some annotations that were there 4 years ago that might be valid

[ValWood]

Various reasons they could have disappeared, I nearly finished checking and most things that have disappeared were bad.

These might be OK:

nucleobase-containing small molecule metabolic process consider

• [x] gda1 https://github.com/pombase/curation/issues/1876
• [ ] ynd1

[ValWood]

carbohydrate

• [x] exg1 fungal-type cell wall beta-glucan metabolic process

• [x] eng2 oligosaccharide catabolic process/ some carbohydrate term +cell wall polysaccharide catabolic process

• [ ] alpha amylases

• [x] eng1 +cell wall polysaccharide catabolic process -GO:0009311 oligosaccharide metabolic process IEA with IPR004888

  • [x] alg11, shouldn’t be oligosaccharide +GO:0006488 dolichol-linked oligosaccharide biosynthetic process

• [x] alg2 +GO:0006488 dolichol-linked oligosaccharide biosynthetic process

  • [x] any1, indirect GO:1905533 negative regulation of leucine import across plasma membrane

[ValWood]

transmembrane transport

• [x] SPAC4G8.08 https://github.com/pombase/website/issues/682

• [x] SPCC1682.11c (family is called choline-transporter like but there is no evidence that they are transporters

• [x] SPAC9G1.04 not tm transport

[ValWood]

cytoskeleton (actin)

• [x] slm1 SPAC637.13c cytoskeletal signaling protein Slm1 (predicted)

• [x] vps1 SPAC767.01c dynamin family protein Vps1 (nope getting mixed up)

  kinases regulation of actin cyto?

• [x] pom1

• [x] plo1

• [x] syp1 SPBC4C3.06 F-BAR domain protein Syp1 (predicted) move down to negative regulation

• [x] SPAC926.03 myosin II regulatory light chain Rlc1 check- should be fixed by https://github.com/geneontology/go-ontology/issues/15082

  • [x] check esyN files too (this is probably because I didn't update the slim file, I always forget to do this...)

[ValWood]

DNA repair?

• [x] ASTRA complex telomere maintenance and DNA repair?
• [x] Smc5-Smc6 complex
• [x] Ino80 complex
• [x] hus5 (sumo related)

[ValWood]

conjugation @Antonialock

• [x] git1
• [x] cgs2
• [x] (gpa1 and pka1 are annotated)

[Antonialock]

ohh, yes, all of these should be negative regulation of conjugation with cellular fusion I guess

(pka1 phosphorylates rst2 resulting in rst2 exclusion from the nucleus. rst2 when in the nucleus acts as a TF fror ste11 which drives mating

[Antonialock]

all genes annotated to "adenylate cyclase-activating glucose-activated G-protein coupled receptor signaling pathway" now also have the annotation negative regulation of induction of conjugation with cellular fusion.

[ValWood]

• [x] pep3 vesicle docking

[ValWood]

meiotic nuclear division

• [x] SPBC27.02c
• [x] SPAC16A10.05c
• [x] SPAC1805.07c
• [x] SPAC14C4.16
• [x] SPBC3B9.22c
• [x] SPCC417.02
• [x] SPAC589.08c
• [x] SPBC32F12.08c
• [x] SPCC1223.15c
• [x] SPAC8C9.17c /GO="aspect=P; term=attachment of spindle microtubules to kinetochore involved in homologous chromosome segregation; GOid=GO:0051455; evidence=IC; db_xref=GO_REF:0000111; from=GO:0042729; date=20180307"

NMS complex

Systematic ID

• [x] SPBC409.04c
• [x] SPBC409.09c
• [x] SPAC688.02c
• [x] SPAC29E6.04
• [x] SPAC27F1.04c
• [x] SPAPB17E12.06
• [x] SPBC11C11.03
• [x] SPBC336.08
• [x] SPCC188.04c
• [x] SPCC1020.02

/GO="aspect=P; term=attachment of spindle microtubules to kinetochore involved in homologous chromosome segregation; GOid=GO:0051455; evidence=IC; db_xref=GO_REF:0000111; from=GO:0031617; date=20180307"

[ValWood]

cell cycle transition

• [x] nuc2
• [x] cut4
• [x] rad26???
• [x] par1 ?
• [x] par2 ?
• [x] ppa3? ~- [ ] cut1/2~
• [x] slp1
• [x] bir1 will sort if applicable https://curation.pombase.org/pombase-trac/wiki/ChromosomeSegregation

APC can have /GO="aspect=P; term=positive regulation of mitotic metaphase/anaphase transition; GOid=GO:0045842; evidence=IC; db_xref=GO_REF:0000111; from=GO:0005680; date=20180307"

[ValWood]

cytokinesis

• [x] myo1 not sure maybe not cytokinesis? ~- [ ] mcp1?~ ~- [ ] fim1~

[ValWood]

carbohydrate derivative

• [x] SPCC191.05c | nucleoside 2-deoxyribosyltransferase (predicted) ? ~- [ ] SPBP18G5.02 | CDP-diacylglycerol-glycerol-3-phosphate3-phosphatidyltransferase Pgs1~ ~- [ ] mde1 | SPAC20H4.05c | 5'-methylthioribulose-1-phosphate dehydratase, adducin Mde~

[ValWood]

I've done most of these.

When you get chance @mah11 could you check the "DNA repair complexes, will need to be done by ISS or IC if evidence at SGD is good enough that there are part of repair.

@Antonialock can you see if there is an easy/quick way to get "meiotic nuclear division" onto those where it is valid?

[mah11]

progress so far:

• Smc5-Smc6 complex: did IC for nse5, nse6, smc5; the others already had DNA repair annotations
• ASTRA complex: The GO:0070209 definition calls it "part of the chromatin remodeling machinery" and doesn't say anything about DNA repair, so it doesn't look safe to infer a repair annotation from the GO CC annotation.
• Ino80 complex: Similar to ASTRA - the GO definition (GO:0031011) has "chromatin remodeling activity and 3' to 5' DNA helicase activity", which doesn't narrow it down to necessarily DNA repair. That said, ino80 and nht1 have ISO annotations from the cerevisiae orthologs (the latter only from phenotypes at SGD).
• hus5: It looks like there's data in PMID:21444718. For now I've just done an IGI with rad60 in artemis as a stopgap.

Should I look into individual Ino80 complex subunits in more detail (post-hols)?

[ValWood]

No leave it at that ...just wanted to make sure we were missing nothing obvious....

[mah11]

OK. I like that answer ;)

[ValWood]

The only outstanding part of this ticket is to try to annotate these to meiotic nuclear division (or regulation of) in some way

• [x] sad1 | SPBC12D12.01 | spindle pole body SUN domain protein Sad1
• [x] cdc2
• [x] cdc13
• [x] cam1
• [x] spo15
• [x] cut2 -ve reg meiotic chromosome separation
• [x] cut7 IC from GO:0008574 +GO:0072687

[Antonialock]

cdc2 done, doing 25688135 for sad1

[Antonialock]

I don't think spo15 should have meiotic nuclear division....it's a sporulation protein, meiosis I and II are normal. It's involved in spindle pole body remodelling. This maps to sexual reproduction / meiotic cell cycle process

[Antonialock]

same with cam1

[ValWood]

OK makes sense. The SPB remodelling occurs quite far upstream of events of division (prophase?)

[Antonialock]

no it's when it remodels to form a crescent during sporulation

[ValWood]

Ah OK yes even further upstream...