ntr's: subtypes of phospholipid scrambling

[gocentral]

Hi,

I have been annotating a few papers about anoctamin proteins and I think it would be good to have some more specific child terms under "phospholipid scrambling" (GO:0017121). The Anoctamin family has 10 members in mouse and other vertebrates. Two proteins are characterized as being "intracellular calcium activated chloride channel activity". However, five of the others have been shown to possess "calcium activated phospholipid scrambling" activity, with some differences in specificity towards: phosphoserine, phosphocholine, and galactosylceramide (PMID:23532839), so it might also be useful to have specific terms for specific substrates, especially since the other three anoctamins were shown not to be active on those three phospholipid substrates.

phospholipid scrambling (GO:0017121) -calcium activated phospholipid scrambling --calcium activated phosphoserine scrambling --calcium activated phosphocholine scrambling --calcium activated galactosylceramide scrambling

In addition, another paper (PMID:22936354) discusses phosphatidylserine exposure in osteoblasts as part of the bone mineralization process. Since we already have two terms for specific types of "phosphatidyl serine exosure on ...", it might be good to have a term for "phosphatidylserine exposure on osteoblasts" with a relationship to "bone mineralization".

thanks,

-Karen

Reported by: krchristie

Original Ticket: geneontology/ontology-requests/10597

[gocentral]

• assigned_to: David Hill

Original comment by: ukemi

[gocentral]

Hi Karen,

Would it be better to make molecular function terms, ie. calcium activated phosphoserine scramblase?

-D

Original comment by: ukemi

[gocentral]

Hi David,

That's a good question. The experiments were done by expressing individual constructs in a cell line which was deleted for Ano6, and which was shown to lack phospholipid scramblase activity. Then the activity and substrate specificity for each transfected construct was measured. While there are some differences in specificity, there is also a lot of overlap.

So, at this early stage, I think it would be fine to make the more specific BP terms for different kinds of substrates, e.g. PS, PC, Gal-Cer, etc., and not go to that level of specificity in MF.

However, since the scramblase function of anoctamins is Ca2+ activated/dependent, I think it would be good to make a MF term for "calcium activated phospholipid scramblase" to indicate the calcium dependent nature of these scramblases.

-Karen

Original comment by: krchristie

[gocentral]

• status: open --> closed-accepted

Original comment by: ukemi

[gocentral]

+[Term] +id: GO:0061589 +name: calcium activated phosphatidylserine scrambling +namespace: biological_process +def: "The movement of a population of phosphatidylserine molecules from one leaflet of the plasma membrane bilayer to the opposite leaflet as a result of a calcium stimulus." [GOC:krc, PMID:23532839] +is_a: GO:0061588 ! calcium activated phospholipid scrambling +created_by: dph +creation_date: 2014-02-05T15:17:21Z + +[Term] +id: GO:0061590 +name: calcium activated phosphatidylcholine scrambling +namespace: biological_process +def: "The movement of a population of phosphatidylcholine molecules from one leaflet of the plasma membrane bilayer to the opposite leaflet as a result of a calcium stimulus." [GOC:krc, PMID:23532839] +is_a: GO:0061588 ! calcium activated phospholipid scrambling +created_by: dph +creation_date: 2014-02-05T15:23:03Z + +[Term] +id: GO:0061591 +name: calcium activated galactosylceramide scrambling +namespace: biological_process +def: "The movement of a population of galactosylceramide molecules from one leaflet of the plasma membrane bilayer to the opposite leaflet as a result of a calcium stimulus." [GOC:krc, PMID:23532839] +is_a: GO:0061588 ! calcium activated phospholipid scrambling +created_by: dph +creation_date: 2014-02-05T15:25:52Z + +[Term] +id: GO:0061592 +name: phosphatidylserine exposure on osteoblast involved in bone mineralization +namespace: biological_process +def: "A phospholipid scrambling process that results in the appearance of phosphatidylserine on the surface of osteoblasts, and contributes to bone mineralization." [GOC:krc, PMID:22936354] +is_a: GO:0017121 ! phospholipid scrambling +relationship: part_of GO:0030282 ! bone mineralization +created_by: dph +creation_date: 2014-02-05T15:27:39Z

Original comment by: ukemi