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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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GO:0019933 cAMP-mediated signaling #20712

Open pgaudet opened 3 years ago

pgaudet commented 3 years ago

Hello,

Following on the Signaling workshop of the Fall 2017 (see slides here: https://docs.google.com/presentation/d/1xR6EFbRyCSwruXVeMYZtJfwWEbIr6U8zei8IwGG3OrA/edit#slide=id.g26be66c50c_0_6) and on #20487

"GO:0007188 adenylate cyclase-modulating" G protein-coupled receptor signaling pathway and "GO:0019933 cAMP mediated signalling" are 2 names for the same pathway

ValWood commented 3 years ago

I would be happy if "cAMP-mediated signalling" was obsoleted and made a related synonym of GO:0007188 adenylate cyclase-modulating" G protein-coupled receptor signaling pathway.

I just want people to find this pathway if they search on "cAMP-mediated signalling"

ValWood commented 3 years ago

or merged...

pgaudet commented 3 years ago

I think we can also do the same merge with

Annotations are here: https://docs.google.com/spreadsheets/d/11VqCZrr_xy3pLGDBtEGksjncw1a1EDoOdif9V_ppO-U/edit#gid=0 (see also this analysis from 2017 https://docs.google.com/presentation/d/1xR6EFbRyCSwruXVeMYZtJfwWEbIr6U8zei8IwGG3OrA/edit#slide=id.g26be66c50c_0_91

Will might need to obsolete, because it looks like there are many receptors, as annotations are too inconsistent to merge: ligands and adenylate cyclases annotate to 'regulation of cAMP-mediated signaling' (since they are upstream). Also, phosphodiesterases, that degrade cAMP and stop the signaling, are often annotated to negative regulation of cAMP signaling.

There are not so many annotations

Group  Number of EXP annotations
AgBase 3
dictyBase 13 @pfey03
FlyBase 3 @hattrill
MGI 6 @ukemi
PomBase 6 OK
RGD 37 @gthayman
SGD 3 @srengel
UniProt 30
WB 1 @vanaukenk

This really is a case where the start and end of the pathway would be useful to have. The 'canonical' ACA-activating GPCR pathway activates PKA, which activates gene expression, see https://docs.google.com/presentation/d/1xR6EFbRyCSwruXVeMYZtJfwWEbIr6U8zei8IwGG3OrA/edit#slide=id.g26cb322782_0_61 so - do we also need to merge/obsolete GO:0010737 protein kinase A signaling ? But other pathways also feed into PKA signaling.

Maybe we can do the cAMP bit and see PKA later ?

ValWood commented 3 years ago

~I only see 2 direct annotations at PomBase? stm1 and pka1~

ignore 2 genes, multiple annotations

ValWood commented 3 years ago

PomBase done!

ValWood commented 3 years ago

another commonly used name for is GO:0007188 adenylate cyclase-modulating" G protein-coupled receptor signaling pathway in fission yeast is glucose-sensing PKA pathway

pgaudet commented 3 years ago

@ValWood We have a term for this, adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway

ValWood commented 3 years ago

Yes "GO:0007188 adenylate cyclase-modulating" G protein-coupled receptor signaling pathway needs synonyms glucose-sensing PKA pathway (exact?) and cAMP-mediated signaling (related or broad? ) after merge?

pgaudet commented 3 years ago

Sorry I was talking about GO:0010619 - can you not use this ?

ValWood commented 3 years ago

We already use this, https://www.pombase.org/term/GO:0010619 but it is no longer linked to "cAMP-mediated signalling" which used to be an ancestor and is what users are more likely to use in searching... All these terms need

either glucose-sensing PKA pathway and cAMP-mediated signaling

or just cAMP-mediated signaling as synonyms (depending whether they mention glucose or not)

pgaudet commented 3 years ago

I see links between those terms -

image

Do you want me to add

OK ?

ValWood commented 3 years ago

Yes! thanks.

pfey03 commented 3 years ago

@pgaudet I know we said maybe exclude Dicty from GO:0019933 cAMP-mediated signaling' , but I need to check if it can really be excluded as cAMP also plays role in later development. not sure if anything is intracellular but need to check into that again to be really sure.

pfey03 commented 3 years ago

I checked and it's always via an extracellular receptor as far as I could find and cAMP is always secreted. So I think GO:0019933 can be 'not in Dictyostelium'

pgaudet commented 3 years ago

Added Never in taxon GO:0019933 cAMP-mediated signaling NCBITaxon:33083 Dictyostelids

pfey03 commented 3 years ago

THanks @pgaudet

pgaudet commented 3 years ago

We need to obsolete the following 4 terms:

Annotations are here (downloaded again today): https://docs.google.com/spreadsheets/d/11VqCZrr_xy3pLGDBtEGksjncw1a1EDoOdif9V_ppO-U/edit#gid=0

Contributor (Assigned by)

AgBase | 3 BHF-UCL | 1 CGD | 10 dictyBase | 40 FlyBase | 8 MGI | 14 ParkinsonsUK-UCL | 1 RGD | 44 SGD | 10 UniProt | 54 WB | 1

ukemi commented 3 years ago

What about soluble adenylate cyclase? PMID:25308880

ValWood commented 3 years ago

Isn't adenylate cyclase always soluble? I presume you would only use "adenylate cyclase-activating G protein-coupled receptor signaling pathway" if the adenylate cyclase is part of this pathway.

Is adenylate cyclase part of other pathways too? I presume there would be other terms for that?

pgaudet commented 3 years ago

This paper also helps: https://pubmed.ncbi.nlm.nih.gov/21490586/

sAC is distinct from the more widely studied source of cAMP, the transmembrane adenylyl cyclases (tmACs); its activity is uniquely regulated by bicarbonate anions, and it is distributed throughout the cytoplasm and in cellular organelles. Due to its unique localization and regulation, sAC has various functions in a variety of physiological systems that are distinct from tmACs

The authors also write

However, in a seeming conundrum, cAMP has also been implicated in a wide variety of often-contradictory physiological processes, including different aspects of metabolism, proliferation, apoptosis, differentiation, migration, development, ion transport, pH regulation, and gene expression. Only recently has it become clear how this single second messenger could simultaneously mediate so many processes. In current models of cyclic nucleotide signal transduction, cAMP is locally generated within independently regulated microdomains (most recently reviewed in 39).

supporting multiple pathways, in fact. I dont find any term(s) that would represent the other ACA/cAMP signaling pathways.

pfey03 commented 3 years ago

I already updated all Dicty from dictyBase on 22. Feb, hope it will soon come through with next EBI release

pgaudet commented 3 years ago

Thanks @pfey03 !

pfey03 commented 3 years ago

@pgaudet noticed I missed some regulation of cAMP mediated signaling and updating those today or tomorrow

hattrill commented 3 years ago

Just to add to the soluble AC thread, I am currently looking at cAMP signaling in the mitochondrial matrix: https://pubmed.ncbi.nlm.nih.gov/29694829/

pgaudet commented 3 years ago

Thanks @hattrill let us know what you find, it sounds like we can create other pathways.

Where I dont know what to do is for PDE - it degrades cAMP, but would we be able to tell from which pathway cAMP was produced?

hattrill commented 3 years ago

I think for my purposes as they stand (looking at PMID:25648146), I could do with a negative term for GO:0010738 regulation of protein kinase A signaling

In D.mel, it's not clear if the cAMP is generated in the mitochondrion or not as the sAC is unknown. So, I don't think I can point to a specific pathway.

For mammalian systems it seems like cAMP can be generated by sACs in the matrix.

srengel commented 3 years ago

SGD done.

pgaudet commented 3 years ago

AgBase done

pfey03 commented 3 years ago

dictyBase all checked and done

pgaudet commented 3 years ago

Group | Number of annotations

dictyBase | 3 FlyBase | 2 MGI | 6 RGD | 37 UniProt | 31 WB | 1

vanaukenk commented 3 years ago

WB checked and updated.

pfey03 commented 3 years ago

done with dicty

suzialeksander commented 2 months ago

Annotation Review is out-of-date and was closed