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Review annotations to GO:0004584 dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase activity #2872

Closed pgaudet closed 4 years ago

pgaudet commented 4 years ago

GO:0004584 dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase activity is mapped to EC:2.4.1.130, which has been replaced by: Transferred entry: 2.4.1.258: Dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichol alpha-1,3-mannosyltransferase. Transferred entry: 2.4.1.259: Dolichyl-P-Man:Man(6)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase. Transferred entry: 2.4.1.260: Dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichol alpha-1,6-mannosyltransferase. Transferred entry: 2.4.1.261: Dolichyl-P-Man:Man(8)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase.

There are 3 EXP annotations left by GeneDB and 1 InterPro mapping to InterPro:IPR007315

https://docs.google.com/spreadsheets/d/1MNrfYhqCimhrM9Xsxr2GiCk5DhmoDCQGUunmGBvXWyE/edit#gid=0

This term will be obsoleted.

Thanks, Pascale

Achchuthan commented 4 years ago

Hi @pgaudet, Thanks a lot for letting me know. I have updated the annotation for the gene from Trypanosoma brucei with GO:0052925 (2.4.1.258) in our Chado database. @uliboehme will be able to update the Plasmodium annotations.

typhainepl commented 4 years ago

Hi, I have replaced the GO term in the InterPro entry by GO:0000030: mannosyltransferase activity.

uliboehme commented 4 years ago

Hi @pgaudet, Thanks for letting me know. The GO term in Plasmodium (PF3D7_1341600) has been changed last year in the annotation database as indicated in the google spread sheet. https://docs.google.com/spreadsheets/d/1lhBpUjWQMNe6gY9oCYZxajwTTlr1L9cE1h7ZiGEBzi8/edit#gid=0 I'm not able to change GO terms in UniProt (Q8IDS3, PF3D7_1341600).

pgaudet commented 4 years ago

@alexsign Are GeneDB:PF3D7_1341600 and and UniProtKB:Q8IDS3 the same ? It looks the same in Protein2GO; do you know why we would get this listed twice in AmiGO ? Its as if the IDs are not reconciled... ?

pgaudet commented 4 years ago

also there is one pombase annotation @ValWood please fix: https://docs.google.com/spreadsheets/d/1lhBpUjWQMNe6gY9oCYZxajwTTlr1L9cE1h7ZiGEBzi8/edit#gid=0

alexsign commented 4 years ago

@pgaudet I can see 3 records in the P2GO database from GeneDB:

Q8IDS3 GO:0004584 ECO:0000316 PMID 24489949 Q8IDS3 GO:0005783 ECO:0000314 PMID 12117963 Q8IDS3 GO:0006506 ECO:0000316 PMID 24489949

looks like 3 different annotations to PF3D7_1341600 = Q8IDS3

ValWood commented 4 years ago

Does anyone know the actual activities for

gpi10 | pig-B (predicted) gpi18 | pig-V, dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase (predicted)

ValWood commented 4 years ago

pigB according to UniProt https://www.uniprot.org/uniprot/Q92521 Mannosyltransferase involved in glycosylphosphatidylinositol-anchor biosynthesis. Transfers the third alpha-1,2-mannose to Man2-GlcN-acyl-PI during GPI precursor assembly.1 Publication but has GO glycolipid mannosyltransferase activity

SGD has alpha-1,2-mannosyltransferase activity

ValWood commented 4 years ago

pigV human https://www.uniprot.org/uniprot/Q9NUD9 glycolipid mannosyltransferase activity

SGD enables alpha-1,6-mannosyltransferase activity

deustp01 commented 4 years ago

A useful review, with material on budding yeast - human homology: PMID: 29679465

ValWood commented 4 years ago

MT-III (Gpi10),

MT-II (Gpi18) A second Man is added to the GPI intermediate by MT-II which consists of two subunits, Gpi18 and Pga1 in S. cerevisiae (100,101). Based on homology to Pmt2 family of O- mannosyltransferases, Gpi18 is predicted to be the catalytic sub- unit and Pga1 an accessory subunit (101). Metabolic labeling experiments suggest that (EtnP)Mana1–4GlcNa1–6(2-acyl)inositol- phospholipid is the major intermediate that accumulates in gpi18 mutants and could be its major substrate (100). However, a GPI precursor without EtnP may also be a substrate.

So now I only need to find out what MTII and MTIII refer to!

ValWood commented 4 years ago

I can't figure this out but go ahead with the obsoletion anyway - if we can't work it out we'll just go up to mannosyltransferase.

pgaudet commented 4 years ago

@uliboehme You should be able to remove

PFAL | Q8IDS3 | PF3D7_1341600 |   | GO:0004584 | dolichyl-phosphate-mannose-glycolipid alpha-mannosyltransferase activity | ECO:0000316(IGI) | ECO:0000316 | (IGI) |   | PMID:24489949 ECO:0000316 | (IGI)

I will remove the IBA annotation.

Thanks, Pascale

hattrill commented 4 years ago

@sjm41 and @phanivg you may want to review PIG-V based on this obsoletion proposal

pgaudet commented 4 years ago

I dont see any annotations by FlyBase to this term - did I miss some ?

hattrill commented 4 years ago

No - no issue here. It's an ISS with a yeast protein - when Stacia updated the SGD annotation, ours automatically updated in P2GO. But Steven & Phani have an enzyme project on the go (I have a feeling that they've looked over this, but I wanted to double check with them)

uliboehme commented 4 years ago

@pgaudet Thanks for your message. I've already removed GO:0004584 from PF3D7_1341600 in our annotation database (chado Artemis). I'm not able to remove the GO term from UniProtKB:Q8IDS3.

pgaudet commented 4 years ago

Got it. I assume that will be done in the next load Is this right @alexsign ?

uliboehme commented 4 years ago

Thanks @pgaudet

alexsign commented 4 years ago

@pgaudet should be removed after this weekend load.

pgaudet commented 4 years ago

Great - this looks like it's all done.

sjm41 commented 4 years ago

@ValWood You probably realise this, but note that the 'GPI mannosyltransferases' should not be annotated with any of the 4 activities mentioned at the top of this ticket - those activities describe the actions of the 'dolichyl pyrophosphate mannosyltransferases' (i.e. Alg3, Alg9, Alg12) that act earlier in glycan synthesis. The two sets of enzymes are distinguished by substrate: dolichol pyrophosphate (PP-Dol) vs dolichol phosphate (P-Dol).

This distinction may be the reason we have the GO:0004584 term, as it's specific for dolichyl-phosphate, and may be a reason for not obsoleting it - I'll mention this on the related ticket (https://github.com/geneontology/go-ontology/issues/16022).

Synthesizing data from UniProt/EC/SGD/GO, I believe the following summarizes the situation:

Dolichyl pyrophosphate mannosyltransferases:

GPI mannosyltransferases: