PMID: 23629718 Molecular mechanisms of drug resistance in clinical Candida species isolated from Tunisian hospitals

[MPiovesana]

Curated by @MPiovesana https://canto.phi-base.org/curs/1d956c6785fd3798

[MPiovesana]

This is quite a long paper which describes the antifungal susceptibility phenotypes of several clinical isolates and laboratory-generated strains of Candida albicans and Candida tropicalis. In brief, a fluconazole-resistant clinical isolate (JEY355) of C. albicans was found to carry a mutant allele of MRR1 (MRR1-V877F). To test the link between azole resistance and this mutant allele, authors generated a deleted MRR1 line (MRR1Δ), followed by the introduction of the mutant allele in the deleted background. Similarly, an azole-resistant isolate of C. tropicalis was found to carry mutant alleles of ERG3 (aaS258F) and ERG11 (44aa deletion + D275V). These alleles were introduced in the genomic loci of ERG3 and ERG11, respectively, in a wild type strain DSY140 (derived from ATCC 750). Single and double mutant lines were generated. The antifungal susceptibility of the resulting lines was tested (Table 3, Figure 3), and results were curated. I focused on annotations of susceptibility to azoles (fluconazole and voriconazole), amphotericin B, and brefeldin A, which seem to be the most relevant ones from the paper.

[MPiovesana]

Uniprot IDs: C. albicans: Reference proteome UP000000559 includes strain SC5314, used in this paper, and was used to search for MRR1 protein. A single entry was found and used for the curation session (Q5A4G2).

AC - this reviewed entry looks fine https://www.uniprot.org/uniprotkb/Q5A4G2/entry

C. tropicalis: Authors provide a GenBank accession number but I believe those were for the deposition of the mutant allele sequences; plus, it only refers to erg11 when searching it on Uniprot. Furthermore, finding these IDs was a little trickier as the reference proteome suggested by Uniprot for C. tropicalis does not include reference strain ATCC 750 used in this study. So by doing a normal search on Uniprot with gene and species name, the following entries were retrieved: ERG3: N0A5G3; organism is linked to strain ATCC 750. First entry returned on search. However, another entry of same length is also shown (N0A3T1).

Ac - this is an unreviewed entry https://www.uniprot.org/uniprotkb/N0A5G3/entry

ERG11: P14263; single reviewed entry for this gene, linked to strain ATCC 750.

AC - this reviewed entry looks fine https://www.uniprot.org/uniprotkb/P14263/entry

IDs might need revising.

[MPiovesana]

Strains: C. albicans: SC5314 was selected. C. tropicalis: I searched for strain ATCC 750, from which recipient strain DSY140 is derived. PHI-Canto suggested strain 1909 as a synonym to ATCC 750, so I selected it. Is this ok?

[MPiovesana]

Genotypes creation: as all genotypes (except for MRR1 deletion) were created by introducing a mutant allele of a clinical isolate into a wild type recipient strain, they were classified as transformant alleles.

C. albicans: MRR1Δ: deletion of MRR1 (AC - DSY4278)

MRR1 transformant (JEY355-MRR1(V877F)): introduction of mutant allele of MRR1 derived from strain JEY355 in strain SC5314 harbouring MRR1 deletion (MRR1Δ was added in background).

C. tropicalis: ERG11 transformant(JEY162-ERG11(824-955bpΔ + D275V): introduction of mutant allele of ERG11 derived from strain JEY162 in genomic loci of wild type ERG11; mutant allele carries a deletion (bp 824 to 955) and mutation leading to aa substitution (D275V). ERG11Δ was added in background.

ERG3 transformant(JEY162-ERG3(S258F): introduction of mutant allele of ERG3 derived from strain JEY162 in genomic loci of wild type ERG3; ERG3Δ added in background.

ERG11 transformant(JEY162-ERG11(824-955bpΔ + D275V) + ERG3 transformant(JEY162-ERG3(S258F): multilocus genotype describing the introduction of both mutant alleles derived from strain JEY162.

[MPiovesana]

Genotype annotations: genotypes were annotated accordingly with the following PHIPO terms: normal growth on fluconazole (suggested) normal growth on voriconazole normal growth on brefeldin A (suggested) resistance to fluconazole resistance to brefeldin A

[MPiovesana]

Curation completed pending review.

[CuzickA]

Added 'MDR1' for Candida albicans

https://www.uniprot.org/uniprotkb/Q5ABU7/entry swiss-prot reviewed entry.

I want to make a GO MF annotation to indicate that MRR1 regulates MDR1 expression

[CuzickA]

Hi @ValWood, do you think the above GO MF annotations are reasonable?

[ValWood]

Looks good! v

[CuzickA]

Thanks @ValWood

[CuzickA]

Pathogen phenotype annotations look fine.

Considered trying to add AE alteration in archetype for Ct ERG11/CYP51B but decided against it. There was no archetype information in Nichola's S file or the Mair et al 2026 paper for Candida tropicalis. It may have been possible to use FRAST but this would not be straight forward as its not clear where to get the sequence for 'JEY162-ERG11(824-955bpΔ + D275V)' to do a FRAST alignment against CYP51B and how to cope with the 132nt deletion. Therefore, AE not added.

Next steps for this session 1) wait for PHIPO terms to be loaded into PHI-Canto

Then session ready for approval.

[CuzickA]

Terms now added. Session approved. Closing ticket.