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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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new term: macropinocytic cup #6164

Closed gocentral closed 9 years ago

gocentral commented 15 years ago

Hello, Dicty in liquid medium feeds by macropinocytosis (no process like that in GO, not needed at the moment), and the actin cytoskeleton forms so-called "crowns", which are 'macropinocytic cups'. I'm curating PMID:12538772 where formin C localizes to these macropinocytic cups or 'crowns'. However, these 'crowns' are heavily enriched in F-actin, so it cannot be a simple sibling to GO:0001891 phagocytic cup, which is a child of 'plasma membrane part'. I rather think of this as a child of the 'cortical actin cytotskeleton', similar to the fungal GO:0030479 actin cortical patch.

GO:0030864 cortical actin cytoskeleton GO:new macropinocytic cup

Ref: F-actin rich structures found at the plasma membrane in cells, at the site of macropinocytosis, a from of endocytosis for the uptake of relatively large amounts of extracellular fluid.

For dicty it would be nice to add the synonym 'crown', or 'F-actin crown'. It might also be useful to add 'ruffling' somewhere.

Thanks, Petra

Reported by: pfey

Original Ticket: geneontology/ontology-requests/6183

gocentral commented 15 years ago

From the paper, and a couple of others it cites, I wonder if crowns are a type of cell projection (GO:0042995)? I thought they looked like cell projections, with membrane and cortical cytoskeleton, in some of the micrographs. If we do make the term is_a cell projection, it could have part_of children for the membrane and cytoskeletal parts (if they'd be useful).

How does that sound? m

Original comment by: mah11

gocentral commented 15 years ago

Original comment by: mah11

gocentral commented 15 years ago

Yes, looking at all the children of GO:0042995, I think macropinocytic cup is_a cell projection would work very well and for completeness the part_of children could be added (not sure those are needed for annotation).

Thanks a lot! Petra

Original comment by: pfey

gocentral commented 15 years ago

added macropinocytic cup GO:0070685 macropinocytic cup membrane GO:0070686 macropinocytic cup cytoskeleton GO:0070687

Original comment by: mah11

gocentral commented 15 years ago

Original comment by: mah11