9 LC Concepts in Molecular Biology 19.10.2022
Autophagy and quality control 2
When we’ll be talking about autophagy, we’ll refer to macroautophagy
which is characterized by the formation of a membrane structure called
isolation membrane, its forms next to the ER endoplasmic reticulum
but its not a continuation or extension of it, it’s a membrane structure
that’s form de novo. This membrane structure grows in 3 dimensions,
while growing it encapsulates cytoplasmic cargo material and then
when the isolation membrane encloses, by a fission reaction, results in
two final membranes: inner membrane and outer membrane. Finally
the outer membrane wioll fuse with the lysosome and the inner
membrane and the cargo will be degraded.
Autophagy can be induced by starvation:
- Upon starvation TOR kinase activity is lost and qill
no longer phosphorylate, and this activates Atg1.
- Atg1 will become active and assemble into a
macromolecular ondensarte and will induce
autophagosome formation.
- This process can be also induced by rapamycin
Autophagy a major pathway for the clearance of cells from
dangerous and harmful material, even when cells are not
starving and with presence of nutrients (f.e. if
mitochondria is damaged).
SELECTED TYPES OF AUTOPHAGY
Initially autophagy was characterized as a starvation induced process, and
then when people looked at the content of autophagosomes it was more
less the same that was also present on average on the cell. It also became
clear that autophagy can also very selectively target all sorts of components
such as:
- Protein aggregates
- Demaged organelles
- Cyctosolic pathogens
- And so on
What all these pathways, including autophagy, do is actuallyreplacing
damaged components every time. This is what our cells do, the individual
molecules are replaced and identified if they’re damaged.
How is all of this material actually recognized by the autophagosome
machinery?
We have a cargo material and the isolation membrane; the problem this
has been solved is that isolation membrane is selectively attacked with atg8
proteins.
atg8 is one of these genes discovered in genes, required for autophagosome
formation.
Also out cells express atg8 proteins, called differently but structurally very
similar. In particular they are folded like ubiquitine, so they have a ubiquitine
fold and short extensions at the n-terminus; these are ubiquitine proteins.
, 9 LC Concepts in Molecular Biology 19.10.2022
Just like ubiquitine is conjugated generally to a Lys redidue,
atg8 proteins are conjugated to the membrane of it (in
particular a membrane that is called phospho-esanolamin
PE).
o UBIQUITINATION
Ubiquitin is usually activated by E1 and then
transferred to the E2 enzyme, from it is
transferred to the target (at leat in the
canonical pathway) and this linking of the
loaded E2 to the substrate is mediated
generally by E3 ligases.
In autophagy we do have a similar
cascade:
1. We have atg7(E1) that will activate
atg8, also under the consumption of
atp
2. this loaded E1 will then transfer atg8
to atg3 (E2)
3. E3 will attache atg8 by two PE this
is aidded by E3 complex that’s also
composed by several atg proteins
(12, 5, 16) (in total called ATG8 conjugation machinery, that in our cells are called
GABARAP proteins) y
When they are in the membrane, this atg8 proteins can be recognized by
the cargo receptors or adaptors, this receptor is a short peptide that will
poke into two hydrophobic pockets called LIR motifs for LC3- interacting
regions. these short motifs can bind this atg8 family proteins, in this
case Lc3, that decorate the isolation membranes. Thereby you can
recruit proteins very specifically to the isolate membrane.
Autophagy and quality control 2
When we’ll be talking about autophagy, we’ll refer to macroautophagy
which is characterized by the formation of a membrane structure called
isolation membrane, its forms next to the ER endoplasmic reticulum
but its not a continuation or extension of it, it’s a membrane structure
that’s form de novo. This membrane structure grows in 3 dimensions,
while growing it encapsulates cytoplasmic cargo material and then
when the isolation membrane encloses, by a fission reaction, results in
two final membranes: inner membrane and outer membrane. Finally
the outer membrane wioll fuse with the lysosome and the inner
membrane and the cargo will be degraded.
Autophagy can be induced by starvation:
- Upon starvation TOR kinase activity is lost and qill
no longer phosphorylate, and this activates Atg1.
- Atg1 will become active and assemble into a
macromolecular ondensarte and will induce
autophagosome formation.
- This process can be also induced by rapamycin
Autophagy a major pathway for the clearance of cells from
dangerous and harmful material, even when cells are not
starving and with presence of nutrients (f.e. if
mitochondria is damaged).
SELECTED TYPES OF AUTOPHAGY
Initially autophagy was characterized as a starvation induced process, and
then when people looked at the content of autophagosomes it was more
less the same that was also present on average on the cell. It also became
clear that autophagy can also very selectively target all sorts of components
such as:
- Protein aggregates
- Demaged organelles
- Cyctosolic pathogens
- And so on
What all these pathways, including autophagy, do is actuallyreplacing
damaged components every time. This is what our cells do, the individual
molecules are replaced and identified if they’re damaged.
How is all of this material actually recognized by the autophagosome
machinery?
We have a cargo material and the isolation membrane; the problem this
has been solved is that isolation membrane is selectively attacked with atg8
proteins.
atg8 is one of these genes discovered in genes, required for autophagosome
formation.
Also out cells express atg8 proteins, called differently but structurally very
similar. In particular they are folded like ubiquitine, so they have a ubiquitine
fold and short extensions at the n-terminus; these are ubiquitine proteins.
, 9 LC Concepts in Molecular Biology 19.10.2022
Just like ubiquitine is conjugated generally to a Lys redidue,
atg8 proteins are conjugated to the membrane of it (in
particular a membrane that is called phospho-esanolamin
PE).
o UBIQUITINATION
Ubiquitin is usually activated by E1 and then
transferred to the E2 enzyme, from it is
transferred to the target (at leat in the
canonical pathway) and this linking of the
loaded E2 to the substrate is mediated
generally by E3 ligases.
In autophagy we do have a similar
cascade:
1. We have atg7(E1) that will activate
atg8, also under the consumption of
atp
2. this loaded E1 will then transfer atg8
to atg3 (E2)
3. E3 will attache atg8 by two PE this
is aidded by E3 complex that’s also
composed by several atg proteins
(12, 5, 16) (in total called ATG8 conjugation machinery, that in our cells are called
GABARAP proteins) y
When they are in the membrane, this atg8 proteins can be recognized by
the cargo receptors or adaptors, this receptor is a short peptide that will
poke into two hydrophobic pockets called LIR motifs for LC3- interacting
regions. these short motifs can bind this atg8 family proteins, in this
case Lc3, that decorate the isolation membranes. Thereby you can
recruit proteins very specifically to the isolate membrane.
