search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
222 stars 40 forks source link

ntr: centrosomal corona #2839

Closed gocentral closed 9 years ago

gocentral commented 19 years ago

Hi,

I'd like the new component term:

centrosomal corona

suggested def:

The periphery of the microtuble organizing center, consisting of an amorphous corona from which microtubules emerge.

Child of GO: 0005813 ; centrosome

This structure, according to the literature, is Dicty specific -- possible sensu term?

Original publications describing the Dictyostelium centrosome:

Thanks,

Karen

Reported by: kpilcher

Original Ticket: "geneontology/ontology-requests/2848":https://sourceforge.net/p/geneontology/ontology-requests/2848

gocentral commented 19 years ago

Logged In: YES user_id=436423

From the proposed def, it sounds possibly related to 'pericentriolar material' (GO:0000242; def: A network of small fibers that surrounds the centrioles in cells; contains the microtubule nucleating activity of the centrosome). Should we use a synonym for GO:242 or add a new term? If we add a new term, what is the difference from the existing term?

thanks, m

Original comment by: mah11

gocentral commented 19 years ago

Logged In: YES user_id=1056932

Hmm...I'm not sure if they are the same. The original papers describing the centrosomal corona are from the 80s and I don't have access to the full text.

I emailed the authors with your questions so I will let you know what they say. If they don't get back to me, I guess I'll have to go to the library and find the original papers! :)

Thanks!

Original comment by: kpilcher

gocentral commented 19 years ago

Logged In: YES user_id=1056932

I got a response from the authors of the paper I'm annotating (PMID:15800059). This is what they say:

right, the corona is the functional Dicty homologue of the pericentriolar material (PCM) of higher cells. However, I think you'll have to use the term "corona"; PCM makes no sense because Dicty has no centrioles in its centrosome. Instead Dicty has a box-shaped, layered core structure, which is surrounded by the corona with electron-dense nodules. The nodules contain gamma tubulin and, thus, the microtubule-nucleation centers.

So it looks like we either need a new term or a definition change for PCM (and also GO:0005813 centrosome, def: "A structure comprised of a pair of centrioles and peri-centriolar material...")

Original comment by: kpilcher

gocentral commented 19 years ago

Logged In: YES user_id=436423

OK, I've reworded the def of centrosome so the first sentence is now: 'A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule spindle apparatus is organized.'

and added centrosomal corona GO:0031592 with a slightly adjusted def and a comment, both to help clarify the similarities and differences from PCM.

thanks for chasing up the additional info!

m

Original comment by: mah11

gocentral commented 19 years ago

Original comment by: mah11

gocentral commented 19 years ago

Logged In: YES user_id=1056932

Hi Midori,

Thanks so much. This is really great for us -- now we can correctly use centrosome for Dicty.

Another thing I noticed about centrosome (GO:0005813) is that the part "microtubule spindle apparatus" refers to mitosis, but the part "...during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle" suggests this term may be used for mitosis OR interphase. This could be corrected by changing "microtubule spindle apparatus" to "microtubule cytoskeleton" or just "microtubules."

Another problem is that centrosome, in addition to its MTOC parentage, is a child of spindle pole (GO:0000922). This necessarily dictates that centrosome must be used for mitosis, however, I am fairly certain that people use centrosome for both interphase AND mitosis.

I know I've used this for interphase centrosomes and here's a couple of example annotatations from other db's:

http://www.godatabase.org/cgi-bin/amigo/go.cgi?search\_constraint=gp&view=details&session\_id=3716b1125426733&gp=MGI:2143311

http://www.godatabase.org/cgi-bin/amigo/go.cgi?search\_constraint=gp&view=details&session\_id=3716b1125426733&gp=Q9Y3P9

In both those cases, the paper showed staining centrosome during interphase...

Karen

Original comment by: kpilcher

gocentral commented 19 years ago

Logged In: YES user_id=436423

Good catch, I've fixed both problems, and added a new term: spindle pole centrosome GO:0031616

m

Original comment by: mah11