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#9568 O-GlcNAcylation - add synonym or new term

FlyBase
closed-accepted
5
2012-08-08
2012-06-25
No

I'm curating PMID:22158438 and struggling to decide what the correct terms are. I'm not sure if this needs to be a new term or a synonym of an existing term:

O-GlcNAcylation (aka O-linked-N-acetylglucosamine modification)

I think this is a type of protein O-linked glycosylation.

Also the corresponding enzyme activity that adds this sugar is O-GlcNAc transferase which is currently a synonym of protein N-acetylglucosaminyltransferase activity (aka N-GlcNAc transferase activity). Are the N-GlcNAc transferase activity and O-GlcNAc transferase activity truly the same activity? I am a bit concerned about the N v O discrepancy but then I don't really understand the chemistry of sugar linking.

Thanks,
Susan

Discussion

  • susantweedie

    susantweedie - 2012-06-25
    • summary: GlcNAcylation - add synonym or new term --> O-GlcNAcylation - add synonym or new term
     
  • John S. Garavelli

    Yes, it can be very confusing if you don't understand the chemistry.
    First, get straight what the name of the sugar is, what is the abbreviation, and what it is the sugar is attached to. The name of the sugar spelled out is N-acetylglucosamine, that is a glucose where the 2-position alcohol is converted to an acetylated amine. Here the "N-" refers to the position of a substitution within the sugar. When the sugar is abbreviated, "glucose" becomes "Glc" and "N-acetylglucosamine" becomes "GlcNAc" --- the "N-" is now inside the abbreviation, and it is important to capitalize it that way.
    Second, the 1-position of that sugar is being attached to a protein at a particular amino acid side chain. There are different enzymes that do this.
    An enzyme that attaches GlcNAc to the alcohol group of a serine, threonine, or tyrosine is performing O-glycosylation, in this case O-GlcNAcylation. The enzyme that does this usually works on intracellular proteins.
    An enzyme that attaches GlcNAc to the amido group of asparagine is performing N-glycosylation, so it is a different process, N-GlcNAcylation. The enzyme that does this works on extracellular proteins.
    Where you got confused is where you said "which is currently a synonym of protein N-acetylglucosaminyltransferase activity (aka N-GlcNAc transferase activity)", you should have said "which is currently a synonym of protein N-acetylglucosaminyltransferase activity (aka O-GlcNAc transferase activity)". The "N-acetylglucosaminyltransferase" is spelled out, so an "N-" is at the front describing the sugar structure. The "O-GlcNAc" is abbreviated, so the "O-" is at the front describing the atom in the protein the sugar is attached to.
    To help keep it straight, you can indicate the protein atom that the enzyme is attaching the sugar to by saying "O-transferase" or "N-transferase". Your enzyme activity is an "GlcNAc O-transferase".

     
  • susantweedie

    susantweedie - 2012-06-26

    Thanks for the helpful explanation John. I didn't explain very well, when I said "which is currently a synonym of protein N-acetylglucosaminyltransferase activity (aka N-GlcNAc transferase
    activity)" I should have made it clear that the aka reflects a synonym that is currently in the GO -
    i.e. protein N-acetylglucosaminyltransferase activity ; GO:0016262 currently has both of these as exact synonyms:

    N-GlcNAc transferase activity
    O-GlcNAc transferase activity

    I wanted to make sure this was correct. Perhaps this is correct because the scope of the term is to cover GlcNAc transfer to protein via both N and O linkages - in which case I think it would be useful to add the linkage specific child terms and include your suggestion as the primary name or synonym:

    GlcNAc O-transferase
    GlcNAc N-transferase

    As for process terms, would you support the idea of O-GlcNAcylation becoming a new child term of O-glycosylation or is more appropriate to have it as a narrow synonym? The glycosylated amino acid in this case is threonine so I guess the logical new term is:

    protein O-GlcNAcylation via threonine ; GO:NEW
    Is_a protein O-linked glycosylation via threonine ; GO:0018243

    Maybe this is a step too far in which case I'll use GO:0018243 for process.

     
  • Paola Roncaglia

    Paola Roncaglia - 2012-06-27
    • assigned_to: nobody --> paolaroncaglia
     
  • Paola Roncaglia

    Paola Roncaglia - 2012-07-18

    Dear John,
    Would you have any more comments on Susan's questions below?
    Many thanks,
    Paola

     
  • Paola Roncaglia

    Paola Roncaglia - 2012-07-24

    Hi Susan, these are done:

    Removed synonym O-GlcNAc transferase activity from GO:0016253 protein N-acetylglucosaminyltransferase activity.

    Added new term: [this is the one you'll need]
    GO:0097363 protein O-GlcNAc transferase activity

    As for the process term, please go ahead and use protein O-linked glycosylation via threonine ; GO:0018243.

    Thanks,
    Paola

     
  • Paola Roncaglia

    Paola Roncaglia - 2012-07-24
    • status: open --> closed-accepted
     
  • Paola Roncaglia

    Paola Roncaglia - 2012-07-25
    • status: closed-accepted --> open-accepted
     
  • Paola Roncaglia

    Paola Roncaglia - 2012-07-25

    Agreed to add new process term as below. Will do soon.

     
  • Paola Roncaglia

    Paola Roncaglia - 2012-08-06

    Hi Susan,

    Here's your new process term:
    GO:0097370 protein O-GlcNAcylation via threonine

    Note for self:
    I'll leave this item open until I've fixed the entire node of protein glycosylation ; GO:0006486
    (see discussion http://wiki.geneontology.org/index.php/Ontology_meeting_2012-07-25#PROTEIN_GLYCOSYLATION\)

    Paola

     
  • Paola Roncaglia

    Paola Roncaglia - 2012-08-08

    Fixed node of protein glycosylation ; GO:0006486.

     
  • Paola Roncaglia

    Paola Roncaglia - 2012-08-08
    • status: open-accepted --> closed-accepted
     

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