Antifungal drug resistance evoked via RNAi-dependent epimutations

• Published in: Nature (London) 2014-09, Vol.513 (7519), p.555-558
• Main Authors: Calo, Silvia, Shertz-Wall, Cecelia, Lee, Soo Chan, Bastidas, Robert J., Nicolás, Francisco E., Granek, Joshua A., Mieczkowski, Piotr, Torres-Martínez, Santiago, Ruiz-Vázquez, Rosa M., Cardenas, Maria E., Heitman, Joseph
• Format: Article
• Language: English
• Subjects: 38; 38/1; 38/22; 38/23; 38/71; 38/77; 45; 631/208/176/2016; 631/208/505; 631/326/193/2542; 82; 82/29; 82/80; Antifungal agents; Calcineurin - genetics; Calcineurin - metabolism; Calcineurin Inhibitors; Complications and side effects; Dosage and administration; Drug resistance; Drug resistance in microorganisms; Drug Resistance, Fungal - genetics; Drug therapy; Epigenesis, Genetic - genetics; Fungal infections; Genes; Genetic aspects; Genomes; Humanities and Social Sciences; Humans; Hyphae - drug effects; Hyphae - genetics; Hyphae - growth & development; Hypotheses; Kinases; letter; Microorganisms; Molecular Sequence Data; Mucor - drug effects; Mucor - genetics; Mucor - growth & development; Mucormycosis - drug therapy; Mucormycosis - microbiology; multidisciplinary; Mutation; Mutation - genetics; Mycoses; Phenotype; Proteins; Risk factors; RNA Interference; RNA polymerase; Science; Studies; Tacrolimus - metabolism; Tacrolimus - pharmacology; Tacrolimus Binding Protein 1A - deficiency; Tacrolimus Binding Protein 1A - genetics; Tacrolimus Binding Protein 1A - metabolism; Yeasts
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature13575

The human fungal pathogen Mucor circinelloides develops spontaneous resistance to an antifungal drug both through mutation and through a newly identified epigenetic RNA-mediated pathway; RNA interference is spontaneously triggered to silence the fkbA gene, giving rise to drug-resistant epimutants that revert to being drug-sensitive once again when grown in the absence of drug. Epimutants confer drug resistance RNA interference (RNAi) is a mechanism conserved across eukaryotes that controls multiple cellular functions. This study reports that the opportunistic human pathogen Mucor circinelloides can develop spontaneous resistance to the antifungal drug FK506 (tacrolimus) via two distinct mechanisms. One is through conventional Mendelian mutation, whereas the other, surprisingly, is via a newly identified epigenetic RNAi-mediated pathway. Joseph Heitman and colleagues show that RNAi is spontaneously triggered to silence a gene, fkbA , that encodes the peptidylprolyl isomerase FKBP12. This enzyme interacts with the drug to form a complex that inhibits calcineurin, blocking the transition to hyphae. The resulting drug-resistant 'epimutants' revert to drug sensitivity when grown in the absence of drug. Microorganisms evolve via a range of mechanisms that may include or involve sexual/parasexual reproduction, mutators, aneuploidy, Hsp90 and even prions. Mechanisms that may seem detrimental can be repurposed to generate diversity. Here we show that the human fungal pathogen Mucor circinelloides develops spontaneous resistance to the antifungal drug FK506 (tacrolimus) via two distinct mechanisms. One involves Mendelian mutations that confer stable drug resistance; the other occurs via an epigenetic RNA interference (RNAi)-mediated pathway resulting in unstable drug resistance. The peptidylprolyl isomerase FKBP12 interacts with FK506 forming a complex that inhibits the protein phosphatase calcineurin 1 . Calcineurin inhibition by FK506 blocks M. circinelloides transition to hyphae and enforces yeast growth 2 . Mutations in the fkbA gene encoding FKBP12 or the calcineurin cnbR or cnaA genes confer FK506 resistance and restore hyphal growth. In parallel, RNAi is spontaneously triggered to silence the fkbA gene, giving rise to drug-resistant epimutants. FK506-resistant epimutants readily reverted to the drug-sensitive wild-type phenotype when grown without exposure to the drug. The establishment of these epimutants is accompanied by generation of abundant fkbA small R