query GO:0120024 glucagon-like peptide binding and GO:0120022 glucagon binding

[RLovering]

Hi There are 2 terms describing the binding of peptides encoded by the pro-glucagon gene (GCG), but no specific terms for the binding of peptides related to the glucagon gene. Neither of these terms have been associated with any proteins.

GO:0120022 glucagon binding Definition Interacting selectively and non-covalently with glucagon, a polypeptide hormone involved in glucose response. It is produced by pancreatic alpha cells and raises the concentration of glucose in the blood.

GO:0120024 glucagon-like peptide binding Interacting selectively and non-covalently with glucagon-like peptide, a antihyperglycemic hormone. Glucagon-like peptide is derived from the glucagon gene produced by pancreatic alpha cells.

In UniProt GCG recod: https://www.uniprot.org/uniprot/P01275 there are five isoforms listed: Glucagon: Glucagon-like peptide 1: Glucagon-like peptide 2: Oxyntomodulin: Glicentin:

In human there are 10 members of the glucagon family https://www.uniprot.org/uniprot/?query=family:%22glucagon%20family%22&fil=organism%3A%22Homo+sapiens+%28Human%29+%5B9606%5D%22&sort=score 1 is glucagon (with 5 isoform options) and 5 others.

Before looking at the GCG UniProt record I used the GO:0120024 glucagon-like peptide binding term to curate PMID:17715056 P48546 GIPR which binds both GCG and GIP https://www.uniprot.org/uniprot/P09681.

I am not convinced that we need a GO term for every member and isoform of the glucagon family, instead do you think it would be sensible to merge the 2 terms listed above

GO:0120022 glucagon binding GO:0120024 glucagon-like peptide binding

and rename as: glucagon family binding Definition: Interacting selectively and non-covalently with any member of the glucagon family (e.g. glucagon, glucagon-like peptides, oxyntomodulin, glicentin, ADCYAP1, GHRH, secretin, VIP, GIP).

Following the GO term available for proteins that bind members of the calcitonin family: GO:0097644 calcitonin family binding Definition: Interacting selectively and non-covalently with any member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs)).

PS I am still unconvinced that there should be no link in the ontology between peptide (1-50aa) and protein (>50aa). I am not convinced that the cell really appreciates the difference between a peptide hormone and a protein hormone. In fact for GCG https://www.uniprot.org/uniprot/P01275 one isoform Glicentin is 69aa whereas Glucagon is 29. So I guess metabolism/cleavage or binding of this protein/peptides would need to be curated under both protein and peptide branches of the ontology.

Thanks

Ruth

[pgaudet]

See history of the terms here: #13143

It seems a merge would be reasonable here; I dont see why glucagon should be treated differently from other members of the family.

[pgaudet]

Hi @RLovering

A few more terms mention glucagon. Here's what I propose to do:

Term	ID	Number of annotations	Proposed action
DONE 'glucagon-like peptide binding'	GO:0120024	0	merge into GO:0120022 glucagon binding' ; change label to glucagon family peptide binding
'glucagon processing'	GO:0120116	0	change label to 'glucagon family hormone processing' or 'glucagon family peptide processing'
'glucagon receptor binding'	GO:0031769		change label to 'glucagon family hormone receptor binding' or 'glucagon family receptor binding' _probably should add isa parent GO:0051428 peptide hormone receptor binding
'glucagon-like peptide 1 receptor activity'		GO:0044508	merge into GO:0004967 'glucagon receptor activity' ;
'glucagon secretion'	GO:0070091		change label to 'glucagon family hormone secretion'
'negative regulation of glucagon secretion'	GO:0070093		change label to 'negative regulation of glucagon family hormone secretion'
'positive regulation of glucagon secretion'	GO:0070094		change label to 'positive regulation of glucagon family hormone secretion'
'regulation of glucagon secretion'	GO:0070092		change label to 'regulation of glucagon family hormone secretion'
'response to glucagon'	GO:0033762		change label to 'response to glucagon family hormone'
'cellular response to glucagon stimulus'	GO:0071377		change label to 'cellular response to glucagon family hormone'

[RLovering]

This looks good to me except do you think you could reduce the use of 'hormone' in the name. I have put possible different names in the table above in italics, where I think 'hormone' maybe could not be included, but I guess if for consistency you want to keep hormone in all terms then that is fair enough. I think these revisions are good

Best Ruth

[pgaudet]

I was trying to avoid the term 'peptide' because of your comment

I am not convinced that the cell really appreciates the difference between a peptide hormone and a protein hormone.

[deustp01]

But I think "peptide" is part of the generally used name for these molecules, which might justify an exception?

[RLovering]

Hi Pascale

I don't like this suggestion as other things bind to the receptor not just the ligand.

merge into GO:0004967 'glucagon receptor activity' ; rename glucagon family hormone receptor binding or 'glucagon family receptor binding' probably should add is_a parent GO:0051428 peptide hormone receptor binding

merge into GO:0004967 'glucagon receptor activity' ; rename glucagon family hormone receptor activity or 'glucagon family receptor activity' probably should add is_a parent GO:0051428 peptide hormone receptor binding

I have edited the table and added the parent binding term to the row above

Thanks

Ruth