Advanced Molecular Cell Biology - Lecture 19

what is (macro)autophagy?

a mechanism to digest intracellular material

what are the stages of autophagy?

initiation → expansion (phagophore formation) → closure (autophagosome) → lysosome fusion → acidification and maturation → degradation (autolysosome)

why do cells need degradation?

homeostasis, removing damaged components, signalling, recycling nutrients, reprogramming cells (differentiation)

What are some of the multiple mechanisms of degradation?

the ubiquitin/proteasome system (UPS), macroautophagy, chaperone-mediated autophagy and microautophagy

describe the ubiquitin/proteasome system:

Cytosolic proteins that cells get rid of in response to signalling get ubiquitin tags by ubiquitin ligases, ubiquitin tags target for degradation, allowing recognition by the proteasome, the protein gets fed through the barrel-shaped proteasome and degraded

describe the key characteristics of a proteosome:

• Non-lysosomal

• Degrades individual proteins

• Major turnover route for short-lived proteins

describe the key characteristics of macroautophagy:

• Lysosomal

• Bulk digestion pathway

• Can remove whole organelles

• Molecules released can support metabolism

describe the key characteristics of chaperone-mediated autophagy/microautophagy:

• Lysosomal

• Only degrades individual proteins

• Turns over specific, generally long-lived proteins

• Relatively low capacity

autophagy is rapidly upregulated under __________. It causes ____-_________ bulk degradation of the cytosol

starvation, non-selective

What gene has been proven important to allow wild-type amoeba to survive through amino acid starvation?

atg 1

cells lacking _________ die under starvation, autophagy-deficient mice die during __________ starvation, ________ cells in solid _______ need autophagy to survive

autophagy, neonatal, cancer, tumours

autophagy has a functional role in cellular remodelling, autophagy is the only mechanism to degrade ________, it is essential to form some specific cell types

organelles

name 2 examples of autophagy carrying out cellular remodelling:

erythropoiesis and removal of sperm-derived mitochondria

Why is the removal of damaged components an important function of autophagy?

cellular components accumulate damage over time; these need to be removed selectively

why is reduced autophagy is the major reason for age-related degeneration?

• Cells continuously acquire damage

• Lysosomal capacity decreases as we age

• Long-lived or highly metabolic cells such as neurons and muscle are most susceptible

what is the dietary restriction hypothesis:

During starvation or exercise, there is an increase in autophagy, and there is an increase in damage repair; therefore there is evidence that you can live longer

Some pathogens can escape immune cells' engulfment and enter the cytoplasm. What is a function of autophagy associated with this issue?

Autophagy allows the killing of intracellular pathogens (i.e. TB or Salmonella)

what are the 4 functions of autophagy?

• nutrient recycling

• cellular remodelling

• removal of damaged components

• killing intracellular pathogens

why is recycling nutrients important?

for surviving starvation and cancer

why can a lack of removal of damaged protein/organelle cause?

ageing, muscular dystrophy, neurodegeneration and cancer

intracellular pathogen removal it is important to remove;

• tuberculosis

• MRSA

• viruses

how do you make an autophagosome:

Autophagy has also been shown to occur in yeast, but to observe the proteasomal enzymes that live in the lysosome in yeast, they have to be knocked out. If the cells are then starved, vesicles appear, and then a visual screen was done to identify 15 autophagy genes

identifying the Atg genes allowed?

• disruption of autophagy to investigate its functions

• a start on dissecting how the machinery works

• observation of autophagy in live cells

What are the 3 key components of the autophagy machinery involved in making autophagosomes:

• ULK 1 complex (regulatory part), AMPK (tells you how much ATP the cells have), mTORC1 (general regulator of cell metabolism)

• VPS34 (defines membranes that will become autophagosomes in the future, largely on the ER surface)

• SNAREs

how is selective autophagy carried out?

a family of adaptor proteins which have an Atg8-interacting motif which can bind specifically to Atg8

cell will ubiquitinate the substances they want to get rid of; then the adaptor protein comes in, binds to both ubiquitin and the Atg8 on the autophagosomes, targeting it for degradation