signaling pattern recognition receptor activity disambiguation and true path violations

[ValWood]

defined GO:0008329 signaling pattern recognition receptor activity Combining with a pathogen-associated molecular pattern (PAMP), a structure conserved among microbial species, or damage-associated molecular pattern (DAMP), an endogenous molecule released from damaged cells), and transmitting a signal to initiate a change in cell activity.

this is clearly the term for a PAMP receptor, when a host receptor binds to a pathogen cell surface molecule called a PAMP

However, it has children that are NOT specific to PAMPs lipoarabinomannan receptor activity
lipopolysaccharide receptor activity
lipoteichoic acid receptor activity
peptidoglycan receptor activity
polysaccharide receptor activity

or at least not defined as being specific for PAMPS....

[ValWood]

Suggest, in addition to fixing the descendants, renaming this "pathogen-associated molecular pattern receptor activity" so that it cannot be misused.

[ukemi]

@addiehl Could you have a look at this one too? Thanks!!

[addiehl]

will do

[ValWood]

Thanks Alex, no hurry for this. I'd also be interested whether you know about the location of these. According to this plant paper, PMID:20601497

I think that the pathogenic fungi that is recognised by the "pattern recognition receptor" is recognising the cell surface of the pathogen (a fungi) , but it is inside the host (plant leaf cell). I don't think it's a cell surface receptor but I could be wrong.....

[hattrill]

Agree with @ValWood suggestion of renaming/defining term to "pathogen-associated molecular pattern receptor activity". We have also been looking at the pattern recognition pathway process terms, which we think could do with some revision along the same lines, and some rewiring. We are thinking about them wrt to Drosophila - which I need to discuss with the rest of our group next week.

[hattrill]

See you've openned a discussion on pathways here #16615

[ValWood]

Yes, I got a bit lost down there to be honest, it isn't very consistent with how we are supposed to annotate pathways. You could describe everything in about 20 different ways!

[hattrill]

Having second thoughts: if this were renamed to "pathogen-associated molecular pattern receptor activity", we would be excluding the DAMPs, that are included as activating ligands for pattern recognition receptors.

[ValWood]

Good point. Any suggestions?

I worry about "molecular pattern recognition receptor" because "molecular pattern" is a bit vague (although I guess this could be covered in the def?).

Or, separate DAMP and PAMP receptors?

Or just use "signalling receptor activity"

Since the type will become obvious from "has_input" and part_of connection to the process.

[ValWood]

@ukemi @pgaudet thoughts how best to do this?

[hattrill]

Perhaps it would be good to separate out PAMPs and DAMPs - think that it would be a shame to lose them from the GO, as there is a lot of interest in these types of activities wrt disease. For DAMPs, the has_input won't make it obvious as these can be things like mtDNA fragments.

[deustp01]

Listening to immunologist colleagues talk, I get the impression that the "molecular pattern" terminology arises because they want their own distinctive way of describing the behavior of a receptor (TOLL or other) with a broad and incompletely described specificity for ligands. And the DAMP - PAMP distinction is at least in part a way of specifying what the ultimate result of receptor activation will be: innate responses to set off a full immune reaction to a pathogen, or innate responses that lead to autoimmunity. At the level of describing the molecular details of a receptor:ligand interaction, this distinction may be out of scope. But a real cellular immunologist should jump in here; I'm out of date and guessing to fill in gaps. You might ask Ludovic.Desvignes@nyulangone.org .

[ValWood]

That's a nice summary of expectations.

Maybe we should do this by

signalling receptor activity part_of GO:0080185 effector dependent induction by symbiont of host immune response (or whatever).

I'm happy to go either way.....

[ValWood]

Note that GO:0038187 is not currently positioned under "innate immune receptor"

[ValWood]

out of date