BIOL402: Bacterial Defenses Against Bacteriophage

E4

3 strategies to counter phage infections:

1. receptor adaptations to limit attachment

2. host defense mechanisms

3. phage-derived phage defenses (superinfection prevention)

receptor adaptations:

point mutations

extracellular matrix

phase variation

masking proteins

regulation of receptor gene expression

outer membrane vesicles

what are point mutations:

changes to the receptor proteins which change their shape, limiting viral attachment

what is the function of masking proteins?

they cover receptors to prevent attachment

what is phase variation?

the rapid turnover of receptor expression

what is the function of outer membrane decoys?

they act as decoys

host defense systems:

restriction modification systems

DISARM

BREX

Argonaut

CRISPR

superinfection exclusion systems

toxin-antitoxin systems

secondary metabolites/ chemical defenses

what are restriction modification systems:

nuclei acid interference which differentiated=s between host and phage genomes

type 1 restriction modification system:

protein complex with methyltransferase, restriction endonuclease, and specificity will cut and methylate DNA far from its recognition site

type 2 restriction modification system:

separate methyltransferases and restriction endonucleases which cut close to their recognition site

type 3 restriction system:

separate methyltransferases and restriction endonucleases which work together in a complex to cut far from the recognition site

type 4 restriction system:

only a restriction endonuclease which cuts methylated DNA

the Dnd system:

phosphothiolation of dnDNA by DndABCDE, unthiolated DNA is cut by DndFGH

the Ssp system:

phosphothiolation of ssDNA by SspABCD

sspE recognizes SspABCD activation and cuts unmodified DNA

ssP FGH damages unmodified DNA

DISARM stands for:

defense island system associated with restriction modification

DISARM system:

methyltransferase, helicase, and nuclease activity which are recruited to 5’ overhangs to initiate damage

BREX:

bacterial exclusion which interferes with phage replication

Argonaut:

binds target DNA and interferes with its function

TtAgo function:

uses guide DNA to target DNA

RsAgo function:

small RNA is used to target DNA

CRISPR:

clustered regularly interspaced short palindromic sequences, a bacterial immune system

CRISPR class 1:

uses multiple small subunits as effector molecules to cleave DNA

CRISPR class 2:

one small effector molecule to cleave DNA

classification of CRISPR Cas 9 system:

class 2

phase 1 CRISPR cas 9 system:

bacteriophage nucleic acids are digested into spacers by Cas 9 and integrated into the genome

RNase 3 cleaves the preCRISPR RNA into guide and tracr RNA

phase 2 CRISPR cas9 system:

bacteriophage infection alerts Cas9 to the location of phage DNA and CRISPR RNA binds phage DNA, cleaving it

superinfection exclusion systems:

prevent entry of other phage into an already infected cell

proteins involved in superinfection exclusion:

Imm

Sim

SicA

Lip

function of Imm, Sim, and SicA proteins:

binds the inner membrane to prevent translocation

function of Lip protein:

blocks receptors for bacteriophage attachment

anti T4 lysozyme protein function:

prevents peptidoglycan degradation

abortive infection systems:

sense phage replication and turn off gene expression or shutdown metabolism

types of abortiveinfection systems:

RexA/RexB

Gabija

RexA/RexB system:

viral nuclei acids are bound be cellular proteins to activate RexA, which dimerizes with RexB (a transmembrane ion channel which disrupts cell membrane potential)

Gabija system:

localized ATP depletion activated GajA, an ATP binding protein with an open ATP cleft when the concentration of ATP is low

an empty ATP GajA domain causes nicks in phage DNA to activate GajB

GajB has endonuclease activity and digests phage DNA

type 2 toxin-antitoxin system:

responds to cellular stress to activates proteases to destroy the antitoxin

the toxin degrades cellular DNA

type 3A toxin-antitoxin system:

respond to bacteriophage infections, causing dissociation of the toxin from the antitoxin

secondary metabolites which can interfere with the phage replicative cycle:

doxorubicin

daunorubicin

doxorubicin function:

uses an OH group to become a free radical to damage DNA by oxidation

daunorubicin function:

uses a H to interrupt circularization of phage DNA

phage counter measures for bacterial defenses:

increase protease production

sloppy replication

anti-restriction modification processes

anti-CRISPR systems

anti-abi systems

mechanisms for countering restriction modification systems:

phage encoded methyltransferases

OCR protein production to mimic restriction endonuclease sites

DarA/DarB prevents DNA cutting by binding restriction endonuclease site

Ra1 increases host methyltransferase activity

Stp disrupts modification systems

anti-CRISPR systems:

produce Acr proteins to inhibit CRISPR phases

anti-abi systems:

encode the Gad1 protein to block DNA binding domains in GajA