#10828 NTR? Terms for protein glycosylation activities.

None
closed-rejected
None
5
2014-05-12
2014-05-04
Jim Hu
No

Should there be terms intermediate between GO:0016757_!_transferase_activity,_transferring_glycosyl_groups and its children?

e.g. differentia for N vs O linked products? Protein vs nonprotein substrates?

I'm working on a student annotation from

http://jb.asm.org/content/189/22/8088.full

Figure 3 shows expression of the PglL protein and its protein substrate in E. coli lead to generation of an O-glycosylated product. I can do this as a process annotation, but I was wondering if there should be activity terms.

Discussion

1 2 > >> (Page 1 of 2)
  • Molecular function term GO:0006486 protein glycosylation has exactly the needed N- and O- children. Could additional is_a links to show that the glycosylation process occurs by means of transferase reactions show the relationship without creating path violations?

     
  • Jim Hu
    Jim Hu
    2014-05-05

    You mean process term, right?

     
  • Sorry for the fuzziness - I'm not sure. Process terms parallel to the molecular function ones would make sense, but I think I've also seen parent-child relationships created between a process and a molecular function, and either might be appropriate here.

     
    • assigned_to: Tanya Berardini
     
  • Investigating MF-BP links vs. new MF terms as options.

     
  • We could link specific functions that are only involved in protein N/O glycosylation using part_of relationships to the appropriate process. I'm not familiar enough with the catalytic activity subgraph to know if there is a precedent for broader grouping categories that are not EC-based as that's the origin of this section of the ontology. It seems to me that that kind of classification is better suited to BP, where it already exists. Can you find the specific function in GO that you could use for annotation?

    How about:
    oligosaccharyl transferase activity
    http://amigo.geneontology.org/amigo/term/GO:0004576

     
  • Don't know anything about the bacterial process, but in humans and budding yeast, the process starts with the synthesis of an oligosaccharide block that is transferred onto an appropriate side chain (asn or tyr) of the protein that is to be glycosylated, and that oligosaccharide is modified by the addition of more saccharide units as the protein proceeds through the ER and Golgi, to yield the final glycopeotein. Terms need to be broad enough to cover this range of chemical processes, with part_of children perhaps to cover the distinctive successive steps, so GO:0004576 oligosaccharyl transferase activity looks like it might be one of these children, not the whole-process parent.

     
  • Peter - I was trying to suggest an MF term for Jim to use in annotation in conjunction with the protein O-linked glycosylation one from BP. We do need to make more links between MFs and BPs.

    Jim - Will 'oligosaccharyl transferase activity' + 'protein O-linked glycosylation' work? If yes, we can close this issue.

     
  • Jim?

     
  • Jim Hu
    Jim Hu
    2014-05-12

    Yes

     
1 2 > >> (Page 1 of 2)