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1.  Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection 
mBio  2012;3(5):e00259-12.
ABSTRACT
The major cause of athlete’s foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response.
IMPORTANCE
Athlete’s foot, jock itch, ringworm, and nail infections are common fungal infections, all caused by fungi known as dermatophytes (fungi that infect skin). This report presents the genome sequences of Trichophyton rubrum, the most frequent cause of athlete’s foot, as well as four other common dermatophytes. Dermatophyte genomes are enriched for four gene classes that may contribute to the ability of these fungi to cause disease. These include (i) proteases secreted to degrade skin; (ii) kinases, including pseudokinases, that are involved in signaling necessary for adapting to skin; (iii) secondary metabolites, compounds that act as toxins or signals in the interactions between fungus and host; and (iv) a class of proteins (LysM) that appear to bind and mask cell wall components and carbohydrates, thus avoiding the host’s immune response to the fungi. These genome sequences provide a strong foundation for future work in understanding how dermatophytes cause disease.
doi:10.1128/mBio.00259-12
PMCID: PMC3445971  PMID: 22951933
2.  Comparison of Sterol Import under Aerobic and Anaerobic Conditions in Three Fungal Species, Candida albicans, Candida glabrata, and Saccharomyces cerevisiae 
Eukaryotic Cell  2013;12(5):725-738.
Sterol import has been characterized under various conditions in three distinct fungal species, the model organism Saccharomyces cerevisiae and two human fungal pathogens Candida glabrata and Candida albicans, employing cholesterol, the sterol of higher eukaryotes, as well as its fungal equivalent, ergosterol. Import was confirmed by the detection of esterified cholesterol within the cells. Comparing the three fungal species, we observe sterol import under three different conditions. First, as previously well characterized, we observe sterol import under low oxygen levels in S. cerevisiae and C. glabrata, which is dependent on the transcription factor Upc2 and/or its orthologs or paralogs. Second, we observe sterol import under aerobic conditions exclusively in the two pathogenic fungi C. glabrata and C. albicans. Uptake emerges during post-exponential-growth phases, is independent of the characterized Upc2-pathway and is slower compared to the anaerobic uptake in S. cerevisiae and C. glabrata. Third, we observe under normoxic conditions in C. glabrata that Upc2-dependent sterol import can be induced in the presence of fetal bovine serum together with fluconazole. In summary, C. glabrata imports sterols both in aerobic and anaerobic conditions, and the limited aerobic uptake can be further stimulated by the presence of serum together with fluconazole. S. cerevisiae imports sterols only in anaerobic conditions, demonstrating aerobic sterol exclusion. Finally, C. albicans imports sterols exclusively aerobically in post-exponential-growth phases, independent of Upc2. For the first time, we provide direct evidence of sterol import into the human fungal pathogen C. albicans, which until now was believed to be incapable of active sterol import.
doi:10.1128/EC.00345-12
PMCID: PMC3647772  PMID: 23475705
3.  Discovery of Cryptic Polyketide Metabolites from Dermatophytes using Heterologous Expression in Aspergillus nidulans 
ACS synthetic biology  2013;2(11):10.1021/sb400048b.
Dermatophytes belonging to the Trichophyton and Arthroderma genera cause skin infections in humans and animals. From genome sequencing data, we mined a conserved gene cluster among dermatophytes that are homologous to one that produces an immunosuppressive polyketide in Aspergillus fumigatus. Using a recombination-based cloning strategy in yeast, we constructed fungal heterologous expression vectors that encode the cryptic clusters. When integrated into the model Aspergillus nidulans host, a structurally related compound neosartoricin B was formed, suggesting a possible role of this compound in the pathogenesis of these strains.
doi:10.1021/sb400048b
PMCID: PMC3795930  PMID: 23758576
natural products; polyketide; heterologous expression; prenyltransferase
4.  Pharmacokinetics of Posaconazole Within Epithelial Cells and Fungi: Insights Into Potential Mechanisms of Action During Treatment and Prophylaxis 
The Journal of Infectious Diseases  2013;208(10):1717-1728.
Background. The antifungal posaconazole concentrates within host cells and protects against Aspergillus fumigatus. The specific subcellular location of posaconazole and the mechanism by which cell-associated posaconazole inhibits fungal growth remain uncharacterized.
Methods. Posaconazole was conjugated with the fluorophore boron-dipyrromethene (BDP-PCZ). A549 pulmonary epithelial cells and A. fumigatus were exposed to BDP-PCZ individually and in coculture. BDP-PCZ subcellular localization and trafficking were observed using confocal microscopy and flow cytometry.
Results. BDP-PCZ concentrated within A549 cell membranes, and in particular within the endoplasmic reticulum. Epithelial cell-associated BDP-PCZ rapidly transferred to and concentrated within A. fumigatus cell membranes on contact. BDP-PCZ transfer to conidia did not require phagocytosis and was markedly enhanced by the conidial hydrophobin RodA. Within AF, BDP-PCZ also concentrated in membranes including the endoplasmic reticulum and colocalized with the azole target enzyme CYP51a. Concentration of BDP-PCZ within host and fungal cell membranes persisted for >48 hours and could be competitively inhibited by posaconazole but not voriconazole.
Conclusions. Posaconazole concentrates within host cell membranes and rapidly transfers to A. fumigatus, where it accumulates to high concentrations and persists at the site of its target enzyme. These intracellular and intercellular pharmacokinetic properties probably contribute to the efficacy of PCZ.
doi:10.1093/infdis/jit358
PMCID: PMC3805237  PMID: 23908482
posaconazole; localization; pharmacokinetics; endoplasmic reticulum; epithelial cells; Aspergillus; postantifungal effect; hydrophobin rodA
5.  Sequenced dermatophyte strains: growth rate, conidiation, drug susceptibilities, and virulence in an invertebrate model 
Although dermatophytes are the most common cause of fungal infections in the world, their basic biology is not well understood. The recent sequencing and annotation of the genomes of five representative dermatophyte species allows for the creation of hypotheses as to how they cause disease and have adapted to their distinct environments. An understanding of the microbiology of these strains will be essential for testing these hypotheses. This study is the first to generally characterize these five sequenced strains of dermatophytes for their microbiological aspects. We measured the growth rate on solid medium and found differences between species, with Microsporum gypseum CBS118893 having the fastest growth and Trichophyton rubrum CBS118892 the slowest. We also compared different media for conidia production and found that the highest numbers of conidia were produced when dermatophytes were grown on MAT agar. We determined the Minimum Inhibitory Concentration (MIC) of nine antifungal agents and confirmed susceptibility to antifungals commonly used as selectable markers. Finally, we tested virulence in the Galleria mellonella (wax moth) larvae model but found the results variable. These results increase our understanding of the microbiology and molecular biology of these dermatophyte strains and will be of use in advancing hypothesis-driven research about dermatophytes.
doi:10.1016/j.fgb.2010.11.010
PMCID: PMC3035951  PMID: 21145410
dermatophytes; Galleria; antifungal; drug susceptibilities
6.  Dermatophyte Virulence Factors: Identifying and Analyzing Genes That May Contribute to Chronic or Acute Skin Infections 
Dermatophytes are prevalent causes of cutaneous mycoses and, unlike many other fungal pathogens, are able to cause disease in immunocompetent individuals. They infect keratinized tissue such as skin, hair, and nails, resulting in tinea infections, including ringworm. Little is known about the molecular mechanisms that underlie the ability of these organisms to establish and maintain infection. The recent availability of genome sequence information and improved genetic manipulation have enabled researchers to begin to identify and study the role of virulence factors of dermatophytes. This paper will summarize our current understanding of dermatophyte virulence factors and discuss future directions for identifying and testing virulence factors.
doi:10.1155/2012/358305
PMCID: PMC3185252  PMID: 21977036
7.  Zinc Finger Transcription Factors Displaced SREBP Proteins as the Major Sterol Regulators during Saccharomycotina Evolution 
PLoS Genetics  2014;10(1):e1004076.
In most eukaryotes, including the majority of fungi, expression of sterol biosynthesis genes is regulated by Sterol-Regulatory Element Binding Proteins (SREBPs), which are basic helix-loop-helix transcription activators. However, in yeasts such as Saccharomyces cerevisiae and Candida albicans sterol synthesis is instead regulated by Upc2, an unrelated transcription factor with a Gal4-type zinc finger. The SREBPs in S. cerevisiae (Hms1) and C. albicans (Cph2) have lost a domain, are not major regulators of sterol synthesis, and instead regulate filamentous growth. We report here that rewiring of the sterol regulon, with Upc2 taking over from SREBP, likely occurred in the common ancestor of all Saccharomycotina. Yarrowia lipolytica, a deep-branching species, is the only genome known to contain intact and full-length orthologs of both SREBP (Sre1) and Upc2. Deleting YlUPC2, but not YlSRE1, confers susceptibility to azole drugs. Sterol levels are significantly reduced in the YlUPC2 deletion. RNA-seq analysis shows that hypoxic regulation of sterol synthesis genes in Y. lipolytica is predominantly mediated by Upc2. However, YlSre1 still retains a role in hypoxic regulation; growth of Y. lipolytica in hypoxic conditions is reduced in a Ylupc2 deletion and is abolished in a Ylsre1/Ylupc2 double deletion, and YlSre1 regulates sterol gene expression during hypoxia adaptation. We show that YlSRE1, and to a lesser extent YlUPC2, are required for switching from yeast to filamentous growth in hypoxia. Sre1 appears to have an ancestral role in the regulation of filamentation, which became decoupled from its role in sterol gene regulation by the arrival of Upc2 in the Saccharomycotina.
Author Summary
All but a few eukaryotes die without oxygen and respond dynamically to changes in the level of oxygen available to them. One ancient oxygen-requiring biochemical pathway in eukaryotes is the pathway for the biosynthesis of sterols, leading to cholesterol in animals and ergosterol in fungi. Mutations in this pathway are a frequent cause of azole drug resistance in pathogenic fungi. The regulatory mechanism for the sterol pathway is also widely conserved between animals and fungi and is centred on a transcription activator, SREBP, which forms part of a sterol-sensing complex. However, in one group of yeasts – the Saccharomycotina, which includes the major pathogen Candida albicans – control of the sterol pathway has been taken over by an unrelated regulatory protein, Upc2. We show here by analysis of the yeast Yarrowia lipolytica that the evolutionary switch from SREBP to Upc2 was a two-step process in which Upc2 appeared in an ancestor of Saccharomycotina, and SREBP subsequently lost its sterol-regulatory function while retaining an ancient role in filamentation.
doi:10.1371/journal.pgen.1004076
PMCID: PMC3894159  PMID: 24453983
8.  Cytoplasmic localization of sterol transcription factors Upc2p and Ecm22p in S.cerevisiae 
Fungal genetics and biology : FG & B  2008;45(10):1430-1438.
Ergosterol homeostasis is a critical process for fungal cells. Paralogous zinc cluster transcription factors Upc2p and Ecm22p are major regulators of ergosterol biosynthesis in Saccharomyces cerevisiae. Upc2p and Ecm22p sense and respond to sterol depletion but their mechanism of activation has not been defined. Subcellular localization and functional expression of Upc2p–GFP and Ecm22p-GFP was monitored by fluorescence microscopy and flow cytometry in live yeast cells. Both fusion proteins localized to intracellular membranes and to perinuclear foci. Perinuclear localization of Upc2p-GFP and Ecm22p-GFP was increased when ergosterol biosynthesis was blocked by azole drug treatment. Nuclear localization in response to sterol depletion is consistent with the hypothesis that Upc2p and Ecm22p are trafficked from a membrane to the nucleus as a post-translational mechanism of sterol sensing.
doi:10.1016/j.fgb.2008.07.004
PMCID: PMC2580778  PMID: 18675371
Ergosterol; UPC2; ECM22; SREBP; Azole Resistance; GFP; FACS
9.  Polyene susceptibility is dependent on nitrogen source in the opportunistic pathogen Candida albicans 
Objective
Polyene antifungal drugs, including amphotericin B or nystatin, target ergosterol in the fungal plasma membrane and are used to treat systemic, vaginal and oral fungal infections. In the oral cavity, the available nitrogen sources are primarily in the form of proteins, which are poor nitrogen sources. This study evaluates the effect of protein as a nitrogen source on drug susceptibilities.
Methods
Candida albicans were grown in protein [bovine serum albumin (BSA) or casein (CSN)] as a sole nitrogen source, in ammonium sulfate (AS) as a nitrogen source, or in both protein and AS.
Results
Cells grown in BSA or CSN were 4 to 16-fold less susceptible to amphotericin B and nystatin than cells grown in AS. Similar results were observed for cycloheximide, but not for fluconazole or caspofungin, and were observed for many C. albicans clinical isolates. The results are observed in two different media, and in broth and on agar. Cells grown under these nitrogen poor conditions have a reduction in ergosterol sterol levels and a reduction in overall sterol synthesis. QRT-PCR analyses shows that some genes involved in sterol biosynthesis are induced under nitrogen limiting conditions, consistent with the lower sterol levels.
Conclusion
The results demonstrate that nitrogen source has a significant effect on polyene susceptibilities. As these nitrogen-limiting conditions mimic oral nitrogen availability, they suggest that in vitro polyene susceptibilities may overestimate the in vivo susceptibilities to polyene drugs in the mouth.
doi:10.1093/jac/dkn101
PMCID: PMC2424025  PMID: 18343803
Amphotericin B; ergosterol; sterol; secreted aspartyl proteinase
10.  A Flucytosine-Responsive Mbp1/Swi4-Like Protein, Mbs1, Plays Pleiotropic Roles in Antifungal Drug Resistance, Stress Response, and Virulence of Cryptococcus neoformans 
Eukaryotic Cell  2012;11(1):53-67.
Cryptococcosis, caused by the basidiomycetous fungus Cryptococcus neoformans, is responsible for more than 600,000 deaths annually in AIDS patients. Flucytosine is one of the most commonly used antifungal drugs for its treatment, but its resistance and regulatory mechanisms have never been investigated at the genome scale in C. neoformans. In the present study, we performed comparative transcriptome analysis by employing two-component system mutants (tco1Δ and tco2Δ) exhibiting opposing flucytosine susceptibility. As a result, a total of 177 flucytosine-responsive genes were identified, and many of them were found to be regulated by Tco1 or Tco2. Among these, we discovered an APSES-like transcription factor, Mbs1 (Mbp1- and Swi4-like protein 1). Expression analysis revealed that MBS1 was regulated in response to flucytosine in a Tco2/Hog1-dependent manner. Supporting this, C. neoformans with the deletion of MBS1 exhibited increased susceptibility to flucytosine. Intriguingly, Mbs1 played pleiotropic roles in diverse cellular processes of C. neoformans. Mbs1 positively regulated ergosterol biosynthesis and thereby affected polyene and azole drug susceptibility. Mbs1 was also involved in genotoxic and oxidative stress responses. Furthermore, Mbs1 promoted production of melanin and capsule and thereby was required for full virulence of C. neoformans. In conclusion, Mbs1 is considered to be a novel antifungal therapeutic target for treatment of cryptococcosis.
doi:10.1128/EC.05236-11
PMCID: PMC3255937  PMID: 22080454
11.  A Foot in the Door for Dermatophyte Research 
PLoS Pathogens  2012;8(3):e1002564.
doi:10.1371/journal.ppat.1002564
PMCID: PMC3315479  PMID: 22479177
12.  The role of Candida albicans homologous recombination factors Rad54 and Rdh54 in DNA damage sensitivity 
BMC Microbiology  2011;11:214.
Background
The fungal pathogen Candida albicans is frequently seen in immune suppressed patients, and resistance to one of the most widely used antifungals, fluconazole (FLC), can evolve rapidly. In recent years it has become clear that plasticity of the Candida albicans genome contributes to drug resistance through loss of heterozygosity (LOH) at resistance genes and gross chromosomal rearrangements that amplify gene copy number of resistance associated genes. This study addresses the role of the homologous recombination factors Rad54 and Rdh54 in cell growth, DNA damage and FLC resistance in Candida albicans.
Results
The data presented here support a role for homologous recombination in cell growth and DNA damage sensitivity, as Candida albicans rad54Δ/rad54Δ mutants were hypersensitive to MMS and menadione, and had an aberrant cell and nuclear morphology. The Candida albicans rad54Δ/rad54Δ mutant was defective in invasion of Spider agar, presumably due to the altered cellular morphology. In contrast, mutation of the related gene RDH54 did not contribute significantly to DNA damage resistance and cell growth, and deletion of either Candida albicans RAD54 or Candida albicans RDH54 did not alter FLC susceptibility.
Conclusions
Together, these results support a role for homologous recombination in genome stability under nondamaging conditions. The nuclear morphology defects in the rad54Δ/rad54Δ mutants show that Rad54 performs an essential role during mitotic growth and that in its absence, cells arrest in G2. The viability of the single mutant rad54Δ/rad54Δ and the inability to construct the double mutant rad54Δ/rad54Δ rdh54Δ/rdh54Δ suggests that Rdh54 can partially compensate for Rad54 during mitotic growth.
doi:10.1186/1471-2180-11-214
PMCID: PMC3197502  PMID: 21951709
13.  An A643V Amino Acid Substitution in Upc2p Contributes to Azole Resistance in Well-Characterized Clinical Isolates of Candida albicans▿  
The Candida albicans Upc2p transcription factor regulates ERG11, encoding the target of azole drugs. Gain-of-function mutations that contribute to resistance were recently identified in a series of sequential clinical isolates (N. Dunkel, T. T. Liu, K. S. Barker, R. Homayouni, J. Morschhauser, and P. D. Rogers, Eukaryot. Cell 7:1180-1190, 2008). In the present study, UPC2 was sequenced from a matched set of 17 isolates. An A643V substitution was present in all of the isolates in the series that overexpressed ERG11. Azole susceptibility, ergosterol levels, and expression of ERG genes were elevated in the A643V clinical isolates and in reconstructed strains.
doi:10.1128/AAC.00995-10
PMCID: PMC3028767  PMID: 21078937
14.  Overexpression of TUF1 restores respiratory growth and fluconazole sensitivity to a Cryptococcus neoformans vad1Δ mutant 
Microbiology  2010;156(Pt 8):2558-2565.
The yeast-like fungus Cryptococcus neoformans favours respiration as a mechanism of energy production, and thus depends heavily on mitochondrial function. Previous studies of a C. neoformans vad1Δ mutant revealed reduced expression of the mitochondrial elongation factor TUF1 and defects in glycerol utilization, consistent with mitochondrial dysfunction. In this study, we found that in trans expression of TUF1 in the vad1Δ mutant suppressed the mitochondrial defects, including growth on respiration-dependent carbon sources and fluconazole resistance, associated with VAD1 deletion. Tetracycline, an inhibitor of mitochondrial translation, was found to confer resistance to fluconazole in the wild-type and vad1Δ mutant, whereas the fluconazole susceptibility of the TUF1-overexpressing strain was unaffected by tetracycline treatment. In the presence of fluconazole, the vad1Δ mutant exhibited increased activation of the global transcriptional regulator Sre1. TUF1 overexpression failed to alter cleavage of Sre1 in response to fluconazole in the vad1Δ mutant, suggesting that TUF1 repression in the vad1Δ mutant is distal to Sre1, or that it occurs through an independent pathway.
doi:10.1099/mic.0.035923-0
PMCID: PMC3068674  PMID: 20430817
15.  The UPC2 Promoter in Candida albicans Contains Two cis-Acting Elements That Bind Directly to Upc2p, Resulting in Transcriptional Autoregulation▿† 
Eukaryotic Cell  2010;9(9):1354-1362.
In Candida albicans, ergosterol biosynthetic genes, including ERG11, which encodes the target of azole antifungal drugs, are regulated by the transcriptional regulator Upc2p. To initially characterize the promoter of the UPC2 gene, 5′ rapid amplification of cDNA ends was used to identify two transcriptional initiation sites upstream of the ATG codon. The regions within the UPC2 promoter required for azole regulation of the UPC2 promoter were then identified using nested deletions fused to a luciferase reporter which were tested for azole inducibility in wild-type (WT) and upc2Δ/upc2Δ strains. Two distinct regions important for azole induction were identified: a Upc2p-dependent region (UDR) between bp −450 and −350 upstream of the ATG codon and a Upc2p-independent region (UIR) between bp −350 and −250 upstream of the ATG codon. Within the UDR, loss or mutation of the sterol response element (SRE), so named because of homology to the Saccharomyces cerevisiae Upc2p binding site, resulted in a decrease in both basal and induced expression in the WT strain but did not affect azole inducibility in the upc2Δ/upc2Δ deletion strain. Gel shift analyses using the DNA binding domain of Upc2p confirmed binding of the protein to two SRE-related sequences within the UPC2 promoter, with strongest binding to the UDR SRE. Detailed gel shift analyses of the UDR SRE shows that Upc2p binds to a bipartite element within the UPC2 promoter, including the previously identified SRE and a new, adjacent element, the short direct repeat (SDR), with partial homology to the SRE.
doi:10.1128/EC.00130-10
PMCID: PMC2937341  PMID: 20656915
16.  Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi 
Genome Biology  2011;12(1):R7.
Background
Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans.
Results
97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species.
Conclusions
Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens.
doi:10.1186/gb-2011-12-1-r7
PMCID: PMC3091305  PMID: 21247460
17.  Azole Drugs Are Imported By Facilitated Diffusion in Candida albicans and Other Pathogenic Fungi 
PLoS Pathogens  2010;6(9):e1001126.
Despite the wealth of knowledge regarding the mechanisms of action and the mechanisms of resistance to azole antifungals, very little is known about how the azoles are imported into pathogenic fungal cells. Here the in-vitro accumulation and import of Fluconazole (FLC) was examined in the pathogenic fungus, Candida albicans. In energized cells, FLC accumulation correlates inversely with expression of ATP-dependent efflux pumps. In de-energized cells, all strains accumulate FLC, suggesting that FLC import is not ATP-dependent. The kinetics of import in de-energized cells displays saturation kinetics with a Km of 0.64 uM and Vmax of 0.0056 pmol/min/108 cells, demonstrating that FLC import proceeds via facilitated diffusion through a transporter rather than passive diffusion. Other azoles inhibit FLC import on a mole/mole basis, suggesting that all azoles utilize the same facilitated diffusion mechanism. An analysis of related compounds indicates that competition for azole import depends on an aromatic ring and an imidazole or triazole ring together in one molecule. Import of FLC by facilitated diffusion is observed in other fungi, including Cryptococcus neoformans, Saccharomyces cerevisiae, and Candida krusei, indicating that the mechanism of transport is conserved among fungal species. FLC import was shown to vary among Candida albicans resistant clinical isolates, suggesting that altered facilitated diffusion may be a previously uncharacterized mechanism of resistance to azole drugs.
Author Summary
Azole antifungals are used to treat a wide variety of fungal infections of humans, animals and plants. A great deal is known about how the azoles interact with their target enzyme within fungal cells and how the azoles are exported from the fungal cell through various efflux pumps. Altered interactions with the target enzyme and altered efflux pump expression are common mechanisms of azole resistance in fungi. However, the mechanism by which azoles enter a fungal cell is not clear—many have assumed that azoles passively diffuse into the cell. This study demonstrates that azoles are not passively diffused, or actively pumped, into the cell. Instead, azoles are imported by facilitated diffusion, mediated by a transporter. Facilitated diffusion of azoles is saturable. All clinically important azoles, and many structurally related compounds, compete for FLC import, while structurally unrelated drugs do not compete. Azole import by facilitated diffusion is shown in four species of fungi, suggesting that it is common for most if not all fungi. Altered facilitated diffusion is observed in a collection of clinical isolates, suggesting that altered import is a previously uncharacterized mechanism of resistance.
doi:10.1371/journal.ppat.1001126
PMCID: PMC2947996  PMID: 20941354
18.  Genetic Basis of Antifungal Drug Resistance 
Current fungal infection reports  2009;3(3):163-169.
Antifungal resistance caused by mutations of the drug target, overexpression of the drug target, and drug efflux by the upregulation of transporters is increasingly common. Recently our understanding of fungal drug resistance has been advanced by the identification of three key transcriptional regulators of resistance: Tac1p, Upc2p, and Mrr1p. The discovery of hyperactive variants of these regulators in resistant clinical isolates confirms the importance of transcriptional regulation in the development of antifungal resistance. Alternative mechanisms of drug resistance including aneuploidy and biofilm formation have recently been documented in fungi; as well as the phenomenon of drug tolerance. Characterization of the transcriptional regulation of fungal drug resistance and the identification of novel mechanisms of resistance has implications for current therapy and for the development of future antifungal drugs.
doi:10.1007/s12281-009-0021-y
PMCID: PMC2790137  PMID: 20161440
19.  Organization and Evolutionary Trajectory of the Mating Type (MAT) Locus in Dermatophyte and Dimorphic Fungal Pathogens▿ †  
Eukaryotic Cell  2009;9(1):46-58.
Sexual reproduction in fungi is governed by a specialized genomic region, the mating type (MAT) locus, whose gene identity, organization, and complexity are diverse. We identified the MAT locus of five dermatophyte fungal pathogens (Microsporum gypseum, Microsporum canis, Trichophyton equinum, Trichophyton rubrum, and Trichophyton tonsurans) and a dimorphic fungus, Paracoccidioides brasiliensis, and performed phylogenetic analyses. The identified MAT locus idiomorphs of M. gypseum control cell type identity in mating assays, and recombinant progeny were produced. Virulence tests in Galleria mellonella larvae suggest the two mating types of M. gypseum may have equivalent virulence. Synteny analysis revealed common features of the MAT locus shared among these five dermatophytes: namely, a small size (∼3 kb) and a novel gene arrangement. The SLA2, COX13, and APN2 genes, which flank the MAT locus in other Ascomycota are instead linked on one side of the dermatophyte MAT locus. In addition, the transcriptional orientations of the APN2 and COX13 genes are reversed compared to the dimorphic fungi Histoplasma capsulatum, Coccidioides immitis, and Coccidioides posadasii. A putative transposable element, pogo, was found to have inserted in the MAT1-2 idiomorph of one P. brasiliensis strain but not others. In conclusion, the evolution of the MAT locus of the dermatophytes and dimorphic fungi from the last common ancestor has been punctuated by both gene acquisition and expansion, and asymmetric gene loss. These studies further support a foundation to develop molecular and genetic tools for dermatophyte and dimorphic human fungal pathogens.
doi:10.1128/EC.00259-09
PMCID: PMC2805302  PMID: 19880755
20.  Candida albicans UPC2 is transcriptionally induced in response to antifungal drugs and anaerobicity through Upc2p dependent and independent mechanisms. 
Microbiology (Reading, England)  2008;154(Pt 9):2748-2756.
Many genes in the Candida albicans ergosterol biosynthetic pathway are controlled by the transcriptional activator Upc2p, which is upregulated in the presence of azole drugs and has been suggested to regulate its own transcription by an autoregulatory mechanism. The UPC2 promoter was cloned upstream of a luciferase reporter gene (RLUC). UPC2-RLUC activity is induced in response to ergosterol biosynthesis inhibitors and in response to anaerobicity. In both conditions, induction correlates with the magnitude of sterol depletion. Azole inducibility in the parental strain was approximately 100-fold, and in a UPC2 homozygous deletion strain was 17-fold, suggesting that in addition to autoregulation, UPC2 transcription is controlled by a novel, Upc2p-independent mechanism(s). Curiously, basal UPC2-RLUC activity is 5-fold higher in the deletion strain, which may be an indirect consequence of the lower sterol level in this strain, or a direct consequence of repression by an autoregulatory mechanism. These results suggest that transcriptional regulation of UPC2 expression is important in the response to antifungal drugs, and that this regulation occurs through Upc2p-dependent as well as novel Upc2p-independent mechanisms.
doi:10.1099/mic.0.2008/017475-0
PMCID: PMC2577385  PMID: 18757808
Candida albicans; UPC2; azoles; resistance; ergosterol biosynthesis; autoregulation
21.  Micafungin activity against Candida albicans with diverse azole resistance phenotypes 
Objectives
The purpose of this study was to investigate whether mechanisms of azole resistance in Candida albicans contribute to reduced micafungin activity in vitro.
Methods
MICs were determined for a collection of strains with well-characterized mechanisms of azole resistance obtained from systemic, oral and vaginal infections. This collection of strains includes those with resistance-associated phenotypes. All known molecular mechanisms of azole resistance are included in this set of isolates (alone or in combination). Micafungin activity was further investigated for a subset of isolates by agar dilution.
Results
There was no correlation between any of the azole resistance mechanisms or resistance phenotypes and micafungin activity as determined by MIC, even in isolates with cross-resistance to multiple azole drugs. Overexpression of the ABC transporter CDR2 has been suggested to contribute to reduced echinocandin activity in agar dilution studies. By broth microdilution, there was no difference in MIC between the pump overexpressors and the collection as a whole. However, azole-resistant isolates from matched strains exhibited a small increase in their micafungin MICs relative to their susceptible controls. By agar dilution analysis, multiple CDR2-overexpressing strains exhibited reduced growth in the presence of micafungin relative to the laboratory strain SC5314.
Conclusions
Azole resistance mechanisms do not contribute to increased micafungin MIC. However, within sets of matched isolates, strains overexpressing CDR2 had a slight increase in micafungin MIC. Changes in micafungin susceptibility are associated with CDR2 overexpression in agar dilution tests.
doi:10.1093/jac/dkn156
PMCID: PMC2532560  PMID: 18436555
echinocandins; antifungals; XTT
22.  Micafungin activity against Candida albicans with diverse azole resistance phenotypes 
Objectives
The purpose of this study was to investigate whether mechanisms of azole resistance in Candida albicans contribute to reduced micafungin activity in vitro.
Methods
MICs were determined for a collection of strains with well-characterized mechanisms of azole resistance obtained from systemic, oral and vaginal infections. This collection of strains includes those with resistance-associated phenotypes. All known molecular mechanisms of azole resistance are included in this set of isolates (alone or in combination). Micafungin activity was further investigated for a subset of isolates by agar dilution.
Results
There was no correlation between any of the azole resistance mechanisms or resistance phenotypes and micafungin activity as determined by MIC, even in isolates with cross-resistance to multiple azole drugs. Overexpression of the ABC transporter CDR2 has been suggested to contribute to reduced echinocandin activity in agar dilution studies. By broth microdilution, there was no difference in MIC between the pump overexpressors and the collection as a whole. However, azole-resistant isolates from matched strains exhibited a small increase in their micafungin MICs relative to their susceptible controls. By agar dilution analysis, multiple CDR2-overexpressing strains exhibited reduced growth in the presence of micafungin relative to the laboratory strain SC5314.
Conclusions
Azole resistance mechanisms do not contribute to increased micafungin MIC as determined by broth microdilution. However, within sets of matched isolates, strains overexpressing CDR2 had a slight increase in micafungin MIC. Changes in micafungin susceptibility are associated with CDR2 overexpression in agar dilution tests.
doi:10.1093/jac/dkn156
PMCID: PMC2532560  PMID: 18436555
echinocandins; antifungals; XTT
23.  Polyene susceptibility is dependent on nitrogen source in the opportunistic pathogen Candida albicans 
Objectives
Polyene antifungal drugs, including amphotericin B or nystatin, target ergosterol in the fungal plasma membrane and are used to treat systemic, vaginal and oral fungal infections. In the oral cavity, the available nitrogen sources are primarily in the form of proteins, which are poor nitrogen sources. This study evaluates the effect of protein as a nitrogen source on drug susceptibilities.
Methods
Candida albicans was grown in protein [bovine serum albumin (BSA) or casein (CSN)] as a sole nitrogen source, in ammonium sulphate (AS) as a nitrogen source, or in both protein and AS.
Results
Cells grown in BSA or CSN were 4- to 16-fold less susceptible to amphotericin B and nystatin than those grown in AS. Similar results were observed for cycloheximide, but not for fluconazole or caspofungin, and were observed for many C. albicans clinical isolates. The results were observed in two different media, and in broth and on agar. Cells grown under these nitrogen-poor conditions have a reduction in ergosterol sterol levels and a reduction in overall sterol synthesis. Quantitative real-time reverse transcription–polymerase chain reaction analysis shows that some genes involved in sterol biosynthesis are induced under nitrogen-limiting conditions, consistent with the lower sterol levels.
Conclusions
The results demonstrate that nitrogen source has a significant effect on polyene susceptibilities. As these nitrogen-limiting conditions mimic oral nitrogen availability, they suggest that in vitro polyene susceptibilities may overestimate the in vivo susceptibilities to polyene drugs in the mouth.
doi:10.1093/jac/dkn101
PMCID: PMC2424025  PMID: 18343803
amphotericin B; ergosterol; sterol; secreted aspartyl proteinase
24.  Characterization of caspofungin susceptibilities by broth and agar in Candida albicans clinical isolates with characterized mechanisms of azole resistance 
Summary
In Candida albicans, caspofungin (CSP) susceptibilities, determined by broth microdilution methods, have not been found to be related to azole susceptibilities or resistance. In contrast, it has been observed that azole-resistant clinical isolates that overexpress the efflux pump gene CDR2 are less susceptible to CSP when tested using an agar dilution method commonly used with Saccharomyces cerevisiae. The goal of this study is to further understand the effects of azole resistance mechanisms on CSP susceptibility testing. A collection of 69 isolates exhibiting known mechanisms of azole resistance and resistance-associated phenotypes were analyzed by broth microdilution methods to determine standard minimum inhibitory concentrations (MIC) for CSP. The same isolates were then analyzed for MIC by Etest strips, an agar based method that has been shown generally to be comparable to broth methods. The MIC as analyzed by both methods were not significantly different. However, a collection of strains overexpressing the efflux pump CDR2 does exhibit a spectrum of CSP susceptibilities when examined by agar dilution susceptibility tests, ranging from standard to reduced susceptibilities. This work demonstrates that a change in CSP susceptibility with CDR2 overexpressing cells in agar dilution studies is a variable phenotype and it is not the result of growth conditions (broth versus agar).
doi:10.1080/13693780701816557
PMCID: PMC2562740  PMID: 18404551
Candida albicans; Caspofungin; drug resistance; Etest
25.  Tetracycline alters drug susceptibility in Candida albicans and other pathogenic fungi 
Microbiology (Reading, England)  2008;154(Pt 3):960-970.
Summary
The tetracycline (TET) promoter has been used in several systems as an inducible regulator of gene expression. In control analyses, the standard Candida albicans laboratory strain SC5314 was found to have altered susceptibility to a variety of antifungal drugs in the presence of relatively high concentrations (50 to 200 μg/ml) of TET. Altered susceptibility was most notable with exposure to amphotericin B (AMB) with a 32 fold increase in susceptibility, and terbinafine (TRB) with a 32 fold decrease in susceptibility. The TET/AMB synergy was observed in several clinical isolates of C. albicans and in distantly related species Aspergillus fumigatus, and Cryptococcus neoformans. The TET/AMB synergy is not related to efflux pump activity, as determined by FACS analyses and by analysis of a strain containing efflux pump deletions. Gene expression analyses by luciferase and by quantitative real time reverse transcriptase PCR failed to identify significant alterations in expression of any genes associated with resistance. C. albicans grown in TET for 48 h does show a reduction in total cellular ergosterol. Analysis of growth curves suggests that the TET effect is associated with lack of a diauxic shift, which is related to a loss of mitochondrial function. MitoTracker fluorescent dye was used to demonstrate that TET has a direct effect on mitochondrial function. These results demonstrate the need for careful analysis of TET effects when using a TET-inducible promoter, especially in studies that involve antifungal drugs. This study defines some limits to the use of the TET inducible promoter, and identifies effects on cells that are the result of TET exposure alone, not the result of expression of a targeted gene.
doi:10.1099/mic.0.2007/013805-0
PMCID: PMC2615396  PMID: 18310042
Candida albicans; tetracycline; drug resistance; MIC; amphotericin B

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