#107 interleukin receptors

[Melanie Courtot]

Hi,

A request for update to interleukins came through the GO tracker at https://github.com/geneontology/go-ontology/issues/12375
Specifically:

• update definition of IL receptors to say "A protein complex that consists of, at a minimum, a dimeric interleukin and its two receptor subunits."
• update definition of IL12R and IL23R to add "[...] as well as optional additional kinase subunits."
• add link ILRs part_of GO:0005887 integral component of plasma membrane.
• in addition to potentially create a "cytokine complex" grouping term.

Cheers,
Melanie

[Birgit Meldal]

Actually, delete 'optional' as in these specific receptors they are required, and add specific kinases:

• update definition of IL12R and IL23R: "A protein complex that consists of a dimeric interleukin, its two receptor subunits and additional JAK2 & TYK2 kinase subunits."

Should the 'cytokine complex' term be created in PRO or GO??? I can do it through TG templates (we already have GO:0005125 cytokine activity).

Birgit

[Darren Natale]

Hi Melanie and Birgit,

Can you clarify the request? Are you asking for these complexes in a specific organism? At the moment, we do not have terms for these receptor-ligand complexes, only the receptor components, so there is nothing to "update" in PRO. I can see that the complexes you speak of are GO terms, however. Take a look at the following link to an Amigo search. After the page loads, drop down the ontology source, then click the "-" to remove everything except cellular component terms.

http://amigo.geneontology.org/amigo/search/ontology?q=interleukin+receptor

You'll see 18 results. Fifteen are from GO and 3 are from PRO. One of the PRO terms is "interleukin-23 receptor" (PR:000009001) which, along with "interleukin-12 receptor subunit beta-1" (PR:000001367) forms the receptor itself. Based on Birgit's last revision to this ticket, the full receptor complex is "interleukin-23 receptor complex" (GO:0072536, also shown in the search result) that would have the following components:

PR:000009001 interleukin-23 receptor
PR:000001367 interleukin-12 receptor subunit beta-1
PR:000009197 tyrosine-protein kinase JAK2
PR:000016874 non-receptor tyrosine-protein kinase TYK2
GO:0070743 interleukin-23 complex

Note the unfortunate naming of TYK2 (which comes from UniProtKB). The last component, interleukin-23 complex, is made up of:

PR:000001384 interleukin-23 subunit alpha
PR:000001369 interleukin-12 subunit beta

For "interleukin-12 receptor complex" (GO:0042022) the components would be the same, except replace "interleukin-23 receptor" with "interleukin-12 receptor subunit beta-2" (PR:000008980) and replace "interleukin-23 complex" with "interleukin-12 complex" (GO:0043514). That latter complex is similar to the interleukin-23 complex except the alpha subunit is "interleukin-12 subunit alpha" (PR:000001368).

It thus seems to me that the revisions originally requested do indeed need to be made in GO. If species-specific terms are needed for any of these, I'll be glad to supply them.

Best regards,
Darren

[Birgit Meldal]

My request is definitiely species agnostic (applies at least to human and mouse which I curated) and I thought it was the GO terms that needed updating... Over to Melanie.