autophagy 2

Question 1

interactions between atg8 and autophagy adaptors/ receptors

Answer 1

atg8 are small ub like molecules
ub-binging domains are varied in size and sequence
proteins interact with atg8 through lc3 interaction region

Question 2

lc3 interaction region

Answer 2

also called atg8 interaction motif
short linear peptide sequence found in disordered regions of proteins
LIR/AIM mediates protein interactions with atg8/lc3/gabarap protein

Question 3

lc3 interaction motif

Answer 3

classical core motif: tryptophan - amino acid - amino acid - leucine
expanded includes acidic or serine residues
serine can be phosphorylated

Question 4

lc3 structure

Answer 4

globular
2 deep hydrophobic pockets - vary in sizer and depth
helps regulate the lir motif
presence of n terminal extension allows lir interactions

Question 5

gabarap interaction

Answer 5

modified lir for valine drives interaction with gabarap

Question 6

specificity from lir to gabarap

Answer 6

intro of valine in x1 or val in x1 in L position increases gabarap production

Question 7

lir/atg8 interaction

Answer 7

hydrophobic residues of lirs sit in hp1 of atg8
interaction is stabilised bu acidic/phosphorylated serine residues preceeding hydrophobic residues
interaction is sufficient to recruit protein to the growing ap
can then be used to recruit specific complexes/structures to ap for degradation by autophagy/ lysosomal pathway

Question 8

autophagy receptor

Answer 8

degraded with cargo
p62 and nbr1 both target protein aggregates for degradation
receptors are not degraded when autophagy doesnt occur - so they can accumulate
mimicked by inhibiting lysosome

Question 9

xenophagy

Answer 9

targetting intracellular pathogens for degradation
s thyphi - fatal side effects
s typhimurium - non fatal side effects
classical model use din salmonella

Question 10

life cycle of salmonella

Answer 10

epithelium induces formation of vacuole
vacuole is in the vesicle and matures
vacuoles rupture leading to salmonella being coated in ubiquitin

defect in autophagy leads to hyperprolif of salmonella
normal proliferation of samonella through vesicle maturation

Question 11

specialised receptors

Answer 11

used to target intracellular bacteria to the autophagy pathway
lack of autophagy receptors increases proliferation of cystolic salmonella
autophagy activated by invading pathogens can be marked by ub for targetting by autophagy receptors

Question 12

optineurin

Answer 12

ub and autophagy receptor
ub binding domain in hte c terminal
lir present
serine after lir activates tlr4 and tbr4
e5ok mut is linked to primary open angle glaucoma
defects associated with pagets disease of bone and amyotrophic lateral sclerosis

Question 13

phosphorylated optineurin

Answer 13

tbk1 p’s optn at lir

pOPTN activates autophagy activity

Question 14

pathogens avoiding autophagy

Answer 14

bacterial effectors - secreted by protein into host cytosol that target specific functions
SpeB targets for degradation
RavZ is the cleaved form

Question 15

shigella

Answer 15

escape vacuole to cytosol and proliferate to infect other cells
exposed to innate immune system once they enter the cytosol
avoid detection through iscB to act as a cloaking device
virA targets rab1 and inhibits autophagy

Question 16

non-canonical autophagy

Answer 16

atg proteins not required for formation of ap
double membrane doesnt necessarily elongate from one source
atg proteins can be recruited to a pre existing membrane different from phagospore
can be activated by tlrs
tlr9 activation by forgein dna induces lc3 associated phagocytosis of tlr9 into ifn signalling compartment and induced ifn alpha
noncannonical is dependent on lap
lap is improtant for pathogen clearing and antigen presentation
lap is also key for immune signalling by tlrs