A Human IRE1 Inhibitor Blocks the Unfolded Protein Response in the Pathogenic Fungus Aspergillus fumigatus and Suggests Noncanonical Functions within the Pathway

The unfolded protein response (UPR) is a signaling pathway that maintains endoplasmic reticulum (ER) homeostasis, with functions that overlap virulence mechanisms in the human-pathogenic mold Aspergillus fumigatus. The canonical pathway centers on HacA, its master transcriptional regulator. Translation of this protein requires the removal of an unconventional intron from the cytoplasmic mRNA of the hacA gene, which is achieved by an RNase domain located in the ER-transmembrane stress sensor IreA. Here, we show that targeting this RNase activity with a small-molecule inhibitor effectively blocked UPR activation, resulting in effects that mirror the consequences of genetic deletion of the RNase domain. However, these phenotypes were surprisingly narrow in scope relative to those associated with a complete deletion of the hacA gene. These findings expand the understanding of UPR signaling in this species by supporting the existence of noncanonical functions for the unspliced hacA mRNA in ER stress response.

ABSTRACT

The unfolded protein response (UPR) is a signaling network that maintains homeostasis of the endoplasmic reticulum (ER). In the human-pathogenic fungus Aspergillus fumigatus, the UPR is initiated by activation of an endoribonuclease (RNase) domain in the ER transmembrane stress sensor IreA, which splices the downstream mRNA hacA^u into its active form, hacAⁱ, encoding the master transcriptional regulator of the pathway. Small-molecule inhibitors against IRE1, the human ortholog of IreA, have been developed for anticancer therapy, but their effects on the fungal UPR are unexplored. Here, we demonstrate that the IRE1 RNase inhibitor 4μ8C prevented A. fumigatus from increasing the levels of hacAⁱ mRNA, thereby blocking induction of downstream UPR target gene expression. Treatment with 4μ8C had minimal effects on growth in minimal medium but severely impaired growth on a collagen substrate that requires high levels of hydrolytic enzyme secretion, mirroring the phenotype of other fungal UPR mutants. 4μ8C also increased sensitivity to carvacrol, a natural compound that disrupts ER integrity in fungi, and hygromycin B, which correlated with reduced expression of glycosylation-related genes. Interestingly, treatment with 4μ8C was unable to induce all of the phenotypes attributed to the loss of the canonical UPR in a ΔhacA mutant but showed remarkable similarity to the phenotype of an RNase-deficient IreA mutant that is also unable to generate the hacAⁱ mRNA. These results establish proof of principle that pharmacological inhibition of the canonical UPR pathway is feasible in A. fumigatus and support a noncanonical role for the hacA^u mRNA in ER stress response.

IMPORTANCE The unfolded protein response (UPR) is a signaling pathway that maintains endoplasmic reticulum (ER) homeostasis, with functions that overlap virulence mechanisms in the human-pathogenic mold Aspergillus fumigatus. The canonical pathway centers on HacA, its master transcriptional regulator. Translation of this protein requires the removal of an unconventional intron from the cytoplasmic mRNA of the hacA gene, which is achieved by an RNase domain located in the ER-transmembrane stress sensor IreA. Here, we show that targeting this RNase activity with a small-molecule inhibitor effectively blocked UPR activation, resulting in effects that mirror the consequences of genetic deletion of the RNase domain. However, these phenotypes were surprisingly narrow in scope relative to those associated with a complete deletion of the hacA gene. These findings expand the understanding of UPR signaling in this species by supporting the existence of noncanonical functions for the unspliced hacA mRNA in ER stress response.

INTRODUCTION

The unfolded protein response (UPR) is a eukaryotic signaling network that communicates information on the protein folding environment of the endoplasmic reticulum (ER) to the nucleus (1). In fungi, studies on the UPR have demonstrated that several species that infect plants, animals, or humans have uniquely adapted this stress response pathway to support the expression of pathogenicity traits, such as antifungal drug resistance, nutrient acquisition, host-temperature adaptation, cell wall or membrane homeostasis, and effector protein secretion (2–12). The pathway detects and responds to the accumulation of unfolded proteins, which is a situation that arises whenever the demand for increased output by the secretory pathway exceeds the protein folding capacity of ER-resident chaperones and folding enzymes (13). When unfolded proteins reach a critical threshold in the ER lumen, they activate an ER transmembrane protein known in humans as IRE1 (IreA in Aspergillus fumigatus [Fig. 1]). IRE1/IreA directs the most evolutionarily conserved branch of the UPR, and the basic paradigm of signaling is conserved across most fungal species, including A. fumigatus (14).

FIG 1.

Schematic representation of the UPR pathway in A. fumigatus and alignment of the amino acid sequence of the RNase domain of human IRE1 with orthologs in fungi. (A) The UPR is activated by ER stress, which occurs when the demand for secretion exceeds the protein folding capacity of the ER or when the cell encounters stimuli that disrupt ER homeostasis. The resulting accumulation of unfolded proteins activates the cytosolic RNase domain of the ER transmembrane stress sensor IreA, which removes an intron from the uninduced mRNA hacA^u, converting it into the induced mRNA hacAⁱ, which is translated into the bZIP transcription factor HacA that coordinates a transcriptional program to augment ER folding capacity. The small-molecule inhibitor 4μ8C blocks the activity of the IreA RNase domain required for hacA mRNA processing. (B) Alignment of the RNase domain of human IRE1 with the corresponding region in A. fumigatus, C. albicans, and C. neoformans. The arrow indicates the conserved lysine residue targeted by 4μ8C. Black shading indicates identity to the column consensus and gray indicates similarity.

All species homologs of the IRE1 protein contain an ER luminal stress-sensing domain and a cytosolic effector region containing kinase and endoribonuclease (RNase) domains (15, 16). Interactions between the sensor and unfolded proteins trigger oligomerization in the ER membrane, resulting in trans-autophosphorylation and activation of the RNase domain. The RNase then removes an unconventional intron from a cytoplasmic mRNA that is known in A. fumigatus as hacA^u (uninduced), creating a frameshift in the activated form of the mRNA, hacAⁱ (induced), that is an obligatory step for the translation of the bZIP transcription factor HacA (1, 3, 5) (Fig. 1A). This master transcriptional regulator of the canonical UPR pathway helps to buffer physiological fluctuations in ER stress by orchestrating a transcriptional program that augments the folding of proteins trafficking through the secretory pathway (3, 13, 17).

Selective inhibitors of the kinase or RNase domain of human IRE1 have been developed as tools to experimentally dissect the contribution of the UPR to cell physiology and human disease, particularly with respect to cancer (18–24). Among these compounds, salicylaldehyde-based inhibitors have shown high efficacy by directly blocking the RNase domain (25). The compounds 4μ8C and STF-083010 are two well-described examples of this class (26–29), but their effects on a fungal pathogen are still unexplored. Here, we demonstrate that 4μ8C (30) is an inhibitor of the canonical UPR pathway in A. fumigatus, effectively blocking the accumulation of hacAⁱ mRNA and downstream target gene induction. We found that treatment with 4μ8C failed to recapitulate the entire collection of phenotypes associated with a ΔhacA deletion mutant but was similar to phenotypes displayed by an IreA RNase domain mutant that is unable to process hacA^u mRNA into hacAⁱ. These data demonstrate the feasibility of pharmacological disruption of the canonical UPR pathway in a fungal pathogen and support emerging evidence that both the unspliced and spliced hacA mRNAs have functions in ER stress responses.

RESULTS

The human IRE1 RNase inhibitor 4μ8C blocks the canonical UPR of A. fumigatus.

We previously showed that the canonical UPR pathway of A. fumigatus involves a linear order of molecular events triggered by the activation of IreA in the presence of ER stress (3). Upon activation, the endoribonuclease domain of IreA splices an intron from the uninduced cytoplasmic mRNA hacA^u, converting it to its induced form, hacAⁱ, which is subsequently translated into the encoded transcription factor HacA (Fig. 1A). Subsequent studies revealed that deleting the ireA gene, or the ortholog in other fungal species (5, 31), is more deleterious than deleting the gene encoding the downstream transcription factor, suggesting that additional branches of the pathway emanating from IreA contribute to the ER stress response independently of HacA (Fig. 1A). To further examine the possibility of more complexity in the pathway, we focused in this study on the RNase domain, incorporating both small-molecule and genetic inhibition approaches.

The synthetic coumarin derivative 8-formyl-7-hydroxy-4-methylcoumarin (abbreviated as 4μ8C) was initially identified in a high-throughput screen for selective inhibitors of the human IRE1 RNase (30). The molecule forms a Schiff base with a lysine residue in the active site of the RNase domain, which prevents IRE1 from splicing its target mRNA (XBP1^u in humans). Since the homologous lysine is conserved in A. fumigatus IreA (Fig. 1B), we hypothesized that 4μ8C could be used to modulate the processing of hacA^u mRNA into its activated form, hacAⁱ (Fig. 1A). To test this, we used quantitative reverse transcription-PCR (RT-qPCR) analysis to monitor the induction of hacAⁱ levels during acute ER stress. Dithiothreitol (DTT) is the most widely used approach to experimentally induce ER stress because it reduces the disulfide bridges that stabilize many proteins in the secretory pathway, resulting in a rapid increase in the level of unfolded proteins that activate the IRE1/IreA sensor (32). Consistent with previous reports (33), DTT treatment of A. fumigatus hyphae induced accumulation of hacAⁱ mRNA, reflecting activation of the IreA RNase domain (Fig. 2A). Since the hacA gene promoter is a target of the HacA transcription factor (34), this surge in hacAⁱ mRNA levels in the presence of DTT is due to a positive feedback loop that involves three linked events: first, initial activation of the IreA RNase converts basally expressed hacA^u mRNA into hacAⁱ; second, translation of hacAⁱ mRNA into the HacA transcription factor increases transcription from the hacA gene promoter itself, thereby replenishing the pool of hacA^u mRNA; and third, splicing of hacA^u into hacAⁱ continues as long as the IreA RNase remains activated (5, 35). We found that incorporation of 4μ8C into the medium prevented DTT from triggering an increase in hacAⁱ mRNA abundance, demonstrating that the canonical UPR is not responsive to an acute ER stress stimulus in the presence of this compound. The lowest concentration for blocking the UPR under these conditions was determined to be 10 mg/liter (see Fig. S1 in the supplemental material), so this concentration was used for all subsequent experiments in this study.

FIG 2.

The human IRE1 inhibitor 4μ8C blocks the induction of the canonical hacA^u-hacAⁱ pathway in A. fumigatus. (A) RT-qPCR analysis of hacA^u and hacAⁱ mRNA levels during acute ER stress induced by 1 mM DTT for 1 h in the presence or absence of 10 mg/liter 4μ8C. (B) RT-qPCR analysis of hacA^u, hacAⁱ, and sod1 mRNA levels in the presence of 10 mg/liter 4μ8C. (C) RT-qPCR analysis of the expression of the UPR-independent gene Afu8g05720 in the presence of 1 mM DTT and 4μ8C. (D) RT-qPCR analysis of UPR target gene expression (bipA, pdiA, and eroA) in the presence of 10 mg/liter 4μ8C and/or 1 mM DTT. Values represent the mean ± SD of results from three biological replicates per strain and condition (ns, not significant; *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001 [one-way ANOVA with Dunnett’s post hoc test for panels A, B, and D or Tukey’s post hoc test for panel C]).

FIG S1

A minimal concentration of 4μ8C is required to block induction of the UPR. RT-qPCR analysis of mRNA levels from the UPR target genes bipA, pdiA, and eroA in liquid AMM at 37°C and 200 rpm in the A. fumigatus strain KU80. Cultures were simultaneously treated with DTT and two different concentrations of 4μ8C for 1 h prior to harvest. Data represent mean values of three technical replicates ± SD from one representative experiment. The experiment was repeated once with similar results. Download FIG S1, TIF file, 0.2 MB ^{(180.7KB, tif)} .

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We have previously reported that low levels of hacAⁱ are also detectable in the absence of added ER stress, representing a basal UPR that functions to buffer fluctuations in protein folding that arise during normal vegetative growth (5). We found that treatment with 4μ8C also reduced the steady-state levels of hacAⁱ mRNA under these conditions (Fig. 2B), consistent with the ability of the compound to impair basal IreA activation. In contrast, expression of the sod1 gene, which does not depend on the UPR for its expression (36), was unaffected by 4μ8C treatment (Fig. 2B), suggesting that downregulation of hacAⁱ mRNA levels by 4μ8C is not due to a general downregulation of transcription. Moreover, since the effects of DTT on cell physiology are not limited to ER protein folding (37, 38), we also compared the effects of 4μ8C on the expression of Afu8g05720, representing a gene that we have previously shown to be induced by DTT independently of the UPR (5). As shown in Fig. 2C, 4μ8C did not block the induction of this gene by DTT, illustrating specificity of 4μ8C treatment for the inhibition of UPR target genes.

Since 4μ8C effectively blocks hacAⁱ induction during acute ER stress (Fig. 2A), the compound should also prevent the upregulation of UPR target genes that are under the control of the HacA transcription factor. To test this, we compared the expression levels of three genes that are established UPR targets across multiple species: the Hsp70 chaperone gene bipA, the protein disulfide isomerase gene pdiA, and the oxidoreductase gene eroA (34, 39). As expected, all three of these UPR markers were strongly induced by DTT in A. fumigatus (Fig. 2D). However, no induction was detected in the presence of 4μ8C, consistent with the ability of this compound to prevent the accumulation of hacAⁱ mRNA (Fig. 2D). The compound also blocked the ability of DTT to induce the expression of srcA and pmrA (Fig. S2A), encoding ER/Golgi P-type Ca²⁺ ATPases that we have recently identified as targets of the UPR in A. fumigatus (33). Interestingly, we found that a ΔsrcA/ΔpmrA double deletion mutant was hypersensitive to the effects of 4μ8C relative to its parental strain (Fig. S2B). Since the absence of these Ca²⁺ ATPases exacerbates ER stress (33), the increased sensitivity of this mutant to 4μ8C is likely to be due to the ability of the compound to prevent the canonical UPR from mounting an adaptive response to low Ca²⁺ levels in the secretory pathway caused by the absence of these Ca²⁺ pumps. We conclude that 4μ8C is able to enter the fungus and reach the IreA sensor, thereby inhibiting the RNase activity that is required for hacA^u mRNA processing and downstream activation of UPR target genes.

FIG S2

The compound 4μ8C blocks the transcriptional upregulation of genes encoding P-type Ca²⁺-ATPases during ER stress. (A) Fold change in the expression levels of the srcA and pmrA genes by RT-qPCR during acute ER stress induced by 1 mM DTT for 1 h in the presence or absence of 10 mg/liter 4μ8C. Values represent the mean ± SD of the results from three technical replicates per strain and condition. (B) The ΔsrcA/ΔpmrA mutant is hypersensitive to 4μ8C. Serial dilutions of conidia from the indicated strains were spotted onto AMM plates containing 4μ8C and incubated for 72 h at 37°C. Download FIG S2, TIF file, 1.3 MB ^{(1.4MB, tif)} .

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4μ8C impairs growth on a polymeric protein substrate.

Mutants of A. fumigatus that harbor deletions of the hacA gene grow relatively well on medium containing simple carbon and nitrogen sources (3). Similarly, we found that the growth rate of the A. fumigatus parental strain KU70 on solid minimal medium supplemented with 4μ8C was only slightly reduced, comparable in magnitude to the mild growth inhibition displayed by a KU70-derived mutant lacking the hacA gene (Fig. 3A). In liquid culture, both KU70 and the unmodified wild-type strain CEA10 showed only a 10% reduction in metabolic activity in the presence of 4μ8C (Fig. 3B), making it unlikely that the inhibitory effect of 4μ8C on UPR gene expression is due to broad inhibition of fungal metabolism. In addition, although a slight reduction in spore germination rate was observed in the presence of 4μ8C, the total biomass accumulation after 24 h of incubation in liquid culture was indistinguishable in the presence or absence of the compound (Fig. S3). We conclude that pharmacological inhibition of the IreA RNase domain has minimal growth-impairing effects on A. fumigatus, consistent with the relatively normal growth characteristics of the ΔhacA mutant in the absence of stress.

FIG 3.

Growth on a complex protein polymer is impaired in the presence of 4μ8C. (A) Conidia were spot inoculated onto the center of plates containing AMM in the presence/absence of 10 mg/liter 4μ8C, and colony diameter was measured after 6 days at 37°C. (B) Overnight cultures in liquid AMM at 37°C were treated with 4μ8C at the indicated concentrations for 1 h, and metabolic activity was determined using resazurin. (C) Conidia from the indicated strains were inoculated onto the surface of a collagen gel matrix containing 10 mg/liter 4μ8C. Images of mycelial growth were captured after 72 h at 37°C. Bars show mean values ± SD of the results from three biological replicates per strain and condition (****, P < 0.0001; ns, not significant [one-way ANOVA with Tukey’s post hoc test]).

FIG S3

The compound 4μ8C delays germination but has minimal effects on total biomass formation. Microscopic analysis of the parental strain KU70 (A) and the unmodified wild-type isolate CEA10 (B) in the presence of 4μ8C. Scale bar represents 20 μm. (C) Quantification of the germination rate of CEA10 cultures treated with 4μ8C for 16 h. Values represent the mean ± SD of four biological samples per condition. (D) Effect of 4μ8C on biomass formation in liquid culture. The mycelial dry weight was determined from overnight cultures of CEA10 inoculated at 1 × 10⁶ conidia/ml and incubated for 24 h at 37°C. Values represent the mean ± SD of four biological samples per condition (****, P < 0.0001 [one-way ANOVA with Dunnett’s post hoc test]). Download FIG S3, TIF file, 2.5 MB ^{(2.6MB, tif)} .

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The ability of 4μ8C to block the induction of hacAⁱ mRNA and downstream UPR target gene activation under ER stress predicted that treatment with this compound would have similar effects as deleting the hacA gene under conditions that require UPR activity. Filamentous fungi that lack the hacA gene grow poorly on polymeric substrates because their secretory pathways are unable to meet the demand for hydrolytic enzyme secretion (3, 9, 40, 41). To determine how 4μ8C would impact utilization of a complex protein substrate, conidia were inoculated into a solution of type I collagen as the only source of carbon and nitrogen. Although both KU70 and CEA10 isolates grew well on this medium, the inclusion of 4μ8C strongly impaired growth (Fig. 3C). The ΔhacA mutant also grew poorly on this substrate, indicating that loss of the canonical UPR, either by genetic deletion of hacA or by treatment with 4μ8C, impairs the ability to grow on a protein substrate that requires enzymatic breakdown by secreted hydrolases prior to absorption.

4μ8C increases sensitivity to the antimicrobial agents carvacrol and hygromycin.

The inability of A. fumigatus to activate the canonical UPR in the presence of 4μ8C suggests that the fungus would be hypersensitive to a drug that causes ER stress. To test this, the effects of 4μ8C on growth were compared in the presence of carvacrol, a plant-derived compound that disrupts ER homeostasis in Candida albicans and triggers UPR intervention (42). As shown in Fig. 4A, carvacrol induced accumulation of the hacAⁱ mRNA in the CEA10 strain, confirming that this compound has similar adverse effects on ER homeostasis in A. fumigatus as it does in C. albicans. In addition, the ΔhacA mutant was hypersensitive to carvacrol relative to its parental strain KU70, indicating a role for the canonical UPR in protecting against carvacrol-induced ER stress (Fig. 4B). We found that treatment with 4μ8C prevented carvacrol-induced hacAⁱ accumulation (Fig. 4A), which was associated with increased susceptibility to carvacrol in both the KU70 and CEA10 backgrounds (Fig. 4B). An isobolographic analysis (43) in liquid culture confirmed that the combination of 4μ8C and carvacrol treatment had synergistic toxicity toward the fungus (Fig. 4C). We conclude that preventing the canonical UPR from responding to carvacrol-induced ER stress, either by chemical treatment with 4μ8C or by genetic deletion of hacA, is toxic to A. fumigatus.

FIG 4.

4μ8C increases susceptibility to carvacrol and hygromycin. (A) Fold change in the expression of hacA^u and hacAⁱ mRNAs by RT-qPCR after treatment for 1 h with 10 mg/liter 4μ8C and/or 75 mg/liter carvacrol or 60 mg/liter hygromycin B (HygB) (strain CEA10). (B) Serial dilutions of conidia from the indicated strains were spotted onto AMM plates containing carvacrol or hygromycin B in the presence or absence of 10 mg/liter 4μ8C and incubated for 48 h at 37°C. A ΔhacA mutant that lacks the HygB resistance marker was used in this assay (strain 467). (C) Isobolographic analysis of the synergism between 4μ8C and carvacrol against the wild-type strain CEA10. Solid circles represent the MICs displayed by different combinations of the drugs. (D) Fold change in the expression levels of the glycosylation-related genes WBP1 (Afu5g08970), ROT2 (Afu5g03500), and msdS (Afu1g14560) in the presence or absence of 10 mg/liter 4μ8C. Values represent the mean ± SD of the results from three biological replicates per strain and condition (*, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001; ns, not significant [one-way ANOVA with Dunnett’s post hoc test]).

Other plant-derived compounds that are structurally related to carvacrol have been shown to enhance the toxicity of drugs that target translation fidelity, such as aminoglycosides (44). Aminoglycosides are a therapeutically important class of antimicrobials that reduce the discrimination between cognate and near-cognate tRNAs, causing the incorporation of incorrect amino acids that promotes the accumulation of toxic protein aggregates (45). As shown in Fig. 4A, the aminoglycoside hygromycin B (HygB) induced hacAⁱ in A. fumigatus, which was blocked by treatment with 4μ8C (Fig. 4A), suggesting a role for the UPR in countering protein folding stress associated with HygB-induced translational errors. In support of this, we found that the ΔhacA mutant was hypersensitive to HygB and that treatment of either KU70 or CEA10 strains with 4μ8C increased sensitivity to this compound (Fig. 4B). An alternative explanation for this increased HygB susceptibility stems from the observation that yeast glycosylation mutants are hypersensitive to this aminoglycoside, a phenomenon that is attributed to one or more HygB resistance proteins that require glycosylation for optimal activity (46). Our previous demonstration that the ΔhacA mutant is deficient in the expression of genes involved in N-glycan biosynthesis (5) would be consistent with a glycosylation defect that enhances HygB sensitivity. This predicts that UPR inhibition by 4μ8C would also reduce the expression of glycosylation-related genes. To test this, we compared the expression levels of glycosylation genes that were previously shown to be downregulated in the ΔhacA mutant (5): msdS (encoding an α-mannosidase) (47), the DTT-inducible gene Afu5g08970 (WBP1 in Saccharomyces cerevisiae, an oligosaccharyl transferase gene), and Afu5g03500 (ROT2 in S. cerevisiae, a glucosidase I gene). Similarly to ΔhacA (Fig. S4), all three genes were downregulated in A. fumigatus after treatment with 4μ8C as demonstrated by RT-qPCR analysis (Fig. 4D). As expected, the induction of WBP1 and ROT1 upon ER stress with 1 mM DTT was blocked in the presence of the inhibitor (Fig. 4D). We conclude that the canonical UPR is an integral part of the cellular response to HygB in A. fumigatus and that preventing UPR activation, either by treatment with 4μ8C or by genetic deletion of hacA, enhances the toxicity of this aminoglycoside against the fungus.

FIG S4

Glycosylation-related gene expression is reduced by hacA deletion or by treatment with 4μ8C. RT-qPCR analysis of the expression levels of the glycosylation-related genes msdS (Afu1g14560), WBP1 (Afu5g08970), and ROT2 (Afu5g03500) in the presence or absence of 4μ8C. Values represent the mean ± SD of the results from three technical replicates per strain and condition. Download FIG S4, TIF file, 0.2 MB ^{(188.1KB, tif)} .

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4μ8C reveals unexpected complexity in the canonical UPR pathway.

The ΔhacA mutant of A. fumigatus exhibits increased sensitivity to both the triazole and echinocandin classes of antifungals, as well as to the ER stress agents DTT and tunicamycin (3). Although blocking hacAⁱ mRNA induction by 4μ8C treatment increased carvacrol and hygromycin B sensitivity, we were surprised to find that the compound had minimal effects on the sensitivity of the fungus to DTT, tunicamycin, or itraconazole (Fig. 5A). A fundamental difference between the ΔhacA mutant and chemical inhibition of hacA^u processing is that the ΔhacA mutant lacks both hacA^u and hacAⁱ mRNAs due to the absence of the hacA gene, whereas the 4μ8C-treated organism still expresses hacA^u (Fig. 2B). This raises the possibility that residual hacAⁱ levels in cultures treated with 4μ8C are sufficient to provide some protection against ER stress. We therefore examined a mutant that harbors an inactivating deletion in the RNase domain of IreA but still retains the hacA gene (ireA^ΔRNase). As observed with 4μ8C treatment, no hacAⁱ mRNA could be detected by RT-qPCR in the ireA^ΔRNase mutant, even in the presence of a strong ER stress stimulus, confirming that this strain is incapable of mounting a canonical UPR response (Fig. 5B). The levels of hacA^u were notably elevated in the ireA^ΔRNase mutant (Fig. 5B), consistent with a failure to process basally expressed hacA^u mRNA into hacAⁱ. Interestingly, and similar to what we observed with 4μ8C treatment, the ireA^ΔRNase mutant showed no hypersensitivity to DTT, tunicamycin, or itraconazole (Fig. 5A).

FIG 5.

The compound 4μ8C reveals additional complexity in the canonical UPR pathway. (A) Serial dilutions of conidia from the indicated strains were spotted onto AMM plates containing DTT, tunicamycin (Tn), or itraconazole (ITZ) in the presence or absence of 10 mg/liter 4μ8C and incubated for 48 h at 37°C. (B) Fold change in the expression of hacA^u and hacAⁱ mRNAs by RT-qPCR after treatment of the indicated strains for 1 h with 1 mM DTT. Cultures inoculated at 10⁶ conidia/ml were grown in AMM for 16 h at 37°C. (C) The caspofungin sensitivities of the ireA^ΔRNase and ΔhacA mutants were compared to that of the parental strain KU70 in the presence or absence of 4μ8C using the MIC test strip method. (D) Colony diameters on minimal medium at 37°C and 45°C. Conidia from the indicated strains were spot inoculated onto the center of plates containing AMM, and colony diameter was measured after 6 days at 37°C. (E) Serial dilutions of conidia from the indicated strains were spotted onto AMM plates containing carvacrol and incubated for 72 h at 37°C. (F) Conidia from the indicated strains were inoculated onto the surface of a collagen gel matrix, and mycelial growth was photographed after 72 h at 37°C. Values in panels B and D represent the mean ± SD of the results from three biological replicates per strain and condition (*, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001; nd, not detected; ns, not significant [one-way ANOVA with Dunnett’s {B} or Tukey’s {D} post hoc test]).

We have previously shown that the ΔhacA mutant has a lower MIC to caspofungin using an MIC test strip and that the normally fungistatic effects of caspofungin toward A. fumigatus became fungicidal in the absence of hacA (Fig. 5C) (3). In contrast, caspofungin remained fungistatic to the ireA^ΔRNase mutant and the 4μ8C-treated parental strain, with no decrease in the MIC (Fig. 5C). In addition, we found that neither the ireA^ΔRNase mutant nor treatment with 4μ8C increased thermal stress sensitivity as previously reported for the ΔhacA mutant (Fig. 5D) (3). However, the ireA^ΔRNase mutant was hypersensitive to carvacrol and grew poorly on a collagen substrate (Fig. 5E and F), similar to the effects of 4μ8C on the control strain (Fig. 3C and Fig. 4B). Together, these findings indicate that blocking hacAⁱ accumulation under conditions of ER stress by either a chemical or genetic approach is less detrimental to the fungus than the complete absence of the hacA gene, suggesting that there is additional complexity in the pathway that involves functions for the unspliced hacA^u mRNA that are distinct from the spliced mRNA.

DISCUSSION

Selective inhibitors of the kinase and/or RNase domains of human IRE1 are under development for the purpose of creating toxic levels of unfolded proteins in human tumor cells, particularly when used in combination with drugs that exacerbate ER stress (18, 19, 48, 49). These compounds are well tolerated in animal models and have been associated with favorable therapeutic outcomes (21–24, 50). However, their effects on a fungal pathogen have not been reported. Here, we demonstrate that the human IRE1 RNase inhibitor 4μ8C impaired the ability of A. fumigatus to maintain basal levels of hacAⁱ mRNA under vegetative growth conditions, in addition to preventing the accumulation of hacAⁱ under conditions of acute ER stress induced by treatment with DTT or the natural product carvacrol. This correlated with reduced expression levels of known UPR target genes, reflecting inhibition of the canonical UPR. STF-083010 is another inhibitor of the human IRE1 RNase and is structurally related to 4μ8C (21). We found that this compound also impaired hacAⁱ mRNA induction and sensitized the fungus to carvacrol-induced ER stress (see Fig. S5 in the supplemental material), providing additional support for the notion that disabling the fungal UPR is achievable by small-molecule inhibition. However, in contrast to 4μ8C, STF-083010 was only partially effective, so it was not pursued further in this study. Our data on 4μ8C provide the first validation of small-molecule inhibition of the fungal UPR in A. fumigatus, which could provide a valuable tool for future studies into how this stress response pathway integrates with other cellular circuitry to coordinate adaptive responses in fungi. It is also worth mentioning that UPR activity impacts one of the bottlenecks that limit the secretion of proteins by filamentous fungi used in the biotechnology industry (51), suggesting that 4μ8C could have broader utility as a way to understand how the UPR affects industrial secretion processes.

FIG S5

The human IRE1 inhibitor STF-083010 partially impairs the fungal UPR. (A) Treatment with STF-083010 increases sensitivity to carvacrol. Serial dilutions of conidia from the indicated strains were spotted onto AMM plates containing carvacrol and/or STF-083010 and incubated for 48 h at 37°C. (B) Fold change in the expression of hacA^u and hacAⁱ mRNAs by RT-qPCR after overnight cultures (20 h at 37°C) were treated for 1 h with DTT in the presence or absence of STF-083010 (strain CEA10). (C) Treatment with STF-083010 partially blocks DTT induction of the UPR target gene bipA. Fold change in the expression of bipA mRNA by RT-qPCR after overnight cultures (20 h at 37°C) were treated for 1 h with DTT in the presence or absence of STF-083010 (strain CEA10). Values represent the mean ± SD of the results from three technical replicates per strain and condition. Download FIG S5, TIF file, 0.4 MB ^{(416.5KB, tif)} .

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It is well known that filamentous fungi possess a high capacity to secrete large quantities of hydrolytic enzymes that allow them to break down complex substrates (52). Minimal medium that is optimized for the growth of A. fumigatus contains simple forms of carbon and nitrogen that are readily assimilated by the fungus. Treatment with 4μ8C had only a minor inhibitory effect on growth in this medium, similar to the mild growth impairment displayed by a ΔhacA mutant under the same conditions (Fig. 3). In contrast, either deletion of hacA or treatment with 4μ8C severely impaired the ability of A. fumigatus to grow on a collagen substrate. This is consistent with the importance of the UPR in supporting the accurate folding of secreted hydrolytic enzymes that are necessary to break down complex biopolymers (Fig. 3C).

Carvacrol is an essential oil from the oregano plant with in vitro antifungal activity against a variety of fungal species (42, 53–56) and has been shown to have potential in vivo application as a prophylactic agent for the prevention of avian aspergillosis (57). Although the precise molecular target of carvacrol is unknown, its ability to disrupt ER morphology and induce a UPR transcriptional signature in C. albicans clearly indicates that it causes acute ER stress (42). We found that carvacrol also induced the UPR in A. fumigatus, which could be blocked by treatment with 4μ8C (Fig. 4A). The two compounds showed synergistic toxicity against A. fumigatus, suggesting that 4μ8C prevents the accumulation of hacAⁱ mRNA needed to counteract the toxic effects of carvacrol on ER homeostasis (Fig. 4B and C). We also found that 4μ8C increased the susceptibility of C. albicans to carvacrol, suggesting a conserved mechanism of carvacrol between species (Fig. S6). Interestingly, our findings also revealed enhanced toxicity of hygromycin B against A. fumigatus in the presence of 4μ8C. This is likely to be due, in part, to the ability of 4μ8C to prevent the canonical UPR from adequately responding to the ER stress caused by hygromycin-induced errors in protein translation (Fig. 4A). In addition, the adverse effects of 4μ8C on the expression of glycosylation-related genes (Fig. 4D) would be expected to impair glycosylation-assisted protein folding, as well as impair glycosylation-dependent hygromycin B resistance mechanisms that have been well described from studies on yeast glycosylation mutants (46). We conclude that 4μ8C-induced hypersensitivity to hygromycin B is likely to be multifactorial but mediated in part by UPR signaling through the canonical HacAⁱ-directed pathway.

FIG S6

Susceptibility to carvacrol is enhanced by 4μ8C treatment in C. albicans. Serial 10-fold dilutions of C. albicans yeast (ATCC 18804) were spotted onto plates of yeast extract-peptone-dextrose (YPD) agar containing 4μ8C in the presence or absence of carvacrol and incubated at 37°C for 24 h. Download FIG S6, TIF file, 0.5 MB ^{(490.1KB, tif)} .

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Despite the existence of two overlapping reading frames in all species homologs of the mRNA encoding the UPR transcription factor, it is widely assumed that the spliced mRNA is the most relevant to ER homeostasis because it translates a bZIP transcription factor involved in UPR target gene expression. Interestingly, a phylogenetic analysis of vertebrate homologs of this mRNA has indicated that the evolution of the two overlapping reading frames argues for functionality of the unspliced transcript protein (58). Recent studies in human cells have shown that one function of the protein specified by the unspliced transcript is to target the nascent protein-mRNA-ribosome complex to the ER membrane via the signal recognition particle (SRP) pathway (59–62). If the sole purpose of the protein encoded by the unspliced mRNA in A. fumigatus is bringing the hacA^u mRNA in the proximity of the IreA RNase in order to optimize splicing into hacAⁱ, one would predict that preventing hacAⁱ accumulation by treatment with 4μ8C or by IreA RNase domain mutation would have the same effects as deleting the hacA gene (Fig. 1A). However, our data show that the effects of deleting hacA are broader in scope relative to chemical or genetic RNase inhibition (Fig. 5), suggesting that there is unexplained functionality of the unspliced hacA^u mRNA that goes beyond serving as the precursor for hacAⁱ. In Cryptococcus neoformans, the majority of the phenotypes associated with ire1 deletion could be complemented with the spliced transcription factor gene but not by the unspliced version (10). However, in that study complementation was performed in the complete absence of Ire1; in our study Ire1 was still present but rendered incapable of inducing the canonical pathway due to chemical or genetic inhibition of the Ire1 RNase. Ire1 is also present in the ΔhacA mutant of A. fumigatus, but the phenotype of that mutant is more severe than the phenotype of canonical UPR inhibition using 4μ8c treatment or RNase mutation, suggesting that beneficial effects of hacA^u are apparent when the Ire1 sensor is present. This raises the possibility that the unspliced protein augments noncanonical functions of Ire1, which would be consistent with evidence that it is targeted to the ER membrane (59–62). Unique functions for the unspliced protein have also been proposed in human cells (63, 64), as well as in Aspergillus oryzae, where mutants that constitutively express only the spliced form exhibit a transcriptional profile that is different from that of a hacA deletion strain (65). The existence of additional noncanonical branches in the UPR that contribute to ER homeostasis is also consistent with studies showing that the UPR is capable of customizing the regulation of the target gene expression contingent upon the nature and scope of the stress that a cell encounters, rather than acting as a simple “on-off” switch (66, 67). Experiments to explore the mechanisms involved in A. fumigatus are under way and are expected to further unravel the complexity of the UPR in the biology and virulence of this clinically important fungal pathogen.

MATERIALS AND METHODS

Reagents.

Aliquots of 4μ8C (EMD Millipore; 412512) at 25 mg/ml were prepared in dimethyl sulfoxide (DMSO) and stored at −20°C until use. Dithiothreitol (DTT; Thermo Scientific; R0862) was dissolved in water at 1 M prior to use. Tunicamycin (Cayman Chemical; 11445) and itraconazole (Sigma; 16657) were dissolved in DMSO at 10 mg/liter and stored until use at −20°C or −80°C, respectively. Hygromycin B (RPI; H75020) was dissolved in water at 100 mg/ml and stored at −80°C prior to use. A 6.4 M stock solution of carvacrol (Sigma-Aldrich; W224511) was diluted to 0.64 M (96.74 g/liter) in DMSO prior to immediate use.

Strains and culture conditions.

The A. fumigatus strains used in this study are summarized in Table S1 in the supplemental material. Conidia were harvested from cultures grown on OSM plates (Aspergillus minimal medium [AMM] osmotically stabilized with 1.2 M sorbitol). Unless otherwise specified, all experiments were performed in AMM: 1% (wt/vol) d-glucose, 1% (vol/vol) NH₄ tartrate, and 2% (vol/vol) salt solution (2.6% [wt/vol] KCl, 2.6% [wt/vol] MgSO₄ heptahydrate, 7.6% [wt/vol] KH₂PO₄, 5% [vol/vol] trace-element solution). Colony diameters were determined by spotting 5 × 10³ conidia onto the center of a 100-mm plate containing AMM + 0.8% (wt/vol) agarose (UltraPure agarose; Invitrogen) with or without 4μ8C, and colony diameters were measured after 6 days. For analysis of stress sensitivity, serial dilutions of conidia (10⁵ to 10¹ conidia in a 5-μl volume) were spotted onto AMM plates supplemented with 0.8% agarose and the compounds of interest. Plates were incubated at 37°C and photographed after 48 h. For analysis of germination rates, a total of 1 × 10³ spores were inoculated into liquid AMM containing the indicated concentrations of 4μ8C and incubated at 37°C. Controls with DMSO were run in parallel. The number of germinated conidia was then quantified microscopically (90 to 183 cells counted per condition). For analysis of mycelial biomass, liquid AMM was inoculated with CEA10 conidia at a concentration of 1 × 10⁶ conidia/ml and incubated for 24 h at 37°C. The mycelium was then dried and weighed. Growth on a collagen substrate was performed by diluting a 10× stock solution of Aspergillus minimal salts to 1× with a 5-mg/liter solution of type l collagen as the sole source of carbon and nitrogen (Sigma; C3867; 5 mg/liter), and inoculating 100 conidia into the surface of the gel in a 96-well plate. Plates were photographed after 72 h at 37°C. Control cultures in liquid AMM were prepared in parallel.

TABLE S1

Strains of A. fumigatus used in this study. Download Table S1, DOCX file, 0.02 MB ^{(16.9KB, docx)} .

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RNA extraction and RT-qPCR.

Cultures were inoculated with 1 × 10⁶ conidia/ml in 50 ml of AMM and incubated at 37°C and 200 rpm. After 16 h of incubation, cultures were treated for 1 h with the indicated compounds prior to RNA isolation. RNA was isolated using the RNAzol RT column kit according to the manufacturer’s instructions (Molecular Research Center, Inc.). The digestion of genomic DNA and synthesis of cDNA were performed using RNase-free DNase (Roche) and iScript Reverse Transcription Supermix for RT-qPCR (Bio-Rad). The RT-qPCR was performed in a StepOne real-time PCR system (Applied Biosystems) using 1 μg of template per well and iTaq Universal SYBR Green Supermix (Bio-Rad). The primers used in the reaction mix are summarized in Table S2, and their final concentration was 500 nM, with the exception of 200 nM for the housekeeping gene (18S rRNA). Primer efficacy was evaluated using a standard curve. The specificity of the hacA^u and hacAⁱ reverse primers for distinguishing between the unspliced and spliced versions of the hacA mRNA was confirmed by RT-qPCR using the TaqMan probe and primers listed in Table S2. The final concentration for probes and primers was 250 nM and 500 nM, respectively (including the housekeeping gene).The reaction was performed with the Ex Taq master mix (TaKaRa), using the same cycle parameters described above for RT-qPCR. Since expression results obtained with SYBR green were similar to those obtained with a TaqMan probe, the SYBR green method was employed for the results presented in this study, using the same primer concentrations used for TaqMan. For hacA^u and hacAⁱ mRNA detection, the cycle conditions were 20 s at 95°C, 40 cycles of 3 s at 95°C, and 20 s at 66°C. For detection of other genes, the cycle conditions were 20 s at 95°C, 40 cycles of 3 s at 95°C, and 30 s at 60°C. The melting curve was monitored to verify the specificity of the amplification reaction. The 18S rRNA was used as a housekeeping gene. Fold change in mRNA levels was determined in comparison to untreated cultures.

TABLE S2

Oligonucleotides (primers and probes) used for gene expression analyses. Download Table S2, DOCX file, 0.02 MB ^{(16.7KB, docx)} .

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Analysis of metabolic activity and antifungal susceptibility.

For analysis of metabolic activity, conidia were inoculated at a concentration of 1 × 10⁶ conidia/ml in 150 μl of liquid AMM in a 96-well plate and incubated for 16 h at 37°C. The plates were washed three times, and the indicated concentrations of 4μ8C were added to the plates before incubating for an additional hour at 37°C. The final concentration of DMSO was 0.5% (vol/vol) in each well, including the growth controls. The cultures were then washed three times, and the medium was replaced with AMM containing 0.02 mg/ml of the oxidation-reduction metabolic indicator resazurin (14322; Cayman Chemicals). After incubating for 1 h at 37°C, the fluorescence was measured (excitation, 535 nm; emission, 590 nm) in a microplate reader (Synergy H1; BioTek). For analysis of synergy between carvacrol and 4μ8C, conidia were inoculated into liquid AMM containing 0.02 mg/ml of resazurin at a concentration of 2.5 × 10⁴ conidia/ml. Serial 2-fold dilutions of 4μ8C were then dispensed from column 2 in the 96-well plate to column 9. Additionally, 2-fold dilutions of carvacrol were dispensed from row A to H into each well containing 4μ8C. Columns 1 and 11 were used as growth and sterility controls, respectively. Columns 10 and 12 were used to display the individual MICs of carvacrol and 4μ8C. The plates were incubated at 37°C for 24 h, after which the fluorescence was measured as described above. The MIC was defined as the lowest concentration required to inhibit 90% of fungal metabolic activity after 24 h of incubation. An isobologram representation was used to determine if the combination of 4μ8C and carvacrol had synergistic activity. The diagonal line in Fig. 4C connects the individual MICs for each compound (shown by the solid circles on the axis lines), and the remaining circles represent the MICs for different combinations of the two drugs. Synergistic, additive, and antagonistic effects are represented by solid circles that fall below the diagonal line, on top of the diagonal line, or above the diagonal line, respectively. The fractional inhibitory concentration (FIC) index was determined as (MIC carvacrol in combination with 4μ8C/MIC carvacrol alone) + (MIC 4μ8C in combination with carvacrol/MIC 4μ8C alone). The interaction between the drugs was defined as synergistic (FIC < 0.5), indifferent (0.5 < FIC ≤ 4.0), or antagonistic (FIC > 4.0). Antifungal susceptibility using the MIC test strip (MTS) method was determined following the instructions of the manufacturer. A concentration of 10⁶ conidia/ml was spread with a sterile cotton swab onto a plate of RPMI 1640 agar with 0.164 M morpholinepropanesulfonic acid (MOPS) and l-glutamine (pH 7.0). RPMI plates containing 4μ8C were run in parallel. After the surface of the medium appeared dry, an MIC test strip containing caspofungin (Liofilchem; 92154) was applied. Plates were incubated for 48 h at 37°C and photographed.

Statistical analysis.

Statistical analysis was performed using GraphPad Prism version 8 for Windows (GraphPad Software, San Diego, CA, USA). Statistically significant differences were determined using one-way analyses of variance (ANOVA) with Dunnett’s or Tukey’s multiple-comparison tests.