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Antimicrobial Agents and Chemotherapy, February 2009, p. 354-369, Vol. 53, No. 2
0066-4804/09/$08.00+0     doi:10.1128/AAC.01095-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Abc1p Is a Multidrug Efflux Transporter That Tips the Balance in Favor of Innate Azole Resistance in Candida krusei{triangledown}

Erwin Lamping,1* Amrita Ranchod,1 Kenjirou Nakamura,2 Joel D. A. Tyndall,3 Kyoko Niimi,1 Ann R. Holmes,1 Masakazu Niimi,4 and Richard D. Cannon1

Department of Oral Sciences, University of Otago, Dunedin, New Zealand,1 Advanced Research Center, Nippon Dental University, School of Life Dentistry, Niigata, Japan,2 National School of Pharmacy, University of Otago, Dunedin, New Zealand,3 Department of Bioactive Molecules, National Institute of Infectious Diseases, Tokyo, Japan4

Received 14 August 2008/ Returned for modification 16 October 2008/ Accepted 8 November 2008


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ABSTRACT
 
Most Candida krusei strains are innately resistant to fluconazole (FLC) and can cause breakthrough candidemia in immunocompromised individuals receiving long-term prophylactic FLC treatment. Although the azole drug target, Erg11p, of C. krusei has a relatively low affinity for FLC, drug efflux pumps are also believed to be involved in its innate FLC resistance. We describe here the isolation and characterization of Abc1p, a constitutively expressed multidrug efflux pump, and investigate ERG11 and ABC1 expression in C. krusei. Examination of the ERG11 promoter revealed a conserved azole responsive element that has been shown to be necessary for the transcription factor Upc2p mediated upregulation by azoles in related yeast. Extensive cloning and sequencing identified three distinct ERG11 alleles in one of two C. krusei strains. Functional overexpression of ERG11 and ABC1 in Saccharomyces cerevisiae conferred high levels of resistance to azoles and a range of unrelated Abc1p pump substrates, while small molecule inhibitors of Abc1p chemosensitized C. krusei to azole antifungals. Our data show that despite the presence of multiple alleles of ERG11 in some, likely aneuploid, C. krusei strains, it is mainly the low affinity of Erg11p for FLC, together with the constitutive but low level of expression of the multidrug efflux pump Abc1p, that are responsible for the innate FLC resistance of C. krusei.


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INTRODUCTION
 
Paradoxically, medical advances of the 20th century have led to a significant increase in the incidence of life-threatening fungal infections. Most of the more than 100,000 described fungal species live in the environment and do not colonize humans. However, with the increase in the number of immunocompromised individuals due to the AIDS epidemic, the number of organ transplant patients receiving immunosuppressant treatment, or the number of cancer patients undergoing chemotherapy, an increase in the incidence of fungal infections has ensued (19). Most fungal infections are caused by Candida species, with Candida albicans predominating, followed by C. glabrata, C. parapsilosis, C. tropicalis, and, in fifth place, C. krusei (34). While C. albicans and C. parapsilosis are common in neonatal and pediatric age groups C. glabrata and C. krusei infections are becoming more important in the elderly population (33).

A limited choice of antifungal agents, however, is available to the clinician (19). One of the most commonly used class of antifungals is the azoles, which include fluconazole (FLC) and itraconazole (ITC), and the more recently introduced broad-spectrum triazoles voriconazole (VRC) and posaconazole (35), both of which exhibit improved pharmacokinetic properties and a broader spectrum of antifungal activity. The target for the azoles is cytochrome P450 lanosterol 14{alpha}-demethylase, Erg11p, which is also known as Cyp51p, an essential enzyme of the ergosterol biosynthesis pathway (18). FLC is still the most commonly used azole antifungal because it is a well-tolerated drug with few side effects (12). Azoles, however, are fungistatic rather than fungicidal. This azole tolerance is mediated by the Hsp90-dependent calcineurin stress response pathway (3, 5, 6). It allows fungal cells to develop resistance at high frequency using a range of mechanisms. These processes are well documented and include (i) the mutation or the overexpression of the drug target Erg11p leading to medium levels of resistance, (ii) mutations in enzymes of the ergosterol biosynthesis pathway (e.g., ERG3) that compensate for the accumulation of toxic ergosterol intermediates in cells treated with azoles, and (iii) the overexpression of drug efflux pumps that leads to the highest levels of resistance (1, 2, 19, 55).

Drug efflux pumps belong either to the ATP-binding cassette (ABC) family of transporters or the major facilitator superfamily of transporters. These pumps are present in all living organisms and are often involved in protecting cells from the harmful effects of toxic compounds. Their overexpression is associated with the multidrug-resistant phenotype of clinically important pathogenic microorganisms. Although most Candida species are susceptible to azole antifungals, C. krusei and C. glabrata are two Candida species that are often naturally resistant to FLC (25, 34, 35, 38). The two FLC-inducible ABC transporters CgCdr1p and CgPdh1p, whose upregulation is mediated by the transcription factor CgPdr1p, are the main cause for the innate FLC resistance of C. glabrata (29, 41, 46, 48, 51).

The mechanisms causing C. krusei to be innately resistant to FLC are poorly understood. It has been shown that C. krusei Erg11p is significantly less susceptible to FLC inhibition than most other fungal Erg11p proteins (11, 32, 49). Other studies have shown that efflux pumps are at least partially responsible for the high levels of C. krusei resistance (4, 16, 25, 38, 50). Using degenerate primers designed against the highly conserved C-terminal nucleotide binding domain 2 (NBD2) of pleiotropic drug resistance family (PDR) transporters such as Saccharomyces cerevisiae Pdr5p or C. albicans Cdr1p and Cdr2p, Katiyar and Edlind (16) successfully amplified and sequenced a 357-bp DNA fragment from C. krusei genomic DNA (gDNA). The gene was named ABC1. Northern analysis showed that ABC1 expression was upregulated in the presence of azole antifungals, leading these authors to conclude that this potential efflux pump could be an important contributor to the innate FLC resistance of C. krusei, similar to the innate resistance mechanism found for C. glabrata (29). However, a recent report claims that no ABC transporters are involved in the innate FLC resistance of C. krusei (13).

In order to clarify uncertainties arising from these contradictory reports, we used inverse PCR to isolate and characterize the entire genes for both the azole drug target ERG11 and the ABC transporter ABC1 from wild-type C. krusei strains. We also analyzed their potential contributions to the innate azole resistance phenotype of C. krusei cells.


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MATERIALS AND METHODS
 
Strains and culture conditions. The C. krusei isolates and yeast strains used in the present study are listed in Table 1. All S. cerevisiae strains created in the present study were based on strains AD1-8u– (7) and AD{Delta} (20). All fungal strains were grown in yeast extract, peptone, and glucose (YPD) medium composed of 1% (wt/vol) Bacto yeast extract (Difco Laboratories, Detroit, MI), 2% (wt/vol) Bacto peptone (Difco), and 2% (wt/vol) glucose. Yeast transformants were selected on plates containing complete supplement mixture without uracil (CSM-ura; Bio 101, Vista, CA), 0.67% (wt/vol) yeast nitrogen base without amino acids (Difco), 2% (wt/vol) glucose, and 2% (wt/vol) agar (Difco). Plasmids were maintained in Escherichia coli strain DH5{alpha}. E. coli cells were grown in Luria-Bertani medium, to which ampicillin was added (100 µg/ml) as required.


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  		TABLE 1. Fungal and yeast strains used in this study

Materials. Molecular biology reagents and restriction and modifying enzymes were from New England Biolabs (Beverly, MA) or from Roche Diagnostics N.Z., Ltd. (Auckland, New Zealand). High-pressure liquid chromatography-purified DNA oligonucleotides were purchased from Hermann GbR Synthetische Biomoleküle (Denzlingen, Germany). PCR and DNA fragments were purified by using kits from Qiagen Pty., Ltd. (Clifton Hill, Victoria, Australia). gDNA was isolated from yeast by using a Y-DER yeast DNA extraction reagent kit (Pierce, Rockford, IL) or a Qiagen DNeasy tissue kit from Qiagen (Clifton Hill, Victoria, Australia). A random primer kit from Invitrogen New Zealand, Ltd. (Auckland, NZ), was used to radioactively label PCR fragments used in Southern and Northern experiments. Yeast were transformed by using the alkali-cation yeast transformation kit from Bio 101, taking into account the sensitivity of strain AD{Delta} to high concentrations of Li+ cations (20). All plasmids and DNA fragments were verified by DNA sequencing using a DYEnamic ET terminator cycle sequencing kit (v3.1; GE Healthcare UK, Ltd., Buckinghamshire, United Kingdom) and analyzed at the Micromon DNA sequencing facility (Monash University, Melbourne, Australia). PCRs used the high-fidelity KOD+ DNA polymerase (Toyobo, Osaka, Japan or Novagen, San Diego, CA).

Compounds. FLC (Diflucan; aqueous solution) was purchased from Pfizer Laboratories, Ltd. (Auckland, New Zealand). ITC and ketoconazole (KTC) were purchased from Janssen-Kyowa (Tokyo, Japan). Aureobasidin A was purchased from Takara Bio, Inc. (Shiga, Japan). Miconazole (MCZ), rhodamine 6G (R6G), rhodamine 123, nystatin, amphotericin B, cycloheximide, doxycycline, cerulenin, enniatin, oligomycin, flucytosine, terbinafine, nigericin, monensin, cytochalasin D, latrunculin A, and 4-nitroquinoline N-oxide were purchased from Sigma-Aldrich New Zealand, Ltd. (Auckland, New Zealand). FK506 was a gift from Astellas Pharma, Inc. (Tokyo, Japan), and the milbemycins {alpha}11, {alpha}20, {alpha}25, β9, and β11 were a gift from Sankyo Co., Ltd. (Tokyo, Japan).

Genetic manipulations. Plasmids used in the present study are listed in Table 2. Plasmid pBluescript II SK(+) (Stratagene, La Jolla, CA) was used as a cloning vehicle for all inverse PCR fragments. The C. krusei gDNA that was used as a template for inverse PCRs was prepared as follows: <1 µg of gDNA was digested to completion with restriction enzymes that gave bands of 1 to 5 kb in Southern blot experiments and then purified by phenol extraction, followed by ethanol precipitation, and redissolved in 100 µl of Milli-Q water. gDNA (<50 ng) was ligated (20-µl reaction) to form circular DNA molecules. Portions of the ligated gDNA (1 µl) were then used as templates for inverse PCRs. The primer pairs were designed to be close to, but pointing away from, each other (see P1 and P2 in Fig. 1A and C) and contained EcoRI restriction sites. The following PCR cycling protocol was used: 94°C for 5 min (94°C for 20 s, 55°C for 10 s, and 68°C for 1 min/kb) repeated 34 times, with a final extension time of 10 min at 68°C. The PCR amplicons consisted of the gDNA region (except for the small portion between the two primers) representing the restriction fragment that had been self-ligated. These PCR fragments were gel purified and then cut with the same restriction enzymes to split these fragments into their left (5') and right (3') arms, respectively, and with EcoRI (the primers contained EcoRI sites). Left- and right-arm inverse PCR fragments were cloned separately into the multiple cloning site of pBluescript II SK(+) and sequenced.


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  		TABLE 2. Plasmids used in this study


Figure 1
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  		FIG. 1. Cloning and characterization of the C. krusei genomic loci containing ERG11 and ABC1. Graphical representation of the genomic ERG11 (A) and ABC1 (C) loci of C. krusei strain B2399. Open arrows depict all potential ORFs identified. P1 and P2 are the primer pairs that were used in the inverse PCR experiments described in the text. Individual inverse PCR fragments that were cloned into vector pBluescript II SK(+) are numbered 1 to 4 underneath the restriction maps. The gray box within the ABC1 ORF shown in panel C represents the region that was characterized previously by Katiyar and Edlind (16), while the black box indicates the experimentally verified intron in the ABC1 ORF. Ba, BamHI; Bg, BglII; E, EcoRI; H, HindIII; P, PstI; S, SacI; X, XhoI. Restriction enzymes in italics in panel A (H and X) are enzymes that cut only once within the genomic region shown. (B) Autoradiograms for Southern blots performed on gDNA extracted from C. krusei strain B2399 that had been fully digested with the indicated restriction enzymes. The left-hand Southern blot was hybridized with the radioactively labeled fragment called the "5' probe" shown as a light gray box on panel A, and the right-hand Southern blot was hybridized with the "3' probe," also shown as a light gray box on panel A. (D) Autoradiograms for Southern blots performed on gDNA extracted from C. krusei strains B2399 (left panel) and IFO0011 (right panel) using a radioactively labeled fragment of ABC1 (light gray box in panel C named "probe").

Construction of yeast strains overexpressing heterologous membrane proteins. In order to study the function and localization of C. krusei Abc1p, the protein was overexpressed in S. cerevisiae AD{Delta}. The construction of the ABC1 overexpressing yeast strains AD{Delta}/CkABC1g and AD{Delta}/CkABC1g-GFP (both containing the gDNA open reading frame [ORF] including an 88-bp intron) or AD{Delta}/CkABC1 (containing the cDNA ORF) has been described previously (20). Analogous to the heterologous overexpression of C. krusei Abc1p in S. cerevisiae AD{Delta}, the ERG11 ORFs from S. cerevisiae AD1-8u–, C. albicans ATCC 10261, and C. krusei B2399 were cloned into plasmids pABC3 and pABC3-GFP as PacI/NotI fragments to create plasmids pABC3-ScERG11, pABC3-CaERG11A (20), and pABC3-CkERG11C as well as pABC3-ScERG11-GFP, pABC3-CaERG11A-GFP and pABC3-CkERG11C-GFP, respectively. All plasmids were cut with restriction enzyme AscI, and the resulting transformation cassettes were used to transform AD1-8u– or AD{Delta}. Ura+ transformants containing the cassette correctly integrated at the chromosomal PDR5 locus were selected on CSM-ura plates and confirmed by colony PCR, using a previously described cloning procedure (20).

Purification and analysis of PM proteins. Plasma membrane (PM) fractions of S. cerevisiae cells were prepared as described previously (28). Protein samples (30 µg) were separated on 8% acrylamide gels and stained with Coomassie blue R250. S. cerevisiae strains expressing C-terminal green fluorescent protein (GFP) fusion proteins were examined by using a Zeiss 510 Axiovert 200 M inverted confocal laser scanning microscope (Otago Centre for Confocal Microscopy).

Functional analysis of wild-type and recombinant yeast strains. The susceptibility of yeast to antifungal agents was measured by a microdilution assay as described previously (14, 28). To be able to quantify the antifungal susceptibilities of C. krusei strains according to the Clinical and Laboratory Standards Institute (CLSI) standards and recommended breakpoints, we also determined the MICs for C. krusei by using the CLSI microdilution reference method (CLSI guidelines document M27-A2). Agarose diffusion assays were performed to test the susceptibility of S. cerevisiae strains overexpressing C. krusei Erg11p or Abc1p to different xenobiotics. In brief, 10 ml of YPD overnight culture of each test strain was diluted 1:20 into 3 ml of CSM medium, followed by growth at 30°C for another 4 h to mid-logarithmic growth phase (optical density at 600 nm [OD600] of ~1, ~107 cells/ml). The cells were diluted to an OD600 of 0.008 in 5 ml of melted CSM medium containing 0.6% agarose (45°C) and overlaid on 20 ml of CSM agar-based medium. Whatman 3MM paper disks (5 mm in diameter) containing xenobiotics were placed onto the solidified top agarose medium, and the plates were incubated at 30°C for 48 h. The amounts of xenobiotics used are described in the figure legends.

Chemosensitization assays. The chemosensitization of a yeast strain overexpressing C. krusei Abc1p or C. krusei strains B2399 and IFO0011 to ITC was carried out as described previously (28). In brief, cells were cultured in CSM medium as for agarose diffusion assays. Each test strain was diluted to an OD600 of 0.008 in 10 ml of melted CSM containing 0.6% agarose (45°C) with either no ITC (control to determine the toxicity of each drug) or ITC at 0.25x the MIC of ITC (MICITC) determined on solid medium (see explanation below). The cell suspension was poured into a rectangular Omnitray plate (126 by 86 by 19 mm; Nunc, Roskilde, Denmark) that contained 20 ml of CSM solidified with 0.6% agarose either without (control) or with 0.01 µg of ITC/ml. Whatman 3MM paper disks containing potential drug pump inhibitors (5 or 1 µg of milbemycins {alpha}11, {alpha}20, {alpha}25, β9, and β11, 1 µg or 0.2 µg of enniatin, 5 µg of FK506, or 25 nmol of oligomycin as indicated in the figure legends) were placed on the overlay, and the plates were incubated at 30°C for 48 h. The MICITCs on solid media were between 20 to 100 times lower than the MICITCs for the same strains determined in liquid media. This was determined by testing the growth of S. cerevisiae strains AD{Delta} and AD{Delta}/CkABC1g, as well as of C. krusei strains B2399 and IFO0011 on solid medium containing serial twofold dilutions of ITC. The MICITC on solid medium was 0.0008 µg/ml for AD{Delta} compared to its MIC of 0.031 µg/ml in liquid medium, 0.04 µg/ml on solid medium compared to 4 µg/ml in liquid medium for AD{Delta}/CkABC1g, and 0.04 µg/ml compared to 0.5 or 1 µg/ml for C. krusei strains B2399 and IFO0011, respectively. This observation was specific for ITC only. We also tested the growth of the same strains on solid medium containing serial twofold dilutions of FLC or R6G. In both cases the MICs for all of the strains appeared to be similar on solid media to the MICs determined in liquid media.

Northern and Southern analysis. Total RNA was isolated from C. krusei B2399 cells by using the hot-phenol extraction method. Usually about 100 ODU (OD units; defined as the amount of cells corresponding to 1 ml of cells of an OD600 of 1) of cells were harvested by centrifugation for 1 min at 3,000 x g, and the cells were washed once in ice-cold water and snap-frozen in liquid nitrogen and stored at –80°C. Samples (10 µg) of total RNA were separated on 1.2% denaturing agarose gels and stained with ethidium bromide (EtBr). The separated total RNA was photographed, immediately Northern blotted onto nylon+ membranes, and further processed according to standard protocols (40). For Southern blot analysis of C. krusei strains B2399 or IFO0011, 10 µg of gDNA was digested to completion with various restriction enzymes and separated on 0.8% agarose gels. Southern blotting of denatured gDNA, binding to nylon+ membranes, and hybridization of radioactive probes was carried out as described for the Northern blot analysis.


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RESULTS
 
Isolation and sequence analysis of the ERG11 ORF from two C. krusei strains. The entire C. krusei ERG11 ORF was PCR amplified from gDNA templates of C. krusei strains B2399 and IFO0011 (Table 1). Sequencing the purified PCR fragments identified five and four single nucleotide polymorphisms (SNPs), respectively (Table 3). SNP C44T of strain IFO0011 was the only nonsynonymous SNP leading to the conserved amino acid change A15V. Sequence alignment with a number of other fungal Erg11p proteins revealed that both amino acid variants exist in other fungal species (most C. tropicalis and C. dubliniensis Erg11p sequences have a valine, while most C. albicans, C. glabrata, and S. cerevisiae Erg11p sequences found in the GenBank database have an alanine; Fig. 2). Figure 2 also shows the location of secondary structure elements taken from the Mycobacterium tuberculosis MtCyp51p crystal structure, the structure that is often used for modeling eukaryotic Erg11p/Cyp51p proteins (9, 11, 36). While MtCyp51p is a soluble protein, eukaryotic Erg11ps and Cyp51ps contain an amino-terminal membrane anchor that targets them to the endoplasmic reticulum. PredictProtein, a bioinformatics program that predicts the protein topology of membrane proteins (39), predicted one amino-terminal transmembrane domain for C. krusei Erg11p located between amino acids S26 and A43 (Fig. 2). Thus, the first 25 amino acids are predicted to face the lumen of the endoplasmic reticulum, and the bulk of the protein (L44 to N528) faces the cytosol.


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  		TABLE 3. Sequences for individual C. krusei ERG11 ORF alleles from strains B2399 and IFO0011a


Figure 2
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  		FIG. 2. Multiple sequence alignment of C. krusei Erg11p with fungal Erg11ps, human Cyp51Ap and MtCyp51p. Using CLUSTAL W software C. krusei Erg11p was aligned with Erg11p from other important fungal pathogens such as C. albicans (CaErg11p), C. dubliniensis (CdErg11p), C. tropicalis (CtErg11p), C. glabrata (CgErg11p), S. cerevisiae (ScErg11p), Aspergillus fumigatus Erg11Ap (AfuErg11Ap) and Erg11Bp (AfuErg11Bp), and C. neoformans (CneErg11p) and compared to human Erg11p (HsCyp51Ap) and the soluble bacterial homolog M. tuberculosis Cyp51p (MtCyp51p), for which the crystal structure is known. Highly conserved residues are shown in red, conservative amino acid changes are shown in green, and nonconserved residues are shown in black. Shown above the alignments are all of the alpha helices (light gray boxes with their conventional letter designations) and beta strands (dark gray arrows with their conventional number designations) taken from the MtCyp51p structure (PDB ID number 2VKU). With the exception of MtCyp51p, all Erg11ps/Cyp51ps are predicted (using PredictProtein) to contain an amino-terminal membrane anchor domain spanning the endoplasmic reticulum membrane (TMD). The two gray boxes within the sequence alignments represent the two signature motifs common to all Erg11ps, with the most-conserved residues marked with an asterisk above the sequence. The four amino acid residues that are most often found to be associated with azole resistance in clinical Candida isolates are marked with round black dots above the individual amino acids. The plus sign above the essential cysteine residue marks the residue that forms the fifth heme iron ligand.

C. krusei B2399 contains three and IFO0011 contains two ERG11 alleles. In an attempt to identify the DNA sequences of individual ERG11 alleles for strains B2399 and IFO0011, we cloned a number of individual ERG11 ORFs into vector pABC3 and sequenced them. Unexpectedly, we identified three distinct alleles for ERG11 of strain B2399 (Table 3) and two alleles for ERG11 of strain IFO0011, as would be expected for a diploid strain (15, 43, 53, 54) (Table 3). Careful reexamination of the original sequencing chromatograms revealed a 2:1 ratio for all five B2399 SNPs and a 1:1 ratio for the four IFO0011 SNPs, as expected for strains containing three or two separate alleles, respectively. To be absolutely sure that the sequences for each individual allele were determined correctly and to distinguish clones representing individual alleles from clones that represented chimeras between different alleles, we sequenced 20 individual B2399 and 10 individual IFO0011 ERG11 ORF clones from two separate PCRs using independently isolated gDNA as a template. This was necessary because we observed that a significant proportion (10 to 20%) of individually cloned PCR fragments turned out to be chimeric clones due to template switching between individual PCR cycles. The A allele ORFs of both strains were identical, while the other alleles (B and C alleles of strain B2399 and the B allele of strain IFO0011) were unique. The DNA sequences of all five ERG11 alleles have been deposited with GenBank (accession numbers DQ903901 to DQ903905).

Characterization of 10 kb of gDNA surrounding the C. krusei ERG11 locus. Assuming that C. krusei was diploid, we were surprised to identify three unique ERG11 alleles in strain B2399. We initially thought that C. krusei may have acquired additional ERG11 alleles via gene duplication events in the recent past. We hypothesized that the increased copy number for ERG11, together with its reduced affinity for azole antifungals, is the likely cause for its innate azole resistance phenotype. To test this hypothesis, we created a detailed map of the chromosomal ERG11 locus to find evidence for repeats of ERG11 in close proximity to each other. First, we performed Southern blot analysis of gDNA from B2399 using two radioactive probes (Fig. 1A and B). Strain IFO0011 gave identical results (data not shown). Using this information together with the ERG11 ORF sequence obtained we were able to perform two rounds of inverse PCR (using primer pairs P1 and P2) to amplify, clone, and sequence fragments 1, 2, and 4 shown in Fig. 1A (see also Materials and Methods), thus yielding nearly 10 kb of DNA sequence surrounding, and including, the ERG11 ORF.

Four ORFs were identified as illustrated in Fig. 1A. ORFs I (399 bp; 132 amino acids) and II (471 bp; 156 amino acids) were predicted to encode mitochondrial ribosomal proteins MrpL38p and Mrp49p, respectively. ORF IV showed highest homology to the rRNA processing protein 45 (Rrp45p; 1,233 bp; 410 amino acids) that is part of the 3'-5' exonuclease complex (exosome complex). ORFs I, II, and III are all transcribed in the same direction, while ORF IV is encoded by the opposite strand. No evidence for any other ORFs or extra copies of ERG11 was found. An alternative explanation for the presence of three different ERG11 alleles in strain B2399 is that this strain contains three ERG11-containing chromosomes.

C. krusei B2399 is aneuploid with at least three ERG11-containing chromosomes. If strain B2399 has three separate ERG11-containing chromosomes rather than multiple copies of ERG11 on the same chromosome, we should be able to identify three distinct alleles for the whole 10-kb chromosomal region identified above. This was indeed the case. In order to exclude PCR artifacts, more than 10 individual clones from independent PCR amplifications for each of the DNA fragments 1, 2, 3, and 4 shown in Fig. 1A were sequenced, and all contained allele-specific SNPs, including their three overlapping regions. Therefore, we could identify the individual DNA sequences for all three alleles across the whole 10 kb. All B2399 SNPs were verified by directly sequencing the PCR fragments amplified from gDNA, and again all exhibited the expected 2:1 ratio as described above. Aligning the three alleles revealed 74 unique SNPs (18 SNPs specific for the A allele, 31 SNPs specific for the B allele, and 25 SNPs specific for the C allele). On average, there was one allele-specific SNP every 400 bp, which is similar to the SNP frequencies we found for different C. albicans strains (the average allele-specific SNP frequency for CDR1 from six different C. albicans strains was one SNP/425 bp and one SNP/160 bp for CDR2 [14]). Closer inspection revealed that more than 4 kb of the 3' end of the gDNA sequences (starting just downstream of ORF IV as illustrated in Fig. 1A) of both the A and the C alleles of strain B2399 were identical, while the B allele contained 21 of its 31 unique SNPs in that region. As expected, the SNP frequency was lower within the four ORFs (only 12 of the 74 unique SNPs lay within the four identified ORFs), leading to an average SNP frequency within ORFs I to IV of an individual allele of one SNP/900 bp. The sequences for all three B2399 alleles have been deposited with GenBank (accession numbers EU296425 to EU296427).

Isolation and characterization of the genomic locus of ABC1 of strains B2399 and IFO0011. Using degenerate primers against the highly conserved C-terminal Walker A and B motifs of fungal ABC transporters, Katiyar and Edlind (16) were able to isolate two small (357-bp) DNA fragments representing part of the C-terminal NBD2 of two C. krusei ABC transporters, which they named ABC1 and ABC2. ABC1 showed highest homology to the well-characterized multidrug efflux transporters S. cerevisiae Pdr5p and C. albicans Cdr1p and Cdr2p (16). These authors also showed that the expression of ABC1, unlike ABC2, was strongly induced by azole antifungals. This led to the conclusion that Abc1p is likely associated with the innate FLC resistance phenotype of C. krusei. We were able to confirm that C. krusei ABC1 encodes a multidrug efflux pump by isolating the whole gene and heterologously overexpressing Abc1p in S. cerevisiae, leading to an ~100-fold-decreased susceptibility to azole antifungals (20). The present study, however, is the first detailed description of the isolation and characterization of ABC1. Again, due to a lack of C. krusei sequence information, we used inverse PCR to isolate and characterize the entire genomic ABC1 locus. Two rounds of inverse PCR were needed to isolate and sequence the whole ABC1 gene of strain B2399 (see Materials and Methods and Fig. 1C). Cloning and sequencing fragments 1, 2, 3, and 4 yielded the sequence for the entire ABC1 gene, including 664 bp upstream of the ATG start codon and 983 bp downstream of the TAA stop codon (Fig. 1C). Sequence analysis of the ABC1 ORF predicted an 88-bp intron that was experimentally verified (20). Using these sequencing data the ABC1 ORF of strain IFO0011 was also amplified and sequenced. The sequences for the ABC1 ORF of strains B2399 and IFO0011 were identical except for one synonymous SNP (T4549C).

Surprisingly, no SNPs were detected across the whole ABC1 ORF, including the promoter and terminator regions of strains B2399 (6,301 bp) and IFO0011 (5,255 bp), suggesting that both strains are homozygously diploid in ABC1 or, alternatively, both strains are monosomic for ABC1. Southern blot analysis of gDNA from C. krusei strains B2399 and IFO0011 revealed a restriction fragment length polymorphism for EcoRI showing two bands (6 and 8 kb) for EcoRI-digested gDNA (lanes E in Fig. 1D), even though the restriction map of ABC1 (Fig. 1C) predicted only one band larger than 5.5 kb. These data suggest that, unlike for ERG11, both B2399 and IFO0011 strains are homozygous diploid for ABC1. The gDNA and cDNA sequences for ABC1 of C. krusei strain B2399 and the gDNA sequence for ABC1 of strain IFO0011 have been deposited with GenBank (accession numbers DQ903906, DQ903907, and EU296340). Despite extensive efforts, it was not possible to amplify ABC2 by inverse PCR.

C. krusei ABC1 is highly homologous to C. albicans and C. glabrata CDR1 and S. cerevisiae PDR5. Performance of a "protein-blast" search with the predicted Abc1p protein sequence (1,521 amino acids) showed that Abc1p shared highest homology with C. albicans Cdr1p (59% identical and 75% homologous), Cdr4p (59 and 75), Cdr2p (57 and 74), and Cdr3p (55 and 72), followed by C. glabrata CgCdr1p (54 and 71) and S. cerevisiae Pdr5p (53 and 69), all belonging to the cluster I type ABC transporter family with the predicted topology of two amino-terminal NBDs, each followed by a transmembrane domain (TMD) containing six individual transmembrane spanning segments (TMSs) in the order: NBD-TMD-NBD-TMD. PredictProtein revealed that not only is Abc1p highly homologous to other fungal multidrug efflux pumps but the predicted locations of its individual transmembrane segments (TMS 1 to 12) also aligned well (plus or minus one amino acid) with the predicted locations of individual TMSs for Cdr1p, CgCdr1p, and Pdr5p (Fig. 3B). The NBDs were also highly conserved (including Walker A, ABC signature, and Walker B motifs; Fig. 3A). Abc1p NBD1 showed only one conserved amino acid change at the amino-terminal end of the ABC signature motif compared to the other efflux pumps (I317V) with two additional amino acid changes found in the Walker A motifs for both CgCdr1p and Pdr5p (A210S and S213T; Fig. 3A). The NBD2 domains of C. krusei Abc1p and Cdr1p, Cdr2p, CgCdr1p, and ScPdr5p only had one conserved amino acid change (L1027 of Abc1p, Cdr1p, and Cdr2p was replaced by a V in CgCdr1p and Pdr5p) (Fig. 3A). It seems that C. krusei Abc1p shares the same asymmetry in its two NBDs that is a unique feature of the fungal PDR family of ABC transporters (10, 52). It too contains a cysteine (C212) instead of the usually essential lysine in the Walker A motif of its NBD1 and an essential lysine (L906) in the Walker A motif of NBD2 (Fig. 3A), suggesting the functional nonequivalence of the two NBDs of Abc1p as described for CgCdr1p and ScPdr5p (10, 52). Finally, comparing Abc1p with the small part of Abc1p previously isolated (16) revealed three conservative amino acid differences (I990M, D1018E, and V1019L). These changes are likely due to natural strain variations.


Figure 3
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  		FIG. 3. C. krusei Abc1p is an ABC transporter highly homologous to other well-characterized fungal multidrug efflux pumps. (A) Alignment of the highly conserved Walker A, Walker B, and ABC signature motif of NBD1 and NBD2 of Abc1p from C. krusei B2399 with the NBD1 and NBD2 motif of the multidrug efflux pumps C. albicans Cdr1p, Cdr2p, C. glabrata CgCdr1p, and S. cerevisiae Pdr5p. The conserved residues identical to the Abc1p sequence are shaded in gray. The asterisks mark the highly conserved cysteine and lysine residues of the NBD1 and NBD2 domains as described in the text. (B) List of the predicted transmembrane segments TMS1 to TMS12 for the PDR family proteins Abc1p, Cdr1p, CgCdr1p, and Pdr5p using the PredictProtein software program available from Columbia University.

Functional characterization of Abc1p and Erg11p of C. krusei strain B2399 overexpressed in S. cerevisiae AD{Delta}. The overexpression of Abc1p in S. cerevisiae AD{Delta}, a host strain that is highly susceptible to many xenobiotics, resulted in a 100-fold increase in resistance to azole antifungals (20). To confirm that Abc1p is a multidrug efflux transporter, we tested whether its overexpression in AD/CkABC1g could confer increased resistance to 20 other xenobiotics, some of which are known to be substrates of other fungal efflux pumps (Fig. 4). As expected, overexpression of Abc1p conferred increased levels of resistance to a range of unrelated xenobiotics. Apparent substrates of Abc1p included, aside from all of the azoles tested, cerulenin, cycloheximide, nigericin, monensin, rhodamine 123, R6G, cytochalasin D, and latrunculin A. In contrast, aureobasidin A, 4-nitroquinoline N-oxide, doxycycline, nystatin, amphotericin B, flucytosine, and terbinafine appeared not to be substrates of Abc1p (Fig. 4).


Figure 4
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  		FIG. 4. Expression of C. krusei ABC1 or ERG11 confers multidrug resistance on S. cerevisiae. Cells (AD{Delta}, top row; AD{Delta}/CkABC1g, central row; or AD/CkERG11C, bottom row) were grown to mid-logarithmic growth phase and plated on CSM agar plates (pH 7.0). 3MM Whatman filter disks that contained different xenobiotics were then placed onto the agar surface, and the plates were incubated at 30°C for 48 h. The following amounts of xenobiotics were applied to the disks: FLC, 7 µg (23 nmol); ITC, 250 ng (0.36 nmol); KTC, 150 ng (0.28 nmol); MCZ, 12.5 ng (0.026 nmol); nystatin (NYT), 2.5 µg (22 nmol); amphotericin B (AMB), 80 µg (87 nmol); flucytosine (5FC), 2.5 µg (19 nmol); terbinafine (TRB), 15 µg (46 nmol); cerulenin (CER), 502 ng (2 nmol); cycloheximide (CHX), 105 ng (0.37 nmol); nigericin (NIG), 10 µg (8 nmol); monensin (MON), 8 µg (12 nmol); rhodamine 123 (R123), 50 µg (131 nmol); R6G, 7.5 µg (16 nmol); cytochalasin D (CYT-D), 10.2 µg (20 nmol); latrunculin A (LAT-A), 100 ng (0.24 nmol); aureobasidin A (AUR-A), 8 µg (7 nmol); 4-nitroquinoline N-oxide (4-NIT), 0.8 µg (4 nmol); trifluoperazine (TRI), 300 µg (620 nmol); and doxycycline (DOX), 1,200 µg (2.5 µmol).

The resistance pattern for the AD strain overexpressing C. krusei Erg11p was also determined (Fig. 4). C. krusei Erg11p was functionally expressed in the AD strain, and this resulted in increased levels of resistance to azole antifungals only, as expected for the overexpression of the azole drug target. It appeared, however, that the overexpression of C. krusei Erg11p led to a substantially lower increase in resistance to ITC (Fig. 4, lower panel; there is a much smaller reduction of the growth-inhibitory zone around the ITC-containing disk compared to all other azoles tested). Liquid MIC results confirmed that AD/CkERG11C cells were only twice as resistant to ITC as the control AD strain compared to 8 to 16 times more resistant than the AD strain to FLC, VRC, and MCZ (Table 4).


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  		TABLE 4. Susceptibility of C. krusei isolates and S. cerevisiae strains overexpressing different fungal ERG11 alleles or the multidrug efflux pump ABC1 from C. krusei to azoles measured in CSM (pH 7.0) by liquid microdilution assay

PM preparations of S. cerevisiae cells overexpressing Abc1p showed high levels of expression of the 170-kDa Abc1p protein (Fig. 5A). Although expression of Abc1p was achieved for both the gDNA ABC1 ORF (Fig. 5A, lane 2; ABC1 gene contains an 88-bp intron), as well as the cDNA ABC1 ORF (Fig. 5A, lane 3), higher Abc1p expression was achieved (relative to the predominant 100-kDa PM protein Pma1p) from cells containing the ABC1 cDNA ORF. For comparison, Erg11p proteins (~60 kDa) from three different fungal species (S. cerevisiae AD{Delta}, C. albicans ATCC 10261, and C. krusei B2399) were also expressed in S. cerevisiae AD or AD{Delta} strains (Fig. 5B, lanes 2, 3, and 4, respectively). It was evident that C. krusei B2399 Erg11p was expressed at significantly lower levels than Erg11p from S. cerevisiae or C. albicans, although all of them appeared to be expressed functionally, as shown in Fig. 4 and Table 4.


Figure 5
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  		FIG. 5. Expression of Abc1p and Erg11p proteins in C. krusei and recombinant S. cerevisiae. (A and B) Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels of membrane fractions (30 µg; containing PMs together with endoplasmic reticulum) that were isolated from S. cerevisiae AD{Delta} cells overexpressing Abc1p (A) or different fungal Erg11p proteins (B). All strains were grown in YPD medium and harvested in late logarithmic growth phase. Membrane proteins in panel A were isolated from the control strain AD{Delta} (lane 1) and from strains AD{Delta}/CkABC1g (genomic clone containing 1 intron, lane 2) and AD{Delta}/CkABC1 (cDNA clone, lane 3). (B) SDS-PAGE analysis of membrane fractions (30 µg) obtained from AD{Delta} control strain (lane 1), AD{Delta}/ScERG11 (lane 2), AD{Delta}/CaERG11 (lane 3), and AD/CkERG11C (lane 4). (C and D) SDS-PAGE analysis of protein fractions (30 µg) that were isolated from C. krusei B2399 cells grown in YPD medium without FLC (C) or with FLC at a concentration of 1x MICFLC (D) and then harvested at 0, 1, 2, and 3 h. Gray rectangular boxes highlight the 170-kDa protein bands for Abc1p in panels A, C, and D, as well as the 60-kDa protein bands for Erg11p in panels B, C, and D.

ERG11 and ABC1 are constitutively expressed in C. krusei. To study mRNA expression patterns for ABC1 and ERG11, total RNA from B2399 cells grown under a number of different conditions was isolated and subjected to Northern blot analysis (Fig. 6). The housekeeping gene ACT1 from C. krusei B2399 was used as an internal control. Equal loading of total RNA was also confirmed by EtBr staining of the gels. Both ABC1 and ERG11 were constitutively expressed in logarithmically growing cells, and their expression was dramatically reduced in cells about to enter the diauxic growth phase (Fig. 6A, lanes 8.3, 12, and 13 [numbers representing the actual OD600 values]). Exposing early-logarithmic-phase cells (OD600 = 1) for 60 min to different azole antifungals had no significant effects on ABC1 mRNA levels (Fig. 6B). In contrast, ERG11 mRNA levels increased severalfold within 1 h in response to concentrations 2x the MIC of ITC, MCZ, and VRC and 1x the MIC of FLC (Fig. 6B; higher concentrations of FLC [> 200 µg/ml] could not be achieved). During a 320-min time course of exposure of logarithmically grown cells (OD600 = 1) to FLC at a concentration of 1x MIC, no induction in the expression of ABC1 mRNA was observed, whereas ERG11 expression increased significantly compared to control cells (Fig. 6C). The highest levels of ERG11 expression were reached after 80 min of exposure to FLC. This peak of expression coincided with the time when cell growth started to slow down compared to the untreated control cells (data not shown). Decreased levels of ABC1 expression for the control cells at the later time points (160 and 320 min, left panel of Fig. 6C) coincided with the entry of cells into the diauxic phase. To test how ABC1 and ERG11 expression responded to defined stress conditions, exponentially grown cells (OD600 = 1) were harvested, resuspended in fresh media, and exposed to the following for a further 20 min: fresh medium only (control), 2 mM H2O2, pH 7.0, 500 mM NaCl, or 42°C. ERG11 expression was dramatically repressed under all of the conditions tested, but the strongest repression was observed in cells exposed to oxidative stress and high temperature (Fig. 6D). NaCl (500 mM) or a change in pH did not repress ABC1 expression. In contrast, oxidative stress and a high temperature repressed the expression of ABC1 significantly, as it did for ERG11 (Fig. 6D). Serum cholesterol has been shown to reduce azole susceptibilities of fungi such as C. glabrata (27) or A. fumigatus (56) by complementing the cells' need for ergosterol through the uptake of cholesterol from the serum. Therefore, we also tested whether ergosterol at concentrations similar to those found in serum would have any effect on ERG11 or ABC1 expression. Incubating C. krusei cells for 60 min in the presence of ergosterol had no detectable effect, however, on the expression of ERG11 or ABC1 (Fig. 6E). In conclusion, the expression patterns for ERG11 were as expected. Challenging C. krusei cells with azole antifungals at concentrations equal to or higher than their MIC led to a dramatic increase in the expression of ERG11, but only after more than 1 h, when presumably the cell membranes started to become depleted of ergosterol. In contrast, the downregulation of ERG11 in response to stress was much more rapid (20 min). While ABC1 expression was constitutive and relatively high (easy to detect) in growing cells, it was not affected by azole antifungals and the response of ABC1 expression to stress was also more specific than that of ERG11. While ERG11 was repressed under all stress conditions tested, ABC1 was only repressed in response to oxidative stress and high temperature.


Figure 6
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  		FIG. 6. Expression of ERG11 and ABC1 mRNA in C. krusei B2399 grown under a variety of growth conditions. Total RNA was isolated from C. krusei B2399 cells that were grown under a number of different growth conditions. The radioactively labeled probes for ERG11 and ABC1 are shown in Fig. 1A and C, respectively, and the probe that was used for ACT1 is the same as described previously (16). The results for ABC1 are shown in the top panel, and the same RNA samples were used for ERG11 shown directly underneath them. ACT1 mRNA levels were used as an internal control (third panel) and EtBr-stained ribosomal bands shown in the bottom panel indicate RNA loading. (A) Growth-phase-dependent expression of ERG11 and ABC1 mRNA of B2399 cells grown in YPD. The OD600 values at the times of harvest are shown above the corresponding lanes. (B and E) Expression of ABC1 and ERG11 mRNA in logarithmically grown C. krusei B2399 cells exposed for 60 min to different azole antifungals (C, untreated control; FLC, 1x the MICFLC; VRC, 2x the MICVRC; MCZ, 2x the MICMCZ; and ITC, 2x the MICITC) (B) or ergosterol (–erg, sterol solvent Tween 80 control; +erg, 10 µg of ergosterol/ml) (E). (C) Expression of C. krusei ABC1 and ERG11 mRNA in the absence (–FLC) or presence (+FLC) of FLC at a concentration of 1x the MICFLC for the indicated times. (D) Expression of ABC1 and ERG11 mRNA in logarithmically grown C. krusei B2399 cells exposed for 20 min to different stress conditions: C, no stress control; H2O2, 2 mM H2O2; NaCl, 500 mM NaCl; pH 7.0, CSMpH 7.0; and 42°C.

Identification of conserved promoter elements for ERG11. The data presented above show that the expression pattern for C. krusei Erg11p is very similar to that observed for other fungal azole drug targets such as S. cerevisiae and C. albicans Erg11p (31, 44). Recently, Oliver et al. (31) identified an azole responsive element (ARE) that is responsible for the azole-dependent upregulation of C. albicans ERG11 (Fig. 7). Part of the ARE element is the sterol responsive element (SRE; TCGTATA) that is found in a number of ERG genes in S. cerevisiae and C. albicans (23, 31). The zinc cluster transcription factor Upc2p has been shown to bind to the SRE element in the C. albicans ERG11 promoter, leading to the azole-induced expression of Erg11p (31). The ARE for C. albicans ERG11 consists of the SRE and an almost perfect inverted repeat (INV) of that element 13 bp upstream (Fig. 7). Both of these elements are important for the azole-induced Upc2p-dependent upregulation of ERG11 in C. albicans (31). We discovered a very similar ARE-like element that was conserved in all ERG11 alleles at nearly the identical position (–204 versus –236 upstream of the ATG start codon) in the ERG11 promoter of C. krusei. The spacing between the INV and the SRE elements was slightly larger (15 bp versus 13 bp, Fig. 7). Unlike the ERG11 promoters for C. albicans and C. krusei, the search for an ARE in the C. glabrata ERG11 promoter revealed that it possesses two direct repeats of the SRE separated by 29 bp (bp –153 and –189). Clearly, the SRE is conserved between S. cerevisiae, C. albicans, C. glabrata, and C. krusei. The only difference appears to be the way that two of these elements are positioned relative to each other.


Figure 7
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  		FIG. 7. The C. krusei ERG11 promoter contains a conserved ARE. The first 200 to 300 bp of DNA sequence upstream of the ATG start codon of C. krusei ERG11 is compared to the ERG11 promoter sequences of C. albicans and C. glabrata. The ATG start codons are underlined and the predicted TATA boxes are shown in bold face. SREs or their inverted sequences (INV) are shown overlined (SRE) or underlined (parts of SRE and their matching inverted INV sequences), respectively. The INVs and SREs of C. albicans ERG11 have been experimentally verified and contain the ARE that is bound by the zinc cluster transcription factor Upc2p leading to the activation of transcription. The SRE and INV elements for C. glabrata and C. krusei shown for comparison await experimental verification.

Since C. krusei ABC1 is highly homologous to S. cerevisiae PDR5, C. glabrata CDR1 and PDH1, and C. albicans CDR1 and CDR2, its promoter might be expected to possess pleiotropic drug resistance elements (PDREs) found in the S. cerevisiae PDR5 and C. glabrata CDR1 and PDH1 promoters (17, 46, 48) or drug-responsive elements found in C. albicans CDR1 and CDR2 (8). However, no PDREs were present in the ABC1 promoter, and this might explain why ABC1 expression is not induced by FLC (for a review of the family of fungal specific zinc cluster transcription factors such as Pdr1p and Pdr3p of S. cerevisiae and CgPdr1p and Tac1p of C. albicans recognizing PDREs and drug-responsive elements, see reference 24).

Expression of Erg11p and Abc1p proteins in C. krusei B2399 cells. To confirm that not only ERG11 mRNA but actual Erg11p expression is induced by azole antifungals, membrane fractions were isolated from cells that were grown over a 3-h period at the same FLC concentration and under the same conditions that were used for the Northern blot experiments. Figure 5C and D show membrane fractions isolated from B2399 cells grown in the absence (Fig. 5C) or presence (Fig. 5D) of FLC. As was found for ERG11 mRNA, a band of the expected size for the Erg11p protein (~60 kDa) was strongly induced by FLC (lower boxed areas in Fig. 5C and D). However, while ERG11 mRNA levels were highest 80 min after exposure to FLC, Erg11p protein levels were highest 3 h after induction. In contrast, only a faint band at the expected size for the Abc1p protein (170 kDa) could be detected. The amounts of the 170-kDa protein band were very similar between FLC treated and untreated cells and also appeared to be lowest at the 3-h time point when the cells started entering the diauxic phase (upper boxed areas in Fig. 5C and D). This expression pattern appeared to be consistent with the Northern results but was somewhat different compared to C. glabrata cells which, in response to FLC, clearly overexpress both a 61-kDa protein, Erg11p, and a 170-kDa band corresponding to Cdr1p (29). The amounts of C. krusei Erg11p expressed in S. cerevisiae AD/CkERG11C were comparable to the highest levels of Erg11p expressed in C. krusei cells grown in the presence of FLC (compare lane 4 of Fig. 5B with lane 3 of Fig. 5D).

Erg11p is localized in the endoplasmic reticulum and Abc1p in the PM. To test the localization of the fungal Erg11p proteins and the C. krusei multidrug transporter Abc1p expressed in S. cerevisiae strains AD or AD{Delta}, C-terminal GFP fusions of these proteins were created, and their localization was analyzed by confocal microscopy. Addition of the C-terminal GFP tags to Erg11p and Abc1p did not affect the function of either protein (data not shown for Erg11p; see reference 20 for Abc1p). All three fungal Erg11p proteins were properly localized in internal structures reminiscent of membranes of the rough endoplasmic reticulum surrounding the nucleus (Fig. 8). Judging from the intensity of the fluorescent signals (different exposure times were used for fluorescent images in Fig. 8), Erg11ps from both S. cerevisiae and C. albicans were expressed at significantly higher levels than Erg11p from C. krusei. This correlates well with the amounts of the untagged versions of these proteins expressed in AD and AD{Delta} strains (Fig. 5B). Confocal microscopy also revealed that the C-terminal Abc1p-GFP fusion expressed in AD{Delta} cells is localized in the PM, as expected.


Figure 8
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  		FIG. 8. Confocal microscopy of AD or AD{Delta} cells overexpressing C. krusei Abc1p or fungal Erg11p proteins. Multidrug efflux pump C. krusei Abc1p localized to the PM, whereas the fungal azole drug target proteins Erg11p from S. cerevisiae, C. albicans and C. krusei localized exclusively to internal structures mainly around the nucleus reminiscent of rough endoplasmic reticulum. Light microscopy images of the cells are shown above their confocal images, and fused images of the light microscopy images with the confocal images are shown underneath the confocal images. The two CaERG11 images have been taken at different sensitivities in order to see more detail in the right hand image. The right-hand CaERG11 image was taken at the same setting as the CkERG11 image.

Functional characterization of S. cerevisiae cells overexpressing C. krusei Erg11p and Abc1p. Disk diffusion assays indicated that Abc1p is a multidrug efflux pump that can transport azole antifungals (Fig. 4). To get a better understanding of the individual contributions of C. krusei Abc1p and Erg11p to the overall FLC resistance phenotype of wild-type C. krusei cells the azole susceptibilities of S. cerevisiae cells overexpressing a selection of fungal Erg11p proteins or the multidrug transporter Abc1p to five azole antifungals (FLC, ITC, KTC, MCZ, and VRC) was quantified by measuring liquid MICs (Table 4). Assuming that Erg11p protein expression levels for the same construct are more or less constant in each MIC assay (a constitutive overexpression system is being used), comparing the different azole MICs of each fungal Erg11p-overexpressing strain can be used as a direct measure of its relative affinities for different azole antifungals. For example, high MICs (relative to the control strains AD or AD{Delta}) indicate a low affinity of an azole to its drug target Erg11p, whereas low MICs indicate a relatively higher affinity of the azole to that particular fungal Erg11p. The average fold increase for AD{Delta}/ScERG11 was fourfold (twofold for KTC, fourfold for MCZ and FLC, and eightfold for ITC and VRC). Erg11p from C. albicans was overexpressed at levels very similar to those for Erg11p from S. cerevisiae (Fig. 5B), and it led to very similar levels of increased resistance (~4-fold) for all five azoles tested (Table 4). This indicates that Erg11ps from S. cerevisiae and C. albicans have very similar affinities to the five azoles tested. Although Erg11p from C. krusei was expressed at much lower levels than Erg11p from S. cerevisiae or C. albicans (compare lanes 2, 3, and 4 of Fig. 5B), it conferred the highest levels of resistance to FLC and MCZ and similar levels of resistance to VRC and KTC (Table 4). This suggests that C. krusei Erg11p has lower affinities for FLC and MCZ than Erg11p from S. cerevisiae or C. albicans.

The overexpression of the efflux pump Abc1p in S. cerevisiae AD{Delta} led to between 64- and 128-fold-increased levels of resistance for all azoles tested (Table 4). Abc1p from C. krusei appears to be a very efficient azole transporter.

For comparison, the azole susceptibilities of six C. krusei isolates are also shown in Table 4. Since host S. cerevisiae AD cannot be grown in the medium recommended by CLSI for the determination of azole MICs in yeast, though we wanted to compare the azole susceptibilities of these C. krusei isolates with the azole susceptibilities of all S. cerevisiae strains shown in Table 4, and because we wanted to determine the MICs for all strains grown in the medium that was used for the expression studies shown in Fig. 5 and 6, we used CSM (pH 7.0) medium for all measurements. However, in order to interpret the azole susceptibilities of the C. krusei strains according to the interpretative breakpoints defined for the CLSI protocol, we also determined the azole susceptibilities of all six C. krusei strains according to the recommended CLSI method. These data are shown in parentheses in Table 4. According to the CLSI protocol, all six C. krusei isolates were classified as either resistant (n = 2) or susceptible dose dependent (SDD; n = 4) to FLC and KTC; all isolates except C. krusei 89221 (susceptible) were SDD to ITC, while all six strains were sensitive to VRC. No breakpoints are available for MCZ.

Abc1p inhibitors chemosensitize C. krusei and Abc1p overexpressing S. cerevisiae strains to FLC and ITC. We have previously described a number of specific small molecule inhibitors of fungal multidrug transporters, including C. krusei Abc1p (20). To test our hypothesis that Abc1p contributes significantly to the innate azole resistance of C. krusei, we tested the effect of these inhibitors on the azole susceptibilities of C. krusei strains B2399 and IFO0011. We used CSM agar plates containing sub-MIC concentrations of ITC (25% of MICITC) and measured the growth of cells around filter disks that contained known, or suspected, pump inhibitors placed onto the surface of agar plates seeded with C. krusei or AD/CkABC1g cells. All eight small molecule inhibitors tested inhibited Abc1p pump activity and chemosensitized S. cerevisiae cells overexpressing Abc1p to ITC (Fig. 9A). The strongest inhibition was obtained with milbemycins {alpha}11, {alpha}20, and {alpha}25, milbemycin β11, and FK506. C. krusei strains B2399 and IFO0011 were also chemosensitized by the same inhibitors with the exception of milbemycin {alpha}11 which showed only minor chemosensitization. Milbemycin β9, enniatin, and oligomycin showed little chemosensitization of cells overexpressing Abc1p to ITC and had no detectable effect on the C. krusei strains. The chemosensitization of cells overexpressing Abc1p and C. krusei strain B2399 by milbemycin {alpha}20 and β11 was quantified by using a checkerboard susceptibility assay (26). Milbemycin {alpha}20 fully inhibited the pump function of Abc1p at concentrations greater than 2 µg/ml and fully chemosensitized S. cerevisiae AD{Delta}/CkABC1g cells to FLC and ITC so that their susceptibilities became identical to AD{Delta} cells (Fig. 9Bc and d). The same concentrations of milbemycin {alpha}20 also showed synergistic effects with FLC or ITC on C. krusei strain B2399. Milbemycin {alpha}20 (2.5 µg/ml) reduced the MICFLC for strain B2399 to 64 µg/ml and the MICITC to 0.125 µg/ml (Fig. 9Ba and b). The chemosensitization experiments were also performed with milbemycin β11, leading to very similar results (data not shown). The fractional inhibitory concentration indices (FICI) (26) for the combination of milbemycin {alpha}20 and either FLC or ITC for AD{Delta}/CkABC1g cells were 0.112 or 0.104, respectively, and the FICI values for the same combinations for C. krusei B2399 cells were 0.35 or 0.298, respectively. FICI values are a quantitative measure for combination therapies and values of <0.5 indicate synergy between two drugs (26, 30, 45).


Figure 9
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  		FIG. 9. Abc1p-specific inhibitors chemosensitize C. krusei cells and S. cerevisiae cells overexpressing Abc1p to ITC and FLC. A S. cerevisiae AD{Delta} cells overexpressing Abc1p, or C. krusei cells, were analyzed by agarose diffusion assays using CSM solidified with 0.6% agarose and containing either no ITC (top row of agar plates; control to test the toxicity of inhibitors) or ITC at 0.25x the agar MICITC for each test strain (0.01 µg/ml). Whatman 3MM paper disks containing the indicated amounts of drug pump inhibitors (1 µg each of milbemycins {alpha}11, {alpha}20, {alpha}25, β9, and β11; 5 µg of FK506; 0.2 µg of enniatin; and 25 nmol of oligomycin) were placed onto the plate for AD{Delta}/CkABC1g cells. Five times more of the milbemycin inhibitors (5 µg) and enniatin (1 µg) were used for C. krusei strains B2399 and IFO0011. The plates were incubated at 30°C for 48 h. (B) The MICFLC and MICITC of C. krusei B2399 cells (a and b) and AD{Delta}/CkABC1g cells (c and d) were measured at various concentrations of the Abc1p inhibitor milbemycin {alpha}20 as described in Materials and Methods.


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DISCUSSION
 
All C. krusei strains used in this study were isolated from different sources and prior to the clinical use of FLC in the early nineties. Strain B2399 was obtained as a reference C. krusei strain from the CDC. Strain IFO0011 was isolated in Japan and the other strains used here are New Zealand isolates from different parts of the human body or from pig intestine. Despite the diversity of the environmental sources, all six strains exhibited very similar azole susceptibilities. They were all fully resistant or SDD to FLC and KTC and SDD to ITC, with the exception of strain 89221, which was sensitive to ITC. However, all strains appeared susceptible to VRC, a broad-spectrum triazole antifungal. Although C. krusei Erg11p has a significantly diminished sensitivity for FLC, ITC, and VRC and possibly other azole antifungals (11, 32), conflicting reports exist on whether other factors such as ABC multidrug efflux transporters or the reduced uptake of azoles also contribute to the innate FLC resistance of C. krusei (25, 49, 50). Although some studies have described large differences in the steady-state levels for different azoles in C. krusei (25, 50), a recent report claimed that no ABC transporter could be involved in the innate azole resistance phenotype (13).

In the present study we have shown that the functional overexpression of C. krusei Erg11p in our hypersusceptible host S. cerevisiae AD (deleted in seven ABC transporters) at levels similar to the highest, azole-induced, expression levels reached in C. krusei still resulted in a FLC-susceptible yeast (MICFLC = 4 µg/ml compared to MICFLC = 256 µg/ml for wild-type C. krusei using the same CSM [pH 7.0] medium). This finding led us to the hypothesis that C. krusei Erg11p alone is not sufficient to cause the innate azole resistance of most C. krusei strains. Functional overexpression of C. krusei Abc1p in S. cerevisiae AD{Delta} led to a 64- to 128-fold-increased level of resistance to FLC (MICFLC = 64 µg/ml) and other azoles. The fact that Abc1p is constitutively expressed in C. krusei, that it is highly homologous to known multidrug efflux pumps of related yeast, and that it confers high levels of resistance to azole antifungals when overexpressed in S. cerevisiae points to Abc1p being a significant contributor to the low azole susceptibility of C. krusei. To test that hypothesis, we attempted to create an ABC1 knockout strain of C. krusei. Due to the lack of C. krusei auxotrophic markers, we set out to adapt the SAT1 flipper/dominant selection marker technique, which has been used to knock out genes in clinical C. albicans isolates and in C. glabrata (37), to inactivate ABC1 in C. krusei. Unfortunately, all attempts to create ABC1 knockout strains failed due to the high level of C. krusei resistance to nourseothricin (even at 500 µg/ml). So, instead, we used Abc1p inhibitors to test whether Abc1p contributes significantly to the FLC resistance of C. krusei cells. This was achieved by demonstrating that C. krusei cells became four to eight times more sensitive to FLC and ITC when they were grown in the presence of specific nontoxic inhibitors of Abc1p. There may be other pumps contributing to the azole resistance of C. krusei, and it is possible that the fourfold increased susceptibilities of C. krusei to FLC and ITC conferred by milbemycins {alpha}20 and β11 is caused through the inhibition of another related pump and not Abc1p. However, a number of observations indicate that this is unlikely to be the case. As shown in Fig. 9A and as previously shown for FLC (20), the same inhibitors that best chemosensitized S. cerevisiae cells overexpressing C. krusei Abc1p to ITC (milbemycins {alpha}20, {alpha}25, and β11 and FK506) also best chemosensitized C. krusei to ITC. This is significant because when we tested the same set of compounds against a range of other homologous fungal efflux pumps (Pdr5p, Cdr1p and Cdr2p, CgCdr1p, and CgPdh1p) each pump was inhibited by a unique subset of these compounds (20). Even Cdr1p and Cdr2p, highly homologous efflux pumps from C. albicans, were inhibited by a very distinct set of xenobiotics. In addition, the concentrations of milbemycins {alpha}20 and β11 (<2 µg/ml) required to fully chemosensitize C. krusei to FLC and ITC were similar to those required to fully inhibit C. krusei Abc1p expressed in S. cerevisiae. Taken together, it appears that C. krusei Abc1p contributes significantly to azole resistance of C. krusei.

Sequence alignments and functional studies suggest that C. krusei Abc1p is an ortholog of S. cerevisiae Pdr5p. Interestingly, in our hands Abc1p expression was not stimulated by the presence of different azoles, as has been reported previously for Cdrp1, CgCdr1p (46), and also for Abc1p (15). One reason why ABC1 mRNA induction was seen previously by Katiyar and Edlind (16) may be because these authors used more than 10 times the concentrations of azoles, concentrations that were up to 100 times their MICs.

Despite extensive efforts, we were not able to isolate ABC2, the second C. krusei ABC transporter reported by Katiyar and Edlind (16). The reason for this is not clear and requires further investigation.

In view of the data provided here and elsewhere (11, 32, 49), it seems that the lower susceptibility of C. krusei Erg11p really is a major reason for the innate azole resistance of C. krusei. In order to investigate what makes it so much less susceptible to azoles than most other fungal Erg11ps, we compared C. krusei Erg11p with other fungal Erg11ps, human Cyp51Ap, and MtCyp51p (a CLUSTAL W alignment of these proteins is shown in Fig. 2). The most obvious difference between fungal Erg11ps and MtCyp51p, as well as human Cyp51Ap, is a 15- to 24-amino-acid insertion between the K''' and L helices compared to MtCyp51p. Significantly, the insertion is greatest for CkErg11p (an extra 5 amino acids; Fig. 2). The most recent three-dimensional structure for MtCyp51p can be found in PDB (2VKU) (9). It is interesting that this insertion is very close to two important amino acid residues (G464 and R467 of the CaErg11p sequence highlighted with black dots above the alignment in Fig. 2) that, when mutated to S464 and/or K467, lead to azole resistance in clinical C. albicans isolates (36, 42). Only a further three amino acids downstream is the essential cysteine (C470) that forms the fifth ligand of the iron in the prosthetic heme group. This insertion could be important for the lower azole susceptibility of C. krusei Erg11p compared to all other fungal Erg11ps. Since this region is predicted to be close to the base of the heme, it is possible that a change in this region somehow affects the environment adjacent to the heme and potentially the binding of azoles to the heme. Because this region is absent in MtCyp51p upon which fungal Erg11p structures are modeled, it is not possible to visualize the changes. Whether this region is important for the reduced azole susceptibility of C. krusei Erg11p can only be answered by solving the fungal Erg11p structure.

Another interesting and somewhat surprising discovery was that C. krusei strain B2399 contained three ERG11 alleles. However, no obvious correlation between the ERG11 copy number and FLC resistance was observed. The trisomy in the ERG11-containing chromosome observed for C. krusei strain B2399 is clearly due to the presence of three separate alleles that did not arise from a gene duplication event but possibly through the mating of two diploid C. krusei strains, followed by an imperfect loss of chromosomes resulting in aneuploidy. This is reminiscent of C. albicans and its imperfect sexual reproduction that can also lead to aneuploidy. Cryptococcus neoformans is another important fungal pathogen that has been shown to possess somewhat similar properties. The mating of C. neoformans serotype A MATa with serotype D MAT{alpha} variant strains was recently shown to produce diploid and sometimes aneuploid AD hybrid strains with increased fitness to UV (21, 22). In contrast, a recent study of the effects of aneuploidy in S. cerevisiae showed that the possession of one extra copy of any of its 16 chromosomes leads to a range of phenotypes such as defects in cell cycle progression, protein synthesis, protein folding, and biomass production (47). An extra copy of any of the chromosomes tested induced a typical stress response and in this case aneuploidy led to reduced fitness. It may be that the aneuploidy of C. krusei B2399, like that of C. neoformans variants, confers phenotypic characteristics that lead to some fitness advantage. The presence of three chromosomes in one of our isolates raises the possibility that C. krusei is able to reproduce sexually; however, we are not aware of any reports that show that C. krusei isolates can be mated under laboratory conditions. Recently, Jacobsen et al. (15) used multilocus sequence typing to determine the population structure of a large collection of C. krusei isolates, and they, too, found evidence for a departure from the mainly clonal reproduction pattern that is seen for C. albicans strains. These authors concluded that investigating the ability of C. krusei to undergo sexual reproduction was warranted.

To summarize, our data support the model that the innate FLC resistance phenotype of C. krusei is mainly a combination of two factors: the low sensitivity of the drug target Erg11p to azole antifungals, which causes a rather high basal level of resistance to azole antifungals, and the constitutive expression of the multidrug efflux pump Abc1p that most likely tips the balance in favor of innate azole resistance for most C. krusei strains. One could therefore speculate that the future use of broad-spectrum triazoles such as VRC that are effective against C. krusei but are also substrates of Abc1p could lead to the rise of VRC resistant C. krusei strains that overexpress Abc1p analogous to the resistance mechanisms described for other Candida species. In addition, the discovery that one of our six C. krusei isolates possessed three copies of the ERG11 gene (and we have evidence that one other strain contains three copies of ERG11 as well) leads us to speculate that a number of C. krusei strains are aneuploid.


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ACKNOWLEDGMENTS
 
This study was supported by an IADR David B. Scott fellowship awarded to A.R., by the Japan Health Sciences Foundation, by the National Institutes of Health (R21DE015075-RDC and R01DE016885-01-RDC), by the New Zealand Lottery Grants Board, and by the Foundation for Research Science and Technology of New Zealand (IIOF grant UOOX0607-RDC).

We thank A. Goffeau and A. Decottignies for providing strain AD1-8u–; Sankyo Pharmaceuticals, Ltd., Tokyo, Japan, for providing the milbemycins; Astellas Pharma, Inc., Japan, for providing FK506; J. Morschhäuser, Molekulare Infektionsbiologie, Universität Würzburg, Würzburg, Germany, for kindly providing the SAT1 flipper plasmids; and A. McNaughton at the Otago Centre for Confocal Microscopy for expert assistance.


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FOOTNOTES
 
* Corresponding author. Mailing address: Department of Oral Sciences, University of Otago, P.O. Box 647, Dunedin 9054, New Zealand. Phone: 64 3 479 7435. Fax: 64 3 479 7078. E-mail: erwin.lamping{at}otago.ac.nz Back

{triangledown} Published ahead of print on 17 November 2008. Back


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Antimicrobial Agents and Chemotherapy, February 2009, p. 354-369, Vol. 53, No. 2
0066-4804/09/$08.00+0     doi:10.1128/AAC.01095-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.




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