OTR: definition for GO:0034290 ! holin activity

[gocentral]

Current definition is incorrect. Holins do not catalyze the formation of holes, they form the holes. Suggest deleting "Catalysis of the".

Reported by: jimhu

Original Ticket: geneontology/ontology-requests/11789

[gocentral]

Also change the child terms

Original comment by: jimhu

[gocentral]

• assigned_to: David Osumi-Sutherland

Original comment by: dosumis

[gocentral]

Swithching ref to more recent review - PMID:25157079.

Seems like Holin activity is a compound function:

1. Regulated formation of a pore via oligomerisation of an existing pool of subunits in the membrane.
2. Channel activity allowing endolysin (cannonical holin activity) or ions (pinholin activity) through the membrane.

If I make this compound function, then stricly, it shouldn't be classified channel activity, as it does right now, despite its current definition being completely inconsistent with this classification. Instead it should have a has_part relationship to channel activity. (Not ideal for grouping of annotations, but this is a general problem). There isn't an equivalent function term for forming holes in membrane, but there are process terms we could make a part relationship to.

Original comment by: dosumis

[gocentral]

How's this:

label "holin activity" definition "A compound function consisting of the regulated formation of a pore via oligomerisation of an existing pool of subunits in the plasma membrane. The resulting channel activity directly or indirectly allows murein hydrolyases to access their cell wall substrate." is_a: 'channel activity' 'part of' some 'cytolysis by virus via pore formation in host cell membrane'

label "canonical holin activity" definition "A compound function consisting of the regulated formation of a pore via oligomerisation of an existing pool of subunits in the plasma membrane. The resulting channel activity directly allows release of a fully-folded phage-encoded endolysin (murein-degradase) from the cell."^^string is_a: 'holin activity' is_a: 'protein channel activity' <-- new

label "pinholin activity" definition "A compound function consisting of the regulated formation of a pore via oligomerisation of an existing pool of subunits in the plasma membrane. The resulting ion channel activity indirectly allows endolysin (murein hydrolyases) to access their cell wall substrate by collapsing the proton motive force (PMF) across the membrane, allowing the endolysin to fold to an active form and hydrolyze bonds in the peptidoglycan cell wall." is_a: 'holin activity' is_a: 'ion channel activity' <-- new

I decided against the has_part strategy. Even though it is strictly correct. The existing fudge is not bad for grouping and the alternative seems to be to classify this directly under MF.

Original comment by: dosumis

[gocentral]

• status: open --> closed-fixed

Original comment by: dosumis