actin cable organization

[gocentral]

Hi, I am currently curating PMID:23051734

I have annotated myoV to "positive regulation of formin-nucleated actin cable assembly " (this is from the delivery of cargo to the cell tip)

additionally I would like to request two terms:

• actin cable retrograde flow (the extension of the cable parallel to the long axis of the cell)
• protein localization to cell tip (this is from the "Myo52 associates with For3" section where they show that myo52 is involved in the anterograde movement of for3)

does this sound reasonable?

additionally I would also like to know what the difference is between an actin cable and an actin filament (is there a fundamental difference or is it just yeast vs metazoan terminology?)

Reported by: antonialock

Original Ticket: geneontology/ontology-requests/10278

[gocentral]

I requested 'protein localization to cell tip' aeons ago in what is now [ontology-requests:#9737]. GO EDs suggested using it to test a TG template, but I'm tired of waiting, so I'll add it in TG freeform today.

An actin cable is a bundle of actin filaments. 'Actin cable' vs. 'actin filament bundle' pretty much is just yeast vs. metazoan terminology.

Leaving this open for GO Eds to deal with the retrograde flow request. m

Original comment by: mah11

[gocentral]

Thanks Midori.

In that case,could I also request actin filament bundle organization?

also, would GO:0070650 Name actin filament bundle distribution Ontology Biological Process Definition Any cellular process that establishes the spatial arrangement of actin filament bundles within the cell.

be the same as actin cable retrograde flow?

Original comment by: antonialock

[gocentral]

• assigned_to: David Hill

Original comment by: ukemi

[gocentral]

Hi Antonia and Midori,

I think the new term should be a child of GO:0070650 'actin filament bundle distribution'. I don't think there is a need for the organization term because I think they are pretty much synonymous.

Also, are you sure that retrograde flow isn't the redistribution from the cell cortex/periphery to the interior of the cell? I think in general that is what retrograde flow describes.

-David

Original comment by: ukemi

[gocentral]

Would the organization term not follow the standard pattern for CC organization, i.e. assembly OR disassembly OR morphogenesis OR ... ? (That said, I don't know for sure if that's the term Antonia needs.)

(Don't think I can help with the retrograde flow question.)

m

Original comment by: mah11

[gocentral]

yes that is what happens to actin isn't it?

from the intro: "Time-lapse imaging shows that the actin cables in yeasts undergo retrograde flow (Martin and Chang, 2006 blue right-pointing triangle; Buttery et al., 2007 blue right-pointing triangle). Dots of formin reside transiently at the plasma membrane, where they assemble actin filaments that may push the whole actin bundle into the cell interior. Formin dots are then released and move in a directed manner away from the cell tip, probably associated with the barbed ends of actin filaments in the bundle. In the fission yeast, For3 is the formin responsible for actin cable assembly (Feierbach and Chang, 2001 blue right-pointing triangle; Nakano et al., 2002 blue right-pointing triangle). How these flexible structures are able to extend through a dense cytoplasm has not been clear. Here we show that myosin Vs contribute to the organization and dynamics of actin cables, suggesting that motors and cables form a self-organizing system in which the motor shapes its own tracks."

Original comment by: antonialock

[gocentral]

Hi Midori,

We have 'actin filament bundle assembly' and I think the distrubution term covers the arrangement of constituent parts. I could add a disassembly term and then the organization grouping term, but do you think that's necessary? Distribution is usually a result of constituent filament polymerization/depolymerization or movement of the bundle via motors. If you think it is useful I will go ahead and add the organization structure for bundles.

-D

Original comment by: ukemi

[gocentral]

I personally don't need any of these terms; Antonia's the one who is curating the paper in question. My comment was really only directed at the suggestion that the distribution term was synonymous with the (not yet extant) organization term. If Antonia doesn't need an organization term, I have no preference at all whether one is added now, later, or never (tho if anyone needed a disassembly term, then it would make sense to also add organization to group everything).

m

Original comment by: mah11

[gocentral]

ok so one annotation to "positive regulation of formin-nucleated actin cable assembly" and one to "actin filament organization" is ok?

Original comment by: antonialock

[gocentral]

I think I am going to go ahead and add 'actin bundle organization' and 'actin bundle retrograde transport', the latter being a child of 'actin filament bundle distribution'. But I probably won't get to it until tomorrow.

So if you want to wait, you can use those.

-D

Original comment by: ukemi

[gocentral]

TG free-form is back, and this is in the queue:

ID: GO:1990151 Label: protein localization to cell tip

Original comment by: mah11

[gocentral]

Thanks, both! I'll wait for the terms David

Original comment by: antonialock

[gocentral]

• status: open --> closed-accepted

Original comment by: ukemi

[gocentral]

Hi Antonia,

Here are the terms.

[Term] +id: GO:0061572 +name: actin filament bundle organization +namespace: biological_process +def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of an actin filament bundle." [GOC:dph] +synonym: "actin filament cable organization" RELATED [GOC:dph] +is_a: GO:0007015 ! actin filament organization +created_by: dph +creation_date: 2013-08-02T11:24:11Z + +[Term] +id: GO:0061573 +name: actin filament bundle retrograde transport +namespace: biological_process +def: "A process of actin filament bundle distribution that results in the arrangement of actin filament bundles from the periphery toward the interior of the cell." [GOC:dph] +synonym: "actin filament cable retrograde transport" RELATED [GOC:dph] +is_a: GO:0070650 ! actin filament bundle distribution +created_by: dph +creation_date: 2013-08-02T11:31:04Z + +[Term]

-David

Original comment by: ukemi