PMID:28630186 Loss of C-5 Sterol Desaturase Activity Results in Increased Resistance to Azole and Echinocandin Antifungals in a Clinical Isolate of Candida parapsilosis.

[MPiovesana]

Curated by @MPiovesana https://canto.phi-base.org/curs/ab37cd93e3786640

[MPiovesana]

In this study, authors investigate the azole susceptibility of two clinical isolates of Candida parapsilosis, named Isolate 1 (azole sensitive) and Isolate 2 (azole resistant). A point mutation leading to an amino acid substitution in the ERG3 gene of Isolate 2 (ERG3-aaG111R) is found to be associated with the azole resistance displayed by this isolate. Authors generate deletion mutants of ERG3 (ERG3Δ) in both Isolate 1 and 2 backgrounds, and also replace the mutant ERG3 allele in Isolate 2 with the wild type copy of ERG3 from Isolate 1. The effect of the deletion of ERG3 in azole susceptibility is also explored in Candida albicans with the generation of deletion mutants in a wild type reference strain (SC5314).

This is a tricky case as the strains in this study as named Isolate 1 and Isolate 2, and therefore we do not really know to which reference strain of C. parapsilosis they are most similar to. For this reason, I think we can only curate the deletion genotypes below:

C. parapsilosis: ERG3Δ (Unknown strain): deletion of the wild type copy of ERG3 in clinical isolate 1 (Unknown strain selected);

C. albicans: ERG3wtΔ (SC5314): deletion of the wild type copy of ERG3 in reference strain background SC5314.

I thought about creating an allele to represent the replacement of the mutant ERG3 allele of Isolate 2 with the wt allele from Isolate 1, but as both are unknown strains, I am not sure how I could represent this.

AC- I agree with this and have left annotations as they are.

[MPiovesana]

Uniprot IDs: C. parapsilosis: A unique reference proteome of C. parapsilosis was identified in UniprotKB (UP000005221), for which a single entry for the ERG3 protein was found (G8B7T4).

C. albicans: The reference proteome UP000000559 was chosen for C. albicans as this is identified as a "Standard" proteome (a second one is available but is classed as Outlier (high value)). A single entry for ERG3 was identified (Q59VG6).

[MPiovesana]

Genotype creation and annotation: Genotypes were created as described above. Genotypes were annotated based on their susceptibility to three azole antifungals (fluconazole, voriconazole, itraconazole). Susceptibility to other chemicals are also tested, but as the main focus of the paper is on azole resistance, these were chosen as representative results.

[MPiovesana]

Question: a second strain of C. albicans is used by the authors to generate deletion lines of ERG3 (strain BWP17). The background of this strain is not explained in the text, and I found it rather confusing (Table 4). Thus, I decided not to curate the deletion genotype generated in this background, as I was unsure about how to do it. I don't believe it would be necessary as it shows a similar azole resistance profile to strain SC5314.

[MPiovesana]

Curation completed pending review.

[CuzickA]

AE alteration in archetype is N/A as these are deletion genotypes and target site is ERG3.

Current annotations look fine.

Approving session and closing ticket.