PMID: 27799210 Screening and Characterization of a Non-cyp51A Mutation in an Aspergillus fumigatus cox10 Strain Conferring Azole Resistance

[MPiovesana]

Curation by @MPiovesana https://canto.phi-base.org/curs/d2c4a7ceed32cff8

[MPiovesana]

GENOTYPES EDITED AFTER DISCUSSION ABOUT TRANSFORMANT ALLELE TYPES; SEE LATEST COMMENT FOR UPDATE!

In this paper, authors observe that the deletion of the algA gene leads to an increased frequency of spontaneous mutations associated with azole resistance in Aspergillus fumigatus. Among several resistant mutants identified in the delta-algA background, two are selected for whole genome sequencing analysis. Despite the presence of multiple SNPs in both mutants, the only difference between the two is that one carries a single point mutation in a gene homologous to cox10 from yeast, therefore named Afcox10 in the paper, and the other carries a SNP in cyp51A. To confirm whether these SNPs are responsible for the increased resistance to itraconazole in an algA-independent way, the wild strain A1160 was transformed with the respective mutant alleles. It is not clear whether a gene replacement strategy was used, but it is implied given that the authors clone the flanking regions as well as the ORF of Afcox10 and cyp51A during the cloning procedures. Thus, I identified three genotypes for curation:

algAΔ - deletion of algA in wild type background Afcox10(aaR243Q) - introduction of mutant allele of Afcox10 in wild type background; cox10Δ added in background to reflect gene replacement; cyp51A(aaF219L) - introduction of mutant allele of cyp51A in wild type background; cyp51AΔ added in background to reflect gene replacement.

Throughout the text, authors reference two wild type strains, A1160 and A1160c. By carefully reading the Materials and Methods section, figure legend and Results, it is apparent that strain A1160c was used as recipient for all transformation experiments. Thus, have selected this strain for curation.

[MPiovesana]

Uniprot ID: accession numbers are provided for algA and Afcox10, and cyp51A is readily found with a quick search on Uniprot as well. No issues locating IDs.

[MPiovesana]

Genotype annotations: annotations were straightforward; phenotype of algAΔ genotype is found in Figure 1a-b, and phenotypes of transformed strains is found in Figure 5. Other figures of the paper refer to spontaneous mutants generated on plates by the exposure of algAΔ to azoles; these mutants, however, contain several mutations across their genome, and not all were fully sequenced. Therefore, I think the annotation of the above-mentioned strains is sufficient.

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PHIPO terms: new terms were suggested: normal growth on itraconazole normal growth on caspofungin normal growth on terbinafine normal growth on bifonazole

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Curation completed pending review.

[MPiovesana]

Thus, I identified three genotypes for curation:

algAΔ - deletion of algA in wild type background Afcox10(aaR243Q) - introduction of mutant allele of Afcox10 in wild type background cyp51A(aaF219L) - introduction of mutant allele of cyp51A in wild type background

The wild type strain A1160C is transformed with the mutant alleles derived from strains W004 and W601. Thus, this falls under the definition of transformant allele type. I edited the genotypes in this curation session to be recorded as:

cox10 transformant (W004-cox10(R243Q)) = mutant cox10 allele from strain W004 introduced in wt strain;

cyp51A transformant (W601-cyp51A(F219L)) = mutant cyp51A allele from strain W601 introduced in wt strain.

Although not completely clear in Materials and Methods, I believe the mutant alleles were introduced using a gene replacement by homologous recombination strategy, as the 5' and 3' regions of the genes were also amplified during the cloning steps. Thus, I recorded the deletion of the endogenous cox10 and cyp51A genes in the background section.

[CuzickA]

We could also curate the info in Fig 4. algAdelta strains selected on chemistry for spontaneous mutants leading to increased resistance. Strain W004 with cox10 R243Q and strain W601 Cyp51 F219L.

This may have been omitted in preference of curating the transformant genotypes with intact algA in fig 5 indicating chemistry R phenotype is algA independent.

[CuzickA]

Current transformant annotations seem fine. (Above Fig 4 does not seem to be required).

[CuzickA]

No need to add new strain.

Next 1) Need new PHIPO terms. 2) Can I add AE for Cyp51? 3) Any GO annotations?

[CuzickA]

[CuzickA]

AE alteration in archetype

Aspergillus fumigatus (this is also the archetype species) cyp51A transformant(W601-cyp51A(F219L))[Not assayed] 'F219L; Cyp51A; ASPEFU'

No info in Nichola's S file. In Mair et al 2016

[CuzickA]

Next 1) add new PHIPO terms NOW DONE 2) Check AE alteration in archetype with Nichola

Then ready to approve.

[CuzickA]

Session approved without Nichola checking AE alteration in archetype.

Closing ticket.