PAMP-triggered immunity

[ValWood]

PAMP- triggered immunity (PTI) usually first line of defence 
Upon association with PAMPs, the pattern-recognition receptors activate a downstream mitogen-activated protein kinase signaling cascade that culminates in transcriptional activation and generation of the innate immune responses.

For PTI I find . GO:0002221 pattern recognition receptor signaling pathway 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

so NTR could be a child of GO:0002221

NTR PAMP-triggered immunity signalling pathway Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands to activate a plant innate immune response. PAMP-triggered immunity PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species. exact synonym PTI signalling

~I would also be happy for this to be a synonym. BUT I'm a bit concerned about the mention of damage-associated molecular pattern (DAMPs) because these AFAIK are not innate immune response, they are inflammatory response. I really think these should be split.~ the DAMPs are also regulating the immune response via damage detection

Note that I could also use: GO:0035420 MAPK cascade involved in innate immune response (0 annotations) it might be best to get rid of this ?

[ValWood]

Note that GO:0002221 pattern recognition receptor signaling pathway

does not say anything explicityly about "activating" the immune response, but "activation" is a parent.

[ValWood]

NTR PAMP-triggered immunity signalling pathway should also be a descendant of GO:0002220 innate immune response activating cell surface receptor signaling pathway

[pgaudet]

I will remove 'damage-associated molecular pattern (DAMPs)' from all term definitions and synonyms. This is quite a different process in which the organism responds to its own molecules, see https://en.wikipedia.org/wiki/Damage-associated_molecular_pattern

Thanks, Pascale

[addiehl]

Per my comment in #18620, I disagree with changing the definition of GO:0002221. Please do not rely solely on wikipedia for guidance here. PAMPs and DAMPs often bind the same receptors leading to the same downstream processes.

I am happy to have PAMP-triggered immunity signaling pathway added, though again many of these pathways are the same as DAMP-triggered signaling pathways.

[ValWood]

This is a recent summary

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6760519/ Plants detect pathogen attack through the perception of conserved microbial signatures, called microbe-associated molecular patterns (MAMPs) or host-derived damage-associated molecular patterns (DAMPs), thanks to plant plasma membrane pattern recognition receptors (PRRs) (Boutrot and Zipfel, 2017). PRRs are generally receptor-like kinases (RLKs) or receptor-like proteins (RLPs) with an extracellular domain for MAMP/DAMP recognition (Trdá et al., 2015). MAMPs can be microbial structural components such as bacterial flagellin, lipopolysaccharides (LPSs), peptidoglycans (PGNs), rhamnolipids (RLs), fungal chitin, or oomycete β-glucans but also secreted toxins or enzymes like fungal xylanase or endopolygalacturonase (Figure 1). DAMPs are endogenous danger signals, such as oligogalacturonides (OGs) or cutin monomers, released from degraded plant cell wall or cuticle, respectively (Boller and Felix, 2009). The MAMP/DAMP perception triggers a complex cascade of signaling events, including ion fluxes such as Ca2+ influx, the production of reactive oxygen species (ROS) and nitric oxide, and the activation of mitogen-activated protein kinases (MAPKs). These early events induce a massive transcriptional reprogramming of primary and secondary metabolisms. The induction of specific defense-related genes leads to the synthesis of (i) pathogenesis-related (PR) proteins, including hydrolytic enzymes (e.g., β-1,3-glucanases or chitinases), which degrade pathogen cell wall; (ii) antimicrobial compounds like phytoalexins; (iii) compounds involved in cell wall reinforcement; and, in some cases, (iv) proteins involved in the hypersensitive response (HR), a form of programmed host cell death (Garcia-Brugger et al., 2006). Altogether, these defense reactions represent the MAMP-triggered immunity (MTI), which is finely regulated by phytohormones (salicylic acid [SA], jasmonic acid [JA], and ethylene [ET]) to finally prevent or delay pathogen infection, thus ensuring a basal plant resistance to pathogens.

so, we keep DAMP in the term, but this seems to always be related to immunity. It does seem that PRR receptors are always related to immune signalling, so, in this case, they must presumably always be immune receptors ?

I'm trying to find a single term to represent PTI in the common usage of PAMP or MAMP triggered immunity

So you are saying that pattern recognition receptor signaling pathway and PAMP triggered immunity and MAMP triggered immunity and "DAMP triggered immunity" should also be added

are equivalent? and therefore pattern recognition receptor signaling pathway is not broader, is that correct?

[addiehl]

in the ontology of 'AMPs, MAMPs are PAMPs

[addiehl]

I suspect plant (and animal) DAMPs get produced via mechanical injury (wounding) as well, producing the responses in plants mentioned above and inflammatory and wound healing responses in animals. Whether these responses are immune responses somewhat stretches the general concept of immunity, but they are certainly defensive in the sense of trying to both repair the organism and be ready for pathogen entrance via the injury. In reality, bacteria of some types are probably all over the surface of plants and animals and may act as potential pathogens if they gain access to the internal regions.

[ValWood]

here,

• [x] we need to revert to the original def for

GO:0002221 pattern recognition receptor signaling pathway 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

which refers to DAMPs

• [x] add NTR PAMP-triggered immunity signalling pathway Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands to activate a plant innate immune response. PAMP-triggered immunity PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species. exact synonym PTI signalling exact MAMP-triggered immunity signalling

• [x] NTR PAMP-triggered immunity signalling pathway needs parents top BOTH GO:0002221 AND GO:0002758 innate immune response-activating signal transduction ( the immune activation in response to a pathogen is the essence of what we are trying to capture)

• [x] Note that GO:0002221 pattern recognition receptor signaling pathway will not be able to have GO:0002758 innate immune response-activating signal transduction as a parent because @addiehl points out that PRR includes DAMPs activating signalling and this may, or may not, be related to immune response signalling

I think that will resolve @addiehl is that OK?

[ValWood]

It might not be quite optimal as some damage/DAMPs will activate immune response , but when we come across that I think we can add DAMps to the "immune signalling term".

[addiehl]

This sounds good to me.

[ValWood]

@pgaudet I think we. should to this becasue the plant reannotation for "resistance -gene independence" will require this new immune process linked PRR signalling term

[pgaudet]

[Term] id: GO:0140426 name: PAMP-triggered immunity signalling pathway namespace: biological_process def: "Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands to activate a plant innate immune response. PAMP-triggered immunity PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species." [PMID:25744358] comment: Created new term, see https://github.com/geneontology/go-ontology/issues/18588. synonym: "MAMP-triggered immunity signalling" EXACT [] synonym: "pathogen-associated molecular pattern signalling" EXACT [] synonym: "PTI signalling" EXACT [] is_a: GO:0002221 ! pattern recognition receptor signaling pathway is_a: GO:0002758 ! innate immune response-activating signal transduction created_by: pg creation_date: 2020-02-11T11:08:57Z