#11084 Autophagic membrane compartments terms request

[Marc Feuermann]

The formation of autophagic vacuoles (autophagosomes) requires several steps. After autophagy induction omegasomes are derived from ER and serve as intermediates for genesis of pre-autophagosomal structures from ER cisternae membranes. They form a cradle for the formation of pre-autophagosomal structures by membrane invagination.

PubMed: 24591649, 18725538

Terms request:

1- Omegasome
Greek capital letter omega-shaped membrane compartment enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. Omegasomes are the first step of the formation of autophagic vacuoles via the pre-preautophagosomal structures.

Is part of GO:0012505 endomembrane system
Is a GO:0044444 cytoplasmic part
Is a GO:0043231 intracellular membrane-bounded organelle

And corresponding terms:

2- Omegasome membrane
3- Integral component of omegasome membrane
4- Intrinsic component of omegasome membrane
5- Extrinsic component of omegasome membrane

But also

6- Integral component of pre-autophagosomal structure membrane
7- Intrinsic component of pre-autophagosomal structure membrane
8- Extrinsic component of pre-autophagosomal structure membrane
9- Integral component of autophagic vacuole membrane
10- Intrinsic component of autophagic vacuole membrane
11- Extrinsic component of autophagic vacuole membrane

These terms will allow coherent primary GO as well as PAINT annotations of the very conserved autophagic pathway.
Thanks,
Marc.

[Marc Feuermann]

Oups, just saw an error in the definition. It's the pre-autophagosomal structure, not pre-preautophagosomal structure ! Sorry.
Thanks a lot.
Marc.

[Paola Roncaglia]

Thank you Marc

[Paola Roncaglia]

BTW, afraid we can't display Greek characters, so the def would have to say
"Omega-shaped (as in the Greek capital letter) intracellular membrane-bounded organelle..."
I think 'intracellular membrane-bounded organelle' would be less ambiguous than 'membrane compartment' if that's ok with you. Thanks!

Paola

[Marc Feuermann]

It's perfect like that :-)
Thank you very much Paola.
Best regards,
Marc.

[Paola Roncaglia]

Added first term:

[Term]
id: GO:1990462
name: omegasome
namespace: cellular_component
def: "Omega-shaped (as in the Greek capital letter) intracellular membrane-bounded organelle enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. Omegasomes are the first step of the formation of autophagic vacuoles via the pre-autophagosomal structures." [GOC:mf, PMID:18725538, PMID:24591649]
is_a: GO:0043231 ! intracellular membrane-bounded organelle
is_a: GO:0044444 ! cytoplasmic part
relationship: part_of GO:0012505 ! endomembrane system

More later :-)
Thanks,
Paola

[Paola Roncaglia]

Added term 2 (via TG template for cc_part_of_cc):

[Term]
id: GO:1903349
name: omegasome membrane
namespace: cellular_component
def: "Any membrane that is part of an omegasome." [GO_REF:0000064, GOC:mf, GOC:TermGenie, PMID:18725538, PMID:24591649]
is_a: GO:0016020 {is_inferred="true"} ! membrane
intersection_of: GO:0016020 ! membrane
intersection_of: part_of GO:1990462 ! omegasome
relationship: part_of GO:1990462 {is_inferred="true"} ! omegasome

[Marc Feuermann]

Great !
Thanks.
Marc.

[Paola Roncaglia]

Added further links to 'omegasome membrane':

[Term]
id: GO:1903349
name: omegasome membrane
namespace: cellular_component
def: "Any membrane that is part of an omegasome." [GO_REF:0000064, GOC:mf, GOC:TermGenie, PMID:18725538, PMID:24591649]
is_a: GO:0016020 {is_inferred="true"} ! membrane
is_a: GO:0098588 ! bounding membrane of organelle
intersection_of: GO:0016020 ! membrane
intersection_of: bounding_layer_of GO:1990462 ! omegasome
intersection_of: part_of GO:1990462 ! omegasome
relationship: part_of GO:1990462 {is_inferred="true"} ! omegasome

[Chris Mungall]

Minor technical note: the final part_of in the set of elements in the equivalence axiom is superfluous, as bounding_part_of is a sub-relation of part_of. Harmless, but if the logical defs follow a consistent pattern they're easier for humans to grok.

We do require a separate

relationship: part_of GO:1990462 {is_inferred="true"} ! omegasome

axiom though, as users require this

[Paola Roncaglia]

Removed redundant link in GO:1903349: intersection_of: part_of GO:1990462 ! omegasome

[Paola Roncaglia]

Hi Marc,

Added these:

id: GO:0097629
name: extrinsic component of omegasome membrane

id: GO:0097630
name: intrinsic component of omegasome membrane

id: GO:0097631
name: integral component of omegasome membrane

More soon... thanks,
Paola

[Paola Roncaglia]

In preparation for next terms, axiomatised GO:0034045 pre-autophagosomal structure membrane

[Paola Roncaglia]

Hi Marc, I added the last missing terms:

[Term]
id: GO:0097632
name: extrinsic component of pre-autophagosomal structure membrane

[Term]
id: GO:0097633
name: intrinsic component of pre-autophagosomal structure membrane

[Term]
id: GO:0097634
name: integral component of pre-autophagosomal structure membrane

[Term]
id: GO:0097635
name: extrinsic component of autophagic vacuole membrane

[Term]
id: GO:0097636
name: intrinsic component of autophagic vacuole membrane

[Term]
id: GO:0097637
name: integral component of autophagic vacuole membrane

Thanks,
Paola