PMID:28720735 A Nonredundant Phosphopantetheinyl Transferase, PptA, Is a Novel Antifungal Target That Directs Secondary Metabolite, Siderophore, and Lysine Biosynthesis in Aspergillus fumigatus and Is Critical for Pathogenicity.

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PMID:28720735 A Nonredundant Phosphopantetheinyl Transferase, PptA, Is a Novel Antifungal Target That Directs Secondary Metabolite, Siderophore, and Lysine Biosynthesis in Aspergillus fumigatus and Is Critical for Pathogenicity. #36

Closed CuzickA closed 3 years ago

CuzickA commented 5 years ago

curation link https://canto.phi-base.org/curs/326646a152a66e68

CuzickA commented 5 years ago

Note: UniProt use teleomorph name Neosartorya fumigata (and anamorph synonym) whereas NCBI taxonomy use anamorph name Aspergillus fumigatus (most commonly used).

ValWood commented 5 years ago

DO UniProt consistently use the telomorph name? (I forgot).

In this case, I suspect that it will seem strange to curators to see the telomorph name. Could we maintain a 'preferred species name" in the master species file?

CuzickA commented 5 years ago

DO UniProt consistently use the telomorph name? (I forgot).

Me too! I just looked up Marc's email and UniProt use the teleomorph name.

The PHI-Canto config file for pathogen species already displays our preferred 'Aspergillus fumigatus' in PHI-Canto.

CuzickA commented 5 years ago

Another one here for you to check through when you have time @ValWood

ValWood commented 5 years ago

commented in wrong ticket

ValWood commented 5 years ago

I checked this one. I tweaked the GO annotation. It was correct but using "author intent" I made some of the GO annotations IMP instead of TAS. The experiments support these MF & BP.

Everything else looked fine

My only comment is that as we were discussing, the important points (loss of pathogenicity and unaffected pathogenicity) might get a bit lost in the detail.

CuzickA commented 4 years ago

This session is waiting for 3 new condition terms prior to approval.

For longer term review these annotations need 'compared to X' and a review of the AE infective ability for these annotations

CuzickA commented 4 years ago

Conditions added. Session approved for now so closing this ticket. Still needs 'compared to X' and a review of the AE infective ability in the future.

CuzickA commented 3 years ago

Manually updated 'assayed_using' AE by hooking up to UniProts.

Added Figure#s to Figure Column.

Might need new condition for '+ TAFC siderophore' (triacetylfusarinine C). Maybe this could be '+ siderophore' with 'TAFC' as related synonym?

CuzickA commented 3 years ago

@ValWood Another question about 'RNA level' curation

I need to re-annoate this session with all the WT metagenotype controls. Does it make sense to create control annotations here using a new term to indicate 'presence of host RNA involved in a pathogen interaction' or try and capture this control information like this instead?

CuzickA commented 3 years ago

Might need new condition for '+ TAFC siderophore' (triacetylfusarinine C). Maybe this could be '+ siderophore' with 'TAFC' as related synonym?

I think it is ok to use the existing condition term 'iron absent' here.

CuzickA commented 3 years ago

For this annotation

The WT pathogen can inhibit the acidification of host phagolysosomes, whereas the mutants cannot

Therefore, would the control metagenotype be NTR: 'pathogen-induced pH increase in host phagolysome' or 'inhibition of pathogen-induced pH decrease in host phagolysome'? @ValWood and the mutant 'pathogen-induced pH decrease in host phagolysome'.

The structure may need to change here to remove normal/abnormal grouping

CuzickA commented 3 years ago

Manually removed AE 'causes_disease' and used new Disease curation type (I did not record disease on moth host)

CuzickA commented 3 years ago

Also finished control metagenotype annotations, AE compare to and AE disease interaction.

CuzickA commented 3 years ago

See https://github.com/PHI-base/phipo/issues/206

Changed to

as this is a filamentous fungus

CuzickA commented 3 years ago

Two queries to resolve with @ValWood before I can approve this session

1) RNA level 2) pH phenotype query

CuzickA commented 3 years ago

This session still needs 1) new GO BP term 'dihydroxy naphthalene (DHN)-melanin' @ValWood have you requested this?

2) new PHI-ECO term '+ iron' Now added

3) NTR for PHIPO 'pathogen inhibition of host defense induced acidification in phagolysome'

4) edit PHIPO term from 'pathogen-induced pH decrease in host phagolysome' to 'host defense induced acidification in phagolysome'

5) NTR for PHIPO 'host RNA involved in a pathogen interaction, present' Now added

ValWood commented 3 years ago

We are trying to decide if it is appropriate to add every siderophore to GO, there are 100s/1000s? https://github.com/geneontology/go-ontology/issues/20974

but if not broad classes will be added.

ValWood commented 3 years ago

term added to go, so should be available in a few days.

CuzickA commented 3 years ago

Updated RNA annotations, now have

CuzickA commented 3 years ago

Still to do Check on new GO term next week Make PHIPO changes in https://github.com/PHI-base/phipo/issues/317

CuzickA commented 3 years ago

GO term updated NTR PHIPO terms added Approving session and closing ticket

CuzickA commented 1 year ago

This annotation has been flagged up in a search for pathogen phenotype WT allele with WT level expression.

In this case the annotation is for a WT allele with WT level expression but with a chemical treatment added that alters the phenotype. I will leave it for now as I cannot think of another way to make this annotation.