Review annotations to 'cAMP biosynthetic process'

[pgaudet]

Here are the EXP annotations of cAMP biosynthetic process (GO:0006171 ) to proteins OTHER than adenylate cyclase (as far as I was able to tell): Please have a look and see if you rehouse these annotations.

Database	Protein name	ID	Evidence	Date	Reference
CGD		CGD:CAL0000178292	IMP	20140625	CGD_REF:CAL0000143470|PMID:21992526
FlyBase	forkhead box, sub-group O	FB:FBgn0038197	IMP	20130801	FB:FBrf0209006|PMID:19651894
FlyBase	forkhead box, sub-group O	FB:FBgn0038197	IDA	20130801	FB:FBrf0209006|PMID:19651894
PAMGO_MGG		NCBI:AAB66482	IMP	20080225	PMID:9401122
GOC	AT1G62590	TAIR:locus:2203916	IDA	20171002	TAIR:Publication:501755062|PMID:23681569
MTBBASE	Probable lignin peroxidase LipJ	UniProtKB:O07732	IDA	20110725	PMID:15678099
MTBBASE	Probable transcriptional regulatory protein (Probably LuxR/UhpA-family)	UniProtKB:O53720	IDA	20110608	PMID:19516256
UniProt	Receptor activity-modifying protein 2	UniProtKB:O60895	IDA	20111115	PMID:20074556
UniProt	ADM	UniProtKB:P35318	IDA	20111115	PMID:20074556
CAFA	Calmodulin-sensitive adenylate cyclase	UniProtKB:P40136	IMP	20161024	PMID:11807546
MTBBASE	Uncharacterized protein Rv2212	UniProtKB:P9WMU7	IDA	20110724	PMID:16925585
MTBBASE	Uncharacterized protein Rv1319c	UniProtKB:P9WQ31	IDA	20110724	PMID:15182360
MTBBASE	Uncharacterized protein Rv1318c	UniProtKB:P9WQ33	IDA	20110828	PMID:15182360
UniProt	Calcitonin gene-related peptide type 1 receptor	UniProtKB:Q16602	IDA	20111115	PMID:20074556
CACAO	Trace amine-associated receptor 1	UniProtKB:Q96RJ0	IDA	20140404	PMID:11723224
UniProt	Urocortin-2	UniProtKB:Q96RP3	IEP	20030404	PMID:11329063
ZFIN	NME/NM23 nucleoside diphosphate kinase 3	ZFIN:ZDB-GENE-000210-34	IMP	20170815	ZFIN:ZDB-PUB-161209-4|PMID:27927712
ZFIN	parathyroid hormone 2	ZFIN:ZDB-GENE-041102-1	IDA	20041208	ZFIN:ZDB-PUB-040810-7|PMID:15297442
ZFIN	parathyroid hormone 2 receptor	ZFIN:ZDB-GENE-991123-10	IDA	20041208	ZFIN:ZDB-PUB-040810-7|PMID:15297442

[sabrinatoro]

@pgaudet Could you remind me if we made a decision about how to annotate ligands which bind to the receptor? Should we annotate them as regulator of "adenylate cyclase-activating G-protein coupled receptor signaling pathway"? or should we annotate them to the pathway? Thanks!

[pgaudet]

Hi @sabrinatoro

The ligand is part of the pathway, so you would annotate to "adenylate cyclase-activating G-protein coupled receptor signaling pathway" (not regulation of...)

Thanks, Pascale

[sabrinatoro]

Thank you, @pgaudet. The ZFIN annotations have all been updated.

[pgarmiri]

Hi @pgaudet ,

I came across this very interesting case and I would like your opinion, please.

There were a few annotations of GO:0030819 ' positive regulation of cAMP biosynthetic process' to CALCRL in human (Q16602). This protein when pairing with different receptor activity modifying proteins (RAMPs) can produce calcitonin gene-related peptide (CGRP) receptors (CRLR/RAMP1) and adrenomedullin (AM) receptors (CRLR/RAMP2 or -3). In PMID: 10882736, they show that when stably coexpressed with RAMPs, CRLR-GFP appeared on the cell surface and was fully active in intracellular cAMP production and calcium mobilization. This leads to CRLR endocytosis that occurred predominantly through a clathrin-dependent pathway. (http://www.jbc.org/content/275/38/29602.full.pdf)

Now there are specific terms for these pathways (see below) that I have used replaces the offending terms, but it seems that the information that these pathways modulate cAMP production is lost.

GO:1990410 Process adrenomedullin receptor signaling pathway GO:1990408 Process calcitonin gene-related peptide receptor signaling pathway

I have compare the 2 GO terms above with GO:0007189 'adenylate cyclase-activating G-protein coupled receptor signaling pathway' (see the link below). There seem to be under different G-protein coupled receptor terms that they are not related to cAMP signaling, which is a pity.

https://www.ebi.ac.uk/QuickGO/chart?ids=GO:1990410,GO:1990408,GO:0007189

Do you think new terms /relations are needed to capture how these pathways work? Or any other suggestions or how to deal with this case?

Thanks,

Penelope

[pgarmiri]

All the UniProt annotations mentioned above have been updated. ( In the end, I added the specific pathway term plus the suggested one GO:0007189.)

The CAFA annotations will not be updated at this point as the evaluation of the submissions is in progress.

[suzialeksander]

@sandyl27, can you review the above CACAO annotation? Just post back on this issue to let us know you've dealt with it (deleted/changed/kept for reason x). Thanks!

[sandyl27]

I'm going to change it to GO:0030819 positive regulation of cAMP biosynthetic process. Please let me know if you think this is wrong.

[pgaudet]

Hi @sandyl27 I think you can go ahead and annotate to Trace amine-associated receptor 1 - UniProtKB:Q96RJ0 to ' GO:0004930 G-protein coupled receptor activity' See section "Pharmacological Characterization of the Rat Trace Amine Receptor." - the authors clearly test the G-protein coupled receptor activity: "the striking similarity in amino acid sequence between r2-3 and biogenic amine GPCRs (Fig. 1) indicated that catecholamines or related compounds might activate the receptor. When tested in functional assays of cAMP production"

OK ?

Thanks, Pascale

[sandyl27]

@pgaudet That makes sense! I just changed it in protein 2 GO.

[pgaudet]

Hi @happy-lorna @asangrador There are 3 InterPro families with mappings to cAMP biosynthetic process IPR030672 IPR009398 IPR013716

(Do I need to notify you of these or do you have an automatic process to deal with obsolete terms?)

Thanks, Pascale

[pgaudet]

I am going ahead with the obsoletion, https://github.com/geneontology/go-ontology/issues/14718

so I am saving the existing annotations 'for the record': https://docs.google.com/spreadsheets/d/1b5T4XOVd1yOCi0N5yv1cJ_l77WPwLZk8G_63wl4oIGs/edit#gid=0