Transcript Autophagy_Marcx

PAINT autophagy annotation
Lessons learned
Autophagy (or autophagocytosis) (from the Greek auto-, "self"
and phagein, "to eat"), is the basic catabolic mechanism that
involves cell degradation of unnecessary or dysfunctional
cellular components through the actions of lysosomes .
The breakdown of cellular components promotes cellular survival during starvation by
maintaining cellular energy levels. Autophagy allows the degradation and recycling of
cellular components.
During this process, targeted cytoplasmic constituents are isolated from the rest of
the cell within a double-membraned vesicle known as an autophagosome. The
autophagosome then fuses with a lysosome and its cargo is degraded and recycled.
There are three different forms of autophagy that are commonly described;
macroautophagy, microautophagy and chaperone-mediated autophagy.
In the context of disease, autophagy has been seen as an adaptive response to stress
which promotes survival, whereas in other cases it appears to promote cell death and
morbidity.
The 3 types of autophagy
The role of autophagy in Parkinson’s disease.
Lynch-Day M.A., Mao K., Wang K., Zhao M., Klionsky D.J.
Cold Spring Harb Perspect Med. 2012 Apr;2(4):a009357.
What’s the origin of the autophagosome / autophagic vacuole ?
The autophagosome: origins unknown, biogenesis complex
Lamb C.A., Yoshimori T., & Tooze S.A.
Nature Reviews Molecular Cell Biology 14, 759–774 (2013) doi:10.1038/nrm3696
Proteins involved in autophagic vacuole assembly are very
conserved and well known
GO: 0000045 - autophagic vacuole assembly
The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized
membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm
The emerging role of autophagy in alcoholic liver disease.
Ding W.X., Manley S., & Ni H.M. Exp Biol Med (Maywood). 2011 May 1;236(5):546-56.
What’s the origin of the autophagosome / autophagic vacuole ?
The autophagosome: origins unknown, biogenesis complex
Lamb C.A., Yoshimori T., & Tooze S.A.
Nature Reviews Molecular Cell Biology 14, 759–774 (2013) doi:10.1038/nrm3696
Pre-autophagosomal structures
It is very difficult to discriminate between
omegasomes, PAS and autophagosomes.
Only recently specific localisation markers
such as DFCP1/ZFYVE1 for omegasomes
have been identified.
New GO terms:
PAINT autophagy - summary
• 235 primary annotations to autophagy-related
terms
• 137 primary annotations confirmed for
propagation
• 98 indirect annotation (IMP, phenotypes)
• 48 families annotated
• 15 missing families
ATGs and autophagic vacuole assembly
Protein family
PTHR family
Assembly
Localization
Function
ATG1
PTHR24348
YES
Cytoplasm, PAS
Kinase for ATG9 to bind ATG18
ATG2
PTHR13190
YES
PAS
Localizes ATG18 to omegasome and PAS
ATG3
PTHR12866
YES
Cytoplasm
E2 for ATG8-PI conjugation
ATG4
PTHR22624
YES
Cytoplasm
Cleaves ATG8: reveals C-ter Gly for PI conjugation. Also removes PI
ATG5
PTHR13040
YES
Cytoplasm, PAS
ATG12-ATG5 acts as E3 for ATG8-PI conjugation
ATG6/BECN1/VPS30 PTHR12768
YES
Endosome, vacuole, PAS
VPS34 PI3-kinase complex I, ATG8 conjugation and membrane location
ATG7
PTHR10953
YES
Cytoplasm, PAS
E1 for ATG12-ATG5 and ATG8-PI conjugation
ATG8
PTHR10969
YES
Omegasome, PAS, vacuole
Membrane fusion, autophagosome assembly
ATG9
PTHR13038
YES
ER, Golgi, PAS (integral)
Recruites ATG proteins to the PAS (through ATG18-binding)
ATG10
PTHR14957
YES
Cytoplasm, PAS
E2 for ATG12-ATG5 conjugation
ATG101
PTHR13292
YES
Cytoplasm, PAS
Stabilizes ATG13, protecting it from proteasomal degradation
ATG11
PTHR23160
YES
PAS
Scaffold protein that recruits ATG proteins to the PAS
ATG12
PTHR13385
YES
Cytoplasm, PAS
Ubiquitin-like. ATG12-ATG5 acts as E3 for ATG8-PI conjugation
ATG13
PTHR31546
YES
Cytoplasm, PAS
ATG1 kinase activator
ATG14/BAKOR
PTHR13664/15157
YES
Cytoplasm, PAS
VPS34 PI3-kinase complex I. Mediates binding of the complex to the PAS
ATG15
PTHR21493
-
PAS, vacuole
Lipase involved in the lysis of intravacuolar multivesicular body
ATG16
PTHR19878
YES
Cytoplasm, PAS
Stabilizes the ATG5-ATG12 conjugate
ATG18/WIPI1/WIPI2 PTHR11227
YES
Omegasome/PAS
PI(3,5)P2 regulatory complex. ATG9 trafficking to the PAS
ATG20
PTHR10555
YES
Endosome, PAS
Required for proper sorting of the v-SNARE protein SNC1
ATG22
PTHR11360
-
Cytoplasm, PAS
Vacuolar effluxer, mediates the efflux of amino acids resulting from
autophagic degradation
Proteins without a PTHR family
- 17 distinct autophagy-related proteins do not belong to
any PTHR family .
- A small part is excluded from families due to highly
divergent primary sequences.
- The majority were too specific to one species or a small
clad of species, so no family could be created.
Example: Pichia pastoris ATG30
An example: the ATG1/ULK1 family PTHR24348
Autophagy
Response to starvation
Phosphorylation
Regulation of cell size (?)
Regulation of cell growth (?)
DROME_ATG1
CEAEL_Unc-51
BPs: High majority of IMPs and IGIs !
Relevance ?
Issues with annotations:
- Wrong annotations:
Disputes: no real stats; but we could dispute at least one annotation per family .
Too bad stats are not maintained - it would help identify areas where more annotation
guidelines are needed
- BP versus regulation of BP:
When should we use regulation and when not ?
- Over-annotation:
IMP/IGI annotations lead to a lot of phenotypic annotations (cell proliferation, cell
growth, apoptosis, …). Sometimes it is totally indirect.
- Missing annotation:
It would be helpful to annotate directly in PAINT - or have a faster turnover between
Protein2GO and the GO db.
- HTP annotations:
Exclusion list for now; is this the best solution ?
Even if there are many false positives, the majority should be true positives and are
sometimes the only information we have.
Issues with propagation:
- Issue of species-specific terms:
Some terms such as “fungal-type vacuole” are very specific.
What's the advantage of having this as a separate term from vacuole ?
In animals, the corresponding organelle is the “lysosome”.
- Issue of species-specific functions:
Some proteins, functions, or processes are very specific to certain species and
cannot be propagated.
As an example, mitochondrial data should not be propagated in plants, because
could be chloroplastic.
The case of ATG26
"Atg26 is not involved in autophagy-related pathways in Saccharomyces cerevisiae."
Cao Y., Klionsky D.J.
Autophagy 3:17-20(2007)
… and
- PAINT annotation requires to go back to papers most of the time.
This is also why it is better to annote related families (i.e. same
process).
This allows to to:
- Save some time.
- Make a coherent annotation for the processes.
- Annotation of big families is easier when done in teams or based
on subject. Part can be left to curators with certain expertise.
Example:
PTHR24073 (Rab proteins family): over 2700 proteins
Function in vesicular transport.
Autophagy / Apoptosis
The same work has been done by Pascale about Apoptosis
which allows some comparisons of annotation between those 2
processes.
In general, we found the same issues. However, there are by far
less false positive annotations. This is probably due to the fact
that there is no «easy» test such as DNA-fragmentation which
could be applied to every single mutant.
Some suggestions
- Work on specific topics, expertise
- Grouping for big families.
- Direct annotation in PAINT
- Faster turnover between Protein2GO and the GO db.
- Use a new qualifiers ? (upstream_of and participant_in)
- Clean ontology (synonyms, missing relationships,…)