synonyms and readouts/ responses for PTI signalling

[ValWood]

We found the PTI signalling term yesterday, hooray!

so when this is done: https://github.com/geneontology/go-ontology/issues/18033

please add synonyms to GO:0002221 pattern recognition receptor signalling pathway

Pathogen triggered immunity signalling PAMP triggered immunity signalling PTI signalling

this definition probably has a problem: Definition (GO:0002221 GONUTS page) Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species, or damage-associated molecular pattern (DAMPs), endogenous molecules released from damaged cells. PMID:15199967

That the processes for PAMPS and DAMPS appear to be different. We need to find out oif these are the same processes/pathway

DAMP are damage-associate receptors that trigger an inflamatory response so should not be in this term DAMPs include things like host-produced heat-shock proteins

The PTI trigged immunity pathway has MAP kinase signalling Is a innate immune response is a local response

Other features of plant PTI (are any of these true for any other species that use this term?)

• Involved in "FIRST LAYER OF DEFENSE" (need ref)

• Activates RoS (which in plants triggers deposition of lignin and callose to thicken cell walls). Here we would make a concurrent annotation to "positive regulation of callose deposition" or some appropriate term.

• expression of PTI-related pathogen resistance (PR) genes

[ValWood]

This term might be problematic longer term- we probably need different flavors for animals and plants. Here the term is very non-specific for a process (it is describing any type of signalling activated by a PRR receptor, and so is no different from any "immune response signalling".

It would be good to get a common differentia on this term. QUESTION Do they always signal through MAP kinase pathways?

This is a very nice summary of the pathway in plants https://www.sciencedirect.com/science/article/pii/S1674205215000878#fig1

[ValWood]

@hattrill how does this compare with PTI in flys. We also need to get mammalian input too?

[hattrill]

So, we would just class this as an innate immune response and might use the type of pathogen it's against e.g. antifungal innate immune response

We then co-annotate to indicate which pathway is involved - for flies, this is primarily via the NF-kappaB pathways (PMID:20485470): Toll signaling pathway peptidoglycan recognition protein signaling pathway (known as Imd pathway)

[hattrill]

the 'peptidoglycan recognition protein signaling pathway' GO:0061057 could come under GO:0002221 pattern recognition receptor signalling pathway (mainly it's a cell surface pattern recognition receptor signaling pathway GO:0002752 but can also get activated by an intracellular PRR, I think). The 'Toll signaling pathway' in flies is also a developmental pathway, so not so easy.

[pgaudet]

@hattrill I suppose the immune vs developmental Toll pathways must be different pathways - possibly even triggered by different stimuli ? Should we not distinguish those with 2 separate terms ?

Pascale

[ValWood]

the term

'peptidoglycan recognition protein signaling pathway' seems very general but it's quite a specific defense response pathway? Would one of the exact synonyms which mentions "immune signaling" make a better primary term name?

Imd signalling pathway	exact
immune deficiency pathway	related
Imd signaling pathway	exact
PGRP signaling pathway	related
immune deficiency signaling pathway	related

[hattrill]

Yes, it is...... 'Imd signaling pathway' would be the most frequently used in the literature, followed by 'immune deficiency pathway' (practically never 'peptidoglycan recognition protein signaling pathway' - as you say, it is sounds very general, could be mistaken for any pathway with a PGRP-activated receptor) - a name change would be appreciated. The def refers specifically to Imd: "A series of molecular signals initiated by binding of peptidoglycan to a receptor on the surface of the target cell and ending with regulation of a downstream cellular process. The main outcome of the Imd signaling is the production of antimicrobial peptides."

[hattrill]

@hattrill I suppose the immune vs developmental Toll pathways must be different pathways - possibly even triggered by different stimuli ? Should we not distinguish those with 2 separate terms ?

Pascale

Yes, I have had similar thoughts (this is about to have its birthday: #16672 but I might have to go and remind myself about them!