PMID:29567712 A single fungal MAP kinase controls plant cell-to-cell invasion by the rice blast fungus.

[CuzickA]

curation link https://canto.phi-base.org/curs/0d2bc8d23a8667f4

A past session to look over and check through

[CuzickA]

For checking please @ValWood

[ValWood]

GO terms I removed GO:0044001 | migration in host because this term is for directed movement (like along actin cables) It isn't totally wrong but I think pentration covers what we are looking at.

also removing GO:0075053 | formation of symbiont penetration peg for entry into host in favour of the appressorium term

[ValWood]

Also removing

GO:0052542 | defense response by callose deposition from the pathogen MAPK (this is a host process, but we don't have a gene to attach the annotation to)

[ValWood]

I will put migration in host back, but I think GO should have a term "cell to cell migration"

[ValWood]

QUESTION

I'm confused by these 2 annotations. I looked at the supp data and I could not figure out which strains I was looking at, but other similar metagenotypes/conditions are reduced pathogenicity so I can't figure out what it is here that makes the "pathogenicity unaffected"

pmk1-AS(aaQ104G)[Not assayed]Magnaporthe oryzae (Guy11)	wild typeOryza sativa (CO-39)	PHIPO:0001003	normal formation of extra-invasive hyphal membrane	Microscopy	+ 1-Na-PP1, 26hpi		Fig S6a	infects_tissue leaf , infective_ability unaffected pathogenicity	Alayne Cuzick alayne.cuzick@rothamsted.ac.uk	EditCopy and editDelete Clear
pmk1-AS(aaQ104G)[Not assayed]Magnaporthe oryzae (Guy11)	wild typeOryza sativa (CO-39)	PHIPO:0001004	normal pathogen morphology during colonization of host	Microscopy	+ 1-Na-PP1, 26hpi	Normal morphology of invasive hyphae View definition	Fig S6a	infects_tissue leaf , infective_ability unaffected pathogenicity	Alayne Cuzick alayne.cuzick@rothamsted.ac.uk

[ValWood]

PHIPO:0000990 | absent expression of a pathogen gene product involved in host interaction

I changed to absent expression of a pathogen gene product involved in host interaction

but, this has the child term absent expression of a pathogen gene product involved in host interaction Do we need this? I will open a ticket on the FYPO tracker. Can it merge into the parent?

[CuzickA]

QUESTION

I'm confused by these 2 annotations.

I was a bit unsure how to annotate these. The difference is in the timing of the mutation activation. For Fig 2ab the mutant is activated by +1NA-PP1 after pathogen has made appressorium and invaded the first epidermal cell. Therefore the pathogen penetration prior to addition of 1NA-PP1 was present. Actually maybe this annotation is not correct? To discuss. The main phenotype is the abolished cell to cell movement. (although it is important to document that the pathogen was able to get inside the host, otherwise it would not be present for the cell to cell movement!)

In this annotation Text from paper 'Pmk1 inactivation did not affect the structure of BICs or the morphology of invasive hyphae (fig. S6A).' Again the main phenotype here is the lack of cell to cell movement

I think I was trying to capture 'unaffected pathogencitiy' at the earlier time points and 'loss of pathogenicity/reduced virulence' at the later stage of infection due to the lack of pathogen cell to cell movement. We can discuss this further.

[ValWood]

Yes let's discuss. I thought titwas related to the timing. We can think about how best to make this clear.

[CuzickA]

I will put migration in host back, but I think GO should have a term "cell to cell migration"

@ValWood Do you still think we need this GO term? Has it been requested?

[CuzickA]

I have added the 'cell-to-cell migration in host' GO term

A couple of things here still to discuss before this session can be approved @ValWood

[CuzickA]

I have moved a few queries out of the term suggestion column into the comments. I have done this so that the session can be approved and exported as a batch of data for MC to visualise. We can go back into the session and make edits in the future if required. Also closing ticket for now.

[CuzickA]

Have added Figure info. Will continue updating this session after half term.

[CuzickA]

Tricky to add AE disease present/absent in some annotations.

RNA level query to discuss

Added Disease curation type.

Still working though and adding in control metagenotypes (next Figure S12 in order of sorted Figures)

[CuzickA]

Finished adding control metagenotypes.

Queries left for this session

1) Tricky to add AE disease present/absent in some annotations. 2) RNA level query to discuss

3) Timing query as reported above

Below annotations not very clear why phenotypes are so different

[CuzickA]

RNA levels not look like this

[CuzickA]

Deleting these annotations (They are not very helpful and rather confusing. The inactive mutant can penetrate host prior to addition of + 1-Na-PP1).

[CuzickA]

Still need to continue checking this one

[CuzickA]

I have removed condition '+ 1-Na-PP1' from the controls. I have noted noted in the comment that WT control is equivalent to 'pmk1-AS(aaQ104G) without 1-Na-PP1' The main comparisons are therefore WT vs activated pmk1 mutant

@ValWood please could you have a quick check through of this session to make sure it all looks reasonable!

[CuzickA]

I am trying to add additional pathogen alleles with the background Sep5-GFP but am unable to in PHI-Canto, as the non-GFP alleles already exist. Is this correct or a bug?

[mah11]

Hi @CuzickA,

I am trying to add additional pathogen alleles with the background Sep5-GFP but am unable to in PHI-Canto, as the non-GFP alleles already exist. Is this correct or a bug?

It's likely that you've run into the known issue described here.

Could you try the workaround described in the second part of that comment? If it doesn't work, that's a bug. If it does work, it's not exactly a bug because everything is behaving as it has for ages; it's a shortcoming of the Canto interface that we know about but haven't figured out how to improve yet.

[CuzickA]

Thanks @mah11

Used the workaround

[ValWood]

I checked this one too. There are a couple of comments about the GO terms (in the session). Also, I still don't fully understand the difference between the hyphal and pseudohyphal terms and when they should be used/.

[CuzickA]

Yes, its not always clear. Here is what Google says

[CuzickA]

Hmmm this was an old annotation. Good spot @ValWood !

It wasn't a pmk1 localization study, I think I was trying to capture that the whole WT pathogen was present in the host cell plasmodesma and hyphal membrane (biotrophic interfacial complex (BIC)).

I'll delete these annotations.

[CuzickA]

I think this session is just waiting for the new GO term https://github.com/geneontology/go-ontology/issues/21125

I will approve it for now and the term can be updated when available.

[ValWood]

I just made another note in the appressorium annotation . It occurred to me overnight! Could you check this too?

[CuzickA]

Just seen this comment, I think it is correct

The text in the introduction states the following "To study regulatory mechanisms controlling invasive growth, we characterized Pmk1, a fungal mitogen-activated protein kinase (MAPK) essential for appressorium development and pathogenicity that is conserved in many plant-pathogenic fungi (15). Pmk1 null mutants of M. oryzae cannot infect rice plants even when mutants are inoculated onto wounded leaves (15). We decided to conditionally inactivate the Pmk1 MAPK using a chemical genetic approach"

"Addition of 1NA-PP1 selectively inhibited the function of Pmk1AS mutants, preventing appressorium development (fig. S4),"

[ValWood]

Yes I forgot that part. Last night I was wondering how it got into the first cell if it could not make the appressorium. OK ignore!

[CuzickA]

No problem, always worth checking.

Session now approved.

[CuzickA]

GO term now updated, closing ticket

[jseager7]

@CuzickA I think there's an unused gene in this session: I can't find MPS1 (G4N374) in any annotations.

[CuzickA]

Deleting MPS1 (G4N374) as I don't think its required for this session. _(Looks like this didn't happen. I have now deleted MPS1 16_122022)

Updating the second annotation to a metagenotype with a different host strain/cultivar

Now looks like this

Re-approving session.