PMID: 12604551 A point mutation in the 14alpha-sterol demethylase gene cyp51A contributes to itraconazole resistance in Aspergillus fumigatus

[MPiovesana]

https://canto.phi-base.org/curs/1ce053ff9b1dbeab

[MPiovesana]

Uniprot ID: one entry resulting from search for cyp51A and Aspergillus fumigatus. No issues.

[MPiovesana]

Strain: WT strain CM-237 is used as recipient for gene replacement and expression of mutant cyp51A allele in the study. I could locate a strain named "237" in PHI-Canto, but not CM-237. I tried searching online but I don't believe 237 and CM-237 are synonyms, so I added the strain name manually. Should we request it to be added to PHI-Canto list of A. fumigatus strains?

[MPiovesana]

Experimental conditions: added 2 days post-inoculation to indicate length of antifungal susceptibility tests. Same as discussed in other tickets - need for new experimental condition reflecting inoculation of fungus to medium, not host.

AC: https://github.com/PHI-base/phi-eco/issues/12

[MPiovesana]

Needs adding GO term annotations.

[CuzickA]

Needs adding GO term annotations.

@MPiovesana Did you have a GO term in mind? Is this another case of needing it entered in Admin mode with evidence code of TAS?

[MPiovesana]

Needs adding GO term annotations.

@MPiovesana Did you have a GO term in mind? Is this another case of needing it entered in Admin mode with evidence code of TAS?

@CuzickA Actually, I am not sure whether it is necessary to add the GO annotations here. This is a protein that is cited in several papers, and perhaps it is not necessary to annotate its GO terms in every curation session. When looking on Uniprot, the function of this protein has been described by several publications, but I was unsure whether I should check them individually to identify the experiments performed to assign these functions. When would you recommend is best to add GO annotations, and when is it not necessary?

[CuzickA]

Needs adding GO term annotations.

@MPiovesana Did you have a GO term in mind? Is this another case of needing it entered in Admin mode with evidence code of TAS?

@CuzickA Actually, I am not sure whether it is necessary to add the GO annotations here. This is a protein that is cited in several papers, and perhaps it is not necessary to annotate its GO terms in every curation session. When looking on Uniprot, the function of this protein has been described by several publications, but I was unsure whether I should check them individually to identify the experiments performed to assign these functions. When would you recommend is best to add GO annotations, and when is it not necessary?

@MPiovesana, I agree it sounds like we don't need to add GO annotations here, especially if they have already been annotated in UniProt. I think we only really want to add GO annotations when expt in the publication show the normal function of the gene product and occasionally if there is a strong statement in the text made by the author (TAS). This is another topic for the FAQ :-)

[CuzickA]

Session approved. Closing ticket.

[CuzickA]

I think I need to add AE_alteration in archetype to this session.

[CuzickA]

I need to follow up with Nichola about selecting the correct AE_alteration in archetype here.

From Nichola's S file

I don't think it would make sense to use cyp51b from Zt as the annotation is for cyp51a from Af which is listed in FRAST.

In Mair et al 2016 publication

I think the correct alteration in archetype is therefore G54E; Cyp51A; ASPEFU

[CuzickA]

AE alteration_in _archetype

G54E; Cyp51A; ASPEFU

Questions for Nichola 1) is this correct 'G54E; Cyp51A; ASPEFU'. I could not find info on Cyp51A in your S file. I found the above information from Table 2 in Mair et al 2016.

[CuzickA]

AE alteration_in _archetype checked by Nichola. Session now approved.