Autophagy and Disease Flashcards
What happens when a cellular component/organelle becomes damaged?
Eliminate or repair it
How does a cell eliminate an organelle?
Secretes it out of the cell
Proteasomal degradation
Lysosomal degradation
Where does proteasomal degredation occur and what does it degrade?
Only proteins degraded in the CYTOSOL
What are 3 lysosomal degradation pathways?
Autophagy = degrades intracellular components
Endocytosis = degrades components from cell surface
Phago/pinocytosis = degrades extracellular components
How is a autolysosome formed?
Phagophore develops into autophagosome
Autophagosome and lysosome fuse to make an autolysosome
Which stage of autolysosome formation has a DOUBLE-membrane?
Autophagosome
What does ATG1 gene code for?
ULK1
What is autophagy capable of degrading?
Protein
Lipid
Carbohydrate
Nucleic acid = whole organelles
What forms of stress induce autophagy?
Nutrient derprivation
ER stress
Oxidative stress
What are the 3 complexes needed to initiate autophagy?
Protein kinase ULK1
Lipid kinase VPS34
Ubiquitin-like system
What is required for ULK activity and localization to phagophore?
ATP13
FIP200
ATG101
What is required for VPS34 activity and localization to phagophore?
VPS15
Beclin1
ATG14
What does ULK1 phosphoylate?
Beclin1, ATG14 and VPS34
What are the two Ubiquin-like elements?
ATG12
ATG8
For ubiquitin-like element ATG12 what are the E1, E2, and E3?
E1 = Atg7
E2 = ATG10
E3 = ?
For ubiquitin-like element ATG8 what are the E1, E2, and E3?
E1 = Atg7
E2 = Atg3
E3 = Atg12/5
What amino acid does Ub bind?
Glycine
What amino acid does E2 bind?
Cysteine
What proteins are most commonly mutated in Parkinson’s?
LRRK2
PINK1
Parkin
What ATG subfamilies help the phagophore membrane grow?
Different ATG8s may have distinct roles for elongation and fusion
ATG8 subfamilies = LC3 and GATE-16/GABARAP
What mutations in LRRK2 cause Parkinson’s?
LRRK2 is a kinase
Mutation of G2019S cause increased kinase activity
The increased kinase activity of LRRK2 interferes with the proper recruitment of autophagy-related proteins (such as PINK1, Parkin, and others) to damaged mitochondria.
This disrupts the signaling needed to initiate mitophagy.
The accumulation of defective mitochondria results in increased oxidative stress and cellular dysfunction, contributing to the neurodegeneration seen in Parkinson’s disease.
What are potential Parkinson’s therapies to improve mitophagy?
LRRK2 inhibitor
PINK1 activator
UPS30 inhibitor = a mitochondrial deubiquitylating enzyme that negatively regulates mitophagy—the process by which cells remove damaged mitochondria. By inhibiting USP30, MTX325 aims to enhance mitophagy, thereby improving mitochondrial quality and function.
What is the source of the autophagosomal membrane?***
Endoplasmic reticulum
What is DFCP1?
PI3P binding protein that marks the site of autophagosome formation
What does DFCP1 mark?
The omegasome
What is the omegasome?
The omegasome is a membrane structure that serves as a scaffold for the formation of autophagosomes, crucial for autophagy. It has an omega-like shape and is enriched with phosphatidylinositol 3-phosphate (PI(3)P), a lipid produced by the Vps34 complex.
DFCP1 marks the omegasome by binding to PI(3)P through its FYVE domains. This binding recruits other autophagy-related proteins (like WIPI) to the omegasome, enabling the membrane to curve and expand around damaged cellular material.
The omegasome forms near the endoplasmic reticulum (ER), which provides lipids and scaffolding necessary for autophagosome formation. The omegasome thus acts as a scaffold, allowing the phagophore to emerge, which eventually matures into an autophagosome that engulfs and degrades unwanted cellular components.
Can autophagy be selective and if so how?
Yes it can via Sequestosome-like Receptors (SLR)
Name some sequestosome-like receptors
p62
OPTINEURIN
Tax1BP1
NDP52
NBR1
What happens with loss of Beclin1?
Promotes tumourigenesis
Why is autophagy a double-edged sword?
Can also be applied to tumour cell survival
Blocking autophagy in TUMOURS is a good thing but only in tumours
What is mitophagy?
Autophagy of mitochondria
What are PINk1 and Parkin?
Protein kinase = PINK1
E3 ligase = Parking
What happens to PINK1 and Parkin when mutated in Parkinson’s?
PINK1 is a mitochondrial kinase that normally accumulates on the outer mitochondrial membrane when mitochondria are damaged. It acts as a signal to recruit Parkin, an E3 ubiquitin ligase, to the damaged mitochondria. Mutations in PINK1 impair its ability to recognize and bind to damaged mitochondria, preventing the initiation of mitophagy. As a result, damaged mitochondria accumulate, leading to oxidative stress and cellular damage, contributing to Parkinson’s symptoms.
Parkin is normally recruited by PINK1 to damaged mitochondria, where it ubiquitinates mitochondrial proteins, marking them for degradation. Mutations in Parkin prevent it from effectively tagging damaged mitochondria for removal. This leads to defective mitophagy, allowing damaged mitochondria to persist, further increasing cellular stress and promoting neurodegeneration.
What causes parkinsonism in humans and mitochondrial dysfunction in model organisms?
Loss-of-function mutations in PINK1 and Parkin cause parkinsonism and mitochondrial dysfunction.
What is Parkin’s role in relation to damaged mitochondria?
Parkin (Ub E3 ligase) is recruited from the cytosol to damaged mitochondria to trigger their autophagy.
What is currently unknown about Parkin’s recruitment to damaged mitochondria?
How Parkin recognizes damaged mitochondria is unknown.
How is the expression of PINK1 regulated on mitochondria?
The expression of PINK1 on individual mitochondria is regulated by voltage-dependent proteolysis, which maintains low levels on healthy mitochondria but facilitates rapid accumulation on damaged ones.
What happens when PINK1 accumulates on mitochondria?
The accumulation of PINK1 on mitochondria is both necessary and sufficient for the recruitment of Parkin to mitochondria.
What is mitophagy critical for maintaining?
Mitophagy is the selective removal of damaged mitochondria, which is critical for maintaining neuronal homeostasis.
What disease is mitophagy mutation associated with?
Mutations in proteins involved in mitophagy cause neurodegenerative diseases, suggesting defective mitochondrial turnover contributes to neurodegeneration.
What is the localization pattern of mitophagy events in neurons?
The localization of mitophagy events had a robust somal bias, meaning they were predominantly occurring near the cell body.
In primary rat hippocampal neurons, we developed a mitophagy induction paradigm where mild oxidative stress induced low levels of mitochondrial damage, how did mitophagy react compared to basal conditions?
Mild oxidative stress is applied to the neurons, which causes low levels of mitochondrial damage.
As a result, damaged mitochondria trigger the mitophagy process, but the key difference here is that the lysosomal fusion and acidification (the degradation step) happens more slowly.
The autophagosomes efficiently engulf the damaged mitochondria, but they stay in an undigested state (non-acidified) for hours to days before proper degradation happens.
What is optineurin?
A scaffold protein that helps in recruiting other proteins (like Parkin) to damaged mitochondria. It helps mediate the signaling between damaged mitochondria and the cell’s cleanup machinery, playing a crucial role in Parkin activation for mitophagy.
Optineuin-mediated mitophagy occurs in NEURONES (optineurine is also found in other tissues)
When is PINK1/Parkin activated?
Does not normally regulate a majority of mitophagy under normal (basal) conditions
It is a stress reponse pathway to activate mitophagy
