meiosis/ meiotic nuclear division follow up (too specific)

[pombase-admin]

These are all annotated to "meiotic nuclear division" (list generated from and intersect of this term with karyogamy and ascospore formation). I suspect that some should only be annotated to the parent "meiotic cell cycle" if at all...

SPBC651.05c dot2 ESCRT II complex subunit Dot2 SPBC19C2.05 ran1 serine/threonine protein kinase Ran1 SPAC3A11.14c pkl1 kinesin-like protein Pkl1 SPCC417.07c mto1 MT organizer Mto1 SPAC1486.10 thi1 transcription factor Thi1 SPCC306.09c cap1 adenylyl cyclase-associated protein Cap1 SPAC8E11.02c rad24 14-3-3 protein Rad24 SPAC11E3.06 map1 MADS-box transcription factor Map1 SPBC16G5.15c fkh2 forkhead transcription factor Fkh2 SPBC24C6.06 gpa1 G-protein alpha subunit SPAC18B11.04 ncs1 neuronal calcium sensor related protein Ncs1 SPBC1198.12 mfr1 fizzy-related protein Mfr1 SPCC645.06c rgf3 RhoGEF Rgf3 SPAC16C9.07 pom2 DYRK family protein kinase Pom2 SPBC21C3.18 spo4 serine/threonine protein kinase Spo4 SPBC1778.04 spo6 Spo4-Spo6 kinase complex regulatory subunit Spo6 SPAC458.05 pik3 phosphatidylinositol 3-kinase Pik3 SPBC29A10.02 spo5 II meiotic RNA-binding protein 1

Original comment by: ValWood

[pombase-admin]

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 These are all annotated to "meiotic nuclear division" (list generated from and intersect of this term with karyogamy and ascospore formation).
 I suspect that some  should only be annotated to the parent  "meiotic cell cycle" if at all...

• Priority: 5 --> 8

Original comment by: ValWood

[pombase-admin]

can you have a look through this list before the next update (will fix some odd intersections).

Let me know if this doesn't make sense.... and put a note of which ones move for future ref.

tks

val

Original comment by: ValWood

[pombase-admin]

These might be overlapping with the above list:

SPBC119.04.1 GO:0045836 positive regulation of meiotic nuclear division 93c0ecbe5a58d0fe PomBase SPAC3F10.07c.1 GO:0045836 positive regulation of meiotic nuclear division 0f9cbe164dbdc4a4 PomBase SPBC3H7.09.1 GO:0045836 positive regulation of meiotic nuclear division 0f9cbe164dbdc4a4 PomBase

(I think these should likely be 'meiotic cell cycle' rather than nuclear division)

Original comment by: ValWood

[pombase-admin]

Removed from these ones: Dot2: removed the TAS to meiosis I (these guys can't do nuclear fusion, which I assume cause the downstream problems with meiotic chromosome segregation) pat1: this was probably just a remapping problem? moved up to neg reg of meiotic cell cycle mto1: removed "dynein-driven meiotic oscillatory nuclear movement", this was added by you to a community curation session but I don't think it is supported by the paper? cap1: removed regulation of ascospore formation, seems to be regulating adenylate cyclase activity rad24: looks like it is upstream of meiosis itself

Kept for these ones: pkl1: looks ok, in the ref they suggest a minor role for pkl1 in karyogamy & that is most important for meiosis. Thi1: This looks ok. Maybe, I'm not 100% sure. Ref is PMID:16874521

Original comment by: Antonialock

[pombase-admin]

mto1: removed "dynein-driven meiotic oscillatory nuclear movement", this was added by you to a community curation session but I don't think it is supported by the paper? Hi,

this is here:

Live- cell imaging of mal3Δ cells showed that horsetail movement was impaired in all 30 zygotes examined (Fig. 2 and data not shown). We observed a similar defect in mto1Δ mutant cells, where all 10 examined zygotes showed impaired horsetail movement (Fig. 2 and data not shown).

There is a problem though. I think it is with the parentage of dynein-driven meiotic oscillatory nuclear movement. It is currently a descendent of "meiotic nuclear division"...I don't think it should be. Do you both agree? horsetail movement preceded nuclear division?

Original comment by: ValWood

[pombase-admin]

pkl1: looks ok, in the ref they suggest a minor role for pkl1 in karyogamy & that is most important for meiosis.

in this case shouldn't this one only have a karyogamy annotation? There is no relationship between karogamy and meiosis in GO...should there be?

Original comment by: ValWood

[pombase-admin]

Thi1: This looks ok. Maybe, I'm not 100% sure. Ref is PMID:16874521 I can't see where the meiosis anntotation comes from here? but it doesn't sound right. I sounds way upstream/indirect?

Original comment by: ValWood

[pombase-admin]

For the Thi1 the problem also appears to be a parentage problem.

Currently "sexual sporulation" is a descendent of "meiotic nuclear division". I think this parentage should be removed? Especially as sporulation is defined "The formation of spores derived from the products of meiosis." (it should just be to meiotic cell cycle)

I'll submit the 2 parentage issues to the GO tracker. Can you comment on the pkl1 one, I still haven't figured it?

Original comment by: ValWood

[pombase-admin]

I submitted a ticket for the sporulation TPV. [geneontology:ontology-requests] #11660 TPV's under "meiotic nuclear division"

The "dynein-driven meiotic oscillatory nuclear movement" appears to be fine though. It is defined as The cell cycle process in which oscillatory movement of the nucleus during meiotic prophase I occurs....

if it occurs during prophase I guess it must be part of "meiotic nuclear division". I always think that it 'precedes' it. Stumps me every time...

Original comment by: ValWood

[pombase-admin]

Yeah I think it gets a bit confusing too. Something I don't get - I thought that karyogamy/bouquet formation/horsetail movement all sort of happened in what's called prophase 1 - but then when does premeiotic DNA synthesis take place?

I guess it's like ascospore formation and meiosis II in that you can get a bit of "concurrent activity" which muddles things?

Original comment by: Antonialock

[pombase-admin]

This is correct - horsetail movement happens in prophase, which is part of meiosis I (the division).

Original comment by: mah11

[pombase-admin]

There is no relationship between karogamy and meiosis in GO...should there be?

No. Even in budding yeast, diploids can happily grow and divide vegetatively for umpteen generations; they don't have to (and seldom do) proceed straight from karyogamy to meiosis.

And then there are all the habitually-diploid multicellular organisms that only have meiosis going on in specialized cell types ...

Original comment by: mah11

[pombase-admin]

Ok so I added this back in for mto1

Original comment by: Antonialock

[pombase-admin]

when does premeiotic DNA synthesis take place?

during the S phase that precedes meiosis I .. that S phase is part of the meiotic cell cycle but not part of any nuclear division (i.e. not part of meiosis)

Original comment by: mah11

[pombase-admin]

yes I agree, I think?

In this paper they seem to "lump" different mating events (conjugation, meiosis, ascospore formation) under meiosis, which is where the confusion comes from.

It looks like thi1 is needed both for conjugation and ascospore formation, but not meiosis (they say that meiosis II completes in a deletion mutant, but these guys cannot sporulate. These guys also are defective in conjugation)

(I don't know if this is direct or indirect however)

Original comment by: Antonialock

[pombase-admin]

In this paper they seem to "lump" different mating events (conjugation, meiosis, ascospore formation) under meiosis, which is where the confusion comes from.

So this is what spawned the ticket. Meiosis is used interchangeably by researchers to mean "meiotic nuclear division" and "meiotic cell cycle"

It is the example used in my curation-rule slides for "rule number 1"

Original comment by: ValWood

[pombase-admin]

For this one:

It looks like thi1 is needed both for conjugation and ascospore formation, but not meiosis (they say that meiosis II completes in a deletion mutant, but these guys cannot sporulate. These guys also are defective in conjugation) (I don't know if this is direct or indirect however)

I think I would go with just the phenotypes, as we aren't sure....

Original comment by: ValWood

[pombase-admin]

Ok, I'll remove them. I don't really understand how thiamine biosynthesis ties in with mating - it does somehow (like glucose availability and nitrogen starvation) but I don't think it is understood really how.

Original comment by: Antonialock

[pombase-admin]

• status: open --> closed

Original comment by: Antonialock

[pombase-admin]

If you want further changes then reopen?

Original comment by: Antonialock