PMID: 30148881 Structure of the Cladosporium fulvum Avr4 effector in complex with (GlcNAc)6 reveals the ligand-binding mechanism and uncouples its intrinsic function from recognition by the Cf-4 resistance protein.

[CuzickA]

https://canto.phi-base.org/curs/6dd9062354648dc7

[CuzickA]

To maximise the data here and let people know that this is a gene-for-gene interaction I think we should capture Cf-4.
on page 16 there is info that the plant strain/cv 'moneymaker' does not carry cf-4, whilst strain/cv 'purdue 135 does carry functional cf-4.

[ValWood]

To maximise the data here and let people know that this is a gene-for-gene interaction I think we should capture Cf-4.
on page 16 there is info that the plant strain/cv 'moneymaker' does not carry cf-4, whilst strain/cv 'purdue 135 does carry functional cf-4.

This is a good point. However, I wonder if users will do this automatically. It's a weird one. Its bringing in knowledge from a previous paper, which is not included in the experiment. I don't have a problem with this per. se. if this is what the authors are intending to demonstrate, but from this paper who is to say that cf4 presence-absence in these strains is responsible for the difference. This could be correlation, not causation?

[CuzickA]

3. I also have a query about the GfG AE used
   image see above
   Do they look correct?
   In the 3rd annotation here perhaps it should be 'compatible interaction, compromised recognizable pathogen effector, functional host resistance gene present' instead of 'compatible interaction, recognizable pathogen effector absent, functional host resistance gene present' as the pathogen effector has been altered (engineered variant).

I have now updated to below

[CuzickA]

This session still needs

1. NTR: compatible interaction, compromised recognizable pathogen effector, functional host resistance gene present

2. Discuss query on which GfG AE to use when an alteration to a gene causes a partial phenotype shift. eg
   
   or no phenotype shift eg
   
   Are we happy with the GfG AE that I have used in both of these cases?

[CuzickA]

See notes at bottom of this document
section subheading 'Draft GfG Rules (10_02_2021)'
https://docs.google.com/document/d/1Nm5yAHMwFYfhjRWuatlGA4_X2aSK9l12QQI1ffQXFqs/edit

[CuzickA]

waiting for

1. NTR: compatible interaction, compromised recognizable pathogen effector, functional host resistance gene present
2. Emailed Kim H-K about first part of query above ( partial shift in phenotype) (may need to follow up with no shift query)

[CuzickA]

Added NTR: compatible interaction, compromised recognizable pathogen effector, functional host resistance gene present

Waiting for response from Kim H-K to email about above.

Approving session for now but will keep ticket open with tag 'AE 'GeneforGene' query'
regarding 'partial shift in phenotype'

[CuzickA]

After discussion with Kim H-K on 25March2021 regarding my email query above we decided that my suggested annotations were correct.
Closing this ticket.

[CuzickA]

and update PHIPO terms -see google doc for notes

[CuzickA]

Hi @ValWood I've just seen this and it looks like there is no host involved in this paper so we probably need to leave the Trichoderma annotations where they are in the singles species section. Maybe we should add '+ chitinase' to the conditions. These single species PHIPO terms will also still need some work.

I am still going to make the NTRs we have just discussed for the chitin hydrolysis for the LysM1 paper as this DOES mention a host and needs to be annotated as a metagenotype.

[CuzickA]

@jseager7 please could you check which sessions these terms have been used in

PHIPO:0001225 abolished PAMP receptor decoy activity
PHIPO:0001224 decreased PAMP receptor decoy activity

[jseager7]

@CuzickA Here's the sessions:

• PHIPO:0001225 'abolished PAMP receptor decoy activity'
  • PMID:30148881
• PHIPO:0001224 'decreased PAMP receptor decoy activity'
  • PMID:30148881

[CuzickA]

Great, thanks

[CuzickA]

Fig S7

abolished PAMP receptor decoy activity -> chitin hydrolysis present

decreased PAMP receptor decoy activity -> increased chitin hydrolysis present @ValWood is this correct? (increased compared to 'chitin hydrolysis absent' WT but we don't curate controls for single species genotypes)

[ValWood]

I guess we could add a WT genotype, and then add compared to WT here, without specifically making the control annotation? I think the control annotation would be overkill.

[CuzickA]

I have added this WT control annotation (look at term suggestion) to make thinks clearer for this expt. There is no AE compared to control option for the single species annotations but I think this is okay.

I will now go ahead and make/edit the single species PHIPO terms PHI-base/phipo#336

[CuzickA]

Terms added

session approved, closing ticket