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Biofilms & Microbial communities > Bacterial immunity > Flashcards

Bacterial immunity Flashcards

1
Q

what type of phages infect in a vegetative state and virion maturation occurs before release?

type 1

A

Obligately lytic, professionally lytic, strictly lytic, virulent

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2
Q

what phages infect in a vegetative state and virions mature during release?

type 2

A

chronic and non temperate phages

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3
Q

what phages infect in a vegetative state or as a prophage and virions mature before release?

type 3

A

lytic and temperate

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4
Q

what phages infect in a vegetative state or as a prophage and virions mature during release?

type 4

A

chronic and temperate

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5
Q

how are temperate phages, virulent mutants, and professionally lytic phages genetically related?

A

Temperate phage: phage that is genetically able to display lysogenic cycles as well as productive cycles
Virulent mutant: phage that is one or just a few genetic changes separated from a temperate phage ancestor
Professionally lytic: phage that is unrelated or extremely distantly related to temperate phages (no ability to integrate)

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6
Q

give three generic examples of the aims of anti-virus systems

A
  • prevent infection - block entry
  • prevent replication - cleave or block DNA and RNA
  • prevent spreading - dormancy and suicide
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7
Q

what bacterial immune defenses are there for the degredation of phage nucleic acids?

A
  • CRISPR-Cas systems
  • Restriction modification systems
  • Argonaute systems (pAgo)
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8
Q

what bacterial immune defenses are there for abortive infection?

A
  • Signalling systems (CBASS, Pycsar, Thoeris)
  • Retron systems
  • Toxin-antitoxin systems
  • Others (eg PrrC, Bacterial gasdermins)
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9
Q

What bacterial immune defenses are ther for inhibition of DNA and RNA synthesis?

A
  • Chemical defense (prokaryotic viperin pVips, secondary metabolites (anthracyclines, aminoglycosides))
  • Nucleotide depletion (dCTP deaminase, dGTPase)
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10
Q

how common are R-M systems?

A

R-M systems are present in about three quarters of bacterial genomes

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11
Q

what are restriction-modification systems?

A

consist of a modification enzyme that epigenetically methylates a specific DNA sequence, and a restriction endonuclease (restriction enzyme) that cuts DNA lacking this epigenetic mark.

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12
Q

IN general R-M systems have two distinct functions, what are they

what do the R and M stand for

A
  • 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
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13
Q

what does SAM do in restriction modification systems

A

SAM serves as the methyl donor in cytosine methylation

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14
Q

what proportion of bacterial genomes have R-M systems?

A

R-M systems are present in about three quarters of bacterial genomes

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15
Q

what are the three major groups of restriction modification systems?
on what basis are they categorised?

A

type 1
type 2
type 3

subunit composition, cleavage position, sequence specificity, cofactor requirements

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16
Q

what elements are involved in type 1 R-M system?

enzymes, hydrolysis, cut site, type of protein

A
  • Hetero-oligomeric enzymes
  • require ATP hydrolysis for restriction
  • cut DNA at sites remote from the recognition sequence
  • DEAD-box proteins
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17
Q

what features are involved in type 2 R-M systems?

A
  • ENase and MTase separate enzymes
  • cut DNA within recognition sequence
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18
Q

give an example of a type 1 R-M system?

A

EcoKI

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19
Q

what elements are involved in type 3 R-M systems?

A
  • heterooligomeric ENase
  • ATP required for restriction
  • cut DNA close to recognition sequence
  • DEAD-box proteins
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20
Q

give an example of a type 2 R-M system

A

EcoRI

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21
Q

give an example of a type 3 R-M system?

A

StyLTI

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22
Q

what enzymatic reaction occurs in type 1, 2 and 3 R-M systems

A

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).

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23
Q

how do type IV systems differ from type 1-3?

A

Type IV R-M systems have no methyltransferase, and are composed only of a restriction endonuclease that cleaves methylated foreign DNA

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24
Q

how do R-M systems cause cell death?

A

The REase attacks the unmodified host genome, resulting in cell death.

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25
Q

how does the plasmid maintain its own survival?

in R-M system, after cell split

A

When the cell is split, only one gets a plasmid, the one that doesn’t get it will run out of methyl transferase and die – plasmid maintains its own survival, fitness advantage to maintain the plasmid

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26
Q

what are orphan methyltransferases?

A

Not all DNA methylation in bacterial pathogens is associated with R–M system activities. Many pathogenic bacterial species also contain DNA methyltransferases that are not associated with a restriction enzyme activity targeting the same recognition site.
These solitary (or orphan) methyltransferases include Dcm, and Dam

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27
Q

what is the role of R-M sysems in the evolution of new strains?

A

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. According to this model, 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. (after obtaining plasmid containing R-M genes)
With a sufficient accumulation of genetic variation, biotypes might evolve into different species.

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28
Q

what are immigration control regions?

A

In prokaryotes, the horizontal transfer and the vertical transfer of DNA are rampant. 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.

In support of this, many E. coli and Salmonella enterica serovar Typhimurium strains harbour specific genomic loci rich in R-M systems, termed “immigration control regions”.

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29
Q

how does R-M facilitate genetic diversity?

A

The horizontal transfer of DNA in bacteria increases the genetic diversity among them. A bacterial cell which acquires a new R-M gene complex (right) becomes genetically isolated from its clonal population (left). The MTase component of the newly acquired R-M system modifies the genome. Owing to this change in the methylation pattern, the REase prevents the genetic exchange of alleles between closely related strains. Furthermore, mutations acquired in these populations would facilitate genetic diversity, resulting in different genotypes. These populations would further evolve into different strains.

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30
Q

give two examples of solitary DNA methyltransferases

A

DCM and DAM

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31
Q

what does DCM methylate?

A

methylates cytosines in specific DNA motifs

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32
Q

what does DAM methylate?

A

methylates the adenines in specific target sequences.

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33
Q

DNA methylation by DCM and DAM in bacteria does what?

A
  • denfence against foreign DNA
  • chromosome replication and segregation
  • mismatch repair
  • conjugation, packaging of phage DNA
  • regulation of gene expression
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34
Q

what are immigration control regions?

A

specific genome loci rich in R-M systems
These R-M system facilitate genetic isolation by controlling the uptake of DNA from the environment.

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35
Q

give two examples of bacteria with immigration control regions

A

many E. coli and Salmonella enterica serovar Typhimurium

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36
Q

what are biotypes and how do they develop?

A

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. With a sufficient accumulation of genetic variation, biotypes might evolve into different species.

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.

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37
Q

how does horizontal gene transfer increase genetic diversity?

A

A bacterial cell which acquires a new R-M gene complex (right) becomes genetically isolated from its clonal population (left). The MTase component of the newly acquired R-M system modifies the genome. Owing to this change in the methylation pattern, the REase prevents the genetic exchange of alleles between closely related strains. Furthermore, mutations acquired in these populations would facilitate genetic diversity, resulting in different genotypes. These populations would further evolve into different strains.

38
Q

describe the role of R-M systems in genome evolution

bacteria, phage arms race. RNA->u-DNA…

A

(A) Initially, RNA viruses coexisted with bacteria containing RNA genomes. With the evolution of uridine-containing DNA (U-DNA) genomes in bacteria and the acquisition of RNA-dependent endonucleases, a primitive R-M system could have ensured the restriction of the RNA viruses.
(B) Such a selection pressure would enforce the evolution of a U-DNA genome in viruses to evade this primitive R-M system. This in turn would result in the evolution of thymidine-containing DNA (T-DNA) genomes in bacteria to evade phage infection.
(C) The phage adapts to the host defence strategy by evolving a T-DNA genome.
(D) Continuous selection would result in an “arms race” between bacteria and viruses, resulting in the utilization of modified DNA bases in phage and bacterial genomes

39
Q

how does the principle of gult by association help in the discovery of other defence systems?

A

Algorithms used in gene function or disease prioritization tasks generally operate on a principle called guilt by association:
genes with “associations” are more likely to be “guilty” of sharing functions.
Defence systems like R-M and CRISPR-Cas were found to co-localize in prokaryotic genomes, in “defence islands”.
These defence islands allow the prediction of novel defence systems using the ‘guilt by association’ approach. Protein families with unknown functions that are enriched in these islands can be predicted to be new defences.

40
Q

what is BREX?

A

The BREX (Bacteriophage Exclusion) defence system
Composed of six genes:
* brxA - RNA binding
* brxC - ATPase
* pglX - DNA methylation
* pglZ - alkaline phosphatase
* brxL - ion like protease

41
Q

how does BREX work?

A

BREX acts by blocking phage DNA replication
Phage DNA replication does not occur in BREX-containing cells (red), but is observed in the BREX-lacking strain (black). (
Similar to R-M systems, BREX methylates host DNA to differentiate it from foreign DNA. (PGLX)
Does not cleave the DNA it simply blocks the replication

42
Q

what are the similarities and differences between BREX and R-M systems of defence

A

Similar to R-M systems, BREX methylates host DNA to differentiate it from foreign DNA. (PGLX)

Different from R-M systems, BREX does not degrade the non-methylated foreign DNA. This is why deletion of the methylase gene of BREX does not have deleterious effects on the bacteria (since contrary to R-M systems there is no restriction endonuclease cleaving the DNA)

43
Q

how do BREX and type IV R-M provide complementary protection from phages?

A
  • BREX prevents infection by non-methylated phages
  • R-M type IV (BrxU) prevents infection by methylated phages
44
Q

what is DISARM?

A

The DISARM (Defense Island System Associated with Restriction-Modification) defence system
DISARM is a widespread bacterial defence system with broad anti-phage activities

45
Q

class 1 and 2 of the DISARM system share what genes

A

Classes share a common complex, drm A B and C. (own methyl transferases)

46
Q

whats the difference between class 1 and class 2 DISARM system

A

the way the methyl transferase domains is distinguished.

47
Q

Like most R-M systems and BREX, DISARM protects from ….

A

Like most R-M systems and BREX, DISARM protects from foreign unmethylated DNA.

48
Q

For plasmids DISARM efficiency increases with what

A

For plasmids, the efficiency of the protection increases with the number of unmethylated motifs present in the conjugated plasmid DNA.

49
Q

what is the structure of the DrmAB complex in the absence of phage infection?

A

In the absence of phage infection the DrmAB complex is autoinhibited by the trigger loop

50
Q

how does the DISARM system defend against phage infection?

3 steps

A

In the absence of phage infection, DrmAB complex is autoinhibited via trigger loop
1. Upon phage infection, DISARM is recruited to ssDNA with 5’ overhangs which typically occur duting initial phage DNA infection or during rolling circle replication
2. Loading of ssDNA into DrmAB dislodges the trigger loop, resulting in a conformational change that activates DrmAB
3. DISARM may act to defend against phage at this step by loading onto phage DNA ends and physically blocking replication OR DrmAB activation may recruit DrmC or other nucleases to degrade the foreign DNA

51
Q

what is pan-immunity

A

Ability to share immunity, to share their defense systems. Many lines of defense that are shared… maximizing fitness advantage
Prokaryotic genomes can harbor multiple different defense systems

52
Q

what is the benefit for a single microorganism to encode so many different lines of defence?

A

Some defence systems protect only from a specific type of virus
For microorganisms to be protected against a variety of viruses, it should encode a defence arsenal that can overcome multiple types of phages
If systems overlap in the phage of phages targets there is also a benefit.
Phages can develop resistance to defence therefore microorganisms cannot rely on a single defnce and need to have several lines of defence against the same phage type

53
Q

what causes bacteria to lose/get rid of defence systems?

A

Major drawbacks of defence systems are autoimmunity, and an energy burden on the cell. These fitness costs result in selective pressure for bacteria to get rid of defence systems under no phage pressure.

54
Q

what is the pan-immunity model?

A

the available arsenal of immune systems is a resource shared by a population of bacteria or archaea rather than by individual cells.

55
Q

central components of the cell-autonomous innate immune system have ancient evolutionary roots in prokaryotic genes that protect bacteria from phages
give 4 examples

A

1) cyclic GMP–AMP synthase (cGAS)–stimulator of interferon genes (STING) pathway, CBASS;
2) Toll/IL-1 receptor (TIR) domain-containing pathogen receptors;
3) the viperin family of antiviral proteins;
4) gasdermin proteins, etc.

56
Q
A
57
Q

what is the cyclic GMP–AMP synthase (cGAS)–STING pathway

A

a central component of the cell-autonomous innate immune system in animals. Invading DNA is detected, leading to the production of cyclic GMP-AMP, which activate the cGAS-STING pathway and causes an upregulation of transcription of inflammatory genes that lead to death of the infected cell.

58
Q

cGAS homologs in Vibrio cholerae frequently tend to appear near _ genes.

A

cGAS homologs in Vibrio cholerae frequently tend to appear near defence genes.

59
Q

what occurs when cycle GMP-AMP is produced in Vibrio cholera

A

In Vibrio cholera, production of cyclic GMP-AMP activates a phospholipase that degrades the inner membrane leading to arrest of cell growth and death (abortive infection).

60
Q

how many CBASS systems are identified?
how many effector subtypes do they share?

A

Four major CBASS types were identified, sharing at least six effector subtypes that promote cell death by membrane impairment, DNA degradation or other means

61
Q

what does the CBASS system do when theres a phage infection

A

Phage infection activates the cyclase which causes a molecule to be produced leading to multiple types of effectors.
Activated effectors degrade the membrane, degrade DNA or use other means to cause cell death
Each type of CBASS system uses different effectors to cause cell death

62
Q

the checkered pattern of CBASS distribution in closely related genomes suggests what

A

This chequered pattern of CBASS distribution in closely related genomes suggests that CBASS systems are rapidly gained and lost, consistent with the theory of the pan-immune system of bacteria

63
Q

in the Theoris system what determines the phage specificity of the defence

A

the TIR domains

64
Q

Describe what the theoris sytem does upon phage infection

A

Protein ThsB has a toll-interleukin receptor (TIR) domain. THis protein recognises phage infection (unclear how)
The TIR domain becomes active and catalyses the production of an isomer of cyclic ADP-ribose (cADPR)
The cADPR acts as a signalling molecule that binds the ThsA effector via its C-terminal SLOG domain and activates its NADase activity
The NADase effector depletes NAD+ from the cell, generating cellular condtions that cannot support phage replication and presumable lead to cell death before the pahge progeny can mature (abortive infection)

65
Q

how do the plant TIR differ from bacterial
?

A

In plants, TIR domains can use NAD+ for the production of signalling molecules.

66
Q

how are the TIR based signalling systems in bacteria and plants connected?

A

TIR-based antiviral immune signalling in bacteria could have been the ancestral form of plant TIR-containing mechanisms of innate immunity.

67
Q

what potential evolutionary scenario explains the conservation of immune mechanisms between prokaryotes and eukaryotes?

A

Emergence of the first eukaryotic cells via an endosymbiotic event was likely an evolutionary bottleneck. The immune arsenal of the early eukaryote depended on the defences that were present in the specific prokaryotic cells that gave rise to the eukaryote.

The early eukaryotic cell may also have been able to acquire additional prokaryotic immune genes via horizontal gene transfer.
Processes such as domain shuffling, gene duplication and de novo functional innovation continue to diversify the immunity in eukaryotes.

Bacteria and archaea have diverse innate immune mechanisms, with each species encoding different mechanisms

68
Q

how do phages counteract the CBASS system?

A

Using a biochemical screen, some phages were found to encode proteins able to counteract defence by CBASS

These proteins – Acb – counteract CBASS by degrading the cyclic nucleotide signals, therefore blocking downstream effector activation

69
Q

describe what Acb1 in T4 phages does to counteract CBASS defence?

A

Acb1 of phage T4 hydrolysis the 3′ of adenosine bases, enabling broad recognition and degradation of cyclic di- and trinucleotide CBASS signals

70
Q

phage without _ _ _ cannot infect properly

A

Phage without Acb cannot infect properly

71
Q

Active Acb1 enzymes are conserved in phylogenetically diverse phages
what does this demonstrate about defence evasion in phage biology?

A

Active Acb1 enzymes are conserved in phylogenetically diverse phages, demonstrating cleavage of host cyclic nucleotide signals is a key strategy of CBASS evasion in phage biology

72
Q

what are the most common type sof DNA methylation in bacteria

A

N4-methylcytosine (4mC)
5-methylcytosine (5mC)
N6-methyladenine (6mA)

73
Q

what motifs do type 1 RM systems recognise?

A

long, bipartite

74
Q

what motifs do type 2 and 3 RM systems target?

A

short, palindromic

75
Q
A
76
Q

what type of enzymes do type 1 RM systems use?

A

hetero-oligomeric enzymes (complex of REase and MTase)

77
Q

what type of enzymes do type 2 RM systems use?

A

separate REase and MTase

78
Q

what type of enzymes do type 3 RM systems use?

A

REase and MTase complex

79
Q

which types of RM systems require ATP?

A

type 1 and 3

80
Q

where do type 1 RM systems cleave foreign DNA?

A

Cleave variably, often far from recognition site
(remote)

81
Q

where do type 2 RM systems cleave foreign DNA?

A

Cleave within
or at fixed position close to recognition site

82
Q

where do type 3 RM systems cleave foreign DNA?

A

cleave at a fixed position outside (~25bp) of the recognition site
(close to)

83
Q

where do type 4 RM systems cleave foreign DNA?

A

cleave at variable distances from recogntion site

84
Q

how do type 4 RM systems differ from the other 3 types?

A

no methyltransferase (only methylation-dependent REase)
Cleave modified/methylated foreign DNA

85
Q

how do R-M systems propagate as selfish genetic elements

A

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.
when the cell is split, only one gets the plasmid containing the R-M genes.
The post-segregational loss of the R-M gene complex results in the loss of methylation (run out of methyl transferase). The REase, owing to its higher level of stability, attacks the unmodified host genome, resulting in cell death.

86
Q

what is Dcm?

A

5-cytosine DNA methyltransferases

87
Q

what is Dam?

A

N6-methyladenine DNA methyltransferase

88
Q

give an example of a type 4 RM protein?

A

BrxU

89
Q

what processes continue to diversity immunity in eukaryotes?

A

domain shuffling, gene duplication and de novo functional innovation

90
Q
A

Biofilms & Microbial communities (11 decks)

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