Actin cytoskeleton: def changes, term moves, and synonyms

[gocentral]

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def changes

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We'd like to tweak the defs of some children of actin cytoskeleton (GO:0015629) to include "associated proteins."

GO:0030482 : actin cable Definition: A long bundle of actin filaments AND ASSOCIATED PROTEINS found in cells.

GO:0005884 : actin filament Definition: A two-stranded helical polymer of the protein actin AND ASSOCIATED PROTEINS. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.

GO:0031002 : actin rod Definition: A cellular structure consisting of parallel, hexagonally arranged actin tubules AND ASSOCIATED PROTEINS. Found in the germinating spores of Dictyostelium discoideum.

GO:0031002 : cortical actin cytoskeleton Definition: The portion of the actin cytoskeleton AND ASSOCIATED PROTEINS that lie just beneath the plasma membrane.

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term move

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We'd like to remove two terms out of the actin cytoskeleton node because we cannot find a clear reason for their existence here. (They exist as children of the microtubule cytoskeleton, which makes sense.) If anyone knows of a reason for actin cytoskeleton being a parent of these terms, please let us know!

GO:0005858 : axonemal dynein complex

GO:0005868 : cytoplasmic dynein complex

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synonym

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Finally, we'd like to request two synonyms for

GO:0005884 : actin filament

narrow_synonym: "F-actin" narrow_synonym: "filamentous actin"

Thanks,

dictyBase curators

Reported by: kpilcher

Original Ticket: "geneontology/ontology-requests/3011":https://sourceforge.net/p/geneontology/ontology-requests/3011

[gocentral]

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I don't have any comments, or thoughts, either positive or negative about the movement of the two dynein terms, but the rest of it sounds like a good idea to me.

-Karen

Original comment by: krchristie

[gocentral]

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Hi,

About axonemal and cytoplasmic dynein, I asked one of our Tetrahymena dynein experts and got a nice response:

"To my knowledge, there is no good evidence that dynein uses actin as a track. HOWEVER, monomeric/short fragments of actin are found to associate with dynein at the base of the dynein motor, presumably helping to anchor it to its cargo. This was found a long time ago in Chlamydomonas axonemal inner arm dynein (Piperno et al., don't have the reference off the top of my head but can find it) and is also the case with dynactin, which anchors cytoplasmic dynein 1 to its (membrane) cargo."

The issue seems to be specifically whether dynein associates with the actin cytoskeleton, as opposed to smaller fragments of actin that aren't part of the cytoskeleton. Looks to me like the parentage should be removed.

Nick

Original comment by: nastover

[gocentral]

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I was wondering if it would make sense to make a similar definition change to the def for "microtubule cytoskeleton ; GO:0015630" to add the words "and associated proteins" at the end of the current def.

Current Def: The part of the cytoskeleton (the internal framework of a cell) composed of microtubules.

This term already has lots of child terms that surely must contain non- microtubule proteins.

-Karen

Original comment by: krchristie

[gocentral]

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I agree, Karen, it's inconsistent. 'Myosin' is part of the 'actin cytoskeleton', just like 'cytoplasmic dynein complex' is part of the 'microtubule cytoskeleton'. The framework seems right, so the definition should reflect it.

Nick

Original comment by: nastover

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

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Hello,

After discussion with the GO office, and the new rule to include homopolymers in the ontology, we would like to have "filamentous actin" being a new term, child of "actin filament". The definition can be the current definition of actin filament, since actin filament will now include "and associated proteins".

Perhaps a note can be added to filamentous acin, to state that this term do not encompass associated proteins, and to annotate proteins associated with filamentous actin to "actin filament".

The synonyms need to be fixed: "F-actin" is currently an exact synonym of "actin filament"; it should rather be a synonym of filamentous actin.

Thanks, Pascale

Original comment by: pgaudet

[gocentral]

Logged In: YES user_id=436423

all done:

added filamentous actin GO:0031941 (exact synonym F-actin)

removed relationships axonemal dynein complex (5858) part_of actin cytoskeleton (15629) cytoplasmic dynein complex (5868) part_of actin cytoskeleton (15629)

adjusted definitions to mention 'associated proteins' actin filament (5884) actin cytoskeleton (15629) cortical actin cytoskeleton (30864) microtubule cytoskeleton (15630)

removed exact synonym 1F-actin' from actin filament (5884)

m :)

Original comment by: mah11

[gocentral]

• milestone: --> TermGenie
• status: open --> closed-fixed

Original comment by: mah11