Obsoletion request: GO:0035629 N-terminal protein amino acid N-linked glycosylation;

[ValWood]

Please provide as much information as you can:

ALL N-LINKED GLYCOSYLATION IS VIA ASPARAGINE

• GO term ID and Label

• GO:0035629 N-terminal protein amino acid N-linked glycosylation
  (already has a comment)
  Note that the only known alpha amino glycosylation is on an asparagine; see UniProtKB:P58522. However, this feature is not differentiated from normal N-glycosylation of asparagine.

• GO:0042543 protein N-linked glycosylation via arginine
  (1 EXP but the publication used does not mention arginine)

• The sibling
  GO:0018244    protein N-linked glycosylation via tryptophan
  are already proposed for obsoletion here: Bulk obsoletion request: single step processes or regulation of molecular function with no annotations (336 terms) #28482

This would leave
GO:0006487 protein N-linked glycosylation
and single child [GO:0018279]( protein N-linked glycosylation via asparagine
propose to merge and rename after considering which way would be the lease amount of reannotation for curators.

[ValWood]

Because the only annotations is UniProt, and there will be direct replacement I will proceed straight to obsoletion

[ValWood]

Still to do

GO:0006487 protein N-linked glycosylation
--GO:0018279 protein N-linked glycosylation via asparagine

will be single inheritance.
Obsolete one and replace by the other.

[ValWood]

obsolete
GO:0006487 protein N-linked glycosylation
replace by
GO:0018279 protein N-linked glycosylation via asparagine

[nataled]

Since the current definition mentions more than just asparagine, there should be multiple 'consider' used instead of 'replaced_by'.

[ValWood]

Hi @nataled , it seems that all N-linked glycosylation is via asparagine, so I assume this was a mistake in the definition.

the other children
GO:0042543   obsolete protein N-linked glycosylation via arginine |  
GO:0018244   obsolete obsolete protein N-linked glycosylation via tryptophan

were already obsoleted. Do you have an exception?

[ValWood]

Tryptophan (Trp) and arginine cannot undergo N-linked glycosylation because it does not contain the necessary side chain amine group.
v

[jlewsmith]

CGD done

[nataled]

I was going based on the information in PSI-MOD: N-glycosylated residue which shows other amino acids can be N-linked. All are indicated as 'natural'.

[ValWood]

I think these are referring to N-terminal rather than "N-linked"

In the literature, N-linked glycosylation is defined as acting only on Asparagine residues

https://en.wikipedia.org/wiki/N-linked_glycosylation#:~:text=N%2Dlinked%20glycosylation%20is%20the,%2Dglycosylation%2C%20studied%20in%20biochemistry.

N-linked glycosylation is the attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom (the amide nitrogen of an asparagine (Asn) residue of a protein), in a process called N-glycosylation, studied in biochemistry.[1] The resulting protein is called an N-linked glycan, or simply an N-glycan.

[nataled]

Yeah I was a bit confused by that, but figured N-terminal did not rule out N-linked. But I also checked PRO (which contains a very large number of N-linked glycosylated proteins, and none have an amino acid other than asparagine.

BTW, I'm pretty sure the N is for nitrogen, since there is also O-linked glycosylation (which connects via oxygen).

[ValWood]

BTW, I'm pretty sure the N is for nitrogen, since there is also O-linked glycosylation (which connects via oxygen).

Yes you are correct about that!

[ValWood]

I guess the distinction is it is the N of an asparagine side chain rather than N-term.

[nataled]

I found this paper, describing work on N-linked arginines. https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.00185/full

[ValWood]

I think it is OK for now. Part of this branch review is to remove the single step glycosylase terms (i.e molecular functions) . N-glycosylation (in the current GO sense), will likely become merged into the term dolichol linked oligosaccharide biosynthetic process

because it refers to a pathway i.e
: http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?barista_token=sasgrjd2nx44ugmbfn3w&model_id=gomodel:665912ed00000459
rather than a single glycosylase activity, and is now 'single inheritance'

so the examples in the review mentioned wouldn't belong under here anyway.

[nataled]

My original comment is only about the use of 'replaced_by' instead of 'consider'. If there is even one type of N-linked glycosylation that is not to asparagine (and according to PSI-MOD and that paper, there is), then I think it would be misleading to guide a user from a (relatively) general term to one with more specificity.

[ValWood]

Good point. I will change it once the existing annotations are updated. The existing annotations should all be N-linked via asparagine (and will be automatically migrated via replaced by) , once this is done, for future viewers of the obsolete term I will make it "consider".

[ValWood]

Waiting for next GO update to ensure all the remapping is done before changing to "consider"

[pgaudet]

It seems like the 'via asparigine' should anyway be in the definition rather than in the term label; are we only keeping that in the label because we dont think people read definitions?

[ValWood]

I don't think there is any reason to keep it in the label. It should not make any difference to curators now that there is only one term. I will fix this when I finish the ticket to change the tag to "consider". I can't do that until after the next go release, which is presumably when all of the Noctua remapping will occur.

[pgaudet]

Sounds good, thanks!