Autophagy Flashcards
What is autophagy?
A mechanism to digest intracellular material
Why do cells need degradation? (5)
- Homeostasis
- Removing damaged components
- Signalling (degrade receptors)
- Recycling nutrients
- Reprogramming cells (differentiation)
What are the 2 main mechanisms of degradation?
- The ubiquitin/proteasome system (UPS)
- Autophagy
How does the UPS pathway work? (2)
- Target proteins are tagged with ubiquitin
- Ubiquitin tag is recognised by the proteasome and the protein is degraded
What are the 3 types of autophagy?
- Macroautophagy
- Microautophagy
- Chaperone-mediated autophagy
What is macroautophagy? (2)
- Vesicle is formed de novo (autophagosome) in the cytosol which engulfs material to be degraded
- Autophagosome fuses with a lysosome and degrades the material
What is microautophagy? (2)
- Lysosome membrane invaginates to engulf material
- Material is degraded in the lysosome
What is chaperone-mediated autophagy? (2)
- LAMP2 receptor on the lysosome recognises specific amino acid tags on target proteins
- Targets fed into the lysosome and degraded
What are the features of proteasomal degradation? (3)
- No lysosomes involved
- Degrades individual proteins
- Major turnover route for short-lived proteins (e.g. signalling proteins)
What are the features of macroautophagy? (4)
- Lysosomal
- Bulk digestion pathway
- Can remove whole organelles
- Molecules released can support metabolism (proteins, lipids etc.)
What are the features of chaperone-mediated autophagy? (4)
- Lysosomal
- Degrades individual proteins
- Turnover route for specific long-lived proteins
- Relatively low capacity
What are the functions of macroautophagy? (4)
- Nutrient recycling
- Cellular remodelling
- Removal of damaged components
- Killing intracellular pathogens
How is macroautophagy used for nutrient recycling? (2)
- Autophagy is rapidly upregulated under starvation
- Bulk degradation of the cytosol to create nutrients to keep the cells alive
Why do cancer cells need autophagy?
Tumour cells have restricted blood supply (hypoxic, limited nutrient access) so need to do autophagy to survive
How is macroautophagy used for cellular remodelling? (3)
- Autophagy is the only mechanism to degrade entire organelles
- Removal of mitochondria etc. is required in erythropoiesis
- Removal of sperm-derived mitochondria in the fertilised egg (mitochondria is maternally inherited)
What is erythropoiesis?
Red blood cell formation
How is macroautophagy used to remove damaged components? (2)
- Cellular components accumulate damage over time e.g. mitochondria oxidative damage
- Damage removed by autophagy
How is autophagy linked to ageing and neurodegenerative disease? (3)
- Lysosomal capacity decreases as we age
- Reduced autophagy is the major reason for age-related degeneration
- Long-lived or highly metabolic cells (neurons and muscle) are most susceptible
What is the dietary restriction hypothesis? (2)
- Starvation upregulates autophagy in cells
- Increased damage repair extends lifespan
How is macroautophagy used to kill intracellular pathogens? (3)
- Many pathogens evade the immune system and escape into the cytosol
- Cells can use autophagy to have a second go at getting rid of infection
- However some pathogens can prevent vesicle fusion with the lysosome so the pathogen is safe within the vesicle
Why is it hard to know how to manipulate autophagy? (4)
- Autophagy needs to be inhibited/upregulated in different situations
- Cancer: need to inhibit autophagy to kill tumour cells
- Neurodegeneration: need to upregulate autophagy to remove damage
- Pathogens: inhibit/upregulate depending on the pathogen
How was autophagy discovered? (4)
- Mitochondria within a lysosome observed by electron microscopy, named autophagy
- Later observed in yeast, 15 autophagy genes identified
- Disruption of atg genes used to investigate its functions
- Machinery identified and autophagy observed in live cells
Which proteins are involved in autophagy? (4)
- ULK1 complex required to start autophagy
- PIK3 complex makes a specific lipid on the surface of the phagophore
- Multiple genes involved in adding lipids to the membrane as it forms
- SNAREs required for fusion of autophagosomes with lysosomes
How can autophagy be selective? (3)
- The UBD of an adaptor protein binds to a ubiquitinated protein
- The AIM binds to Atg8 on the inside of the autophagosome membrane to drag the cargo inside for degradation
- Some specific proteins contain AIMs anyway which are naturally selected for degradation by autophagosomes
What is the structure of adaptor proteins? (2)
- Ubiquitin binding domain (UBD)
- Atg8 (LC3) interacting motif (AIM)
What is the marker for autophagosome membranes?
Atg8 (LC3)
What is a phagophore?
A double-membrane structure that expands around the cargo and seals to form a double-membrane vesicle called an autophagosome
What common feature is seen in neurodegenerative diseases?
Ubiquitinated protein aggregates
What proteinopathy is seen in Huntington’s disease?
Huntingtin aggregates
What proteinopathy is seen in Alzheimer’s disease?
Amyloid β plaques
What proteinopathy is seen in Parkinson’s
α-synuclein aggregates
What causes Huntington’s disease? (4)
- Polyglutamine expansion (polyQ) in the Huntingtin protein causes misfolding
- Aggregates of misfolded polyQ Huntingtin are normally ubiquitinated and degraded by the proteosome
- Too much build up results in aggresomes forming which are targeted by autophagy
- More glutamine repeats correlates with earlier onset of disease
What could be the mechanism of toxicity in Huntington’s? (6)
- Loss of the normal function of Huntingtin (function unknown)
- Toxic microaggregates (oligomers)
- Toxic aggresomes
- Proteosome damage
- Adaptor sequestration (adaptor proteins held in the aggresomes)
- Interacting protein sequestration
What causes Parkinson’s disease?
Aggregates of α-synuclein (Lewy bodies) build up in dopaminergic neurons causing death of dopaminergic neurons
What are the differences between Huntington’s and Parkinson’s? (3)
- Huntington’s is caused by a single gene but Parkinson’s has complex genetics
- Huntington’s runs in families but only a small percentage of Parkinson’s cases are familial
- Huntington’s is caused by a Huntingtin mutation but in Parkinson’s α-synuclein is rarely mutated
How is α-synuclein normally degraded? (2)
- Chaperone-mediated autophagy
- Recognised by LAMP2 receptor and transported directly into the lysosome
How can mutations in α-synuclin cause familial Parkinson’s? (3)
- A53T mutation causes α-synuclein to block the LAMP2 receptor, therefore can’t enter the lysosome
- α-synuclein builds up and forms aggregates which are targeted by autophagy
- Aggregates overwhelm autophagy, accumulate and cause disease
What is the leading hypothesis for the cause of Parkinson’s? (2)
- Damaged mitochondria accumulate in Parkinson’s, source of ROS which causes damage
- Parkinson’s is caused by mitochondrial-derived oxidative damage
What proteins are mutated in sporadic cases of Parkinson’s? (2)
- PINK1
- PARKIN
What is PINK1? (3)
- Mitochondrial kinase
- Loss of function in sporadic early-onset Parkinson’s
- Responds to mitochondrial damage
What is PARKIN? (3)
- E3 ubiquitin ligase (tags target proteins with ubiquitin)
- Associated with early-onset Parkinson’s
- Responds to mitochondrial damage
How do PINK1 and PARKIN work normally? (2)
- PINK1 and PARKIN recognise damaged mitochondria and ubiquitinate
- Damaged mitochondria are targeted by mitophagy
What is mitophagy?
Degradation of damaged mitochondria via autophagy
What happens when PINK1/PARKIN are mutated? (3)
- Damaged mitochondria accumulate and generate ROS
- ROS causes oxidative damage, protein misfolding and damage to organelles
- Ultimately leads to neuronal death in Parkinson’s
How is autophagy linked to cancer? (2)
- Autophagy protects cells from damaged organelles/ROS/protein toxicity which prevents DNA damage
- Without autophagy, DNA damage can lead to cancer
Which autophagy gene mutation is associated with cancer?
Atg6 gene (Beclin 1) deletion in high proportion of ovarian, breast and prostate cancers
How are autophagy and apoptosis linked in normal cells? (3)
- Autophagy suppresses apoptosis
- When the cell is surviving, Beclin1 is encouraging autophagy and Bcl2 is on the mitochondria blocking apoptosis
- When the cell wants to die, Beclin1 directly interacts with Bcl2 to remove it from the mitochondria, favours apoptosis over autophagy
What largely causes apoptosis? (2)
- Mitochondrial membrane permeabilisation and release of caspases into the cytosol
- Regulated by Bcl protein family
What does Bcl2 do? (2)
- Present on the mitochondrial membrane
- Prevents the release of caspases and blocks apoptosis
What does Beclin1 do?
Involved in making autophagosomes for autophagy
Why is autophagy a concern in cancer? (3)
- Autophagy is upregulated in cancer cells to keep them alive
- This causes inhibition of apoptosis
- This drives tumour survival and chemotherapy resistance
- Inhibit autophagy to activate apoptosis?
How is autophagy anti-oncogenic? (4)
- Removes damage
- Reduces ROS
- Reduces inflammation
- Prevents DNA damage
How is autophagy pro-oncogenic? (3)
- Promotes survival during oxygen/nutrient shortage
- Inhibits apoptosis
- Promotes chemotherapy resistance
How could autophagy be manipulated to tackle cancer? (3)
- Inhibit autophagy to block tumour survival
- Inhibit autophagy to increase apoptosis during chemotherapy
- Activate autophagy to remove damage and prevent cancer
