Bacterial Immunity

Question 1

2 types Chronic infection life cycles

Answer 1

Temperate
Non temperate

Question 2

Can chronic cycle lead to cell death

Answer 2

Yes
But chronic infections don’t perceive the lysis of the cell

Question 3

Increasing genetic distance

Answer 3

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

Question 4

Prokaryotic host virus arms race

Answer 4

Huge diversity of antivirus systems

Prevent infection - block entry
Prevent replication - cleave or block DNA and RNA
Prevent spreading - dormancy and suicide

Question 5

What causes bacterial evolution

Answer 5

Phage infection

Question 6

Pre 2018

Answer 6

Only 2 defence systems known
CRISPR cas
Restriction modification

Question 7

Post 2018

Answer 7

201 defence systems known

Question 8

Restriction modification (R-M) systems

Answer 8

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

Question 9

R-M system type 1

Answer 9

Cuts without recognition (variable distance)

Question 10

R-M system type 2

Answer 10

Cut DNA at site of recognition
Used for cloning
Palindromic sequence

Question 11

R-M systems type 3

Answer 11

Cuts close to site of recognition
~25 bp from site
Requires ATP

Question 12

How are R-M systems classified?

Answer 12

Subunit composition, cleavage position, sequence specificity and cofactor requirements

Question 13

Most common forms of DNA methylation in bacteria

Answer 13

N4-methylcytosine (4mC)
5-methylcyticine (5mC)
N6-methyladinine (6mA)

Question 14

How does DNA methylation in bacteria work?

Answer 14

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)

Question 15

R-M system type 4

Answer 15

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

Question 16

Where can R-M restriction systems found?

Answer 16

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

Question 17

Why does the cell get addicted to the R-M plasmid?

Answer 17

Plasmid has the ability to modify genome upon entry
Loss of plasmid causes cell death
Addiction drives evolution as it also helps survival

Question 18

DNA methyltransferases not associated with R-M system

Answer 18

3 solitary (or Logan) methyltransferases - Dcm, DAM
Epigenetic regulators of gene expression in many host adapted bacterial pathogens

Question 19

What does DNA methylation in bacteria do?

Answer 19

Defence against foreign DNA
Chromosome replication and segregation
Mismatch repair
Conjugation, packaging of phage DNA
Regulation of gene expression

Question 20

Role of R-M systems in the evolution of new strains

Answer 20

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

Question 21

Methylation pattern and horizontal gene transfer (Biotypes)

Answer 21

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

Question 22

Antibiotic resistance adaptation

Answer 22

Modification in surface receptors, pump antibiotic out of cell

Question 23

Steps of R-M systems evolution

Answer 23

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

Question 24

What distinguishes R-M type 4 from the other types of R-M

Answer 24

Does not methylate host DNA and cleaves methylated DNA of phage

Question 25

Discovery of other defence systems: guilt by association

Answer 25

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

Question 26

Defence islands

Answer 26

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

Question 27

PADLOC

Answer 27

Prokaryotic antiviral defence LOCator Proportion change amongst different species of bacterial Ecoli- zorya and druantia most important defence systems keeping them evolving

Question 28

The BREX (bacteriophage exclusion) defence system

Answer 28

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

Question 29

How does BREX work

Answer 29

Blocks phage DNA replication Methylated host DNA to differentiate from foreign Does not degrade non methylated foreign DNA

Question 30

BREX and type 4 R-M provide complementary protection from Phages

Answer 30

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

Question 31

The DISARM (defence island system associciated with restriction modification) defence system

Answer 31

Widespread bacterial defence system with broad anti phage activity Class 1 and class 2 drmA,B,C = core

Question 32

Class 1 DISARM

Answer 32

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

Question 33

How is foreign DNA recognised by DISARM?

Answer 33

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

Question 34

Pan immunity

Answer 34

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

Question 35

Defence systems are known to be frequently lost from microbial genomes

Answer 35

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

Question 36

Pan immunity model

Answer 36

Available arsenal of immune systems is a resource shared by a population of bacteria or arches rather than by individual cells

Question 37

More than half your body is not human

Answer 37

Eg Microbiome in the gut, all infected by virus - herpes

Question 38

Prokaryotic defences at origin of human cell autonomous innate immune mechanisms

Answer 38

Cell autonomous inmate immune system enables animal cells to resist viral infection Sensor detect viruses and activate expression of antiviral proteins and interferon response

Question 39

DOGMA challenge

Answer 39

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

Question 40

CBASS defence system

Answer 40

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

Question 41

CBASS in Vibrio cholera

Answer 41

Production of cyclic GMP-AMP activated phospholipase that degrades inner membrane leading to arrest of cell growth and death (abortive infection)

Question 42

CBASS defence system info

Answer 42

4 types sharing at least 6 effector subtypes that promote cell death by membrane impairment, DNA degradation or other means

Question 43

CBASS in eukaryotes

Answer 43

Production of oligonucleotide nucleotides Generation of antiviral genes

Question 44

CBASS in prokaryotes

Answer 44

Cyclic oligonucleotide Activated by detection of phage infection leading to cell death

Question 45

TIR

Answer 45

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

Question 46

Potential evolutionary scenario to explain conservation of immune mechanisms between prokaryotes and eukaryotes

Answer 46

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

Question 47

Phages have anti defence: phage anti CBASS

Answer 47

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)

Question 48

Phage without Acb cannot infect properly

Answer 48

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

Question 49

What do the defence systems CBASS and theories have in common?

Answer 49

Exert anti phage activity via signalling molecules that activate effectors that lead to abortive infection

Question 50

R-M systems 1,2 and 3 protect against phage infection by?

Answer 50

Methylating specific sites on host chromosome and cleaving invader phage DNA upon recognition of unmethylated sites

Question 51

Principle of guilty by association has been used to find new anti phage defences. This principle postulates that:

Answer 51

Proteins that are closely located in a genome are likely to share similar functions such as anti phage defence

Question 52

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?

Answer 52

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

Question 53

Phages carry proteins (Acb) that inhibit protection by CBASS defence systems by?

Answer 53

Degrading the signalling molecules that activate the effector protein