Mechanisms of multidrug resistance caused by an Ipi1 mutation in the fungal pathogen Candida glabrata

Abstract

Multidrug resistance in the pathogenic fungus Candida glabrata is a growing global threat. Here, we study mechanisms of multidrug resistance in this pathogen. Exposure of C. glabrata cells to micafungin (an echinocandin) leads to the isolation of a mutant exhibiting resistance to echinocandin and azole antifungals. The drug-resistant phenotype is due to a non-synonymous mutation (R70H) in gene IPI1, which is involved in pre-rRNA processing. Azole resistance in the ipi1^R70H mutant depends on the Pdr1 transcription factor, which regulates the expression of multidrug transporters. The C. glabrata Ipi1 protein physically interacts with the ribosome-related chaperones Ssb and Ssz1, both of which bind to Pdr1. The Ipi1-Ssb/Ssz1 complex inhibits Pdr1-mediated gene expression and multidrug resistance in C. glabrata, in contrast to Saccharomyces cerevisiae where Ssz1 acts as a positive regulator of Pdr1. Furthermore, micafungin exposure reduces metabolic activity and cell proliferation in the ipi1^R70H mutant, which may contribute to micafungin tolerance.

Fig. 1. Development and phenotypic characterization of the C. glabrata ipi1^R70H mutant.

a A schema representing sequential exposure of C. glabrata wild-type (CBS138) cells to increasing concentrations of micafungin. C. glabrata cells were spread on YPD plates containing micafungin at the indicated concentrations, incubated at 30 °C for 2 days, and subjected to antifungal susceptibility tests. b, c Spot dilution assay. C. glabrata strain Cg50 was obtained from a plate containing micafungin at the concentration of 0.03 µg/mL as described in (a). Strain Cg51 was obtained after the repeated subculture of Cg50 in YPD broth without micafungin for 20 days. An ipi1^R70H mutant was constructed as described in the methods. Serial 10-fold dilutions of C. glabrata cells were spotted onto an SC plate containing an antifungal agent at the indicated concentrations. Plates were incubated at 30 °C or the indicated temperatures for 2 days. All susceptibility tests were performed on at least three separate occasions. d Doxycycline-mediated transcriptional repression of IPI1 resulted in a growth defect in C. glabrata. Logarithmic-phase cells of the C. glabrata wild-type (ACG22) and tet-IPI1 strain, in which the native IPI1 promoter was replaced with the tetracycline regulatable promoter, were adjusted to ~ 1 × 10⁵ cells/mL in SD broth and incubated at 30 °C for 24 h with or without 20 µg/mL of the tetracycline analog doxycycline (Dox). Data are expressed as mean ± standard deviation for biological triplicates (****P < 0.0001; ns, not significant; one-way ANOVA with Dunnett’s multiple comparison test). The experiment was repeated twice with similar results. Source data are provided as a Source Data file. e Northern blotting. Logarithmic-phase C. glabrata cells grown at 30 °C were subsequently incubated at 42 °C, a non-permissive temperature for the ipi1^R70H mutant. Total RNA was extracted from each strain at the indicated time points. Top, northern hybridization was performed using an ITS2 probe. Bottom, total RNA was analyzed using 1.0% agarose gel with ethidium bromide, and 25S and 18S rRNA are indicated. The experiment was repeated twice with similar results. Source data including uncropped and unprocessed scans with molecular weight markers are provided as a Source Data file.

Fig. 2. Azole resistant mechanisms of the C. glabrata ipi1^R70H mutant.

a Sterol analysis. C. glabrata wild-type (WT) and ipi1^R70H strains were grown in synthetic defined (SD) broth or SD broth with 8 μg/mL fluconazole ( + FLC). Sterol contents were analyzed by reverse-phase HPLC as described in the methods. The means and standard errors for three independent experiments are shown (ns, not significant; ordinary one-way ANOVA with Sidak’s multiple comparison test). b qRT-PCR. C. glabrata wild-type (WT) and the ipi1^R70H mutant were grown as described in (a) and total RNA was extracted. mRNA abundance of ERG11 was measured by qRT-PCR and normalized using ACT1 as an internal control. Data are expressed as the means ± standard deviations (ns, not significant; ordinary one-way ANOVA with Sidak’s multiple comparison test). qRT-PCR was repeated on three independent occasions with similar results. c qRT-PCR. Total RNA was extracted from C. glabrata wild-type, Cg50, and two different clones of ipi1^R70H mutant strains. mRNA abundance was measured by qRT-PCR and normalized using ACT1 as an internal control. Expression of wild-type strain was defined as 1 in each assay, and relative mRNA abundances in other strains were calculated. Data are expressed as the means ± standard deviations (ordinary one-way ANOVA with Dunnett’s multiple comparison test). qRT-PCR was repeated on three independent occasions with similar results. Source data for panels (a–c) are provided as a Source Data file. d Rhodamine 6 G (R6G) accumulation assay. Intracellular concentration of the fluorescent dye R6G, a substrate of azole efflux pumps, was measured by flow cytometry in three different wild-type strains, two different clones of the ipi1^R70H mutant, and a mutant lacking Cdr1 efflux pump (cdr1Δ). Fluorescence intensity of R6G is shown on the X-axis. Left panel: Cells were incubated with R6G under normal growth conditions to examine the activity of R6G efflux. Right panel: Cells were exposed to R6G under the de-energized condition to examine the levels of R6G infused passively into the cells. These experiments were repeated twice with similar results.

Fig. 3. Involvement of Pdr1 and Cdr1 in azole resistance of the C. glabrata ipi1^R70H mutant.

a Effects of CDR1 and PDR1 deletion on azole susceptibility were examined using a spot dilution assay in the wild-type and ipi1^R70H backgrounds. Logarithmic-phase cells of the C. glabrata strains were serially diluted and spotted on SC plates containing fluconazole or voriconazole at the indicated concentrations. Plates were incubated at 30 °C for 2 days. b Pdr1 P927S, which is known as a gain-of-function mutation in C. glabrata, was introduced in the wild-type and ipi1^R70H backgrounds. A spot dilution assay was performed as described above except that plates were incubated at 37  °C. All susceptibility tests were performed on at least three separate occasions.

Fig. 4. Ssb and Ssz1 physically interact with Ipi1, Pdr1, and each other.

Each protein C-terminally tagged with three tandem repeats of FLAG (3 × FLAG) or HA was expressed. Logarithmic-phase cells were lysed, and total protein was extracted. FLAG-tagged proteins were immunoprecipitated (IP) using an anti-FLAG antibody. Proteins were separated by SDS-PAGE, and immunoblotted (IB) using anti-FLAG or HA antibodies. a Ipi1-3×FLAG and Ssb-HA, (b) Ipi1-3 × FLAG and Ssz1-HA, (c) Ssb-3 × FLAG and Ssz1-HA, (d) Pdr1-3×FLAG and Ssb-HA, and (e) Pdr1-3 × FLAG and Ssz1-HA were analyzed. These experiments were repeated twice with similar results. Source data for all panels, including uncropped and unprocessed scans with molecular weight markers, are provided as a Source Data file.

Fig. 5. Effects of SSB1, SSB2 and SSZ1 deletions on antifungal susceptibility in the wild-type and ipi1^R70H backgrounds.

a–d Logarithmic-phase C. glabrata cells were serially 10-fold diluted and spotted onto SC plates containing micafungin, fluconazole, or voriconazole at the indicated concentrations. Plates were incubated at 30 °C for 96 h. e, f Expression levels of CDR1, CDR2, and PDR1 are elevated in the ssb∆ and ssz1∆ strains. qRT-PCR was performed as described in the methods section and in Fig. 2b. Data are expressed as the means ± standard deviations (*P < 0.05; ***P < 0.001; ****P < 0.0001, ordinary one-way ANOVA with Dunnett’s multiple comparison test). qRT-PCR was repeated on three independent occasions with similar results. Source data for panels (e) and (f) are provided as a Source Data file.

Fig. 6. Cell growth/proliferation traits linked to echinocandin resistance.

a Growth curves of C. glabrata wild-type and various mutant strains. C. glabrata cells were grown in SC broth at 37 °C with agitation at 250 rpm. Based on the echinocandin susceptibility, C. glabrata strains were classified into two groups: group S (echinocandin-susceptible [wild-type level susceptibility to echinocandins]) and group R (echinocandin-resistant compared to the wild-type strain), shown as blue and red lines, respectively. The growth curves represent the mean of biological duplicates. b Optical densities at 600 nm (OD 600 nm) were compared at the indicated time points between the groups S and R (n = 7, each). Data are expressed as the means ± standard deviations. Individual dots represent the mean of biological duplicates for each strain as indicated in Fig. 6a. Statistical analysis was performed using Mann–Whitney U test. ns, not significant. Source data for all panels are provided as a Source Data file.

Fig. 7. Genome-wide gene expression profiles of C. glabrata wild-type strain and the ipi1^R70H mutant in response to micafungin treatment.

C. glabrata cells were exposed to 1 µg/mL of micafungin in SC broth at 37 °C for 1 h. RNA-seq analysis was performed as described in the materials and methods. Venn diagrams show the number of differentially expressed genes in cells treated with micafungin relative to untreated controls (>2-fold change in expression, adjusted P -value of <0.05, DESeq2 analysis applying a two-sided test for each gene with multiple comparison adjustments using the Benjamini-Hochberg method). Representative Gene Ontology (GO) terms are shown (P < 0.05, ~5 terms in order from the term with the lowest P-value, one-sided binomial test with multiple comparison adjustments using the Bonferroni method). Note that no statistically significant term was found for genes upregulated only in the ipi1^R70H mutant. Source data are provided in Supplementary Data 2.

Fig. 8. Effects of loss of calcineurin on antifungal susceptibility of the C. glabrata ipi1^R70H mutant.

a Either calcineurin catalytic subunit A (CNA1) or regulatory subunit B (CNB1) was deleted in the wild-type and ipi1^R70H backgrounds, and the antifungal susceptibility was examined using a spot dilution assay. Logarithmic-phase cells of the C. glabrata strains were serially diluted and spotted on SC plates containing an antifungal agent at the indicated concentrations. Plates were incubated at 37 °C for 2 days. b Expression level of FKS2 in the presence and absence of micafungin was determined by qRT-PCR. Logarithmic-phase cells of the C. glabrata strains were exposed to 1 µg/mL of micafungin in SC broth at 37 °C for 1 h. qRT-PCR was performed as described in the materials and methods and in Fig. 2b. Individual dots are shown for biological replicates (n = 6, each). The means ± standard deviations are shown (ns, not significant; Kruskal-Wallis test with Dunnett’s multiple comparison test). c C. glabrata cell survival was assessed before and after exposure to micafungin. Logarithmic-phase cells of the C. glabrata strains were exposed to 0.2 µg/mL of micafungin in SC broth at 37 °C. The CFUs were determined at the indicated time points, and percent CFU was calculated relative to the CFU prior to micafungin exposure. Data are presented as mean values ± standard deviations. The experiments shown in panels (a–c) were repeated on three independent occasions with similar results. Source data for panels (b) and (c) are provided as a Source Data file.

Fig. 9. Virulence and micafungin susceptibility of the C. glabrata ipi1^R70H mutant in vivo.

a Susceptibility of the C. glabrata ipi1^R70H mutant to macrophage killing. Logarithmic-phase cells of C. glabrata wild-type strain (CBS138) and the ipi1^R70H mutant were cocultured with murine RAW 264 macrophages at 37 °C for 2 h. Percent killing is expressed as the percent reduction of CFU recovered from cocultures compared with the CFU from control cultures (C. glabrata cells without macrophages). All data obtained from the two independent experiments were compared between the wild-type and ipi1^R70H strain groups (n = 14, each). The difference was not statistically significant (ns, not significant; two-tailed Mann–Whitney U test). b A mouse model of disseminated candidiasis. Immunocompetent mice were intravenously inoculated with 8 × 10⁷ cells of either C. glabrata wild-type or ipi1^R70H strain (n = 9 for the wild-type strain and n = 10 for the ipi1^R70H mutant). Bilateral kidneys, spleen, and liver were excised 7 days after injection. Appropriate dilutions of organ homogenates were plated, and the numbers of CFU were counted after 2 days of incubation at 30 °C. Numbers of recovered CFU from each organ are indicated for individual mice in the scatter plots. The geometric mean is shown as a bar. ns, not significant (two-tailed Mann–Whitney U test). The representative data of two independent experiments are shown. c, d A silkworm infection model. Larvae were inoculated with 2.0–2.5 × 10⁷ cells of each C. glabrata strain and injected with an echinocandin-class antifungal agent (micafungin, caspofungin, or anidulafungin) dissolved in saline or saline alone (50 μL). Twenty-four hours later, hemolymph was collected and spread on YPD plates to calculate CFU. The number of larvae is shown in parenthesis. Data were analyzed and presented as described above (ns, not significant; two-tailed Mann–Whitney U test). Source data for all panels are provided as a Source Data file.