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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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rename Swi5-Sfr1 complex #5700

Closed gocentral closed 9 years ago

gocentral commented 15 years ago

to Swi5-Sfr1 recombinase mediator complex

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/5718":https://sourceforge.net/p/geneontology/ontology-requests/5718

gocentral commented 15 years ago

and possibly rename GO:0033061 DNA recombinase mediator complex Rad51 recombinase mediator complex

looks like we also need a new term Rad55/rad57 recombination mediator complex synonym Rhp55/Rhp57 recombination mediator complex (I had used GO:0033061 for this by mistake)

Original comment by: ValWood

gocentral commented 15 years ago

Original comment by: mah11

gocentral commented 15 years ago

Hi,

This is a general comment. Do we want to have gene product names in the GO Term name? Can we name the complex based on its function and mention the subunits from a given species in the definition? Because this is going to be a moving target as gene names change sometimes (often!) and one doesn't know if the gene name is that of fission yeast or budding yeast and so on.

2 cents!

Rama

Original comment by: rbalakri

gocentral commented 15 years ago

I personally prefer complxes without product names but in these cases it is how te community refer to them so its difficult to give them another name I would usually call by the S. cerevisiae name if ir exists and give any different pombe names as synonyms. Also if a btter name comes into use later this can be added.

As yet the equivalent complex to this hasn't been identified in S. cerevisiae pombe swi5 is the ortholog of S. cerevisiae SAE3 but we have not yet identified an ortholog of Sfr1

Original comment by: ValWood

gocentral commented 15 years ago

correction, yes there is an equivalent complex

S. pombe Sfr1 is S. cerevisiae MEI5

SAE3/MEI5 does form a heterodimer according to your gene pages. Does it have another name in S. cerevisiae?

Original comment by: ValWood

gocentral commented 15 years ago

correction, yes there is an equivalent complex

S. pombe Sfr1 is S. cerevisiae MEI5

SAE3/MEI5 does form a heterodimer according to your gene pages. Does it have another name in S. cerevisiae?

Original comment by: ValWood

gocentral commented 15 years ago

Swi5-Sfr1 complex could be something like meiosis specific recombinase assembly complex.

The Rad55/rad57 recombination mediator complex could be Rhp51 recombinase assembly complex
I think the Rhp51 is OK here as this is used in every org for this process

I wonder if we defined DNA recombinase mediator complex correctly?

Original comment by: ValWood

gocentral commented 15 years ago

Seems like there are a couple lines of thought interspersed in this thread.

  1. There already exists a "Rhp55-Rhp57 complex" term: GO:0033062
  2. Mei5p and Sae3p do form a heterodimer in S. cerevisiae (PMID: 15620352).
  3. Because Mei5p-Sae3p assemble the meiotic recombinase Dmc1p and not Rad51p (PMID: 15620352), we cannot rename GO:0033061 from "DNA recombinase mediator complex" to "Rad51 recombinase mediator complex".
  4. As for the definition of GO:0033061 - because Mei5p and Sae3p are not Rad51 paralogs, we may want to think about adjusting the definition. What about "A protein complex that promotes nucleoprotein filament formation during homologous recombination."

Original comment by: eurie

gocentral commented 15 years ago

OK, so DNA recombinase mediator complex is referring to "Rhp55-Rhp57 complex" My confusion arose fro m the def

GO:0033061 Name DNA recombinase mediator complex Definition A protein complex containing two or more Rad51 paralogs and promotes nucleoprotein filament formation during homologous recombination.

I think it is misleading to refer to these are 'rad51 paralogs' they are not rad51 paralogs in pombe (except in some organism predating the most recnt common ancestor) but they are all RecA family proteins. Perhaps the def couls be modified to make this clear. Val

Original comment by: ValWood

gocentral commented 15 years ago

So ... I should

1) broaden the def of DNA recombinase mediator complex (GO:0033061) so it's not exclusive to Rad51 homologs;

2) add a term for the Swi5-Sfr1 complex, aka Sae3-Mei5 complex, as an is_a child of GO:0033061

...?

If that's correct, no problem. m

Original comment by: mah11

gocentral commented 15 years ago

Val, in the beginning (late 1990s - early 2000s), they were all Rad51 homologs/paralogs. But as you state, definitely is no longer the case.

So Midori's plan of action sounds good to me.

Original comment by: eurie

gocentral commented 15 years ago

Ok, def adjusted, and the existing Swi5-Sfr1 complex term moved (GO:0032798; also added synonym).

Original comment by: mah11

gocentral commented 15 years ago

Original comment by: mah11

gocentral commented 13 years ago

Original comment by: mah11