PMID:22241993 The cysteine rich necrotrophic effector SnTox1 produced by Stagonospora nodorum triggers susceptibility of wheat lines harboring Snn1.

[CuzickA]

Link to curation session
http://canto.phi-base.org/curs/bd02fdb6831712ca

Stagonospora nodorum is a necrotrophic fungal pathogen producing host selective toxins/necrotrophic effectors.

In virulent/susceptible interaction pathogen SnTox1 interacts with host susceptibility target Wheat Snn1 to promote host necrosis (host programmed cell death, necrotrophs feed on dead matter) and disease. This is effector-triggered susceptibility (in contrast to effector-triggered immunity PCD/HR against biotrophs).

In an avirulent/resistant interaction there is no necrosis/disease.

Links to GO tickets
geneontology/go-ontology#17243

[ValWood]

Actions still to complete for this session

• https://www.uniprot.org/uniprot/A9JX75
  has a name/product update been requested?
  When we do this we should let them know that we are doing the GO curation too.

• submit to Pfam/panther A BlastP search of the NCBI non-redundant database with the SnTox1 protein sequence as a query led to the identification of three putative proteins with unknown functions, one from S. nodorum (SNOG_06487) and two from P. tritici-repentis (PTRT_04748 and PTRT_03544) with similarities of 38%, 56%, and 43%, respectively. The conserved amino acids between SnTox1 and these proteins were mostly distributed in the predicted signal sequence and the N-terminal region of the mature protein (Figure S3)......
  Amino acid alignment with manual adjustment indicated that SnTox1 contained local similarity with cysteine-rich Cladosporium fulvum Avr4-like fungal effectors (Figure 3A) from Cercospora beticola, Mycosphaerella fijiensis [42] and two ascomycete human pathogens, Microsporum gypseum and Geomyces pannorum (this study). These conserved motifs were identified within the chitin-binding domain (ChtBD) including the C-terminal conserved chitin-binding (CB) motif (Figure 3A)....was more similar to those of plant-specific ChtBDs (ChtBD1, or CBM18 superfamily, pfam00187) than to Avr4 proteins, which are related to invertebrate ChtBDs (ChBD2, or the CBM14 superfamily, pfam01607) .....consistent with strong diversifying selection. The 11 protein isoforms involve amino acid changes at eight positions within SnTox1; however, all cysteine residues remain unchanged across all isoforms (Figure 2D).

(I may have already done ths?)

[ValWood]

This is because we are comparing to

Sn2000-Tox1ASn79+SnTox1A3(transformant, no endogenous copy)[Not assayed]Parastagonospora nodorum (Sn79-1087)	Snn1+[Wild type product level]Triticum aestivum (Chinese Spring)

rather than the WT contriol.

but this isn't implicit from the annotation.

This really makes me think we definitey need to implement

#19
I now think we really need to have an additional field for the loss or gain of function phenotypes. We need to capture which genotype we are comparing to otherwise it is too difficult to understand the annotation (sigh). We can chat about this on our next group call?

I have beed adding the [allele] compared to in the sessions I have been checking. Mostly it is the [WT/WT]

I know the the MPO do something similar to this.

[ValWood]

Looks good.

[CuzickA]

After discussion with Kim H-K on 25March2021 regarding my email query above we decided that we could not use a standard (inverse) gene-for-gene AE when the condition altered the outcome (eg heat, light, chemical). The only available options need to be logically correct for a (inverse) gene-for-gene interaction. Therefore the two options we came up with were

1. do not use an (inverse) gene-for-gene interaction - leave field empty, or
2. have a generic AE term available in both inverse GfG and GfG such as 'metagenotype outcome overcome by external condition'

Let's discuss this today @ValWood

[CuzickA]

@ValWood agrees with option 2.

[CuzickA]

was

remove current AE for 2nd and 4th annotation above with condition 'dark'. Obsolete these PHIPO_EXT terms as they are logically incorrect. (incompatible interaction, recognizable pathogen necrotrophic effector present, host susceptibility locus present AND incompatible interaction, gain of recognizable pathogen necrotrophic effector, host susceptibility locus present)

now (waiting for NTR)

was

remove current AE for 2nd annotation with condition 'dark'

now (waiting for NTR)

was

remove current AE for 2nd and 4th annotation with conditions causing shift

now (waiting for NTR)

[CuzickA]

Add new AE term 'metagenotype outcome overcome by external condition' after Easter

[CuzickA]

Added new AE term 'metagenotype outcome overcome by external condition'

Approved session and closing ticket

[CuzickA]

Following up query on incorrect term
inverse_gene_for_gene compatible interaction, compromised recognizable pathogen necrotrophic effector, host susceptibility locus present

Copy of email sent to Kim H-K

Kim H-K agrees with my proposed change.

annotation now updated to

The PHIPO_EXT term will be obsoleted
inverse_gene_for_gene compatible interaction, compromised recognizable pathogen necrotrophic effector, host susceptibility locus present

[CuzickA]

I need to update the 'transformant' genotypes following the new guidance in #157

[CuzickA]

Session now 'unapproved' until 'transformant' genotypes updated.

[CuzickA]

'transformant' genotypes updated. Session approved. Closing ticket.