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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR protein-RNA adaptor activity #19409

Closed Antonialock closed 3 years ago

Antonialock commented 4 years ago

child of GO:0030674 protein-macromolecule adaptor activity

I would use this term to describe how the RNA binding protein ZC3H11, mkt1 and pbp1 bring PABP (polyA binding protein) to RNAs PMID:24470144 rbp

I think it can also be used to describe how the erh1-mmi1 complex recruit CCR4-NOT and the NURS complex to targets.

Does this sound fine?

I was going to use the parent term protein-macromolecule adaptor activity + extension for PABP + SO:mRNA for 24470144, but realized SO is not allowed in P2G

vanaukenk commented 4 years ago

@ukemi @RLovering @pgaudet This sounds very much like what we are also trying to capture with a 'miRNA activity' term. Perhaps @Antonialock 's new term could be a parent of 'miRNA activity'?

RLovering commented 4 years ago

I agree protein-RNA adaptor activity sounds good for miRs that act as adaptors between mRNA and RISC, just need to make sure the definition is broad enough to include miRs

Antonia you should be able to include SO Ids in P2G, you may have selected the wrong relation. Actually I am not sure you can use SO Ids for mRNA. Probably this should be 'occurs_at SO: UAUU element, if there isn't a SO for UAUU element then request it ;) How about AU_rich_element http://purl.obolibrary.org/obo/SO_0001180?

Best

Ruth

hdrabkin commented 4 years ago

@Antonialock Can you supply the proposed def for the term you are requesting?

Antonialock commented 4 years ago

@hdrabkin hdrabkin Proposed def: "The binding activity of a protein that brings another protein and an RNA in contact, permitting those molecules to function in a coordinated way. "

Just to check, do you think it will be fine to use this term for complex members where several proteins contribute to the bridging with the qualifier contributes_to? In the screenshot example for example, ZC3H11 is the RNA binding protein & PBP1 contacts PABP,

Antonia you should be able to include SO Ids in P2G, you may have selected the wrong relation. Actually I am not sure you can use SO Ids for mRNA. Probably this should be 'occurs_at SO: UAUU element, if there isn't a SO for UAUU element then request it ;) How about AU_rich_element http://purl.obolibrary.org/obo/SO_0001180?

@RLovering I wanted to add two substrates so used has_input. There's http://www.sequenceontology.org/browser/current_svn/term/SO:0001180 in SO. It seemed a bit odd to add 'occurs' at for an adaptor activity, but perhaps that's just in my head?

ValWood commented 4 years ago

I see that you used the definition of the parent

The binding activity of a protein that brings together another macromolecule in contact,

but that doesn't quite make sense does it? @pgaudet

it should be just brings together a something and a something ?

Antonialock commented 4 years ago

yeah I thought the parent def was odd, but I thought it was because of my english xD rephrase parent to The binding activity of a protein that brings two other macromolecules in contact, permitting those molecules to function in a coordinated way. The adaptor can bring together two proteins, or a protein and another macromolecule such as a lipid or a nucleic acid. ?

Antonialock commented 4 years ago

(it can't be 'a something and a something', it must be 'a protein and a something', since the term name states "protein-macromolecule adaptor)

ValWood commented 4 years ago

It's the "in contact ' part that doesn't sound correct

it would be into contact. BUt they are not necessarily always in contact. I would get rid of the "in contact' part.

brings two molecules together?

Antonialock commented 4 years ago

yeah beats me what 'in contact' means. I like the "permitting those molecules to function in a coordinated way"

why is it limited to 2 molecules anyway? e.g. a MAPK cascade scaffold brings together many components?, allowing them to function in a coordinated way?

ValWood commented 4 years ago

Personally, I think that scaffolds and adaptors are slightly different, but I was over-ruled because I'm not able to articulate the difference. Maybe that is the difference . A scaffold is a platform (brings together many disparate things, often forms the core of a complex).

An adaptor connects one thing to another thing (usually via a PTM).

A MAP kinase scaffold fits both adaptor and scaffold, but some scaffolds (like the scaffold of a ribosome for example) aren't really adaptors because that are just a scaffold for assembly, not for connecting.

Antonialock commented 4 years ago

Personally, I think that scaffolds and adaptors are slightly different, but I was over-ruled because I'm not able to articulate the difference. Maybe that is the difference . A scaffold is a platform (brings together many disparate things, often forms the core of a complex).

An adaptor connects one thing to another thing (usually via a PTM).

A MAP kinase scaffold fits both adaptor and scaffold, but some scaffolds (like the scaffold of a ribosome for example) aren't really adaptors because that are just a scaffold for assembly, not for connecting.

Ah, I think you are trying to distinguish connectors that bridges things in a pathway, as opposed to structural molecules that just glue machinery together? I'm sure lots of stuff will fall in a grey zone....would the effort put into making these distinctions be worth it?

ValWood commented 4 years ago

Ah, I think you are trying to distinguish connectors that bridges things in a pathway, as opposed to structural molecules that just glue machinery together? I'm sure lots of stuff will fall in a grey zone....would the effort put into making these distinctions be worth it?

Possibly not. But I don't think non-signalling scaffolds sit well as adaptors.

e.g.

apc15 | anaphase-promoting complex, platform subcomplex scaffold subunit Apc15 apc2 | anaphase-promoting complex cullin family subunit Apc2 apc5 | anaphase-promoting complex, platform subcomplex scaffold TPR subunit Apc5 cut20 | anaphase-promoting complex, platform subcomplex scaffold subunit Apc4/Cut20 cut4| anaphase-promoting complex, platform subcomplex scaffold subunit Apc1

especially when the APC and other complexes like this do have dedicated adaptor subunits apc10 | anaphase-promoting complex substrate recognition subunit Apc10

So now I have no way to describe scaffolds.

hdrabkin commented 4 years ago

@Antonialock is there any consensus on this?

ValWood commented 4 years ago

It seems to me that this is not a decision @Antonialock can make, it depends how GO is going to organise these terms. At present the distinction between a scaffold and an adaptor is fuzzy, and the difference is not clear from the definitions.

I would just add the term requested as @Antonialock suggested if you don't want to fix any exiting inconsistencies in the ontology. This is clearly a protein-RNA adaptor however GO structures the definitions.

Antonialock commented 4 years ago

Thanks, yes I don't think anyone is objecting to this term per se.

protein-RNA adaptor activity def: The binding activity of a protein that brings together another protein and an RNA, permitting those molecules to function in a coordinated way. "

Does this sound like it would work for you too @RLovering @vanaukenk ?

pgaudet commented 4 years ago

@hdrabkin I'll take this since I've done most of this branch.

pgaudet commented 4 years ago

+[Term] +id: GO:0140517 +name: protein-RNA adaptor activity +namespace: molecular_function +def: "The binding activity of a protein that brings together another protein and an RNA, permitting those molecules to function in a coordinated way." [PMID:24470144] +is_a: GO:0030674 ! protein-macromolecule adaptor activity +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/19409 xsd:anyURI +created_by: pg +creation_date: 2020-09-11T09:12:05Z

pgaudet commented 4 years ago

I have also updated the definition of 'GO:0030674 protein-macromolecule adaptor activity' to mention 2 or more macromolecules.

pgaudet commented 3 years ago

Not sure why this was left open