pattern recognition receptor signaling pathway - NTR and reorganization

[pgaudet]

Hello,

This comes from the SIB-Virus group @pmasson55 and Chantal

1. pattern recognition receptor signaling pathway GO:0002221

Add as childen of GO:0002221:

• [x] 1.1 Create GO: endolysosomal pattern recognition receptor signaling pathway

1.1.1 Create GO: endolysosomal toll-like receptor signaling pathways

• [x] moved terms under the new term

1.1.1.1 GO:0034138 toll-like receptor 3 signaling pathway 1.1.1.2 GO:0034154 toll-like receptor 7 signaling pathway
1.1.1.3 GO:0034158 toll-like receptor 8 signaling pathway 1.1.1.4 GO:0034162 toll-like receptor 9 signaling pathway 1.1.1.5 GO:0034170 toll-like receptor 11 signaling pathway 1.1.1.6 GO:0034174 toll-like receptor 12 signaling pathway 1.1.1.7 GO:0034178 toll-like receptor 13 signaling pathway -> endolysosomal DNA, rRNA, ssRNA sensors

1.2. GO:0002753: cytosolic pattern recognition receptor signaling pathway

1.2.1 GO:0039529: RIG-I signaling pathway -> cytosolic ssRNA and dsRNA sensor

• [x] added ssRNA and dsRNA in definition

1.2.2 GO:0039530: MDA-5 signaling pathway -> cytosolic dsRNA sensor

• [x] added dsRNA in definition 1.2.3 GO:0039585: PKR signal transduction -> cytosolic dsRNA sensor

• [x] dsRNA was already in in definition

• [x] 1.2.4 Create GO: cGAS/STING pathway

-> cytosolic DNA sensor

1.3 GO:0002752: cell surface pattern recognition receptor signaling pathway

• [x] 1.3.1 Create GO: cell surface toll-like receptor signaling pathway

1.3.1.1 GO:0034130 toll-like receptor 1 signaling pathway 1.3.1.2 GO:0034134 toll-like receptor 2 signaling pathway 1.3.1.3 GO:0034142 toll-like receptor 4 signaling pathway 1.3.1.4 GO:0034146 toll-like receptor 5 signaling pathway 1.3.1.5 GO:0034150 toll-like receptor 6 signaling pathway 1.3.1.6 GO:0034166 toll-like receptor 10 signaling pathway 1.3.1.7 GO:0035681 toll-like receptor 15 signaling pathway -> lipopeptides, dsRNA, ssRNA, LPS, flagellin sensors

GO:0002754 toll-like receptor signaling pathway will have both children “endolysosomal toll-like receptor signaling pathways” and “cell surface toll-like receptor signaling pathways”

Decide if we keep
GO:0039528 cytoplasmic pattern recognition receptor signaling pathway in response to virus The other PRR signaling pathways (membrane, endolysosomal) do not have this granularity

List of terms negative/positive regulation:

Negative/positive regulation of endolysosomal pattern recognition receptor signaling pathway Negative/positive regulation cytosolic pattern recognition receptor signaling pathway

Negative/positive regulation cell surface pattern recognition receptor signaling pathway

Liu, Xing & Wang, Qiang & Chen, Wei & Wang, Chen. (2013). Dynamic regulation of innate immunity by ubiquitin and ubiquitin-like proteins. Cytokine & growth factor reviews. 24. 10.1016/j.cytogfr.2013.07.002.

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Any comments/suggestions ?

Thanks, Pascale

[tberardini]

• [x] I'd like to request a synonym to be added to GO:0002221 pattern recognition receptor signaling pathway. I can open another ticket, if you like.

Current synonyms: PAMP receptor signaling pathway, PRR signaling pathway, pathogen receptor signaling pathway, pathogen receptor signalling pathway

Add synonym (same range as PAMP receptor signaling pathway): pathogen-associated molecular pattern receptor signaling pathway

Thanks.

[SIBvirus]

following

[ValWood]

sounds good. can this be aligned with this too https://github.com/geneontology/go-ontology/issues/16616

[ValWood]

and https://github.com/geneontology/go-ontology/issues/16615

[ValWood]

and https://github.com/geneontology/go-ontology/issues/16672

[pgaudet]

• [x] GO:0039528 cytoplasmic pattern recognition receptor signaling pathway in response to virus -> merge into parent GO:0002753 cytoplasmic pattern recognition receptor signaling pathway (these signaling pathways are not specific to viruses); RIG-I responds to fungi (PMID: 25579795), as does MDA-5 (PMID: 33087405) ; and possibly other organisms
• all IEA annotations are from Ensembl
• [x] add is_a: GO:0002758 innate immune response-activating signaling pathway

@marcfeuermann

[pgaudet]

Updated definitions to widen the range of organisms that trigger these signaling pathways:

• [x] GO:0002753 cytoplasmic pattern recognition receptor signaling pathway -def: "The series of molecular signals initiated by a ligand binding to a cytoplasmic pattern recognition receptor ( PRR). PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [GOC:a dd, GOC:ar, ISBN:0781735149, PMID:15199967] +def: "The series of molecular signals initiated by the binding of a ligand from another organism to a cytoplasmic p attern recognition receptor (PRR). PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved amo ng microbial species." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967, PMID:17328678, PMID:18272355, PMID:19531363, PMID:21187438]

• [x] GO:0039529 RIG-I signaling pathway -def: "The series of molecular signals initiated by the binding of viral RNA to a pattern recognition receptor (PRR) RIG-1 (also known as DDX58). RIG-I is a cytoplasmic receptor that detects RNA synthesized during viral replication and triggers a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines." [GOC:bf, PMID:17328678, PMID:19620789, PMID:21435580] -comment: The apoptosis effect triggered by the RIG-I signaling pathway is inconclusive and may represent an in-vitro phenomenon. Therefore, in GO the term 'RIG-I signaling pathway ; GO:0039529' is positioned under 'regulation of cytokine production' as this is its primary effect. +def: "The series of molecular signals initiated by the binding of a ligand from another organism to the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58). RIG-I detects RNA synthesized during viral replication or shed by non-viral pathogens, and triggers a signaling pathway to protect the host against infection, for example by inducing the expression of cytokines." [GOC:bf, PMID:17328678, PMID:19620789,

• [x] GO:0039530 MDA-5 signaling pathway -def: "The series of molecular signals initiated by viral RNA binding of a cytoplasmic pattern recognition receptor (PRR) MDA-5 (also known as IFIH1). MDA-5 is a cytoplasmic receptor that detects RNA synthesized during viral replication and triggers a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines." [GOC:bf, PMID:19620789] +def: "The series of molecular signals initiated by the binding of a ligand from another organism to the cytoplasmic pattern recognition receptor (PRR) MDA-5 (also known as IFIH1). MDA-5 detects RNA synthesized during viral replication or shed by non-viral pathogens, and triggers a signaling pathway to protect the host against infection, for example by inducing the expression of cytokines." [GOC:bf, PMID:19620789, PMID:33087405]

[pgaudet]

• [x] Change label GO:0140426

-name: PAMP-triggered immunity signalling pathway +name: pathogen-associated molecular pattern receptor signaling pathway

to make is closer to the parent class 'pattern recognition receptor signaling pathway' (no acronym)

[pgaudet]

Fixed labels

• [x] GO:0002757 immune response-activating signal transduction -> immune response-activating signaling pathway
• [x] GO:0002758 innate immune response-activating signal transduction -> innate immune response-activating signaling pathway

[pgaudet]

+[Term] +id: GO:0140894 +name: endolysosomal toll-like receptor signaling pathway +namespace: biological_process +def: "The series of molecular signals initiated by a ligand binding to an endolysosomal pattern recognition recepto r (PRR) of the toll-like family. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [PMID:29679565] +synonym: "endolysosomal pattern recognition receptor signaling pathway" EXACT [] +is_a: GO:0002221 ! pattern recognition receptor signaling pathway +is_a: GO:0030522 ! intracellular receptor signaling pathway +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/17080 xsd:anyURI +created_by: pg +creation_date: 2022-07-22T12:48:12Z + +[Term] +id: GO:0140895 +name: cell surface toll-like receptor signaling pathway +namespace: biological_process +def: "The series of molecular signals initiated by a ligand binding to a cell surface pattern recognition receptor (PRR) of the toll-like family." [GOC:add, GOC:ar, ISBN:0781735149, PMID:15199967] +synonym: "cell surface PAMP receptor signaling pathway" EXACT [] +synonym: "cell surface pathogen receptor signaling pathway" EXACT [] +synonym: "cell surface pattern recognition receptor signalling pathway" EXACT [] +synonym: "cell surface PRR signaling pathway" EXACT [] +is_a: GO:0002220 ! innate immune response activating cell surface receptor signaling pathway +is_a: GO:0002752 ! cell surface pattern recognition receptor signaling pathway +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/18588 xsd:anyURI +created_by: pg +creation_date: 2022-07-22T13:13:17Z

[pgaudet]

+[Term] +id: GO:0140896 +name: cGAS/STING signaling pathway +namespace: biological_process +def: "The series of molecular signals initiated by the binding of a DNA from another organism to cytosolic cyclic GMP-AMP (cGAMP) synthase (cGAS) that activates innate immune responses through production of the second messenger cGAMP, which activates the adaptor STING." [PMID:27648547] +is_a: GO:0002753 ! cytosolic pattern recognition receptor signaling pathway +property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/17080 xsd:anyURI +created_by: pg +creation_date: 2022-07-22T13:43:11Z

@sylvainpoux maybe you'd like to use this term?

[sylvainpoux]

Hi Pascale,

thanks, I will clearly use this term! On the down side, I will have to completely update the cGAS-STING pathway in Noctua when the term is public.

A naive question: is the term related to inflammation process? Because the cGAS-STING pathway is really the master of inflammation

Thanks

Sylvain

[pgaudet]

Ha! great question. Right now it's under 'innate immune response-activating signaling pathway'; I guess this is not correct?

I can move it under inflammatory response (we dont have an inflammatory response signaling grouping term, maybe we need that?)

Thanks, Pascale

[sylvainpoux]

"innate immune response-activating signaling pathway" is correct, actually it is at the crossroad of both processes. I think it is ok then Thanks Sylvain

[pgaudet]

OK, so you'll need to annotate inflammatory response separately.

[pgaudet]

During these edits I had changed the label of GO:0002753 cytoplasmic pattern recognition receptor signaling pathway to cytosolic pattern recognition receptor signaling pathway, but this was not right, since some children are not cytoplasmic ('endosomal pattern recognition receptor signaling pathway', 'endolysosomal toll-like receptor signaling pathway'), and the literature uses "cytoplasmic".

@marcfeuermann @thomaspd

Thanks, Pascale