Open ValWood opened 4 years ago
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
@hattrill how does this compare with PTI in flys. We also need to get mammalian input too?
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)
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.
@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
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 |
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 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!
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