BIO211 Autophagy Notes

Heterozygotes

  • Alleles are uneven.

Autophagy

  • Process by which proteins are removed due to damage or regulation of activity.

  • Two main pathways:

    • Proteasome: Direct degradation of short-lived proteins and misfolded monomers.

    • Autophagy: Delivery to lysosome for degradation of long-lived proteins and misfolded oligomers/monomers.

  • Both pathways involve tagging with ubiquitin.

    • Ubiquitination signals which pathway a protein will be degraded by.

    • Short-lived native proteins and misfolded monomers are degraded by the proteasome.

    • Long-lived native proteins and misfolded oligomers/monomers are degraded by autophagy.

Purpose of Autophagy

  • Nutrient and energy homeostasis.

  • Removal of damaged organelles.

  • Removal of aggregate proteins.

  • Removal of intracellular pathogens.

  • Discovery of the double membrane structure lead to a Nobel Prize

Types of Autophagy

  • Macroautophagy: Molecules are enveloped by a membrane to form an autophagosome, which then fuses with a lysosome.

  • Microautophagy: Small debris are sequestered directly into the lysosome.

  • Chaperone Mediated Autophagy (CMA): Proteins are transported through a channel into the lysosome.

Process of Autophagy

  1. Phagophore (or isolation membrane) forms from a membrane source.

  2. Cargo is brought to the autophagosome.

  3. Autophagosome fuses with an endosome, forming an amphisome.

  4. Amphisome fuses with a lysosome, forming an autolysosome.

Forming the Phagophore

  • Requires a specialized membrane.

  • The exact origin of the membrane for the phagophore is unknown.

  • All autophagosomes start as an isolation membrane (IM).

  • Membrane for IM could come from the Golgi, endosomes, ER, or mitochondria-associated membrane (MAM) interface.

Membrane Tagging for Phagophore Formation

  • Complex mechanisms enable the formation of the autophagic vesicle.

  • Key components:

    • PI3P (phosphatidylinositol-3-phosphate).

    • VPS34 complex.

    • ATG9 (membrane receptor).

    • LC3 (autophagy receptor).

VPS34 and PI3P

  • VPS34 phosphorylates PI (phosphatidylinositol) to PI3P.

  • VPS34 is a phosphotidylinositol kinase (PI3K).

  • Each version of PIP has a different kinase

  • PI3P is sensed by other proteins involved in autophagy.

ATG9

  • ATG9 brings new membrane to areas tagged with PI3P.

  • ATG9-containing vesicles bud from a source membrane.

  • Vesicles assemble into a preautophagosomal structure (PAS).

  • PAS forms the isolation membrane.

  • ATG9 senses PI3P to bring new membrane to forming autophagosomes.

LC3-II

  • LC3-II is a phospholipid tag found only in autophagosomes.

  • LC3-II is the lipidated form of LC3-I.

  • Lipidation occurs when phosphatidylethanolamine (PE) is added to LC3.

  • LC3-II is a molecule used to “tag” PE.

  • Found only in autophagosomes

  • PE part of LC3-II can be inserted to membranes to allow ‘tag’ to be associated with membrane.

Autophagy Regulation

  • Starvation induces autophagy.

  • TOR (target of rapamycin) complex inhibits autophagy.

  • Inhibiting TOR activates autophagy, and vice versa.

  • Insulin and amino acids activate TOR.

  • Class III PI3K (kinase) activates autophagy.

  • ATG proteins (autophagy-related) work with kinases to form protein complexes.

Simplified Autophagy Regulation

  • Starvation: \text{TOR activity} \downarrow , Autophagy \uparrow

  • Nutrient Rich: \text{TOR activity} \uparrow , Autophagy \downarrow

Cargo Loading

  • Cargo is loaded into the phagophore, forming the isolation membrane.

Mitophagy

  • Damaged mitochondria are tagged with ubiquitin.

  • Ubiquitin recognizes LC3II, potentially using an adaptor protein.

  • Mitochondria are loaded into the autophagosome.

Consequences for Diseases

  • Aging: Removes damaged organelles.

  • Neurodegeneration: Prevents the accumulation of aggregate proteins.

  • Infection: Cells get rid of viruses and bacteria that get inside.

  • Cancer: Removes damaged organelles.

Autophagy: Pro vs. Con

  • Neurodegeneration: Accumulation of autophagic vesicles may be involved in Alzheimer's Disease.

  • Infection: Some bacteria have evolved to subvert the system for their lifestyle.

  • Cancer: Can help cancer cells resist cancer drugs and survive with low nutrients.

Autophagy Pathway Summary

  1. Phagophore forms.

  2. Cargo is targeted to the phagophore.

  3. Phagophore membrane expands to encapsulate cargo (now called autophagosome).

  4. Autophagosome fuses with endosome to form amphisome.

  5. Amphisome fuses with lysosome to form autolysosome.

Autophagy “Special Membrane” Summary

  • Autophagy starts by making a phagophore and tagging it with modified phospholipids, allowing two things to occur:

    • PI3P: Modified PI allows ATG9 to recognize the phagophore and bring new membrane to expand the autophagic membrane.

    • LC3-II: Modified PE allows adaptors to recognize the phagophore and bring "cargo" that will be transported by the completed autophagosome to the lysosome.

Blocking Autophagy

  • Blocking different components of the autophagy pathway can affect the overall process. Some example blocks include: Amino Acids, Insulin, TOR, ATG9, and P62.