regulation of gene expression
Role of R-M systems in the evolution of new strains
Facilitate genetic isolation
Control of uptake if DNA from environment
Horizontal transfer increases genetic diversity
New R-M complex = new strain so isolated from original clonal population
Methylation pattern and horizontal gene transfer (Biotypes)
Different recognition specificities in various strains divides the species into variant strains - BIOTYPES
different biotypes don’t exchange genetic material due to different methylation patterns
Antibiotic resistance adaptation
Modification in surface receptors, pump antibiotic out of cell
Steps of R-M systems evolution
1)RNA virus coexisted with bacteria (RNA). Evolution of uDNA in bacteria and acquisition of RNA dependent endonucleases, primitive R-M system
2) pressure = uDNA in cities to evade primitive R-M system. Lead to tDNA in bacteria to evade infection
3) phage adapts to host defence by evolving tDNA system
D) continuous selection, arms race. Modified DNA bases in phage and bacteria
What distinguishes R-M type 4 from the other types of R-M
Does not methylate host DNA and cleaves methylated DNA of phage
Discovery of other defence systems: guilt by association
Genes with associations are more likely to be guilty if sharing functions
Genes in close proximity to known defence system genes that are enriched in cells that can defend themselves against mobile elements
Defence islands
Prediction of novel defence systems using guilt by association approach
Protein families with unknown functions that are enriched on these islands can be predicted to be new defences
Usually flanked genes
Genes on same operon likely to be associated
Eg R-M and CRISPR-Cas found to colocalise in prokaryotic genomes in defence islands
PADLOC
Prokaryotic antiviral defence LOCator
Proportion change amongst different species of bacterial
Ecoli- zorya and druantia most important defence systems keeping them evolving
The BREX (bacteriophage exclusion) defence system
Made if 6 genes: brxA, B,C, L & pglZ, X
Combination of genes does not resemble classical convo of genes known to be involved in phage defence
Localisation in genomic vicinity of other defence genes
How does BREX work
Blocks phage DNA replication
Methylated host DNA to differentiate from foreign
Does not degrade non methylated foreign DNA
BREX and type 4 R-M provide complementary protection from Phages
BREX - prevents infection by non methylated Phages
R-M type 4 (BrxU) - prevents infection by methylated Phages
SYNERGY - 1 fence island, 2 complementary defence systems, 2 types of phage DNA neutralised
The DISARM (defence island system associciated with restriction modification) defence system
Widespread bacterial defence system with broad anti phage activity
Class 1 and class 2
drmA,B,C = core
Class 1 DISARM
Methylases methylate body DNA at specific motifs
DISARM protects from foreign unmenthylated DNA
For plasmids, efficiency of protection increases with number of Unmethylated motifs present in conjugated plasmid DNA
How is foreign DNA recognised by DISARM?
Genes drmA and B form complex that has trigger loop that partially occluded DNA binding site autoinhibitong activity of complex
Binding to DNA substrates containing 5’ overhang dialogues trigger loop, initiating structural rearrangement for DrmAB activation
Can then either defend against phage by loading onto phage DNA ends and physically blocking replication or recruit DrmC or other nucleuses to degrade foreign DNA
Pan immunity
Sharing of information/resources
Prokaryotic genomes can harbour multiple defence systems
Systems overlapping in range of Phage targets
Microorganisms cannot rely on one defence due to resistance so need several lines of defence
Defence systems are known to be frequently lost from microbial genomes
Drawbacks of defence systems: autoimmunity and energy burden
So get rid of unused defences
Frequent gain and loss = high variable pattern of presence and absence of systems in microbial genomes
Related strains can have very different defence compositions
Pan immunity model
Available arsenal of immune systems is a resource shared by a population of bacteria or arches rather than by individual cells
More than half your body is not human
Eg Microbiome in the gut, all infected by virus - herpes
Prokaryotic defences at origin of human cell autonomous innate immune mechanisms
Cell autonomous inmate immune system enables animal cells to resist viral infection
Sensor detect viruses and activate expression of antiviral proteins and interferon response
DOGMA challenge
Initial recognition and mitigation of infection often occur within non immune cells
Central components of cell autonomous inmate immune system have ancient evolutionary roots in prokaryotic genes that protect bacteria from pages
Eg 1) cyclic GMP-AMP synthase (cGAS), simulator of interferon genes (STING) pathway, CBASS
2) toll/il1 receptor (TIR) domain containing pathogen receptors
3) viper in family of antiviral proteins
4) gasdermin proteins
CBASS defence system
Cyclic GMP-AMP synthase (cGAS)-STING pathway is a central component of the cell autonomous inmate immune systems in animals
Invading DNA detected, leading to production of cyclic GMP-AMP. activated cHAS-STING pathway and causes upreg of transcription of inflammatory genes that leads to death of infected cells
CHAS homologous in vibrio cholera’s frequently appear near defence genes
CBASS in Vibrio cholera
Production of cyclic GMP-AMP activated phospholipase that degrades inner membrane leading to arrest of cell growth and death (abortive infection)
CBASS defence system info
4 types sharing at least 6 effector subtypes that promote cell death by membrane impairment, DNA degradation or other means
CBASS in eukaryotes
Production of oligonucleotide nucleotides
Generation of antiviral genes
CBASS in prokaryotes
Cyclic oligonucleotide
Activated by detection of phage infection leading to cell death
TIR
Theories system seems to operate via abortive infection mechanism
TIR domain of ThsB protein activated after detection of phage
Catalyses production of isomer of cyclic ADP ribose (cADPR)
cADPR binds ThsA effector via terminal c SLOG domain
Activates NADase, depletes NAD
Cell death
Potential evolutionary scenario to explain conservation of immune mechanisms between prokaryotes and eukaryotes
Bacteria and archaea have diverse innate immune mechanisms. Both encode different
Emergence of first eukaryotic cells cia endosymbiotic event, may have gotten immune systems via horizontal transfer
Processes like domain shuffling, gene duplication and de novo functional innovation continue to diversify immunity in eukaryotes
Phages have anti defence: phage anti CBASS
Acb counteracts CBASS by degrading cyclic nucleotide signals therefore blocking downstream effector activation
(Acb1 of T4 hydrolysis of 3’ adenosine bases, enable braid recognition and degradation of cyclic di- and trinucleotide CBASS signals)
Phage without Acb cannot infect properly
Active Acb1 enzymes conserved in phylogenetically diverse Phages demonstrating cleavage of host cyclic nucleotide signals is a key strategy of CBASS evasion in phage biology
What do the defence systems CBASS and theories have in common?
Exert anti phage activity via signalling molecules that activate effectors that lead to abortive infection
R-M systems 1,2 and 3 protect against phage infection by?
Methylating specific sites on host chromosome and cleaving invader phage DNA upon recognition of unmethylated sites
Principle of guilty by association has been used to find new anti phage defences. This principle postulates that:
Proteins that are closely located in a genome are likely to share similar functions such as anti phage defence
Pan immunity model proposes that diversity of immune systems is a resource shared by a population of bacteria or archaea rather than individual cells. This means that?
An individual cell can have access to other defence systems via horizontal gene transfer from other cells
A population of multiple cells carrying distinct defence systems has high chances of survival upon phage infection because at least one cell is likely to carry a defence system to protect against phage
Individual cells have less fitness costs associated with carrying multiple defence systems
Phages carry proteins (Acb) that inhibit protection by CBASS defence systems by?
Degrading the signalling molecules that activate the effector protein
