platelet dense granule org and biogen

[gocentral]

id: GO:new1 term:platelet dense granule organization and biogenesis def: A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a platelet dense granule. A platelet dense granule is an electron-dense granule occurring in blood platelets that stores and secretes adenosine nucleotides and serotonin. [GOC:dph] is_a:secretory granule organization and biogenesis synonym: platelet dense body organization and biogenesis synonym: bull's eye body organization and biogenesis

id: GO:new2 term:secretory granule organization and biogenesis def: A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a single-layered membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. is_a:vesicle organization and biogenesis ; GO:0016050 synonym:secretory vesicle organization and biogenesis

Use this for MGI:1929230 and J:61187 with IMP for the cappuchino mutant.

Reported by: ukemi

Original Ticket: "geneontology/ontology-requests/4267":https://sourceforge.net/p/geneontology/ontology-requests/4267

[gocentral]

Logged In: YES user_id=865072 Originator: NO

David,

These terms are fine by me but for some nitpicky points:

Term 1) If you are going to define the contents of platelet dense granules, I think you should mention that they contain histamine as well as magnesium, calcium, and pyrophophates (PMID:11487378, this would be a good external reference to add here).

Term 2) I am uncomfortable with a blanket statement that secretory granules have single membrane (as opposed to a bipolar membrane). In platelets this is true of dense granules and alpha-granules, but not of lysosomes, which also function as secretory granules in platelets (again PMID:11487378, "The third category of granules involved in the release reaction concerns lysosomes."). Also, other cell types have secretory granules, about which I do not know the structure, so I would prefer a less restrictive definition.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=631592 Originator: YES

Alex,

These are defs taken straight from the CC ontology, so we would have to change exisiting defs.

Dvid

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=865072 Originator: NO

This is complicated further by the definition of secretory granule membrane ; GO:0030667 : "The lipid bilayer surrounding a secretory granule."

Obviously this needs to be changed to something like "The lipid single layer or bilayer surrounding a secretory granule."

-- Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Hi Alex & David,

I'm quite happy to reword the definition of GO:0030667 - when I created the term (some time ago!) I just modeled the def on other vesicle membrane defs, and the current def isn't intended to exclude double membranes.

I would use "The single or double lipid bilayer surrounding a secretory granule" because each "layer" of membrane is a phospholipid bilayer. The def of secretory granule (GO:0030141) should also be changed accordingly; I would change "surrounded by a single-layered membrane" to "surrounded by a single or double membrane" (or "surrounded by a single or doubl lipid bilayer").

Let me know if you want me to make the changes. Otherwise I'll assume David will do it when he adds the new terms.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=865072 Originator: NO

Midori,

I think the problem here is the interpretation of the phrase "single-layered membrane" which I interpreted as meaning not a lipid bilayer, but a single layer of lipids. Although I've seen the phrase "single-layered membrane" in reviews, I can't find any description of it as whether this means a bilayer or something other than bilayer, so it's logical to assume that it is a bilayer. On the other hand, I don't know whether double bilayered secretory granules exist either, although it wouldn't surprise me if they do. Thus, I'll drop any requirement to change definitions in regard to the membrane structure.

Sorry for the delay,

Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=436423 Originator: NO

I can't remember why I put "single-layered membrane" in there ... it's a stupid wording!

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=631592 Originator: YES

When I read this def. I thought it meant a single lipid bilayer, differentiating it from the stacked layers of the golgi??

David

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=436423 Originator: NO

I think it did mean a single bilayer, as opposed to the double bilayers that nuclei and plastids have ... but now I think "why not just say 'single lipid bilayer' if that's what it means?"

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=631592 Originator: YES

Term 2 actually existed but not under the correct parent. I moved the term and expanded the def. I also modified the def of secretory granule.

platelet dense granule organization and biogenesis ; GO:0060155

Original comment by: ukemi

[gocentral]

• status: open --> closed

Original comment by: ukemi