#10992 fix def for glycosylation

None
closed-fixed
None
4
2014-07-17
2014-07-10
Chris Mungall
No
id: GO:0070085
name: glycosylation
def: "The covalent attachment of a glycosyl residue to a substrate molecule." [GOC:mah]

This definition looks like a single step / MF. But glycosylation can involve other steps. The definition should be changed to reflect this. Examples should be added in comments field.

Discussion

  • I'll use wiki as a starting source here (aka devil's advocate):
    Glycosylation (see also chemical glycosylation) is the reaction in which a carbohydrate, i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor). In biology glycosylation mainly refers in particular to the enzymatic process that attaches glycans to proteins, lipids, or other organic molecules.

    It almost sounds as if some authorities consider only the first attachment, and nothing beyond that?

    However, considering that there can be different glycosyl groups, maybe something as simple as "The covalent attachment of glycosyl residues to a substrate molecule."?

     
  • Navigating down to the grandchild, GO:0006486 protein glycosylation, the definition there looks good: "A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins." Could this be generalized and propagated upwards?

     
  • Answered my own question: No. It needs an additional bit (Harold's point) to say that the new bit can be added to an existing glycan as well as to an amino acid side chain.

    Another complication: for mammals (and others?) the overall process that generates a mature glycoprotein can include removing some residues from an added oligosaccharide before additional ones are added onto the trimmed structure. If the process is intended to span all the events that convert a nascent polypeptide chain to a mature glycoprotein, removal steps need to be accommodated within the definition.

     
  • Chris Mungall
    Chris Mungall
    2014-07-11

    I can't say for sure if the intent is to include removal steps but we should make a commitment one way or another.

    It seems that even if the current def tends towards single-step, the graph says otherwise:

      is_a GO:0070085 ! glycosylation
        is_a GO:0043413 ! macromolecule glycosylation
         is_a GO:0006486 ! protein glycosylation
          is_a GO:0006487 ! protein N-linked glycosylation
           *PART_OF* GO:0006491 ! N-glycan processing
    

    So post-processing must be included to avoid inconsistencies with the graph

    [Term]
    id: GO:0006491
    name: N-glycan processing
    def: "The conversion of N-linked glycan (N = nitrogen) structures from the initially transferred oligosaccharide to a mature form, by the actions of glycosidases and glycosyltransferases. The early processing steps are conserved and play roles in glycoprotein folding and trafficking." [ISBN:0879695595, PMID:12736198]
    synonym: "N-glycan catabolism" RELATED []
    synonym: "N-glycan degradation" RELATED []
    synonym: "N-linked glycoprotein maturation" EXACT []
    is_a: GO:0009311  ! oligosaccharide metabolic process
    ***relationship: part_of GO:0006487 ! protein N-linked glycosylation
    
     
  • How about "The covalent attachment and further modification of carbohydrate residues to a substrate molecule."

     
  • Chris Mungall
    Chris Mungall
    2014-07-11

    That's looking better. That would justify a precise "starts_with some MF" axiom.

    Is this correct:

    glycosylation starts_with some
    GO:0016757 'transferase activity, transferring glycosyl groups'

    It's harder to specify ends_with as it's deliberately open end (but circumscribed to only include activities on the attached carbohydrate).

    So the text def looks good from an ontology perspective.

     
  • I think so; could that starts_with some GO:0016757 be construed to also mean not just a single sugar (which can happen), but possible some more complex carbohydrate "pre-built" core structure where its one of the units that is getting linked to the protein (like in GPI anchors). If that seems reasonable, then we should be good.

     
  • Changed text def to "The covalent attachment and further modification of carbohydrate residues to a substrate molecule."

     
    • status: open --> closed-fixed