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Zhou X, Hilk A, Solis NV, Scott N, Beach A, Soisangwan N, Billings CL, Burrack LS, Filler SG, Selmecki A. Single-cell detection of copy number changes reveals dynamic mechanisms of adaptation to antifungals in Candida albicans. Nat Microbiol 2024:10.1038/s41564-024-01795-7. [PMID: 39227665 DOI: 10.1038/s41564-024-01795-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 07/24/2024] [Indexed: 09/05/2024]
Abstract
Genomic copy number changes are associated with antifungal drug resistance and virulence across diverse fungal pathogens, but the rate and dynamics of these genomic changes in the presence of antifungal drugs are unknown. Here we optimized a dual-fluorescent reporter system in the diploid pathogen Candida albicans to quantify haplotype-specific copy number variation (CNV) and loss of heterozygosity (LOH) at the single-cell level with flow cytometry. We followed the frequency and dynamics of CNV and LOH at two distinct genomic locations in the presence and absence of antifungal drugs in vitro and in a murine model of candidiasis. Copy number changes were rapid and dynamic during adaptation to fluconazole and frequently involved competing subpopulations with distinct genotypes. This study provides quantitative evidence for the rapid speed at which diverse genotypes arise and undergo dynamic population-level fluctuations during adaptation to antifungal drugs in vitro and in vivo.
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Affiliation(s)
- Xin Zhou
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Audrey Hilk
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Norma V Solis
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Nancy Scott
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Annette Beach
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Natthapon Soisangwan
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Clara L Billings
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Laura S Burrack
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Scott G Filler
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA.
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2
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Woodruff AL, Berman J, Anderson M. Strain background of Candida albicans interacts with SIR2 to alter phenotypic switching. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001444. [PMID: 38446018 PMCID: PMC10999749 DOI: 10.1099/mic.0.001444] [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: 09/22/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
The genetic background between strains of a single species and within a single strain lineage can significantly impact the expression of biological traits. This genetic variation may also reshape epigenetic mechanisms of cell identity and environmental responses that are controlled by interconnected transcriptional networks and chromatin-modifying enzymes. Histone deacetylases, including sirtuins, are critical regulators of chromatin state and have been directly implicated in governing the phenotypic transition between the 'sterile' white state and the mating-competent opaque state in Candida albicans, a common fungal commensal and pathogen of humans. Here, we found that a previously ambiguous role for the sirtuin SIR2 in C. albicans phenotypic switching is likely linked to the genetic background of mutant strains produced in the RM lineage of SC5314. SIR2 mutants in a specific lineage of BWP17 displayed increased frequencies of switching to the opaque state compared to the wild-type. Loss of SIR2 in other SC5314-derived backgrounds, including newly constructed BWP17 sir2Δ/Δ mutants, failed to recapitulate the increased white-opaque switching frequencies observed in the original BWP17 sir2Δ/Δ mutant background. Whole-genome sequencing revealed the presence of multiple imbalanced chromosomes and large loss of heterozygosity tracts that likely interact with SIR2 to increase phenotypic switching in this BWP17 sir2Δ/Δ mutant lineage. These genomic changes are not found in other SC5314-derived sir2Δ/Δ mutants that do not display increased opaque cell formation. Thus, complex karyotypes can emerge during strain construction that modify mutant phenotypes and highlight the importance of validating strain background when interpreting phenotypes.
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Affiliation(s)
- Andrew L. Woodruff
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Matthew Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
- Department of Medical Genetics, Laboratory of Genetics, University of Wisconsin – Madison, Madison, WI, 53706, USA
- Center for Genomic Science Innovation, University of Wisconsin – Madison, Madison, WI, 53706, USA
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Druseikis M, Mottola A, Berman J. The Metabolism of Susceptibility: Clearing the FoG Between Tolerance and Resistance in Candida albicans. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023; 10:36-46. [DOI: 10.1007/s40588-023-00189-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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4
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Kakade P, Sircaik S, Maufrais C, Ene IV, Bennett RJ. Aneuploidy and gene dosage regulate filamentation and host colonization by Candida albicans. Proc Natl Acad Sci U S A 2023; 120:e2218163120. [PMID: 36893271 PMCID: PMC10089209 DOI: 10.1073/pnas.2218163120] [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: 10/24/2022] [Accepted: 02/02/2023] [Indexed: 03/11/2023] Open
Abstract
Aneuploidy is a frequent occurrence in fungal species where it can alter gene expression and promote adaptation to a variety of environmental cues. Multiple forms of aneuploidy have been observed in the opportunistic fungal pathogen Candida albicans, which is a common component of the human gut mycobiome but can escape this niche and cause life-threatening systemic disease. Using a barcode sequencing (Bar-seq) approach, we evaluated a set of diploid C. albicans strains and found that a strain carrying a third copy of chromosome (Chr) 7 was associated with increased fitness during both gastrointestinal (GI) colonization and systemic infection. Our analysis revealed that the presence of a Chr 7 trisomy resulted in decreased filamentation, both in vitro and during GI colonization, relative to isogenic euploid controls. A target gene approach demonstrated that NRG1, encoding a negative regulator of filamentation located on Chr 7, contributes to increased fitness of the aneuploid strain due to inhibition of filamentation in a gene dosage-dependent fashion. Together, these experiments establish how aneuploidy enables the reversible adaptation of C. albicans to its host via gene dosage-dependent regulation of morphology.
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Affiliation(s)
- Pallavi Kakade
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
| | - Shabnam Sircaik
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
| | - Corinne Maufrais
- Institut Pasteur Bioinformatic Hub, Université Paris Cité, Paris75015, France
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Lab, Paris75015, France
| | - Iuliana V. Ene
- Institut Pasteur, Université Paris Cité, Fungal Heterogeneity Lab, Paris75015, France
| | - Richard J. Bennett
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI02912
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5
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Antifungal Tolerance and Resistance Emerge at Distinct Drug Concentrations and Rely upon Different Aneuploid Chromosomes. mBio 2023; 14:e0022723. [PMID: 36877011 PMCID: PMC10127634 DOI: 10.1128/mbio.00227-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Antifungal drug tolerance is a response distinct from resistance, in which cells grow slowly above the MIC. Here, we found that the majority (69.2%) of 133 Candida albicans clinical isolates, including standard lab strain SC5314, exhibited temperature-enhanced tolerance at 37°C and 39°C, and were not tolerant at 30°C. Other isolates were either always tolerant (23.3%) or never tolerant (7.5%) at these three temperatures, suggesting that tolerance requires different physiological processes in different isolates. At supra-MIC fluconazole concentrations (8 to 128 μg/mL), tolerant colonies emerged rapidly at a frequency of ~10-3. In liquid passages over a broader range of fluconazole concentrations (0.25 to 128 μg/mL), tolerance emerged rapidly (within one passage) at supra-MICs. In contrast, resistance appeared at sub-MICs after 5 or more passages. Of 155 adaptors that evolved higher tolerance, all carried one of several recurrent aneuploid chromosomes, often including chromosome R, alone or in combination with other chromosomes. Furthermore, loss of these recurrent aneuploidies was associated with a loss of acquired tolerance, indicating that specific aneuploidies confer fluconazole tolerance. Thus, genetic background and physiology and the degree of drug stress (above or below the MIC) influence the evolutionary trajectories and dynamics with which antifungal drug resistance or tolerance emerges. IMPORTANCE Antifungal drug tolerance differs from drug resistance: tolerant cells grow slowly in drug, while resistant cells usually grow well, due to mutations in a few known genes. More than half of Candida albicans clinical isolates have higher tolerance at body temperature than they do at the lower temperatures used for most lab experiments. This implies that different isolates achieve drug tolerance via several cellular processes. When we evolved different strains at a range of high drug concentrations above inhibitory levels, tolerance emerged rapidly and at high frequency (one in 1,000 cells) while resistance appeared only later at very low drug concentrations. An extra copy of all or part of chromosome R was associated with tolerance, while point mutations or different aneuploidies were seen with resistance. Thus, genetic background and physiology, temperature, and drug concentration all influence how drug tolerance or resistance evolves.
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Sun LL, Li H, Yan TH, Fang T, Wu H, Cao YB, Lu H, Jiang YY, Yang F. Aneuploidy Mediates Rapid Adaptation to a Subinhibitory Amount of Fluconazole in Candida albicans. Microbiol Spectr 2023; 11:e0301622. [PMID: 36853047 PMCID: PMC10101127 DOI: 10.1128/spectrum.03016-22] [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: 08/02/2022] [Accepted: 02/04/2023] [Indexed: 03/01/2023] Open
Abstract
Candida albicans is a prevalent, opportunistic, human fungal pathogen. Antifungal drug resistance and tolerance are two distinct mechanisms of adaptation to drugs. Studies of mechanisms of drug resistance are limited to the applications of high doses of drugs. Few studies have investigated the effects of subinhibitory amounts of drugs on the development of drug resistance or tolerance. In this study, we found that growth in a subinhibitory amount of fluconazole (FLC), a widely used antifungal drug, for just a short time was sufficient to induce aneuploidy in C. albicans. Surprisingly, the aneuploids displayed fitness loss in the presence of subinhibitory FLC, but a subpopulation of cells could tolerate up to 128 μg/mL FLC. Particular aneuploidy (ChrR trisomy) caused tolerance, not resistance, to FLC. In the absence of FLC, the aneuploids were unstable. Depending on the karyotype, aneuploids might become completely euploid or maintain particular aneuploidy, and, accordingly, the tolerance would be lost or maintained. Mechanistically, subinhibitory FLC was sufficient to induce the expression of several ERG genes and as well as the drug efflux gene MDR1. Aneuploids had a constitutive high-level expression of genes on and outside the aneuploid chromosomes, including most of the ERG genes as well as the drug efflux genes MDR1 and CDR2. Therefore, aneuploids were prepared for FLC challenges. In summary, aneuploidy provides a rapid and reversible strategy of adaptation when C. albicans is challenged with subinhibitory concentrations of FLC. IMPORTANCE Genome instability is a hallmark of C. albicans. Aneuploidy usually causes fitness loss in the absence of stress but confers better fitness under particular stress conditions. Therefore, aneuploidy is considered to be a double-edged sword. Here, we extend the understanding of aneuploidy. We found that aneuploidy arose under weak stress conditions but that it did not confer better fitness to the stress. Instead, it was less fit than its euploid counterparts. If the stress was withdrawn, aneuploidy spontaneously reverted to euploidy. If the stress became stronger, aneuploidy enabled subpopulation growth in a dose-independent manner of the stress. Therefore, we posit that aneuploidy enables the rapid and reversible development of drug tolerance in C. albicans. Further studies are required to investigate whether this is a general mechanism in human fungal pathogens.
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Affiliation(s)
- Liu-liu Sun
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Physiology and Pharmacology, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hao Li
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Physiology and Pharmacology, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Tian-hua Yan
- Department of Physiology and Pharmacology, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Ting Fang
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hao Wu
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yong-bing Cao
- Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hui Lu
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuan-ying Jiang
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feng Yang
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
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Todd RT, Selmecki A. Copy Number Variation and Allele Ratio Analysis in Candida albicans Using Whole Genome Sequencing Data. Methods Mol Biol 2023; 2658:105-125. [PMID: 37024698 PMCID: PMC10676714 DOI: 10.1007/978-1-0716-3155-3_8] [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] [Indexed: 04/28/2023]
Abstract
Whole genome sequencing of human fungal pathogens has revolutionized the speed and accuracy in which sequence variants that cause antifungal resistance can be identified. Genome rearrangements resulting in copy number variation (CNV) are a significant source of acquired antifungal drug resistance across diverse fungal species. Some CNVs are transient in nature, while other CNVs are stable and well tolerated even in the absence of antifungal drugs. By visualizing whole genome sequencing read depth as a function of genomic location, CNVs and CNV breakpoints (genomic positions where the copy number changes occur relative to the rest of the genome) are rapidly identified. A similar analysis can be used to visualize allele ratio changes that occur across the genomes of heterozygous fungal species, both in the presence and absence of CNVs. This protocol walks through the bioinformatic analysis of CNVs and allele ratios utilizing free, open-source visualization tools. We provide code to use with an example dataset (matched antifungal drug-sensitive and drug-resistant Candida albicans isolates) and notes on how to expand this protocol to other fungal genomes.
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Affiliation(s)
- Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA.
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8
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Sun LL, Li H, Yan TH, Cao YB, Jiang YY, Yang F. Aneuploidy enables cross-tolerance to unrelated antifungal drugs in Candida parapsilosis. Front Microbiol 2023; 14:1137083. [PMID: 37113223 PMCID: PMC10126355 DOI: 10.3389/fmicb.2023.1137083] [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: 01/04/2023] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
Candida parapsilosis is an emerging major human fungal pathogen. Echinocandins are first-line antifungal drugs for the treatment of invasive Candida infections. In clinical isolates, tolerance to echinocandins in Candida species is mostly due to point mutations of FKS genes, which encode the target protein of echinocandins. However, here, we found chromosome 5 trisomy was the major mechanism of adaptation to the echinocandin drug caspofungin, and FKS mutations were rare events. Chromosome 5 trisomy conferred tolerance to echinocandin drugs caspofungin and micafungin and cross-tolerance to 5-flucytosine, another class of antifungal drugs. The inherent instability of aneuploidy caused unstable drug tolerance. Tolerance to echinocandins might be due to increased copy number and expression of CHS7, which encodes chitin synthase. Although copy number of chitinase genes CHT3 and CHT4 was also increased to the trisomic level, the expression was buffered to the disomic level. Tolerance to 5-flucytosine might be due to the decreased expression of FUR1. Therefore, the pleiotropic effect of aneuploidy on antifungal tolerance was due to the simultaneous regulation of genes on the aneuploid chromosome and genes on euploid chromosomes. In summary, aneuploidy provides a rapid and reversible mechanism of drug tolerance and cross-tolerance in C. parapsilosis.
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Affiliation(s)
- Liu-liu Sun
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Physiology and Pharmacology, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hao Li
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Physiology and Pharmacology, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Tian-hua Yan
- Department of Physiology and Pharmacology, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yong-bing Cao
- Department of Vascular Diseases, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuan-ying Jiang
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- Yuan-ying Jiang
| | - Feng Yang
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Feng Yang
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9
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Genome plasticity in Candida albicans: A cutting-edge strategy for evolution, adaptation, and survival. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105256. [PMID: 35231665 DOI: 10.1016/j.meegid.2022.105256] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/12/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022]
Abstract
Candida albicans is the most implicated fungal species that grows as a commensal or opportunistic pathogen in the human host. It is associated with many life-threatening infections, especially in immunocompromised persons. The genome of Candida albicans is very flexible and can withstand a wide assortment of variations in a continuously changing environment. Thus, genome plasticity is central to its adaptation and has long been of considerable interest. C. albicans has a diploid heterozygous genome that is highly dynamic and can display variation from small to large scale chromosomal rearrangement and aneuploidy, which have implications in drug resistance, virulence, and pathogenicity. This review presents an up-to-date overview of recent genomic studies involving C. albicans. It discusses the accumulating evidence that shows how mitotic recombination events, ploidy dynamics, aneuploidy, and loss of heterozygosity (LOH) influence evolution, adaptation, and survival in C. albicans. Understanding the factors that affect the genome is crucial for a proper understanding of species and rapid development and adjustment of therapeutic strategies to mitigate their spread.
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Abstract
Aneuploidy, a genomic alternation characterized by deviations in the copy number of chromosomes, affects organisms from early development through to aging. Although it is a main cause of human pregnancy loss and a hallmark of cancer, how aneuploidy affects cellular function has been elusive. The last two decades have seen rapid advances in the understanding of the causes and consequences of aneuploidy at the molecular and cellular levels. These studies have uncovered effects of aneuploidy that can be beneficial or detrimental to cells and organisms in an environmental context-dependent and karyotype-dependent manner. Aneuploidy also imposes general stress on cells that stems from an imbalanced genome and, consequently, also an imbalanced proteome. These insights provide the fundamental framework for understanding the impact of aneuploidy in genome evolution, human pathogenesis and drug resistance.
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11
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Colabardini AC, Wang F, Miao Z, Pardeshi L, Valero C, de Castro PA, Akiyama DY, Tan K, Nora LC, Silva-Rocha R, Marcet-Houben M, Gabaldón T, Fill T, Wong KH, Goldman GH. Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus. PLoS Genet 2022; 18:e1010001. [PMID: 35007279 PMCID: PMC8782537 DOI: 10.1371/journal.pgen.1010001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 01/21/2022] [Accepted: 12/17/2021] [Indexed: 12/21/2022] Open
Abstract
Invasive Pulmonary Aspergillosis, which is caused by the filamentous fungus Aspergillus fumigatus, is a life-threatening infection for immunosuppressed patients. Chromatin structure regulation is important for genome stability maintenance and has the potential to drive genome rearrangements and affect virulence and pathogenesis of pathogens. Here, we performed the first A. fumigatus global chromatin profiling of two histone modifications, H3K4me3 and H3K9me3, focusing on the two most investigated A. fumigatus clinical isolates, Af293 and CEA17. In eukaryotes, H3K4me3 is associated with active transcription, while H3K9me3 often marks silent genes, DNA repeats, and transposons. We found that H3K4me3 deposition is similar between the two isolates, while H3K9me3 is more variable and does not always represent transcriptional silencing. Our work uncovered striking differences in the number, locations, and expression of transposable elements between Af293 and CEA17, and the differences are correlated with H3K9me3 modifications and higher genomic variations among strains of Af293 background. Moreover, we further showed that the Af293 strains from different laboratories actually differ in their genome contents and found a frequently lost region in chromosome VIII. For one such Af293 variant, we identified the chromosomal changes and demonstrated their impacts on its secondary metabolites production, growth and virulence. Overall, our findings not only emphasize the influence of genome heterogeneity on A. fumigatus fitness, but also caution about unnoticed chromosomal variations among common laboratory strains.
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Affiliation(s)
- Ana Cristina Colabardini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Fang Wang
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Intensive Care Unit, Biomedical Research Center, Shenzhen Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhengqiang Miao
- Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Lakhansing Pardeshi
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Clara Valero
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Daniel Yuri Akiyama
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Macau SAR of China
| | - Luisa Czamanski Nora
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafael Silva-Rocha
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Taicia Fill
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau SAR of China
- Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau SAR of China
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR of China
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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12
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Mishra A, Forche A, Anderson MZ. Parasexuality of Candida Species. Front Cell Infect Microbiol 2021; 11:796929. [PMID: 34966696 PMCID: PMC8711763 DOI: 10.3389/fcimb.2021.796929] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/19/2021] [Indexed: 12/03/2022] Open
Abstract
While most fungi have the ability to reproduce sexually, multiple independent lineages have lost meiosis and developed parasexual cycles in its place. Emergence of parasexual cycles is particularly prominent in medically relevant fungi from the CUG paraphyletic group of Candida species. Since the discovery of parasex in C. albicans roughly two decades ago, it has served as the model for Candida species. Importantly, parasex in C. albicans retains hallmarks of meiosis including genetic recombination and chromosome segregation, making it a potential driver of genetic diversity. Furthermore, key meiotic genes play similar roles in C. albicans parasex and highlights parallels between these processes. Yet, the evolutionary role of parasex in Candida adaptation and the extent of resulting genotypic and phenotypic diversity remain as key knowledge gaps in this facultative reproductive program. Here, we present our current understanding of parasex, the mechanisms governing its regulation, and its relevance to Candida biology.
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Affiliation(s)
- Abhishek Mishra
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Anja Forche
- Department of Biology, Bowdoin College, Brunswick, ME, United States
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, United States.,Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
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13
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Yang F, Lu H, Wu H, Fang T, Berman J, Jiang YY. Aneuploidy Underlies Tolerance and Cross-Tolerance to Drugs in Candida parapsilosis. Microbiol Spectr 2021; 9:e0050821. [PMID: 34612700 PMCID: PMC8510177 DOI: 10.1128/spectrum.00508-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/31/2021] [Indexed: 11/20/2022] Open
Abstract
Candida species are the most common human fungal pathogens worldwide. Although C. albicans remains the predominant cause of candidiasis, infections caused by non-albicans Candida species, including C. parapsilosis, are increasing. In C. albicans, genome plasticity has been shown to be a prevalent strategy of adaptation to stresses. However, the role of aneuploidy in C. parapsilosis is largely unknown. In this study, we found that six different aneuploid karyotypes conferred adaptation to the endoplasmic reticulum stress inducer tunicamycin (TUN) in C. parapsilosis. Interestingly, a specific aneuploidy including trisomy of chromosome 6 (Chr6x3) also enabled cross-tolerance to aureobasidin A (AbA), a sphingolipid biosynthesis inhibitor. Consistent with this, selection on AbA identified adaptors with three different aneuploid karyotypes, including Chr6x3, which also enabled cross-tolerance to both AbA and TUN. Therefore, as in other Candida species, recurrent aneuploid karyotypes enable the adaptation of C. parapsilosis to specific stresses, and specific aneuploidies enable cross-adaptation to different stresses. IMPORTANCE Candida parapsilosis is an emerging human fungal pathogen, especially prevalent in neonates. Aneuploidy, having uneven numbers of chromosomes, is a well-known mechanism for adapting to stress in Candida albicans, the most common human fungal pathogen. In this study, we exposed C. parapsilosis to two very different drugs and selected for rare cells that grew in one of the drugs. We found that the majority of isolates that grew in the drugs had acquired an extra copy of one of several aneuploid chromosomes and that specific aneuploid chromosomes appeared in several independent cell clones. Importantly, an extra copy of chromosome 6 was detected following selection in either one of the drugs, and this extra chromosome conferred the ability to grow in both drugs, a property called cross-adaptation, or cross-tolerance. Thus, this study highlights the genome plasticity of C. parapsilosis and the ability of an extra copy of a single chromosome to promote cell growth in the presence of more than one drug.
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Affiliation(s)
- Feng Yang
- Department of Pharmacy, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hui Lu
- Department of Pharmacy, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hao Wu
- Department of Pharmacy, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ting Fang
- Department of Pharmacy, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yuan-ying Jiang
- Department of Pharmacy, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
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14
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Abstract
How cells exposed to one stress are later able to better survive other types of stress is not well understood. In eukaryotic organisms, physiological and pathological stresses can disturb endoplasmic reticulum (ER) function, resulting in “ER stress.” Here, we found that exposure to tunicamycin, an inducer of ER stress, resulted in the acquisition of a specific aneuploidy, chromosome 2 trisomy (Chr2x3), in Candida albicans. Importantly, the resulting aneuploidy also conferred cross-tolerance to caspofungin, a first-line echinocandin antifungal, as well as to hydroxyurea, a common chemotherapeutic agent. Exposure to a range of tunicamycin concentrations induced similar ER stress responses. Extra copies of one Chr2 gene, MKK2, affected both tunicamycin and caspofungin tolerance, while at least 3 genes on chromosome 2 (ALG7, RTA2, and RTA3) affected only tunicamycin and not caspofungin responses. Other Chr2 genes (RNR1 and RNR21) affected hydroxyurea tolerance but neither tunicamycin nor caspofungin tolerance. Deletion of components of the protein kinase C (PKC) or calcineurin pathways affected tolerance to both tunicamycin and caspofungin, supporting the idea that the ER stress response and echinocandin tolerance are regulated by overlapping stress response pathways. Thus, antifungal drug tolerance can arise rapidly via ER stress-induced aneuploidy.
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15
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Uddin W, Dhabalia D, Prakash SMU, Kabir MA. Systematic truncations of chromosome 4 and their responses to antifungals in Candida albicans. J Genet Eng Biotechnol 2021; 19:92. [PMID: 34152516 PMCID: PMC8217416 DOI: 10.1186/s43141-021-00197-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/10/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Candida albicans is an opportunistic human fungal pathogen responsible for superficial and systemic life-threatening infections. Treating these infections is challenging as many clinical isolates show increased drug resistance to antifungals. Chromosome (Chr) 4 monosomy was implicated in a fluconazole-resistant mutant. However, exposure to fluconazole adversely affects Candida cells and can generate numerous mutations. Hence, the present study aimed to truncate Chr4 and challenge the generated Candida strains to antifungals and evaluate their role in drug response. RESULTS Herein, Chr4 was truncated in C. albicans using the telomere-mediated chromosomal truncation method. The resulting eight Candida strains carrying one truncated homolog of Chr4 were tested for response to multiple antifungals. The minimal inhibitory concentration (MIC) for these strains was determined against three classes of antifungals. The MIC values against fluconazole, amphotericin B, and caspofungin were closer to that of the wild type strain. Microdilution assay against fluconazole showed that the mutants and wild type strains had similar sensitivity to fluconazole. The disc diffusion assay against five azoles and two polyenes revealed that the zones of inhibition for all the eight strains were similar to those of the wild type. Thus, none of the generated strains showed any significant resistance to the tested antifungals. However, spot assay exhibited a reasonably high tolerance of a few generated strains with increasing concentrations of fluconazole. CONCLUSION This analysis suggested that Chr4 aneuploidy might not underlie drug resistance but rather drug tolerance in Candida albicans.
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Affiliation(s)
- Wasim Uddin
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, 673601, India
| | - Darshan Dhabalia
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, 673601, India
| | - S M Udaya Prakash
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, 673601, India
| | - M Anaul Kabir
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, 673601, India.
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16
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Gorkovskiy A, Verstrepen KJ. The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi. Genes (Basel) 2021; 12:699. [PMID: 34066718 PMCID: PMC8150848 DOI: 10.3390/genes12050699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 01/12/2023] Open
Abstract
Mutations in DNA can be limited to one or a few nucleotides, or encompass larger deletions, insertions, duplications, inversions and translocations that span long stretches of DNA or even full chromosomes. These so-called structural variations (SVs) can alter the gene copy number, modify open reading frames, change regulatory sequences or chromatin structure and thus result in major phenotypic changes. As some of the best-known examples of SV are linked to severe genetic disorders, this type of mutation has traditionally been regarded as negative and of little importance for adaptive evolution. However, the advent of genomic technologies uncovered the ubiquity of SVs even in healthy organisms. Moreover, experimental evolution studies suggest that SV is an important driver of evolution and adaptation to new environments. Here, we provide an overview of the causes and consequences of SV and their role in adaptation, with specific emphasis on fungi since these have proven to be excellent models to study SV.
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Affiliation(s)
- Anton Gorkovskiy
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Gaston Geenslaan 1, 3001 Leuven, Belgium;
- Laboratory for Systems Biology, VIB—KU Leuven Center for Microbiology, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
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17
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Germination of a Field: Women in Candida albicans Research. CURRENT CLINICAL MICROBIOLOGY REPORTS 2021. [DOI: 10.1007/s40588-021-00169-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Thomson GJ, Kakade P, Hirakawa MP, Ene IV, Bennett RJ. Adaptation to the dietary sugar D-tagatose via genome instability in polyploid Candida albicans cells. G3-GENES GENOMES GENETICS 2021; 11:6219300. [PMID: 33836061 PMCID: PMC8495922 DOI: 10.1093/g3journal/jkab110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
The opportunistic fungal pathogen Candida albicans undergoes an unusual parasexual cycle wherein diploid cells mate to form tetraploid cells that can generate genetically diverse progeny via a non-meiotic program of chromosome loss. The genetic diversity afforded by parasex impacts clinically relevant features including drug resistance and virulence, and yet the factors influencing genome instability in C. albicans are not well defined. To understand how environmental cues impact genome instability, we monitored ploidy change following tetraploid cell growth in a panel of different carbon sources. We found that growth in one carbon source, D-tagatose, led to high levels of genomic instability and chromosome loss in tetraploid cells. This sugar is a stereoisomer of L-sorbose which was previously shown to promote karyotypic changes in C. albicans. However, while expression of the SOU1 gene enabled utilization of L-sorbose, overexpression of this gene did not promote growth in D-tagatose, indicating differences in assimilation of the two sugars. In addition, genome sequencing of multiple progeny recovered from D-tagatose cultures revealed increased relative copy numbers of chromosome 4, suggestive of chromosome-level regulation of D-tagatose metabolism. Together, these studies identify a novel environmental cue that induces genome instability in C. albicans, and further implicate chromosomal changes in supporting metabolic adaptation in this species.
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Affiliation(s)
- Gregory J Thomson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Pallavi Kakade
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
| | - Matthew P Hirakawa
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.,Department of Systems Biology, Sandia National Laboratories, Livermore, CA 94550, USA
| | - Iuliana V Ene
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA.,Mycology Department, Pasteur Institute, Paris 75015, France
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, USA
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Yang F, Todd RT, Selmecki A, Jiang YY, Cao YB, Berman J. The fitness costs and benefits of trisomy of each Candida albicans chromosome. Genetics 2021; 218:6218773. [PMID: 33837402 DOI: 10.1093/genetics/iyab056] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/01/2021] [Indexed: 01/05/2023] Open
Abstract
Candida albicans is a prevalent human fungal pathogen. Rapid genomic change, due to aneuploidy, is a common mechanism that facilitates survival from multiple types of stresses including the few classes of available antifungal drugs. The stress survival of aneuploids occurs despite the fitness costs attributed to most aneuploids growing under idealized lab conditions. Systematic study of the aneuploid state in C. albicans has been hindered by the lack of a comprehensive collection of aneuploid strains. Here, we describe a collection of diploid C. albicans aneuploid strains, each carrying one extra copy of each chromosome, all from the same genetic background. We tested the fitness of this collection under several physiological conditions including shifts in pH, low glucose, oxidative stress, temperature, high osmolarity, membrane stress, and cell wall stress. We found that most aneuploids, under most conditions, were less fit than their euploid parent, yet there were specific conditions under which specific aneuploid isolates provided a fitness benefit relative to the euploid parent strain. Importantly, this fitness benefit was attributable to the change in the copy number of specific chromosomes. Thus, C. albicans can tolerate aneuploidy of each chromosome and some aneuploids confer improved growth under conditions that the yeast encounters in its host niches.
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Affiliation(s)
- Feng Yang
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200086, China.,Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Yuan-Ying Jiang
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yong-Bing Cao
- Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200086, China
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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20
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Reddy PK, Pullepu D, Dhabalia D, Udaya Prakash SM, Kabir MA. CSU57 encodes a novel repressor of sorbose utilization in opportunistic human fungal pathogen Candida albicans. Yeast 2020; 38:222-238. [PMID: 33179314 DOI: 10.1002/yea.3537] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/11/2022] Open
Abstract
Human fungal pathogen Candida albicans cannot utilize L-sorbose as a sole carbon source. However, chromosome 5 monosomic strains can grow on sorbose as repressors present on this chromosome get diminished allowing the expression of sorbose utilization gene (SOU1) located on chromosome 4. Functional identification of these repressors has been a difficult task as they are scattered on a large portion of the right arm of chromosome 5. Herein, we have applied the telomere-mediated chromosomal truncation approach to identify a novel repressor for sorbose utilization in this pathogen. Multiple systematic chromosomal truncations were performed on the right arm of Chr5 in the background of csu51∆/CSU51 to minimize the functional region to 6-kb chromosomal stretch. Further, truncation that removes the part of Orf19.3942 strongly suggested its role in sorbose utilization. However, compelling evidence comes from the observation that truncation at 1,044.288-kb position of Chr5 in the strain csu51∆/CSU51 orf19.3942∆/Orf.19.3942 produced Sou+ phenotype; otherwise, the strain remains Sou- . This confirms beyond doubt the role of Orf.19.3942 in the regulation of sorbose utilization and designated as CSU57. Comparison of SOU1 gene expression of Sou+ strains with wild type suggested its role at transcriptional level. Strain carrying double disruption of CSU57 remains Sou- . Co-overexpression of SOU1 and CSU57 together does not make the recipient strain Sou- ; however, multiple tandem copies of CSU57 produced diminished growth compared with control suggesting that it is a weak repressor. Taken together, we report that CSU57 encodes a novel repressor of L-sorbose utilization in this pathogen. TAKE AWAY: CSU57 encodes a repressor for L-sorbose utilization in Candida albicans. Csu57p acts in combination with Csu51p and other regulators. Csu57p exerts its repressing effect at transcriptional level of SOU1 gene. Utilization of sorbose positively correlates to the expression of SOU1 gene. Multiple copies of CSU57 can partially suppress Sou+ phenotype.
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Affiliation(s)
- Praveen Kumar Reddy
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut, India
| | - Dileep Pullepu
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut, India
| | - Darshan Dhabalia
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut, India
| | | | - Mohammad Anaul Kabir
- Molecular Genetics Laboratory, School of Biotechnology, National Institute of Technology Calicut, Calicut, India
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21
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A conserved regulator controls asexual sporulation in the fungal pathogen Candida albicans. Nat Commun 2020; 11:6224. [PMID: 33277479 PMCID: PMC7718266 DOI: 10.1038/s41467-020-20010-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 11/03/2020] [Indexed: 12/16/2022] Open
Abstract
Transcription factor Rme1 is conserved among ascomycetes and regulates meiosis and pseudohyphal growth in Saccharomyces cerevisiae. The genome of the meiosis-defective pathogen Candida albicans encodes an Rme1 homolog that is part of a transcriptional circuitry controlling hyphal growth. Here, we use chromatin immunoprecipitation and genome-wide expression analyses to study a possible role of Rme1 in C. albicans morphogenesis. We find that Rme1 binds upstream and activates the expression of genes that are upregulated during chlamydosporulation, an asexual process leading to formation of large, spherical, thick-walled cells during nutrient starvation. RME1 deletion abolishes chlamydosporulation in three Candida species, whereas its overexpression bypasses the requirement for chlamydosporulation cues and regulators. RME1 expression levels correlate with chlamydosporulation efficiency across clinical isolates. Interestingly, RME1 displays a biphasic pattern of expression, with a first phase independent of Rme1 function and dependent on chlamydospore-inducing cues, and a second phase dependent on Rme1 function and independent of chlamydospore-inducing cues. Our results indicate that Rme1 plays a central role in chlamydospore development in Candida species.
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22
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Todd RT, Selmecki A. Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs. eLife 2020; 9:e58349. [PMID: 32687060 PMCID: PMC7371428 DOI: 10.7554/elife.58349] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Previously, we identified long repeat sequences that are frequently associated with genome rearrangements, including copy number variation (CNV), in many diverse isolates of the human fungal pathogen Candida albicans (Todd et al., 2019). Here, we describe the rapid acquisition of novel, high copy number CNVs during adaptation to azole antifungal drugs. Single-cell karyotype analysis indicates that these CNVs appear to arise via a dicentric chromosome intermediate and breakage-fusion-bridge cycles that are repaired using multiple distinct long inverted repeat sequences. Subsequent removal of the antifungal drug can lead to a dramatic loss of the CNV and reversion to the progenitor genotype and drug susceptibility phenotype. These findings support a novel mechanism for the rapid acquisition of antifungal drug resistance and provide genomic evidence for the heterogeneity frequently observed in clinical settings.
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Affiliation(s)
- Robert T Todd
- Department of Microbiology and Immunology, University of Minnesota Medical SchoolMinneapolis, MinnesotaUnited States
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota Medical SchoolMinneapolis, MinnesotaUnited States
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23
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The Impact of Gene Dosage and Heterozygosity on The Diploid Pathobiont Candida albicans. J Fungi (Basel) 2019; 6:jof6010010. [PMID: 31892130 PMCID: PMC7151161 DOI: 10.3390/jof6010010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/14/2019] [Accepted: 12/18/2019] [Indexed: 12/29/2022] Open
Abstract
Candida albicans is a fungal species that can colonize multiple niches in the human host where it can grow either as a commensal or as an opportunistic pathogen. The genome of C. albicans has long been of considerable interest, given that it is highly plastic and can undergo a wide variety of alterations. These changes play a fundamental role in determining C. albicans traits and have been shown to enable adaptation both to the host and to antifungal drugs. C. albicans isolates contain a heterozygous diploid genome that displays variation from the level of single nucleotides to largescale rearrangements and aneuploidy. The heterozygous nature of the genome is now increasingly recognized as being central to C. albicans biology, as the relative fitness of isolates has been shown to correlate with higher levels of overall heterozygosity. Moreover, loss of heterozygosity (LOH) events can arise frequently, either at single polymorphisms or at a chromosomal level, and both can alter the behavior of C. albicans cells during infection or can modulate drug resistance. In this review, we examine genome plasticity in this pathobiont focusing on how gene dosage variation and loss of heterozygosity events can arise and how these modulate C. albicans behavior.
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24
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Bravo Ruiz G, Ross ZK, Holmes E, Schelenz S, Gow NAR, Lorenz A. Rapid and extensive karyotype diversification in haploid clinical Candida auris isolates. Curr Genet 2019; 65:1217-1228. [PMID: 31020384 PMCID: PMC6744574 DOI: 10.1007/s00294-019-00976-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 11/30/2022]
Abstract
Candida auris is a newly emerged pathogenic microbe, having been identified as a medically relevant fungus as recently as 2009. It is one of the most drug-resistant yeast species known to date and its emergence and population structure are unusual. Because of its recent emergence, we are largely ignorant about fundamental aspects of its general biology, life cycle, and population dynamics. Here, we report the karyotype variability of 26 C. auris strains representing the four main clades. We demonstrate that all strains are haploid and have a highly plastic karyotype containing five to seven chromosomes, which can undergo marked alterations within a short time frame when the fungus is put under genotoxic, heat, or osmotic stress. No simple correlation was found between karyotype pattern, drug resistance, and clade affiliation indicating that karyotype heterogeneity is rapidly evolving. As with other Candida species, these marked karyotype differences between isolates are likely to have an important impact on pathogenic traits of C. auris.
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Affiliation(s)
- Gustavo Bravo Ruiz
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Zoe K Ross
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- MRC Centre for Medical Mycology, University of Aberdeen, Aberdeen, UK
| | - Eilidh Holmes
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Silke Schelenz
- Department of Microbiology, Royal Brompton Hospital, London, UK
| | - Neil A R Gow
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- MRC Centre for Medical Mycology, University of Aberdeen, Aberdeen, UK
- School of Biosciences, University of Exeter, Exeter, UK
| | - Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
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25
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Susceptibility to Medium-Chain Fatty Acids Is Associated with Trisomy of Chromosome 7 in Candida albicans. mSphere 2019; 4:4/3/e00402-19. [PMID: 31243082 PMCID: PMC6595153 DOI: 10.1128/msphere.00402-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Aneuploidy (changes in chromosome number) and loss of heterozygosity (LOH) occur frequently in the human-pathogenic yeast Candida albicans and are associated with adaptation to stress and to antifungal drugs. Aneuploidy and LOH can also be induced during laboratory manipulations, such as during genetic transformation. We find that C. albicans strain SN152, commonly used to generate gene deletions, has undergone a major LOH event on chromosome 2. One deletion strain generated in this background has acquired extra copies of chromosomes 5 and 7. We find that trisomy (three copies) of chromosome 7 is associated with sensitivity to fatty acids. Fatty acids have known antifungal effects and are used in over-the-counter topical treatments. Screening of a collection of gene knockouts in Candida albicans revealed that one strain, carrying a deletion of the transcription factor DAL81, is very susceptible to the medium-chain fatty acid undecanoic acid. However, reintroducing DAL81 does not restore resistance, and editing DAL81 in a different background does not introduce sensitivity. Whole-genome sequencing revealed that the C. albicansdal81Δ/Δ strain has an extra copy of chromosomes 5 and 7. Reversion to resistance to undecanoic acid was induced by growing the sensitive strain in yeast extract-peptone-dextrose with 60 μg/ml undecanoic acid for up to 9 days. Nine isolates that regained some resistance to undecanoic acid lost one copy of chromosome 7. The copy number of chromosome 5 does not appear to affect resistance to fatty acids. Moreover, the sensitivity may be related to having two copies of haplotype B of chromosome 7. In addition, we find that C. albicans strain SN152, used to delete DAL81 and many other genes, has undergone a major loss of heterozygosity event on chromosome 2 and a smaller one on chromosome 3. IMPORTANCE Aneuploidy (changes in chromosome number) and loss of heterozygosity (LOH) occur frequently in the human-pathogenic yeast Candida albicans and are associated with adaptation to stress and to antifungal drugs. Aneuploidy and LOH can also be induced during laboratory manipulations, such as during genetic transformation. We find that C. albicans strain SN152, commonly used to generate gene deletions, has undergone a major LOH event on chromosome 2. One deletion strain generated in this background has acquired extra copies of chromosomes 5 and 7. We find that trisomy (three copies) of chromosome 7 is associated with sensitivity to fatty acids.
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27
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Forche A, Solis NV, Swidergall M, Thomas R, Guyer A, Beach A, Cromie GA, Le GT, Lowell E, Pavelka N, Berman J, Dudley AM, Selmecki A, Filler SG. Selection of Candida albicans trisomy during oropharyngeal infection results in a commensal-like phenotype. PLoS Genet 2019; 15:e1008137. [PMID: 31091232 PMCID: PMC6538192 DOI: 10.1371/journal.pgen.1008137] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/28/2019] [Accepted: 04/15/2019] [Indexed: 12/21/2022] Open
Abstract
When the fungus Candida albicans proliferates in the oropharyngeal cavity during experimental oropharyngeal candidiasis (OPC), it undergoes large-scale genome changes at a much higher frequency than when it grows in vitro. Previously, we identified a specific whole chromosome amplification, trisomy of Chr6 (Chr6x3), that was highly overrepresented among strains recovered from the tongues of mice with OPC. To determine the functional significance of this trisomy, we assessed the virulence of two Chr6 trisomic strains and a Chr5 trisomic strain in the mouse model of OPC. We also analyzed the expression of virulence-associated traits in vitro. All three trisomic strains exhibited characteristics of a commensal during OPC in mice. They achieved the same oral fungal burden as the diploid progenitor strain but caused significantly less weight loss and elicited a significantly lower inflammatory host response. In vitro, all three trisomic strains had reduced capacity to adhere to and invade oral epithelial cells and increased susceptibility to neutrophil killing. Whole genome sequencing of pre- and post-infection isolates found that the trisomies were usually maintained. Most post-infection isolates also contained de novo point mutations, but these were not conserved. While in vitro growth assays did not reveal phenotypes specific to de novo point mutations, they did reveal novel phenotypes specific to each lineage. These data reveal that during OPC, clones that are trisomic for Chr5 or Chr6 are selected and they facilitate a commensal-like phenotype. Opportunistic fungal pathogens commonly acquire extra copies of chromosomes that can provide a fitness benefit under acute stress such as exposure to antifungal agents but how these extra copies affect fungal life-style and interactions with their hosts is poorly understood. Here we show that in C. albicans the acquisition of specific whole chromosome trisomies during oropharyngeal infection in mice results in a commensal-like phenotype. Our data indicate that trisomies of chromosomes 5 and 6 alter several related virulence-associated traits that affect how the host recognizes and responds to C. albicans during oropharyngeal infection, thereby inducing this commensal-like phenotype. Whole genome sequencing revealed that trisomies were mostly maintained in subsequent oral infections and that de novo mutations that arose were not shared among strains. We hypothesize that both in vivo and in vitro phenotypes are likely the result of allelic imbalance of specific genes on the trisomic chromosomes, rather than due to whole chromosome trisomy.
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Affiliation(s)
- Anja Forche
- Department of Biology, Bowdoin College, Brunswick, Maine, United States of America
- * E-mail: (AF); (SGF)
| | - Norma V. Solis
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Marc Swidergall
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Robert Thomas
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Alison Guyer
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Annette Beach
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Gareth A. Cromie
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Giang T. Le
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Emily Lowell
- Department of Biology, Bowdoin College, Brunswick, Maine, United States of America
| | - Norman Pavelka
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Judith Berman
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Aimeé M. Dudley
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Anna Selmecki
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- * E-mail: (AF); (SGF)
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28
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Frazer C, Hernday AD, Bennett RJ. Monitoring Phenotypic Switching in Candida albicans and the Use of Next-Gen Fluorescence Reporters. ACTA ACUST UNITED AC 2019; 53:e76. [PMID: 30747494 DOI: 10.1002/cpmc.76] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Candida albicans is an opportunistic human fungal pathogen that is able to cause both mucosal and systemic infections. It is also a frequent human commensal, where it is typically found inhabiting multiple niches including the gastrointestinal tract. One of the most remarkable features of C. albicans biology is its ability to undergo heritable and reversible switching between different phenotypic states, a phenomenon known as phenotypic switching. This is best exemplified by the white-opaque switch, in which cells undergo epigenetic transitions between two alternative cellular states. Here, we describe assays to quantify the frequency of switching between states, as well as methods to help identify cells in different phenotypic states. We also describe the use of environmental cues that can induce switching into either the white or opaque state. Finally, we introduce the use of mNeonGreen and mScarlet fluorescent proteins that have been optimized for use in C. albicans and which outperform commonly used fluorescent proteins for both fluorescence microscopy and flow cytometry. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Corey Frazer
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island
| | - Aaron D Hernday
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, Merced, California.,Quantitative and Systems Biology Graduate Program, School of Natural Sciences, University of California, Merced, Merced, California
| | - Richard J Bennett
- Molecular Microbiology and Immunology Department, Brown University, Providence, Rhode Island
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29
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Antunes M, Palma M, Sá-Correia I. Transcriptional profiling of Zygosaccharomyces bailii early response to acetic acid or copper stress mediated by ZbHaa1. Sci Rep 2018; 8:14122. [PMID: 30237501 PMCID: PMC6147978 DOI: 10.1038/s41598-018-32266-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/31/2018] [Indexed: 12/18/2022] Open
Abstract
The non-conventional yeast species Zygosaccharomyces bailii is remarkably tolerant to acetic acid, a highly important microbial inhibitory compound in Food Industry and Biotechnology. ZbHaa1 is the functional homologue of S. cerevisiae Haa1 and a bifunctional transcription factor able to modulate Z. bailii adaptive response to acetic acid and copper stress. In this study, RNA-Seq was used to investigate genomic transcription changes in Z. bailii during early response to sublethal concentrations of acetic acid (140 mM, pH 4.0) or copper (0.08 mM) and uncover the regulatory network activated by these stresses under ZbHaa1 control. Differentially expressed genes in response to acetic acid exposure (297) are mainly related with the tricarboxylic acid cycle, protein folding and stabilization and modulation of plasma membrane composition and cell wall architecture, 17 of which, directly or indirectly, ZbHaa1-dependent. Copper stress induced the differential expression of 190 genes mainly involved in the response to oxidative stress, 15 ZbHaa1-dependent. This study provides valuable mechanistic insights regarding Z. bailii adaptation to acetic acid or copper stress, as well as useful information on transcription regulatory networks in pre-whole genome duplication (WGD) (Z. bailii) and post-WGD (S. cerevisiae) yeast species, contributing to the understanding of transcriptional networks’ evolution in yeasts.
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Affiliation(s)
- Miguel Antunes
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
| | - Margarida Palma
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal.
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30
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Abstract
Ploidy, the number of sets of homologous chromosomes in a cell, can alter cellular physiology, gene regulation, and the spectrum of acquired mutations. Advances in single-cell flow cytometry have greatly improved the understanding of how genome size contributes to diverse biological processes including speciation, adaptation, pathogenesis, and tumorigenesis. For example, fungal pathogens can undergo whole genome duplications during infection of the human host and during acquisition of antifungal drug resistance. Quantification of ploidy is dramatically affected by the nucleic acid staining technique and the flow cytometry analysis of single cells. Ploidy in fungi is also impacted by samples that are heterogeneous for both ploidy and morphology, and control strains with known ploidy must be included in every flow cytometry experiment. To detect ploidy changes within fungal strains, the following protocol was developed to accurately and dependably interrogate single-cell ploidy. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Robert T Todd
- Department of Medical Microbiology and Immunology, Creighton University Medical School, Omaha, Nebraska
| | - Ann L Braverman
- Department of Medical Microbiology and Immunology, Creighton University Medical School, Omaha, Nebraska
| | - Anna Selmecki
- Department of Medical Microbiology and Immunology, Creighton University Medical School, Omaha, Nebraska
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31
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Abstract
The ability of an organism to replicate and segregate its genome with high fidelity is vital to its survival and for the production of future generations. Errors in either of these steps (replication or segregation) can lead to a change in ploidy or chromosome number. While these drastic genome changes can be detrimental to the organism, resulting in decreased fitness, they can also provide increased fitness during periods of stress. A change in ploidy or chromosome number can fundamentally change how a cell senses and responds to its environment. Here, we discuss current ideas in fungal biology that illuminate how eukaryotic genome size variation can impact the organism at a cellular and evolutionary level. One of the most fascinating observations from the past 2 decades of research is that some fungi have evolved the ability to tolerate large genome size changes and generate vast genomic heterogeneity without undergoing canonical meiosis.
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32
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Wertheimer NB, Stone N, Berman J. Ploidy dynamics and evolvability in fungi. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0461. [PMID: 28080987 PMCID: PMC5095540 DOI: 10.1098/rstb.2015.0461] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 12/12/2022] Open
Abstract
Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival. Furthermore, the stress of exposure to an antifungal drug can induce elevated levels of LOH and can promote the formation of aneuploids. This occurs via mitotic defects that first produce tetraploid progeny with extra spindles, followed by chromosome mis-segregation. Thus, drug exposure induces elevated levels of aneuploidy, which can alter the copy number of genes that improve survival in a given stress or drug. Selection then acts to increase the proportion of adaptive aneuploids in the population. Because aneuploidy is a common property of many pathogenic fungi, including those posing emerging threats to plants, animals and humans, we propose that aneuploid formation and LOH often accompanying it contribute to the rapid generation of diversity that can facilitate the emergence of fungal pathogens to new environmental niches and/or new hosts, as well as promote antifungal drug resistance that makes emerging fungal infections ever more difficult to contain.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Noa Blutraich Wertheimer
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Britannia 418, Ramat Aviv, Israel
| | - Neil Stone
- Institute of Infection and Immunity, St George's, University of London, London SW17 0RE, UK
| | - Judith Berman
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Britannia 418, Ramat Aviv, Israel
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33
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Wakabayashi H, Tucker C, Bethlendy G, Kravets A, Welle SL, Bulger M, Hayes JJ, Rustchenko E. NuA4 histone acetyltransferase activity is required for H4 acetylation on a dosage-compensated monosomic chromosome that confers resistance to fungal toxins. Epigenetics Chromatin 2017; 10:49. [PMID: 29061172 PMCID: PMC5653997 DOI: 10.1186/s13072-017-0156-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major human fungal pathogen Candida albicans possesses a diploid genome, but responds to growth in challenging environments by employing chromosome aneuploidy as an adaptation mechanism. For example, we have shown that C. albicans adapts to growth on the toxic sugar L-sorbose by transitioning to a state in which one chromosome (chromosome 5, Ch5) becomes monosomic. Moreover, analysis showed that while expression of many genes on the monosomic Ch5 is altered in accordance with the chromosome ploidy, expression of a large fraction of genes is increased to the normal diploid level, presumably compensating for gene dose. RESULTS In order to understand the mechanism of the apparent dosage compensation, we now report genome-wide ChIP-microarray assays for a sorbose-resistant strain harboring a monosomic Ch5. These data show a significant chromosome-wide elevation in histone H4 acetylation on the mCh5, but not on any other chromosome. Importantly, strains lacking subunits of the NuA4 H4 histone acetyltransferase complex, orthologous to a complex previously shown in Drosophila to be associated with a similar gene dosage compensation mechanism, did not show an increase in H4 acetylation. Moreover, loss of NuA4 subunits severely compromised the adaptation to growth on sorbose. CONCLUSIONS Our results are consistent with a model wherein chromosome-wide elevation of H4 acetylation mediated by the NuA4 complex plays a role in increasing gene expression in compensation for gene dose and adaption to growth in a toxic environment.
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Affiliation(s)
- Hironao Wakabayashi
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA.
| | - Christopher Tucker
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Gabor Bethlendy
- Roche Diagnostics Corporation, Indianapolis, IN, USA.,Parabase Genomics, Dorchester, MA, USA
| | - Anatoliy Kravets
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Stephen L Welle
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA.,Department of Pediatrics, Center for Pediatric Biochemical Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael Bulger
- Department of Pediatrics, Center for Pediatric Biochemical Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Elena Rustchenko
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
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34
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Hampe IAI, Friedman J, Edgerton M, Morschhäuser J. An acquired mechanism of antifungal drug resistance simultaneously enables Candida albicans to escape from intrinsic host defenses. PLoS Pathog 2017; 13:e1006655. [PMID: 28953977 PMCID: PMC5633205 DOI: 10.1371/journal.ppat.1006655] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/09/2017] [Accepted: 09/19/2017] [Indexed: 12/23/2022] Open
Abstract
The opportunistic fungal pathogen Candida albicans frequently produces genetically altered variants to adapt to environmental changes and new host niches in the course of its life-long association with the human host. Gain-of-function mutations in zinc cluster transcription factors, which result in the constitutive upregulation of their target genes, are a common cause of acquired resistance to the widely used antifungal drug fluconazole, especially during long-term therapy of oropharyngeal candidiasis. In this study, we investigated if C. albicans also can develop resistance to the antimicrobial peptide histatin 5, which is secreted in the saliva of humans to protect the oral mucosa from pathogenic microbes. As histatin 5 has been shown to be transported out of C. albicans cells by the Flu1 efflux pump, we screened a library of C. albicans strains that contain artificially activated forms of all zinc cluster transcription factors of this fungus for increased FLU1 expression. We found that a hyperactive Mrr1, which confers fluconazole resistance by upregulating the multidrug efflux pump MDR1 and other genes, also causes FLU1 overexpression. Similarly to the artificially activated Mrr1, naturally occurring gain-of-function mutations in this transcription factor also caused FLU1 upregulation and increased histatin 5 resistance. Surprisingly, however, Mrr1-mediated histatin 5 resistance was mainly caused by the upregulation of MDR1 instead of FLU1, revealing a previously unrecognized function of the Mdr1 efflux pump. Fluconazole-resistant clinical C. albicans isolates with different Mrr1 gain-of-function mutations were less efficiently killed by histatin 5, and this phenotype was reverted when MRR1 was deleted. Therefore, antimycotic therapy can promote the evolution of strains that, as a consequence of drug resistance mutations, simultaneously have acquired increased resistance against an innate host defense mechanism and are thereby better adapted to certain host niches. The yeast Candida albicans is part of the normal microflora of most healthy persons, but it can also cause symptomatic infections when host defenses are compromised. C. albicans frequently generates genetically altered variants that are better adapted to changes in its environment during colonization and infection. We investigated if C. albicans can evolve resistance to histatin 5 (Hst 5), an antimicrobial peptide that is produced in the saliva of humans and protects the oral cavity against this pathogen. We found that activated forms of the transcription factor Mrr1 reduce the susceptibility of C. albicans to killing by Hst 5, a phenotype that was partially caused by Mrr1-mediated overexpression of the multidrug efflux pump MDR1. Gain-of-function (GOF) mutations in Mrr1 are a frequent cause of resistance to the antifungal drug fluconazole, especially during long-term treatment of oropharyngeal candidiasis in AIDS patients, but they may also reduce the fitness of the fungus in the absence of the drug. Fluconazole-resistant clinical C. albicans isolates containing GOF mutations in Mrr1 displayed enhanced Hst 5 resistance, demonstrating that antimycotic therapy can promote the evolution of strains that simultaneously have acquired increased resistance against an innate host defense mechanism and are thereby better adapted to specific host niches.
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Affiliation(s)
- Irene A. I. Hampe
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Justin Friedman
- Department of Oral Biology, University at Buffalo, Buffalo, New York, United States of America
| | - Mira Edgerton
- Department of Oral Biology, University at Buffalo, Buffalo, New York, United States of America
| | - Joachim Morschhäuser
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- * E-mail:
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35
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Ostrov N, Jimenez M, Billerbeck S, Brisbois J, Matragrano J, Ager A, Cornish VW. A modular yeast biosensor for low-cost point-of-care pathogen detection. SCIENCE ADVANCES 2017; 3:e1603221. [PMID: 28782007 PMCID: PMC5489263 DOI: 10.1126/sciadv.1603221] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/15/2017] [Indexed: 05/16/2023]
Abstract
The availability of simple, specific, and inexpensive on-site detection methods is of key importance for deployment of pathogen surveillance networks. We developed a nontechnical and highly specific colorimetric assay for detection of pathogen-derived peptides based on Saccharomyces cerevisiae-a genetically tractable model organism and household product. Integrating G protein-coupled receptors with a visible, reagent-free lycopene readout, we demonstrate differential detection of major human, plant, and food fungal pathogens with nanomolar sensitivity. We further optimized a one-step rapid dipstick prototype that can be used in complex samples, including blood, urine, and soil. This modular biosensor can be economically produced at large scale, is not reliant on cold-chain storage, can be detected without additional equipment, and is thus a compelling platform scalable to global surveillance of pathogens.
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Affiliation(s)
- Nili Ostrov
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Miguel Jimenez
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Sonja Billerbeck
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - James Brisbois
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Joseph Matragrano
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Alastair Ager
- Department of Population and Family Health, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
- Institute for Global Health and Development, Queen Margaret University, Edinburgh, UK
| | - Virginia W. Cornish
- Department of Chemistry, Columbia University, New York, NY 10027, USA
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
- Corresponding author.
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36
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Tolerance to Caspofungin in Candida albicans Is Associated with at Least Three Distinctive Mechanisms That Govern Expression of FKS Genes and Cell Wall Remodeling. Antimicrob Agents Chemother 2017; 61:AAC.00071-17. [PMID: 28223384 DOI: 10.1128/aac.00071-17] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/13/2017] [Indexed: 01/07/2023] Open
Abstract
Expanding echinocandin use to prevent or treat invasive fungal infections has led to an increase in the number of breakthrough infections due to resistant Candida species. Although it is uncommon, echinocandin resistance is well documented for Candida albicans, which is among the most prevalent bloodstream organisms. A better understanding is needed to assess the cellular factors that promote tolerance and predispose infecting cells to clinical breakthrough. We previously showed that some mutants that were adapted to growth in the presence of toxic sorbose due to loss of one chromosome 5 (Ch5) also became more tolerant to caspofungin. We found here, following direct selection of mutants on caspofungin, that tolerance can be conferred by at least three mechanisms: (i) monosomy of Ch5, (ii) combined monosomy of the left arm and trisomy of the right arm of Ch5, and (iii) an aneuploidy-independent mechanism. Tolerant mutants possessed cell walls with elevated chitin and showed downregulation of genes involved in cell wall biosynthesis, namely, FKS, located outside Ch5, and CHT2, located on Ch5, irrespective of Ch5 ploidy. Also irrespective of Ch5 ploidy, the CNB1 and MID1 genes on Ch5, which are involved in the calcineurin signaling pathway, were expressed at the diploid level. Thus, multiple mechanisms can affect the relative expression of the aforementioned genes, controlling them in similar ways. Although breakthrough mutations in two specific regions of FKS1 have previously been associated with caspofungin resistance, we found mechanisms of caspofungin tolerance that are independent of FKS1 and thus represent an earlier event in resistance development.
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37
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Gerstein AC, Lim H, Berman J, Hickman MA. Ploidy tug-of-war: Evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen. Evolution 2017; 71:1025-1038. [PMID: 28195309 DOI: 10.1111/evo.13205] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 01/27/2017] [Indexed: 12/18/2022]
Abstract
Variation in baseline ploidy is seen throughout the tree of life, yet the factors that determine why one ploidy level is maintained over another remain poorly understood. Experimental evolution studies using asexual fungal microbes with manipulated ploidy levels intriguingly reveals a propensity to return to the historical baseline ploidy, a phenomenon that we term "ploidy drive." We evolved haploid, diploid, and polyploid strains of the human fungal pathogen Candida albicans under three different nutrient limitation environments to test whether these conditions, hypothesized to select for low ploidy levels, could counteract ploidy drive. Strains generally maintained or acquired smaller genome sizes (measured as total nuclear DNA through flow cytometry) in minimal medium and under phosphorus depletion compared to in a complete medium, while mostly maintained or acquired increased genome sizes under nitrogen depletion. Improvements in fitness often ran counter to changes in genome size; in a number of scenarios lines that maintained their original genome size often increased in fitness more than lines that converged toward diploidy (the baseline ploidy of C. albicans). Combined, this work demonstrates a role for both the environment and genotype in determination of the rate of ploidy drive, and highlights questions that remain about the force(s) that cause genome size variation.
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Affiliation(s)
- Aleeza C Gerstein
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota.,Department of Microbiology & Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota
| | - Heekyung Lim
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota
| | - Judith Berman
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota.,Department of Microbiology & Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota.,Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Meleah A Hickman
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota.,Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, Georgia
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38
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Wellington M, Anaul M, Rustchenko KE. 5-fluoro-orotic acid induces chromosome alterations in genetically manipulated strains ofCandida albicans. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Melanie Wellington
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York 14642
| | | | - Kabir Elena Rustchenko
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
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39
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Chromosome 5 of Human Pathogen Candida albicans Carries Multiple Genes for Negative Control of Caspofungin and Anidulafungin Susceptibility. Antimicrob Agents Chemother 2016; 60:7457-7467. [PMID: 27736768 DOI: 10.1128/aac.01888-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/04/2016] [Indexed: 11/20/2022] Open
Abstract
Candida albicans is an important fungal pathogen with a diploid genome that can adapt to caspofungin, a major drug from the echinocandin class, by a reversible loss of one copy of chromosome 5 (Ch5). Here, we explore a hypothesis that more than one gene for negative regulation of echinocandin tolerance is carried on Ch5. We constructed C. albicans strains that each lacked one of the following Ch5 genes: CHT2 for chitinase, PGA4 for glucanosyltransferase, and CSU51, a putative transcription factor. We demonstrate that independent deletion of each of these genes increased tolerance for caspofungin and anidulafungin, another echinocandin. Our data indicate that Ch5 carries multiple genes for negative control of echinocandin tolerance, although the final number has yet to be established.
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40
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Analysis of Repair Mechanisms following an Induced Double-Strand Break Uncovers Recessive Deleterious Alleles in the Candida albicans Diploid Genome. mBio 2016; 7:mBio.01109-16. [PMID: 27729506 PMCID: PMC5061868 DOI: 10.1128/mbio.01109-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The diploid genome of the yeast Candida albicans is highly plastic, exhibiting frequent loss-of-heterozygosity (LOH) events. To provide a deeper understanding of the mechanisms leading to LOH, we investigated the repair of a unique DNA double-strand break (DSB) in the laboratory C. albicans SC5314 strain using the I-SceI meganuclease. Upon I-SceI induction, we detected a strong increase in the frequency of LOH events at an I-SceI target locus positioned on chromosome 4 (Chr4), including events spreading from this locus to the proximal telomere. Characterization of the repair events by single nucleotide polymorphism (SNP) typing and whole-genome sequencing revealed a predominance of gene conversions, but we also observed mitotic crossover or break-induced replication events, as well as combinations of independent events. Importantly, progeny that had undergone homozygosis of part or all of Chr4 haplotype B (Chr4B) were inviable. Mining of genome sequencing data for 155 C. albicans isolates allowed the identification of a recessive lethal allele in the GPI16 gene on Chr4B unique to C. albicans strain SC5314 which is responsible for this inviability. Additional recessive lethal or deleterious alleles were identified in the genomes of strain SC5314 and two clinical isolates. Our results demonstrate that recessive lethal alleles in the genomes of C. albicans isolates prevent the occurrence of specific extended LOH events. While these and other recessive lethal and deleterious alleles are likely to accumulate in C. albicans due to clonal reproduction, their occurrence may in turn promote the maintenance of corresponding nondeleterious alleles and, consequently, heterozygosity in the C. albicans species. IMPORTANCE Recessive lethal alleles impose significant constraints on the biology of diploid organisms. Using a combination of an I-SceI meganuclease-mediated DNA DSB, a fluorescence-activated cell sorter (FACS)-optimized reporter of LOH, and a compendium of 155 genome sequences, we were able to unmask and identify recessive lethal and deleterious alleles in isolates of Candida albicans, a diploid yeast and the major fungal pathogen of humans. Accumulation of recessive deleterious mutations upon clonal reproduction of C. albicans could contribute to the maintenance of heterozygosity despite the high frequency of LOH events in this species.
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Burrack LS, Hutton HF, Matter KJ, Clancey SA, Liachko I, Plemmons AE, Saha A, Power EA, Turman B, Thevandavakkam MA, Ay F, Dunham MJ, Berman J. Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome. PLoS Genet 2016; 12:e1006317. [PMID: 27662467 PMCID: PMC5035033 DOI: 10.1371/journal.pgen.1006317] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023] Open
Abstract
Assembly of kinetochore complexes, involving greater than one hundred proteins, is essential for chromosome segregation and genome stability. Neocentromeres, or new centromeres, occur when kinetochores assemble de novo, at DNA loci not previously associated with kinetochore proteins, and they restore chromosome segregation to chromosomes lacking a functional centromere. Neocentromeres have been observed in a number of diseases and may play an evolutionary role in adaptation or speciation. However, the consequences of neocentromere formation on chromosome missegregation rates, gene expression, and three-dimensional (3D) nuclear structure are not well understood. Here, we used Candida albicans, an organism with small, epigenetically-inherited centromeres, as a model system to study the functions of twenty different neocentromere loci along a single chromosome, chromosome 5. Comparison of neocentromere properties relative to native centromere functions revealed that all twenty neocentromeres mediated chromosome segregation, albeit to different degrees. Some neocentromeres also caused reduced levels of transcription from genes found within the neocentromere region. Furthermore, like native centromeres, neocentromeres clustered in 3D with active/functional centromeres, indicating that formation of a new centromere mediates the reorganization of 3D nuclear architecture. This demonstrates that centromere clustering depends on epigenetically defined function and not on the primary DNA sequence, and that neocentromere function is independent of its distance from the native centromere position. Together, the results show that a neocentromere can form at many loci along a chromosome and can support the assembly of a functional kinetochore that exhibits native centromere functions including chromosome segregation accuracy and centromere clustering within the nucleus. The accurate segregation of chromosomes during cell division is essential for maintaining genome integrity. The centromere is the DNA region on each chromosome where assembly of a large protein complex, the kinetochore, is required to maintain proper chromosome segregation. In addition, active centromeres exhibit a specific three-dimensional organization within the nucleus: the centromeres associate with one another in a clustered manner. Neocentromeres, or new centromeres, appear at new places along the chromosome when a native centromere becomes non-functional. We used a yeast model, Candida albicans, and isolated twenty instances in which neocentromeres had formed at different positions. All of these neocentromeres were able to direct chromosome segregation, but some had increased error rates. Like native centromeres, these neocentromeres cluster in the nucleus with the other active centromeres. This implies that formation of a neocentromere leads to reorganization of the three-dimensional structure of the nucleus so that different regions of the chromosome are in closer contact to regions of other chromosomes. Recent work suggests that approximately 3% of cancers may contain chromosomes with neocentromeres. Our observations that many neocentromeres have increased error rates provides insight into genome instability in cancer cells. Changes in chromosome copy number may benefit the cancer cells by increasing numbers of oncogenes and/or drug resistance genes, but may also sensitize the cells to chemotherapy approaches that target chromosome segregation mechanisms.
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Affiliation(s)
- Laura S. Burrack
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biology, Grinnell College, Grinnell, Iowa, United States of America
- Department of Biology, Gustavus Adolphus College, Saint Peter, Minnesota, United States of America
- * E-mail: (LSB); (JB)
| | - Hannah F. Hutton
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Kathleen J. Matter
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Shelly Applen Clancey
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ivan Liachko
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | | | - Amrita Saha
- Department of Biology, Grinnell College, Grinnell, Iowa, United States of America
| | - Erica A. Power
- Department of Biology, Gustavus Adolphus College, Saint Peter, Minnesota, United States of America
| | - Breanna Turman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | | | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Judith Berman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- * E-mail: (LSB); (JB)
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Regional centromeres in the yeast Candida lusitaniae lack pericentromeric heterochromatin. Proc Natl Acad Sci U S A 2015; 112:12139-44. [PMID: 26371315 DOI: 10.1073/pnas.1508749112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Point centromeres are specified by a short consensus sequence that seeds kinetochore formation, whereas regional centromeres lack a conserved sequence and instead are epigenetically inherited. Regional centromeres are generally flanked by heterochromatin that ensures high levels of cohesin and promotes faithful chromosome segregation. However, it is not known whether regional centromeres require pericentromeric heterochromatin. In the yeast Candida lusitaniae, we identified a distinct type of regional centromere that lacks pericentromeric heterochromatin. Centromere locations were determined by ChIP-sequencing of two key centromere proteins, Cse4 and Mif2, and are consistent with bioinformatic predictions. The centromeric DNA sequence was unique for each chromosome and spanned 4-4.5 kbp, consistent with regional epigenetically inherited centromeres. However, unlike other regional centromeres, there was no evidence of pericentromeric heterochromatin in C. lusitaniae. In particular, flanking genes were expressed at a similar level to the rest of the genome, and a URA3 reporter inserted adjacent to a centromere was not repressed. In addition, regions flanking the centromeric core were not associated with hypoacetylated histones or a sirtuin deacetylase that generates heterochromatin in other yeast. Interestingly, the centromeric chromatin had a distinct pattern of histone modifications, being enriched for methylated H3K79 and H3R2 but lacking methylation of H3K4, which is found at other regional centromeres. Thus, not all regional centromeres require flanking heterochromatin.
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Overlapping Functions between SWR1 Deletion and H3K56 Acetylation in Candida albicans. EUKARYOTIC CELL 2015; 14:578-87. [PMID: 25862154 DOI: 10.1128/ec.00002-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/03/2015] [Indexed: 11/20/2022]
Abstract
Nucleosome destabilization by histone variants and modifications has been implicated in the epigenetic regulation of gene expression, with the histone variant H2A.Z and acetylation of H3K56 (H3K56ac) being two examples. Here we find that deletion of SWR1, the major subunit of the SWR1 complex depositing H2A.Z into chromatin in exchange for H2A, promotes epigenetic white-opaque switching in Candida albicans. We demonstrate through nucleosome mapping that SWR1 is required for proper nucleosome positioning on the promoter of WOR1, the master regulator of switching, and that its effects differ in white and opaque cells. Furthermore, we find that H2A.Z is enriched adjacent to nucleosome-free regions at the WOR1 promoter in white cells, suggesting a role in the stabilization of a repressive chromatin state. Deletion of YNG2, a subunit of the NuA4 H4 histone acetyltransferase (HAT) that targets SWR1 activity through histone acetylation, produces a switching phenotype similar to that of swr1, and both may act downstream of the GlcNAc signaling pathway. We further uncovered a genetic interaction between swr1 and elevated H3K56ac with the discovery that the swr1 deletion mutant is highly sensitive to nicotinamide. Our results suggest that the interaction of H2A.Z and H3K56ac regulates epigenetic switching at the nucleosome level, as well as having global effects.
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Abstract
Only few Candida species, e.g., Candida albicans, Candida glabrata, Candida dubliniensis, and Candida parapsilosis, are successful colonizers of a human host. Under certain circumstances these species can cause infections ranging from superficial to life-threatening disseminated candidiasis. The success of C. albicans, the most prevalent and best studied Candida species, as both commensal and human pathogen depends on its genetic, biochemical, and morphological flexibility which facilitates adaptation to a wide range of host niches. In addition, formation of biofilms provides additional protection from adverse environmental conditions. Furthermore, in many host niches Candida cells coexist with members of the human microbiome. The resulting fungal-bacterial interactions have a major influence on the success of C. albicans as commensal and also influence disease development and outcome. In this chapter, we review the current knowledge of important survival strategies of Candida spp., focusing on fundamental fitness and virulence traits of C. albicans.
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Affiliation(s)
- Melanie Polke
- Research Group Microbial Immunology, Hans-Knoell-Institute, Jena, Germany; Department Microbial Pathogenicity Mechanisms, Hans-Knoell-Institute, Jena, Germany
| | - Bernhard Hube
- Department Microbial Pathogenicity Mechanisms, Hans-Knoell-Institute, Jena, Germany; Friedrich-Schiller-University, Jena, Germany; Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Ilse D Jacobsen
- Research Group Microbial Immunology, Hans-Knoell-Institute, Jena, Germany; Friedrich-Schiller-University, Jena, Germany
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Hirakawa MP, Martinez DA, Sakthikumar S, Anderson MZ, Berlin A, Gujja S, Zeng Q, Zisson E, Wang JM, Greenberg JM, Berman J, Bennett RJ, Cuomo CA. Genetic and phenotypic intra-species variation in Candida albicans. Genome Res 2014; 25:413-25. [PMID: 25504520 PMCID: PMC4352881 DOI: 10.1101/gr.174623.114] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Candida albicans is a commensal fungus of the human gastrointestinal tract and a prevalent opportunistic pathogen. To examine diversity within this species, extensive genomic and phenotypic analyses were performed on 21 clinical C. albicans isolates. Genomic variation was evident in the form of polymorphisms, copy number variations, chromosomal inversions, subtelomeric hypervariation, loss of heterozygosity (LOH), and whole or partial chromosome aneuploidies. All 21 strains were diploid, although karyotypic changes were present in eight of the 21 isolates, with multiple strains being trisomic for Chromosome 4 or Chromosome 7. Aneuploid strains exhibited a general fitness defect relative to euploid strains when grown under replete conditions. All strains were also heterozygous, yet multiple, distinct LOH tracts were present in each isolate. Higher overall levels of genome heterozygosity correlated with faster growth rates, consistent with increased overall fitness. Genes with the highest rates of amino acid substitutions included many cell wall proteins, implicating fast evolving changes in cell adhesion and host interactions. One clinical isolate, P94015, presented several striking properties including a novel cellular phenotype, an inability to filament, drug resistance, and decreased virulence. Several of these properties were shown to be due to a homozygous nonsense mutation in the EFG1 gene. Furthermore, loss of EFG1 function resulted in increased fitness of P94015 in a commensal model of infection. Our analysis therefore reveals intra-species genetic and phenotypic differences in C. albicans and delineates a natural mutation that alters the balance between commensalism and pathogenicity.
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Affiliation(s)
- Matthew P Hirakawa
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA
| | - Diego A Martinez
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Matthew Z Anderson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA; Department of Molecular, Cellular Biology and Genetics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Aaron Berlin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sharvari Gujja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ethan Zisson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA
| | - Joshua M Wang
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA
| | - Joshua M Greenberg
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA
| | - Judith Berman
- Department of Molecular, Cellular Biology and Genetics, University of Minnesota, Minneapolis, Minnesota 55455, USA; Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912, USA;
| | - Christina A Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA;
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Abbey DA, Funt J, Lurie-Weinberger MN, Thompson DA, Regev A, Myers CL, Berman J. YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens. Genome Med 2014; 6:100. [PMID: 25505934 PMCID: PMC4263066 DOI: 10.1186/s13073-014-0100-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/30/2014] [Indexed: 12/13/2022] Open
Abstract
The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleotide polymorphisms and loss of heterozygosity events in these pathogens, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains of Candida albicans, the most prevalent human fungal pathogen. The YMAP pipeline (http://lovelace.cs.umn.edu/Ymap/) automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other pathogens with small genomes.
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Affiliation(s)
- Darren A Abbey
- Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, Minneapolis, MN 55415 USA
| | - Jason Funt
- Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, MA 02142 USA
| | - Mor N Lurie-Weinberger
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 418 Britannia Building, Ramat Aviv, 69978 Israel
| | - Dawn A Thompson
- Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, MA 02142 USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, MA 02142 USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, 200 Union St SE, Minneapolis, MN 55455 USA
| | - Judith Berman
- Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, Minneapolis, MN 55415 USA ; Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 418 Britannia Building, Ramat Aviv, 69978 Israel
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Lo HJ, Chu WL, Liou CH, Huang SH, Khoo KH, Yang YL. Ndt80p is involved in L-sorbose utilization through regulating SOU1 in Candida albicans. Int J Med Microbiol 2014; 305:170-3. [PMID: 25497969 DOI: 10.1016/j.ijmm.2014.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 10/30/2014] [Accepted: 11/04/2014] [Indexed: 01/21/2023] Open
Abstract
Ndt80p, a known transcriptional factor, regulates various targets involved in stress responses, filamentous growth, and virulence in Candida albicans. Potential targets of Ndt80p have been identified at the transcriptional level. The present study was conducted to identify genes regulated by Ndt80p from the protein level. We found that the levels of Ahp1p, Fma1p, Hsp21p, Rfa2p, Snz1p, Sod1p, Sou1p, Trp99p, orf19.251, orf19.1862, and orf19.5620, were affected by the null mutation of NDT80 by two-dimensional polyacrylamide gel-electrophoresis analysis. Among the 11 proteins, all but Sou1p and Rfa2p are suggested to be involved in known functions of Ndt80p. Here, we demonstrate that Ndt80p plays a role in l-sorbose utilization through regulating SOU1 in C. albicans.
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Affiliation(s)
- Hsiu-Jung Lo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan; School of Dentistry, China Medical University, Taichung, Taiwan
| | - Wen-Li Chu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Ci-Hong Liou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Szu-Hsuan Huang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yun-Liang Yang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan.
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Bennett RJ, Forche A, Berman J. Rapid mechanisms for generating genome diversity: whole ploidy shifts, aneuploidy, and loss of heterozygosity. Cold Spring Harb Perspect Med 2014; 4:cshperspect.a019604. [PMID: 25081629 DOI: 10.1101/cshperspect.a019604] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Human fungal pathogens can exist in a variety of ploidy states, including euploid and aneuploid forms. Ploidy change has a major impact on phenotypic properties, including the regulation of interactions with the human host. In addition, the rapid emergence of drug-resistant isolates is often associated with the formation of specific supernumerary chromosomes. Pathogens such as Candida albicans and Cryptococcus neoformans appear particularly well adapted for propagation in multiple ploidy states with novel pathways driving ploidy variation. In both species, heterozygous cells also readily undergo loss of heterozygosity (LOH), leading to additional phenotypic changes such as altered drug resistance. Here, we examine the sexual and parasexual cycles that drive ploidy variation in human fungal pathogens and discuss ploidy and LOH events with respect to their far-reaching roles in fungal adaptation and pathogenesis.
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Affiliation(s)
- Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912
| | - Anja Forche
- Department of Biology, Bowdoin College, Brunswick, Maine 04011
| | - Judith Berman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455 Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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Kravets A, Yang F, Bethlendy G, Cao Y, Sherman F, Rustchenko E. Adaptation of Candida albicans to growth on sorbose via monosomy of chromosome 5 accompanied by duplication of another chromosome carrying a gene responsible for sorbose utilization. FEMS Yeast Res 2014; 14:708-13. [PMID: 24702787 DOI: 10.1111/1567-1364.12155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/25/2014] [Indexed: 11/27/2022] Open
Abstract
Candida albicans, a fungus that normally inhabits the digestive tract and other mucosal surfaces, can become a pathogen in immunocompromised individuals, causing severe or even fatal infection. Mechanisms by which C. albicans can evade commonly used antifungal agents are not fully understood. We are studying a model system involving growth of C. albicans on toxic sugar sorbose, which represses synthesis of cell wall glucan and, as a result, kills fungi in a manner similar to drugs from the echinocandins class. Adaptation to sorbose occurs predominantly due to reversible loss of one homolog of chromosome 5 (Ch5), which results in upregulation of the metabolic gene SOU1 (SOrbose Utilization) on Ch4. Here, we show that growth on sorbose due to Ch5 monosomy can involve a facultative trisomy of a hybrid Ch4/7 that serves to increase copy number of the SOU1 gene. This shows that control of expression of SOU1 can involve multiple mechanisms; in this case, negative regulation and increase in gene copy number operating simultaneously in cell.
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Affiliation(s)
- Anatoliy Kravets
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
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Large-Scale Chromosomal Changes and Associated Fitness Consequences in Pathogenic Fungi. CURRENT FUNGAL INFECTION REPORTS 2014; 8:163-170. [PMID: 25685251 DOI: 10.1007/s12281-014-0181-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Pathogenic fungi encounter many different host environments to which they must adapt rapidly to ensure growth and survival. They also must be able to cope with alterations in established niches during long-term persistence in the host. Many eukaryotic pathogens have evolved a highly plastic genome, and large-scale chromosomal changes including aneuploidy, and loss of heterozygosity (LOH) can arise under various in vitro and in vivo stresses. Both aneuploidy and LOH can arise quickly during a single cell cycle, and it is hypothesized that they provide a rapid, albeit imprecise, solution to adaptation to stress until better and more refined solutions can be acquired by the organism. While LOH, with the extreme case of haploidization in Candida albicans, can purge the genome from recessive lethal alleles and/or generate recombinant progeny with increased fitness, aneuploidy, in the absence or rarity of meiosis, can serve as a non-Mendelian mechanism for generating genomic variation.
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