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Song L, Wang S, Zou H, Yi X, Jia S, Li R, Song J. Regulation of Ergosterol Biosynthesis in Pathogenic Fungi: Opportunities for Therapeutic Development. Microorganisms 2025; 13:862. [PMID: 40284698 PMCID: PMC12029249 DOI: 10.3390/microorganisms13040862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 03/22/2025] [Accepted: 04/03/2025] [Indexed: 04/29/2025] Open
Abstract
Ergosterol plays a dual role in fungal pathogenesis and azole resistance, driving key advancements in the understanding of its biosynthesis regulation. This review integrates the latest research progress on the regulation of fungal ergosterol biosynthesis and its role in drug resistance and pathogenicity. We comprehensively discuss the functions of key enzymes (such as Erg11p/Cyp51A, Erg6p, Erg3p, and Erg25p) in the mevalonate, late, and alternative pathways. Notably, we highlight the complex regulation of cyp51A expression by factors such as SrbA, AtrR, CBC, HapX, and NCT in Aspergillus fumigatus, and elucidate the distinctive roles of Upc2, Adr1, and Rpn4 in Candida species. Importantly, we summarize recent discoveries on the CprA-dependent regulation of Cyp51A/Erg11p and heme-mediated stability control. Based on these findings, we propose innovative antifungal strategies, including dual-target inhibition and multi-enzyme inhibition by natural products, which provide novel insights and potential directions for the development of next-generation antifungal therapies.
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Affiliation(s)
- Lingyun Song
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (L.S.); (X.Y.); (S.J.)
| | - Sha Wang
- Huzhou Key Laboratory of Precise Prevention and Control of Major Chronic Diseases, Huzhou University, Huzhou 313000, China;
| | - Hang Zou
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610059, China;
| | - Xiaokang Yi
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (L.S.); (X.Y.); (S.J.)
| | - Shihan Jia
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (L.S.); (X.Y.); (S.J.)
| | - Rongpeng Li
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (L.S.); (X.Y.); (S.J.)
| | - Jinxing Song
- The Key Laboratory of Biotechnology for Medicinal and Edible Plant Resources of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China; (L.S.); (X.Y.); (S.J.)
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Science, Institute of Drug Discovery Technology, Ningbo 315211, China
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2
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Yu P, Zhou M, Yu D, Zhang Z, Ye S, Yu Y, Sun X, Li S, Hu C. Targeted regulation of sterol biosynthesis genes according to perturbations in ergosterol biosynthesis in fungi. J Adv Res 2025:S2090-1232(25)00065-7. [PMID: 39892608 DOI: 10.1016/j.jare.2025.01.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 12/23/2024] [Accepted: 01/27/2025] [Indexed: 02/04/2025] Open
Abstract
INTRODUCTION The synthesis and regulation of ergosterol are vital for fungal growth and stress adaptation. While ergosterol-mediated feedback regulation is a recognized mechanism controlling sterol biosynthesis in fungi, prior research suggests the presence of additional regulatory mechanisms. However, the specifics of the alternative regulatory mechanisms have not been systematically investigated. OBJECTIVES We proposed that a regulatory network is likely to discern disturbances in sterol biosynthesis and trigger responses accordingly. This study aimed to validate the hypothesis and investigate the regulatory mechanisms. METHODS Quantitative Real-time PCR and HPLC-MS/MS were used to explore and compare the regulation of sterol biosynthesis in different fungi. Key transcription factors involved in the alternative regulatory mechanism in Neurospora crassa were identified by phenotypic profiling of a transcription factor mutant library. ChIP-qPCR, fluorescence confocal imaging, RNA sequencing, and gene set enrichment analysis (GSEA) were used to reveal the mechanism of each transcription factor. RESULTS Unlike the canonical ergosterol-mediated feedback regulation in fungi like C. neoformans, our study demonstrated that the inhibitions of ergosterol biosynthesis at specific steps triggered distinct transcriptional responses of erg genes in fungi, including N. crassa and Aspergillus fumigatus. In N. crassa, the responses were orchestrated by different transcription factors. Specifically, the inhibition of ERG24 and ERG2 activated transcription factors SAH-2 and AtrR, resulting in the upregulation of erg24, erg2, erg25, and erg3. Furthermore, the inhibition of ERG11/CYP51 activated transcription factor NcSR, leading to the upregulation of erg11 and erg6. Phenotypic profiles of mutants of various N. crassa erg genes and the aforementioned transcription factors implied that the targeted regulation of ergosterol biosynthesis could fortify fungal viability within complex habitats. CONCLUSION Our study reveals a novel regulatory mechanism in fungi: targeted upregulation of specific sterol biosynthesis genes in response to given perturbations in ergosterol biosynthesis, exhibiting a higher degree of precision and sophistication in sterol biosynthesis regulation.
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Affiliation(s)
- Pengju Yu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101 China
| | - Mi Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 China; National Institute for Radiological Protection, China CDC, Beijing 100101 China
| | - Deshui Yu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin 150010 China
| | - Zhongchi Zhang
- Shanghai Fondin Bio_Tech Company Limited, Shanghai 201204 China
| | - Shuting Ye
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101 China
| | - Yifa Yu
- Nanning Harworld Biological Technology Company Limited, Nanning 530000 China
| | - Xianyun Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101 China
| | - Shaojie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101 China.
| | - Chengcheng Hu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 China.
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Yu P, Ye S, Zhou M, Zhang L, Zhang Z, Sun X, Li S, Hu C. PWWP domain-containing protein Crf4-3 specifically modulates fungal azole susceptibility by regulating sterol C-14 demethylase ERG11. mSphere 2025; 10:e0070324. [PMID: 39670730 PMCID: PMC11774033 DOI: 10.1128/msphere.00703-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 11/22/2024] [Indexed: 12/14/2024] Open
Abstract
The widespread use of azole antifungals in agriculture and clinical settings has led to serious drug resistance. Overexpression of the azole drug target 14α-demethylase ERG11 (CYP51) is the most common fungal resistance mechanism. However, the presence of additional regulatory proteins in the transcriptional response of erg11 is not yet fully elucidated. In this study, leveraging the identified key promoter region of erg11 that controls its response to azoles in Neurospora crassa, we pinpointed a protein, Crf4-3, which harbors a PWWP domain and exerts a positive regulatory influence on azole resistance, as determined by DNA pulldown assays. The removal of Crf4-3 results in heightened sensitivity to azoles while remaining unaffected by other stressors tested. Additionally, the deletion leads to the abolition of transcriptional responses of genes such as erg11 and erg6 to ketoconazole. Interestingly, the basal expression of erg1, erg11, erg25, and erg3A is also affected by the deletion of crf4-3, indicating its role in sterol homeostasis. Crf4-3 homologs are broadly distributed across the Pezizomycotina fungi. The gene deletion for its homologous protein in Aspergillus fumigatus also significantly improves sensitivity to azoles such as voriconazole, primarily through the attenuation of the transcriptional response of erg11. Our data, for the first time, identified Crf4-3 as a novel regulatory protein in the azole stress response of filamentous fungi, offering fresh insights into the mechanisms of azole resistance.IMPORTANCETranscriptional control of pivotal genes, such as erg11, stands as the primary driver of azole resistance. Although considerable effort has been dedicated to identifying transcription factors involved, our knowledge regarding the use of transcriptional regulation strategies to combat azole resistance is currently limited. In this study, we reveal that a PWWP domain-containing protein Crf4-3, which is conserved in Pezizomycotina fungi, modulates fungal azole sensitivity by transcriptionally regulating sterol biosynthetic genes, including erg11. These results also broaden the understanding of fungal PWWP domain-containing proteins regarding their roles in regulating resistance against azole antifungals. Considering research on small molecules targeting the PWWP domain in humans, Crf4-3 homolog emerges as a promising target for designing fungal-specific drugs to combat azole resistance.
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Affiliation(s)
- Pengju Yu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuting Ye
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mi Zhou
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Long Zhang
- Shandong Jinniu Group Co., Ltd., Jinan, China
| | | | - Xianyun Sun
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shaojie Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chengcheng Hu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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4
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Thorn V, Xu J. From patterns to prediction: machine learning and antifungal resistance biomarker discovery. Can J Microbiol 2025; 71:1-13. [PMID: 40233418 DOI: 10.1139/cjm-2024-0248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
Fungal pathogens significantly impact human health, agriculture, and ecosystems, with infections leading to high morbidity and mortality, especially among immunocompromised individuals. The increasing prevalence of antifungal resistance (AFR) exacerbates these challenges, limiting the effectiveness of current treatments. Identifying robust biomarkers associated AFR could accelerate targeted diagnosis, shorten decision time for treatment strategies, and improve patient health. This paper examines traditional avenues of AFR biomarker detection, contrasting them with the increasingly effective role of machine learning (ML) in advancing diagnostic and therapeutic strategies. The integration of ML with technologies such as mass spectrometry, molecular dynamics, and various omics-based approaches often results in the discovery of diverse and novel resistance biomarkers. ML's capability to analyse complex data patterns enhances the identification of resistance biomarkers and potential drug targets, offering innovative solutions to AFR management. This paper highlights the importance of interdisciplinary approaches and continued innovation in leveraging ML to combat AFR, aiming for more effective and targeted treatments for fungal infections.
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Affiliation(s)
- Veronica Thorn
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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5
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Zhu G, Fu M, Zhang Y, Lu L. A ubiquitin-mediated post-translational degradation of Cyp51A contributes to a novel azole resistance mode in Aspergillus fumigatus. Microbiol Res 2024; 289:127891. [PMID: 39244806 DOI: 10.1016/j.micres.2024.127891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/28/2024] [Accepted: 08/31/2024] [Indexed: 09/10/2024]
Abstract
The airborne fungus Aspergillus fumigatus is a major pathogen that poses a serious health threat to humans by causing aspergillosis. Azole antifungals inhibit sterol 14-demethylase (encoded by cyp51A), an enzyme crucial for fungal cell survival. However, the most common mechanism of azole resistance in A. fumigatus is associated with the mutations in cyp51A and tandem repeats in its promoter, leading to reduced drug-enzyme interaction and overexpression of cyp51A. It remains unknown whether post-translational modifications of Cyp51A contribute to azole resistance. In this study, we report that the Cyp51A expression is highly induced upon exposure to itraconazole, while its ubiquitination level is significantly reduced by itraconazole. Loss of the ubiquitin-conjugating enzyme Ubc7 confers resistance to multiple azole antifungals but hinders hyphal growth, conidiation, and virulence. Western blot and immunoprecipitation assays show that deletion of ubc7 reduces Cyp51A degradation by impairing its ubiquitination, thereby leading to drug resistance. Most importantly, the overexpression of ubc7 in common environmental and clinical azole-resistant cyp51A isolates partially restores azole sensitivity. Our findings demonstrate a non-cyp51A mutation-based resistance mechanism and uncover a novel role of post-translational modification in contributing to azole resistance in A. fumigatus.
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Affiliation(s)
- Guoxing Zhu
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Mengjuan Fu
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yuanwei Zhang
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
| | - Ling Lu
- Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
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6
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Ror S, Stamnes MA, Moye-Rowley WS. Gene-specific transcriptional activation by the Aspergillus fumigatus AtrR factor requires a conserved C-terminal domain. mSphere 2024; 9:e0042524. [PMID: 38975761 PMCID: PMC11288021 DOI: 10.1128/msphere.00425-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024] Open
Abstract
Treatment of fungal infections associated with the filamentous fungus Aspergillus fumigatus is becoming more problematic as this organism is developing resistance to the main chemotherapeutic drug at an increasing rate. Azole drugs represent the current standard-of-care in the treatment of aspergillosis with this drug class acting by inhibiting a key step in the biosynthesis of the fungal sterol ergosterol. Azole compounds block the activity of the lanosterol α-14 demethylase, encoded by the cyp51A gene. A common route of azole resistance involves an increase in transcription of cyp51A. This transcriptional increase requires the function of a Zn2Cys6 DNA-binding domain-containing transcription activator protein called AtrR. AtrR was identified through its action as a positive regulator of expression of an ATP-binding cassette transporter (abcC/cdr1B here called abcG1). Using both deletion and alanine scanning mutagenesis, we demonstrate that a conserved C-terminal domain in A. fumigatus is required for the expression of abcG1 but dispensable for cyp51A transcription. This domain is also found in several other fungal pathogen AtrR homologs consistent with a conserved gene-selective function of this protein segment being conserved. Using RNA sequencing (RNA-seq), we find that this gene-specific transcriptional defect extends to several other membrane transporter-encoding genes including a second ABC transporter locus. Our data reveal that AtrR uses at least two distinct mechanisms to induce gene expression and that normal susceptibility to azole drugs cannot be provided by maintenance of wild-type expression of the ergosterol biosynthetic pathway when ABC transporter expression is reduced. IMPORTANCE Aspergillus fumigatus is the primary human filamentous fungal pathogen. The principal chemotherapeutic drug used to control infections associated with A. fumigatus is the azole compound. These drugs are well-tolerated and effective, but resistance is emerging at an alarming rate. Most resistance is associated with mutations that lead to overexpression of the azole target enzyme, lanosterol α-14 demethylase, encoded by the cyp51A gene. A key regulator of cyp51A gene expression is the transcription factor AtrR. Very little is known of the molecular mechanisms underlying the effect of AtrR on gene expression. Here, we use deletion and clustered amino acid substitution mutagenesis to map a region of AtrR that confers gene-specific activation on target genes of this transcription factor. This region is highly conserved across AtrR homologs from other pathogenic species arguing that its importance in transcriptional regulation is maintained across evolution.
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Affiliation(s)
- Shivani Ror
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - W. Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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7
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Gutierrez-Perez C, Puerner C, Jones JT, Vellanki S, Vesely EM, Xatse MA, Viera AFC, Olsen CP, Attiku KO, Cardinale S, Kwasny SM, G-Dayanandan N, Opperman TJ, Cramer RA. Unsaturated fatty acid perturbation combats emerging triazole antifungal resistance in the human fungal pathogen Aspergillus fumigatus. mBio 2024; 15:e0116624. [PMID: 38934618 PMCID: PMC11253624 DOI: 10.1128/mbio.01166-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/02/2024] [Indexed: 06/28/2024] Open
Abstract
Contemporary antifungal therapies utilized to treat filamentous fungal infections are inhibited by intrinsic and emerging drug resistance. Consequently, there is an urgent need to develop novel antifungal compounds that are effective against drug-resistant filamentous fungi. Here, we utilized an Aspergillus fumigatus cell-based high-throughput screen to identify small molecules with antifungal activity that also potentiated triazole activity. The screen identified 16 hits with promising activity against A. fumigatus. A nonspirocyclic piperidine, herein named MBX-7591, exhibited synergy with triazole antifungal drugs and activity against pan-azole-resistant A. fumigatus isolates. MBX-7591 has additional potent activity against Rhizopus species and CO2-dependent activity against Cryptococcus neoformans. Chemical, genetic, and biochemical mode of action analyses revealed that MBX-7591 increases cell membrane saturation by decreasing oleic acid content. MBX-7591 has low toxicity in vivo and shows good efficacy in decreasing fungal burden in a murine model of invasive pulmonary aspergillosis. Taken together, our results suggest MBX-7591 is a promising hit with a novel mode of action for further antifungal drug development to combat the rising incidence of triazole-resistant filamentous fungal infections.IMPORTANCEThe incidence of infections caused by fungi continues to increase with advances in medical therapies. Unfortunately, antifungal drug development has not kept pace with the incidence and importance of fungal infections, with only three major classes of antifungal drugs currently available for use in the clinic. Filamentous fungi, also called molds, are particularly recalcitrant to contemporary antifungal therapies. Here, a recently developed Aspergillus fumigatus cell reporter strain was utilized to conduct a high-throughput screen to identify small molecules with antifungal activity. An emphasis was placed on small molecules that potentiated the activity of contemporary triazole antifungals and led to the discovery of MBX-7591. MBX-7591 potentiates triazole activity against drug-resistant molds such as A. fumigatus and has activity against Mucorales fungi. MBX-7591's mode of action involves inhibiting the conversion of saturated to unsaturated fatty acids, thereby impacting fungal membrane integrity. MBX-7591 is a novel small molecule with antifungal activity poised for lead development.
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Affiliation(s)
- Cecilia Gutierrez-Perez
- Microbiology and Immunology Department, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Charles Puerner
- Microbiology and Immunology Department, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Jane T. Jones
- Microbiology and Immunology Department, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Sandeep Vellanki
- Microbiology and Immunology Department, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Elisa M. Vesely
- Microbiology and Immunology Department, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Mark A. Xatse
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Andre F. C. Viera
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Carissa P. Olsen
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Keren O. Attiku
- Microbiology and Immunology Department, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | | | | | | | | | - Robert A. Cramer
- Microbiology and Immunology Department, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
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8
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Ror S, Stamnes MA, Moye-Rowley WS. Loss of a conserved C-terminal region of the Aspergillus fumigatus AtrR transcriptional regulator leads to a gene-specific defect in target gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595332. [PMID: 38826412 PMCID: PMC11142210 DOI: 10.1101/2024.05.22.595332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Treatment of fungal infections associated with the filamentous fungus Aspergillus fumigatus is becoming more problematic as this organism is developing resistance to the main chemotherapeutic drug at an increasing rate. Azole drugs represent the current standard-of-care in treatment of aspergillosis with this drug class acting by inhibiting a key step in biosynthesis of the fungal sterol ergosterol. Azole compounds block the activity of the lanosterol α-14 demethylase, encoded by the cyp51A gene. A common route of azole resistance involves an increase in transcription of cyp51A. This transcriptional increase requires the function of a Zn2Cys6 DNA-binding domain-containing transcription activator protein called AtrR. AtrR was identified through its action as a positive regulator of expression of an ATP-binding cassette transporter (abcC/cdr1B here called abcG1). Using both deletion and alanine scanning mutagenesis, we demonstrate that a conserved C-terminal domain in A. fumigatus is required for expression of abcG1 but dispensable for cyp51A transcription. This domain is also found in several other fungal pathogen AtrR homologues consistent with a conserved gene-selective function of this protein segment being conserved. Using RNA-seq, we find that this gene-specific transcriptional defect extends to several other membrane transporter-encoding genes including a second ABC transporter locus. Our data reveal that AtrR uses at least two distinct mechanisms to induce gene expression and that normal susceptibility to azole drugs cannot be provided by maintenance of wild-type expression of the ergosterol biosynthetic pathway when ABC transporter expression is reduced.
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Affiliation(s)
- Shivani Ror
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Mark A Stamnes
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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9
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Xi Y, Zhang J, Fan B, Sun M, Cao W, Liu X, Gai Y, Shen C, Wang H, Wang M. Transcriptome Analysis Reveals Potential Regulators of DMI Fungicide Resistance in the Citrus Postharvest Pathogen Penicillium digitatum. J Fungi (Basel) 2024; 10:360. [PMID: 38786715 PMCID: PMC11122302 DOI: 10.3390/jof10050360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/09/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Green mold, caused by Penicillium digitatum, is the major cause of citrus postharvest decay. Currently, the application of sterol demethylation inhibitor (DMI) fungicide is one of the main control measures to prevent green mold. However, the fungicide-resistance problem in the pathogen P. digitatum is growing. The regulatory mechanism of DMI fungicide resistance in P. digitatum is poorly understood. Here, we first performed transcriptomic analysis of the P. digitatum strain Pdw03 treated with imazalil (IMZ) for 2 and 12 h. A total of 1338 genes were up-regulated and 1635 were down-regulated under IMZ treatment for 2 h compared to control while 1700 were up-regulated and 1661 down-regulated under IMZ treatment for 12 h. The expression of about half of the genes in the ergosterol biosynthesis pathway was affected during IMZ stress. Further analysis identified that 84 of 320 transcription factors (TFs) were differentially expressed at both conditions, making them potential regulators in DMI resistance. To confirm their roles, three differentially expressed TFs were selected to generate disruption mutants using the CRISPR/Cas9 technology. The results showed that two of them had no response to IMZ stress while ∆PdflbC was more sensitive compared with the wild type. However, disruption of PdflbC did not affect the ergosterol content. The defect in IMZ sensitivity of ∆PdflbC was restored by genetic complementation of the mutant with a functional copy of PdflbC. Taken together, our results offer a rich source of information to identify novel regulators in DMI resistance.
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Affiliation(s)
- Yue Xi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.X.); (J.Z.); (B.F.); (M.S.); (W.C.); (X.L.); (C.S.); (H.W.)
| | - Jing Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.X.); (J.Z.); (B.F.); (M.S.); (W.C.); (X.L.); (C.S.); (H.W.)
| | - Botao Fan
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.X.); (J.Z.); (B.F.); (M.S.); (W.C.); (X.L.); (C.S.); (H.W.)
| | - Miaomiao Sun
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.X.); (J.Z.); (B.F.); (M.S.); (W.C.); (X.L.); (C.S.); (H.W.)
| | - Wenqian Cao
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.X.); (J.Z.); (B.F.); (M.S.); (W.C.); (X.L.); (C.S.); (H.W.)
| | - Xiaotian Liu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.X.); (J.Z.); (B.F.); (M.S.); (W.C.); (X.L.); (C.S.); (H.W.)
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China;
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.X.); (J.Z.); (B.F.); (M.S.); (W.C.); (X.L.); (C.S.); (H.W.)
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.X.); (J.Z.); (B.F.); (M.S.); (W.C.); (X.L.); (C.S.); (H.W.)
| | - Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (Y.X.); (J.Z.); (B.F.); (M.S.); (W.C.); (X.L.); (C.S.); (H.W.)
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10
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Lockhart SR, Chowdhary A, Gold JAW. The rapid emergence of antifungal-resistant human-pathogenic fungi. Nat Rev Microbiol 2023; 21:818-832. [PMID: 37648790 PMCID: PMC10859884 DOI: 10.1038/s41579-023-00960-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/01/2023]
Abstract
During recent decades, the emergence of pathogenic fungi has posed an increasing public health threat, particularly given the limited number of antifungal drugs available to treat invasive infections. In this Review, we discuss the global emergence and spread of three emerging antifungal-resistant fungi: Candida auris, driven by global health-care transmission and possibly facilitated by climate change; azole-resistant Aspergillus fumigatus, driven by the selection facilitated by azole fungicide use in agricultural and other settings; and Trichophyton indotineae, driven by the under-regulated use of over-the-counter high-potency corticosteroid-containing antifungal creams. The diversity of the fungi themselves and the drivers of their emergence make it clear that we cannot predict what might emerge next. Therefore, vigilance is critical to monitoring fungal emergence, as well as the rise in overall antifungal resistance.
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Affiliation(s)
- Shawn R Lockhart
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Anuradha Chowdhary
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Jeremy A W Gold
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Kühbacher A, Merschak P, Haas H, Liebl M, Müller C, Gsaller F. The cytochrome P450 reductase CprA is a rate-limiting factor for Cyp51A-mediated azole resistance in Aspergillus fumigatus. Antimicrob Agents Chemother 2023; 67:e0091823. [PMID: 37815358 PMCID: PMC10648939 DOI: 10.1128/aac.00918-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/12/2023] [Indexed: 10/11/2023] Open
Abstract
Azole antifungals remain the "gold standard" therapy for invasive aspergillosis. The world-wide emergence of isolates resistant to this drug class, however, developed into a steadily increasing threat to human health over the past years. In Aspergillus fumigatus, major mechanisms of resistance involve increased expression of cyp51A encoding one of two isoenzymes targeted by azoles. Yet, the level of resistance caused by cyp51A upregulation, driven by either clinically relevant tandem repeat mutations within its promoter or the use of high expressing heterologous promoters, is limited. Cytochrome P450 enzymes such as Cyp51A rely on redox partners that provide electrons for their activity. A. fumigatus harbors several genes encoding putative candidate proteins including two paralogous cytochrome P450 reductases, CprA and CprB, and the cytochrome b 5 CybE. In this work, we investigated the contribution of each cprA, cprB, and cybE overexpression to cyp51A-mediated resistance to different medical and agricultural azoles. Using the bidirectional promoter PxylP, we conditionally expressed these genes in combination with cyp51A, revealing cprA as the main limiting factor. Similar to this approach, we overexpressed cprA in an azole-resistant background strain carrying a cyp51A allele with TR34 in its promoter, which led to a further increase in its resistance. Employing sterol measurements, we demonstrate an enhanced eburicol turnover during upregulation of either cprA or cyp51A, which was even more pronounced during their simultaneous overexpression. In summary, our work suggests that mutations leading to increased Cyp51A activity through increased electron supply could be key factors that elevate azole resistance.
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Affiliation(s)
- Alexander Kühbacher
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Petra Merschak
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Hubertus Haas
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Maximilian Liebl
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians Universität München, Munich, Germany
| | - Christoph Müller
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians Universität München, Munich, Germany
| | - Fabio Gsaller
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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Paul S, Stamnes MA, Moye-Rowley WS. Interactions between the transcription factors FfmA and AtrR are required to properly regulate gene expression in the fungus Aspergillus fumigatus. G3 (BETHESDA, MD.) 2023; 13:jkad173. [PMID: 37523774 PMCID: PMC10542180 DOI: 10.1093/g3journal/jkad173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/05/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
Transcriptional regulation of azole resistance in the filamentous fungus Aspergillus fumigatus is a key step in development of this problematic clinical phenotype. We and others have previously described a C2H2-containing transcription factor called FfmA that is required for normal levels of voriconazole susceptibility. Null alleles of ffmA exhibit a strongly compromised growth rate even in the absence of any external stress. Here, we employ an acutely repressible doxycycline-off form of ffmA to rapidly deplete FfmA protein from the cell. Using this approach, we carried out RNA-seq analyses to probe the transcriptome cells acutely deprived of FfmA. A total of 2,000 genes were differentially expressed upon acute depletion of FfmA, illustrating the broad transcriptomic effect of this factor. Interestingly, the transcriptome changes observed upon this acute depletion of FfmA expression only shared limited overlap with those found in an ffmAΔ null strain analyzed by others. Chromatin immunoprecipitation coupled with high throughput DNA sequencing analysis (ChIP-seq) identified 530 genes that were bound by FfmA. More than 300 of these genes were also bound by AtrR, a transcription factor important in azole drug resistance, demonstrating striking regulatory overlap with FfmA. However, while AtrR is an upstream activation protein with known specificity, our data suggest that FfmA is a chromatin-associated factor that binds DNA in a manner dependent on other factors. We provide evidence that AtrR and FfmA interact in the cell and show reciprocal expression modulation. Interaction of AtrR and FfmA is required for normal gene expression in A. fumigatus.
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Affiliation(s)
- Sanjoy Paul
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Mark A Stamnes
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - W Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Yap A, Volz R, Paul S, Moye-Rowley WS, Haas H. Regulation of High-Affinity Iron Acquisition, Including Acquisition Mediated by the Iron Permease FtrA, Is Coordinated by AtrR, SrbA, and SreA in Aspergillus fumigatus. mBio 2023; 14:e0075723. [PMID: 37093084 PMCID: PMC10294635 DOI: 10.1128/mbio.00757-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
Iron acquisition is crucial for virulence of the human pathogen Aspergillus fumigatus. Previous studies indicated that this mold regulates iron uptake via both siderophores and reductive iron assimilation by the GATA factor SreA and the SREBP regulator SrbA. Here, characterization of loss of function as well as hyperactive alleles revealed that transcriptional activation of iron uptake depends additionally on the Zn2Cys6 regulator AtrR, most likely via cooperation with SrbA. Mutational analysis of the promoter of the iron permease-encoding ftrA gene identified a 210-bp sequence, which is both essential and sufficient to impart iron regulation. Further studies located functional sequences, densely packed within 75 bp, that largely resemble binding motifs for SrbA, SreA, and AtrR. The latter, confirmed by chromatin immunoprecipitation (ChIP) analysis, is the first one not fully matching the 5'-CGGN12CCG-3' consensus sequence. The results presented here emphasize for the first time the direct involvement of SrbA, AtrR, and SreA in iron regulation. The essential role of both AtrR and SrbA in activation of iron acquisition underlines the coordination of iron homeostasis with biosynthesis of ergosterol and heme as well as adaptation to hypoxia. The rationale is most likely the iron dependence of these pathways along with the enzymatic link of biosynthesis of ergosterol and siderophores. IMPORTANCE Aspergillus fumigatus is the most common filamentous fungal pathogen infecting humans. Iron acquisition via siderophores has previously been shown to be essential for virulence of this mold species. Here, we demonstrate that AtrR, a transcription factor previously shown to control ergosterol biosynthesis, azole resistance, and adaptation to hypoxia, is essential for activation of iron acquisition, including siderophore biosynthesis and uptake. Dissection of an iron-regulated promoter identified binding motifs for AtrR and the two previously identified regulators of iron acquisition, SrbA and SreA. Altogether, this study identified a new regulator required for maintenance of iron homeostasis, revealed insights into promoter architecture for iron regulation, and emphasized the coordinated regulation of iron homeostasis ergosterol biosynthesis and adaptation to hypoxia.
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Affiliation(s)
- Annie Yap
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Ricarda Volz
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Sanjoy Paul
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - W. Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Hubertus Haas
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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Paul S, Stamnes MA, Moye-Rowley WS. Transcription factor FfmA interacts both physically and genetically with AtrR to properly regulate gene expression in the fungus Aspergillus fumigatus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543935. [PMID: 37333080 PMCID: PMC10274792 DOI: 10.1101/2023.06.06.543935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Transcriptional regulation of azole resistance in the filamentous fungus Aspergillus fumigatus is a key step in development of this problematic clinical phenotype. We and others have previously described a C2H2-containing transcription factor called FfmA that is required for normal levels of voriconazole susceptibility and expression of an ATP-binding cassette transporter gene called abcG1 . Null alleles of ffmA exhibit a strongly compromised growth rate even in the absence of any external stress. Here we employ an acutely repressible doxycycline-off form of ffmA to rapidly deplete FfmA protein from the cell. Using this approach, we carried out RNA-seq analyses to probe the transcriptome of A. fumigatus cells that have been deprived of normal FfmA levels. We found that 2000 genes were differentially expressed upon depletion of FfmA, consistent with the wide-ranging effect of this factor on gene regulation. Chromatin immunoprecipitation coupled with high throughput DNA sequencing analysis (ChIP-seq) identified 530 genes that were bound by FfmA using two different antibodies for immunoprecipitation. More than 300 of these genes were also bound by AtrR demonstrating the striking regulatory overlap with FfmA. However, while AtrR is clearly an upstream activation protein with clear sequence specificity, our data suggest that FfmA is a chromatin-associated factor that may bind to DNA in a manner dependent on other factors. We provide evidence that AtrR and FfmA interact in the cell and can influence one another's expression. This interaction of AtrR and FfmA is required for normal azole resistance in A. fumigatus .
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Affiliation(s)
- Sanjoy Paul
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA. 52242 USA
| | - Mark A. Stamnes
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA. 52242 USA
| | - W. Scott Moye-Rowley
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA. 52242 USA
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Biochemical Identification of a Nuclear Coactivator Protein Required for AtrR-Dependent Gene Regulation in Aspergillus fumigatus. mSphere 2022; 7:e0047622. [PMID: 36374043 PMCID: PMC9769526 DOI: 10.1128/msphere.00476-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Azole drugs represent the primary means of treating infections associated with the filamentous fungal pathogen Aspergillus fumigatus. A central player in azole resistance is the Zn2Cys6 zinc cluster-containing transcription factor AtrR. This factor stimulates expression of both the cyp51A gene, which encodes the azole drug target enzyme, as well as an ATP-binding cassette transporter-encoding gene called abcG1 (cdr1B). We used a fusion protein between AtrR and the tandem affinity purification (TAP) moiety to purify proteins that associated with AtrR from A. fumigatus. Protein fractions associated with AtrR-TAP were subjected to multidimensional protein identification technology mass spectrometry, and one of the proteins identified was encoded by the AFUA_6g08010 gene. We have designated this protein NcaA (for nuclear coactivator of AtrR). Loss of ncaA caused a reduction in voriconazole resistance and drug-induced abcG1 expression, although it did not impact induction of cyp51A transcription. We confirmed the association of AtrR and NcaA by coimmunoprecipitation from otherwise-wild-type cells. Expression of fusion proteins between AtrR and NcaA with green fluorescent protein allowed determination that these two proteins were localized in the A. fumigatus nucleus. Together, these data support the view that NcaA is required for nuclear gene transcription controlled by AtrR. IMPORTANCE Aspergillus fumigatus is a major filamentous fungal pathogen in humans and is susceptible to the azole antifungal class of drugs. However, loss of azole susceptibility has been detected with increasing frequency in the clinic, and infections associated with these azole-resistant isolates have been linked to treatment failure and worse outcomes. Many of these azole-resistant strains contain mutant alleles of the cyp51A gene, which encodes the azole drug target. A transcription factor essential for cyp51A gene transcription has been identified and designated AtrR. AtrR is required for azole-inducible cyp51A transcription, but we know little of the regulation of this transcription factor. Using a biochemical approach, we identified a new protein called NcaA that is involved in regulation of AtrR at certain target gene promoters. Understanding the mechanisms controlling AtrR function is an important goal in preventing or reversing azole resistance in this pathogen.
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