1
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Zhao M, Lamping E, Niimi K, Niimi M, Cannon RD. Functional analysis of Candida albicans Cdr1 through homologous and heterologous expression studies. FEMS Yeast Res 2025; 25:foaf012. [PMID: 40101948 PMCID: PMC11974388 DOI: 10.1093/femsyr/foaf012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2024] [Revised: 02/17/2025] [Accepted: 03/16/2025] [Indexed: 03/20/2025] Open
Abstract
Candida albicans Cdr1 is a plasma membrane ATP-binding cassette transporter encoded by CDR1 that was first cloned 30 years ago in Saccharomyces cerevisiae. Increased expression of Cdr1 in C. albicans clinical isolates results in resistance to azole antifungals due to drug efflux from the cells. Knowledge of Cdr1 structure and function could enable the design of Cdr1 inhibitors that overcome efflux-mediated drug resistance. This article reviews the use of expression systems to study Cdr1. Since the discovery of CDR1 in 1995, 123 studies have investigated Cdr1 using either heterologous or homologous expression systems. The majority of studies have employed integrative transformation and expression in S. cerevisiae. We describe a suite of plasmids with a range of useful protein tags for integrative transformation that enable the creation of tandem-gene arrays stably integrated into the S. cerevisiae genome, and a model for Cdr1 transport function. While expression in S. cerevisiae generates a strong phenotype and high yields of Cdr1, it is a nonnative environment and may result in altered structure and function. Membrane lipid composition and architecture affects membrane protein function and a focus on homologous expression in C. albicans may permit a more accurate understanding of Cdr1 structure and function.
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Affiliation(s)
- Mengcun Zhao
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
| | - Erwin Lamping
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
| | - Kyoko Niimi
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
| | - Masakazu Niimi
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
| | - Richard D Cannon
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
- Department of Oral Sciences, Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
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2
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Liu C, Tan X, Wang J, Sun Y, Xu Q, Han C, Wang Q. Upgrading of the genetic engineering toolkit accelerated the discovery process of the virulence effect of PsGH7d on Phytophthora sojae invasion. PHYSIOLOGIA PLANTARUM 2025; 177:e70083. [PMID: 39936449 DOI: 10.1111/ppl.70083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 12/17/2024] [Accepted: 01/08/2025] [Indexed: 02/13/2025]
Abstract
The genus of Phytophthora includes numerous phytopathogens that have devastating impacts on agricultural production. However, the limited availability of selection markers for numerous pathogenicity pathogens of the genus Phytophthora genetic transformation hinders further research on their pathogenic functional genes. Here we report a gene of NAT I, which serves as a novel selection marker for the Phytophthora sojae transformation. Additionally, we developed a new genetic manipulation toolkit based on vectors containing NAT I, which facilitates gene editing in P. sojae. With the toolkit, the gene PsGH7d of P. sojae, which encodes a glycosyl hydrolase, was edited consecutively via the CRISPR/Cas9 system to obtain gene knockout and enzymatic active site mutation strains. The pathogenicity analysis of these transformants revealed that PsGH7d is a virulence factor dependent on its bifunctional glucanase-xylanase activities. This study develops an updated toolkit for the genus Phytophthora genetic transformation and provides initial insights into the virulence of the bifunctional enzyme PsGH7d.
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Affiliation(s)
- Changqing Liu
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Xinwei Tan
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Jiayu Wang
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Yujing Sun
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Qian Xu
- College of Agronomy, Shandong Agricultural University, Taian, China
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Taian, China
| | - Chao Han
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Qunqing Wang
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Taian, China
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Taian, China
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3
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Li J, Brandalise D, Coste AT, Sanglard D, Lamoth F. Exploration of novel mechanisms of azole resistance in Candida auris. Antimicrob Agents Chemother 2024; 68:e0126524. [PMID: 39480072 PMCID: PMC11619343 DOI: 10.1128/aac.01265-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 10/03/2024] [Indexed: 11/02/2024] Open
Abstract
Candida auris is a pathogenic yeast of particular concern because of its ability to cause nosocomial outbreaks of invasive candidiasis (IC) and to develop resistance to all current antifungal drug classes. Most C. auris clinical isolates are resistant to fluconazole, an azole drug that is used for the treatment of IC. Azole resistance may arise from diverse mechanisms, such as mutations of the target gene (ERG11) or upregulation of efflux pumps via gain of function mutations of the transcription factors TAC1 and/or MRR1. To explore novel mechanisms of azole resistance in C. auris, we applied an in vitro evolutionary protocol to induce azole resistance in a TAC1A/TAC1B/MRR1 triple-deletion strain. Azole-resistant isolates without ERG11 mutations were further analyzed. In addition to a whole chromosome aneuploidy of chromosome 5, amino acid substitutions were recovered in the transcription factor Upc2 (N592S, L499F), the ubiquitin ligase complex consisting of Ubr2 (P708T, H1275P) and Mub1 (Y765*), and the mitochondrial protein Mrs7 (D293H). Genetic introduction of these mutations in an azole-susceptible wild-type C. auris isolate of clade IV resulted in significantly decreased azole susceptibility. Real-time reverse transcription PCR analyses were performed to assess the impact of these mutations on the expression of genes involved in azole resistance, such as ERG11, the efflux pumps CDR1 and MDR1 or the transcription factor RPN4. In conclusion, this work provides further insights in the complex and multiple pathways of azole resistance of C. auris. Further analyses would be warranted to assess their respective role in azole resistance of clinical isolates.
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Affiliation(s)
- Jizhou Li
- Institute of Microbiology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Danielle Brandalise
- Institute of Microbiology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Alix T. Coste
- Institute of Microbiology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dominique Sanglard
- Institute of Microbiology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Frederic Lamoth
- Institute of Microbiology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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4
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Zhou X, Hilk A, Solis NV, Scott N, Beach A, Soisangwan N, Billings CL, Burrack LS, Filler SG, Selmecki A. Single-cell detection of copy number changes reveals dynamic mechanisms of adaptation to antifungals in Candida albicans. Nat Microbiol 2024; 9:2923-2938. [PMID: 39227665 PMCID: PMC11524788 DOI: 10.1038/s41564-024-01795-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 07/24/2024] [Indexed: 09/05/2024]
Abstract
Genomic copy number changes are associated with antifungal drug resistance and virulence across diverse fungal pathogens, but the rate and dynamics of these genomic changes in the presence of antifungal drugs are unknown. Here we optimized a dual-fluorescent reporter system in the diploid pathogen Candida albicans to quantify haplotype-specific copy number variation (CNV) and loss of heterozygosity (LOH) at the single-cell level with flow cytometry. We followed the frequency and dynamics of CNV and LOH at two distinct genomic locations in the presence and absence of antifungal drugs in vitro and in a murine model of candidiasis. Copy number changes were rapid and dynamic during adaptation to fluconazole and frequently involved competing subpopulations with distinct genotypes. This study provides quantitative evidence for the rapid speed at which diverse genotypes arise and undergo dynamic population-level fluctuations during adaptation to antifungal drugs in vitro and in vivo.
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Affiliation(s)
- Xin Zhou
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Audrey Hilk
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Norma V Solis
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Nancy Scott
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Annette Beach
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Natthapon Soisangwan
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Clara L Billings
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Laura S Burrack
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Scott G Filler
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA.
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5
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Thai HD, Trinh MT, Do LTBX, Le TH, Nguyen DT, Tran QT, Tran VKT, Mai LTD, Pham DN, Le DH, Vu TX, Tran VT. Gene function characterization in Aspergillus niger using a dual resistance marker transformation system mediated by Agrobacterium tumefaciens. J Microbiol Methods 2024; 224:106989. [PMID: 38996925 DOI: 10.1016/j.mimet.2024.106989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/14/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Aspergillus niger is a well-known workhorse for the industrial production of enzymes and organic acids. This fungus can also cause postharvest diseases in fruits. Although Agrobacterium tumefaciens-mediated transformation (ATMT) based on antibiotic resistance markers has been effectively exploited for inspecting functions of target genes in wild-type fungi, it still needs to be further improved in A. niger. In the present study, we re-examined the ATMT in the wild-type A. niger strains using the hygromycin resistance marker and introduced the nourseothricin resistance gene as a new selection marker for this fungus. Unexpectedly, our results revealed that the ATMT method using the resistance markers in A. niger led to numerous small colonies as false-positive transformants on transformation plates. Using the top agar overlay technique to restrict false positive colonies, a transformation efficiency of 87 ± 18 true transformants could be achieved for 106 conidia. With two different selection markers, we could perform both the deletion and complementation of a target gene in a single wild-type A. niger strain. Our results also indicated that two key regulatory genes (laeA and veA) of the velvet complex are required for A. niger to infect apple fruits. Notably, we demonstrated for the first time that a laeA homologous gene from the citrus postharvest pathogen Penicillium digitatum was able to restore the acidification ability and pathogenicity of the A. niger ΔlaeA mutant. The dual resistance marker ATMT system from our work represents an improved genetic tool for gene function characterization in A. niger.
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Affiliation(s)
- Hanh-Dung Thai
- National Key Laboratory of Enzyme and Protein Technology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Minh Thi Trinh
- National Key Laboratory of Enzyme and Protein Technology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Loc Thi Binh Xuan Do
- National Key Laboratory of Enzyme and Protein Technology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Thu-Hang Le
- National Key Laboratory of Enzyme and Protein Technology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Duc-Thanh Nguyen
- National Key Laboratory of Enzyme and Protein Technology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Que Thi Tran
- National Key Laboratory of Enzyme and Protein Technology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Van-Khanh Tong Tran
- National Key Laboratory of Enzyme and Protein Technology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Linh Thi Dam Mai
- Faculty of Biology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Duc-Ngoc Pham
- Faculty of Biology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Diep Hong Le
- Faculty of Biology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam
| | - Tao Xuan Vu
- Center for Experimental Biology, National Center for Technological Progress, Ministry of Science and Technology of Vietnam, C6 Thanh Xuan Bac, Thanh Xuan, Hanoi, Viet Nam
| | - Van-Tuan Tran
- National Key Laboratory of Enzyme and Protein Technology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam; Faculty of Biology, University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Viet Nam.
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6
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Acosta-Zaldívar M, Qi W, Mishra A, Roy U, King WR, Li Y, Patton-Vogt J, Anderson MZ, Köhler JR. Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity. PLoS Genet 2024; 20:e1011156. [PMID: 39137212 PMCID: PMC11343460 DOI: 10.1371/journal.pgen.1011156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 08/23/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024] Open
Abstract
Phosphorus is essential in all cells' structural, metabolic and regulatory functions. For fungal cells that import inorganic phosphate (Pi) up a steep concentration gradient, surface Pi transporters are critical capacitators of growth. Fungi must deploy Pi transporters that enable optimal Pi uptake in pH and Pi concentration ranges prevalent in their environments. Single, triple and quadruple mutants were used to characterize the four Pi transporters we identified for the human fungal pathogen Candida albicans, which must adapt to alkaline conditions during invasion of the host bloodstream and deep organs. A high-affinity Pi transporter, Pho84, was most efficient across the widest pH range while another, Pho89, showed high-affinity characteristics only within one pH unit of neutral. Two low-affinity Pi transporters, Pho87 and Fgr2, were active only in acidic conditions. Only Pho84 among the Pi transporters was clearly required in previously identified Pi-related functions including Target of Rapamycin Complex 1 signaling, oxidative stress resistance and hyphal growth. We used in vitro evolution and whole genome sequencing as an unbiased forward genetic approach to probe adaptation to prolonged Pi scarcity of two quadruple mutant lineages lacking all 4 Pi transporters. Lineage-specific genomic changes corresponded to divergent success of the two lineages in fitness recovery during Pi limitation. Initial, large-scale genomic alterations like aneuploidies and loss of heterozygosity eventually resolved, as populations gained small-scale mutations. Severity of some phenotypes linked to Pi starvation, like cell wall stress hypersensitivity, decreased in parallel to evolving populations' fitness recovery in Pi scarcity, while severity of others like membrane stress responses diverged from Pi scarcity fitness. Among preliminary candidate genes for contributors to fitness recovery, those with links to TORC1 were overrepresented. Since Pi homeostasis differs substantially between fungi and humans, adaptive processes to Pi deprivation may harbor small-molecule targets that impact fungal growth, stress resistance and virulence.
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Affiliation(s)
- Maikel Acosta-Zaldívar
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Wanjun Qi
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
| | - Abhishek Mishra
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Udita Roy
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
| | - William R. King
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Yuping Li
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Matthew Z. Anderson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Medical Genetics, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Julia R. Köhler
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
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7
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Determann B, Fu J, Wickes BL. Development of a Shuttle Vector That Transforms at High Frequency for the Emerging Human Fungal Pathogen: Candida auris. J Fungi (Basel) 2024; 10:477. [PMID: 39057362 PMCID: PMC11278357 DOI: 10.3390/jof10070477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Routine molecular manipulation of any organism is inefficient and difficult without the existence of a plasmid. Although transformation is possible in C. auris, no plasmids are available that can serve as cloning or shuttle vectors. C. auris centromeres have been well characterized but have not been explored further as molecular tools. We tested C. auris centromeric sequences to identify which, if any, could be used to create a plasmid that was stably maintained after transformation. We cloned all seven C. auris centromeric sequences and tested them for transformation frequency and stability. Transformation frequency varied significantly; however, one was found to transform at a very high frequency. A 1.7 Kb subclone of this sequence was used to construct a shuttle vector. The vector was stable with selection and maintained at ~1 copy per cell but could be easily lost when selection was removed, which suggested that the properties of the centromeric sequence were more Autonomously Replicating Sequence (ARS)-like than centromere-like when part of a plasmid. Rescue of this plasmid from transformed C. auris cells into E. coli revealed that it remained intact after the initial C. auris transformation, even when carrying large inserts. The plasmid was found to be able to transform all four clades of C. auris, with varying frequencies. This plasmid is an important new reagent in the C. auris molecular toolbox, which will enhance the investigation of this human fungal pathogen.
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Affiliation(s)
| | | | - Brian L. Wickes
- The Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA (J.F.)
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Zhou X, Hilk A, Solis NV, Pereira De Sa N, Hogan BM, Bierbaum TA, Del Poeta M, Filler SG, Burrack LS, Selmecki A. Erg251 has complex and pleiotropic effects on sterol composition, azole susceptibility, filamentation, and stress response phenotypes. PLoS Pathog 2024; 20:e1012389. [PMID: 39078851 PMCID: PMC11315318 DOI: 10.1371/journal.ppat.1012389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 08/09/2024] [Accepted: 07/03/2024] [Indexed: 08/07/2024] Open
Abstract
Ergosterol is essential for fungal cell membrane integrity and growth, and numerous antifungal drugs target ergosterol. Inactivation or modification of ergosterol biosynthetic genes can lead to changes in antifungal drug susceptibility, filamentation and stress response. Here, we found that the ergosterol biosynthesis gene ERG251 is a hotspot for point mutations during adaptation to antifungal drug stress within two distinct genetic backgrounds of Candida albicans. Heterozygous point mutations led to single allele dysfunction of ERG251 and resulted in azole tolerance in both genetic backgrounds. This is the first known example of point mutations causing azole tolerance in C. albicans. Importantly, single allele dysfunction of ERG251 in combination with recurrent chromosome aneuploidies resulted in bona fide azole resistance. Homozygous deletions of ERG251 caused increased fitness in low concentrations of fluconazole and decreased fitness in rich medium, especially at low initial cell density. Homozygous deletions of ERG251 resulted in accumulation of ergosterol intermediates consistent with the fitness defect in rich medium. Dysfunction of ERG251, together with FLC exposure, resulted in decreased accumulation of the toxic sterol (14-ɑ-methylergosta-8,24(28)-dien-3β,6α-diol) and increased accumulation of non-toxic alternative sterols. The altered sterol composition of the ERG251 mutants had pleiotropic effects on transcription, filamentation, and stress responses including cell membrane, osmotic and oxidative stress. Interestingly, while dysfunction of ERG251 resulted in azole tolerance, it also led to transcriptional upregulation of ZRT2, a membrane-bound Zinc transporter, in the presence of FLC, and overexpression of ZRT2 is sufficient to increase azole tolerance in wild-type C. albicans. Finally, in a murine model of systemic infection, homozygous deletion of ERG251 resulted in decreased virulence while the heterozygous deletion mutants maintain their pathogenicity. Overall, this study demonstrates that single allele dysfunction of ERG251 is a recurrent and effective mechanism of acquired azole tolerance. We propose that altered sterol composition resulting from ERG251 dysfunction mediates azole tolerance as well as pleiotropic effects on stress response, filamentation and virulence.
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Affiliation(s)
- Xin Zhou
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Audrey Hilk
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Norma V. Solis
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, California, United States of America
| | - Nivea Pereira De Sa
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, United States of America
| | - Bode M. Hogan
- Gustavus Adolphus College, Department of Biology, Saint Peter, Minnesota, USA
| | - Tessa A. Bierbaum
- Gustavus Adolphus College, Department of Biology, Saint Peter, Minnesota, USA
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, United States of America
- Division of Infectious Diseases, School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Veterans Administration Medical Center, Northport, New York, United States of America
| | - Scott G. Filler
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, California, United States of America
- David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Laura S. Burrack
- Gustavus Adolphus College, Department of Biology, Saint Peter, Minnesota, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
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9
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Guo L, Zheng L, Dong Y, Wang C, Deng H, Wang Z, Xu Y. Miconazole induces aneuploidy-mediated tolerance in Candida albicans that is dependent on Hsp90 and calcineurin. Front Cell Infect Microbiol 2024; 14:1392564. [PMID: 38983116 PMCID: PMC11231705 DOI: 10.3389/fcimb.2024.1392564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
Antifungal resistance and antifungal tolerance are two distinct terms that describe different cellular responses to drugs. Antifungal resistance describes the ability of a fungus to grow above the minimal inhibitory concentration (MIC) of a drug. Antifungal tolerance describes the ability of drug susceptible strains to grow slowly at inhibitory drug concentrations. Recent studies indicate antifungal resistance and tolerance have distinct evolutionary trajectories. Superficial candidiasis bothers millions of people yearly. Miconazole has been used for topical treatment of yeast infections for over 40 years. Yet, fungal resistance to miconazole remains relatively low. Here we found different clinical isolates of Candida albicans had different profile of tolerance to miconazole, and the tolerance was modulated by physiological factors including temperature and medium composition. Exposure of non-tolerant strains with different genetic backgrounds to miconazole mainly induced development of tolerance, not resistance, and the tolerance was mainly due to whole chromosomal or segmental amplification of chromosome R. The efflux gene CDR1 was required for maintenance of tolerance in wild type strains but not required for gain of aneuploidy-mediated tolerance. Heat shock protein Hsp90 and calcineurin were essential for maintenance as well as gain of tolerance. Our study indicates development of aneuploidy-mediated tolerance, not resistance, is the predominant mechanism of rapid adaptation to miconazole in C. albicans, and the clinical relevance of tolerance deserves further investigations.
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Affiliation(s)
- Liangsheng Guo
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lijun Zheng
- Department of Ultrasound Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yubo Dong
- Department of Pharmacy, The 960th Hospital of PLA, Jinan, China
| | - Chen Wang
- Department of Pharmacy, The 960th Hospital of PLA, Jinan, China
| | - Huijie Deng
- Department of Pharmacy, The 960th Hospital of PLA, Jinan, China
| | - Zongjie Wang
- Department of Pharmacy, The 960th Hospital of PLA, Jinan, China
| | - Yi Xu
- Department of Pharmacy, The 960th Hospital of PLA, Jinan, China
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10
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Zhou X, Hilk A, Solis NV, Hogan BM, Bierbaum TA, Filler SG, Burrack LS, Selmecki A. Erg251 has complex and pleiotropic effects on azole susceptibility, filamentation, and stress response phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583770. [PMID: 38496635 PMCID: PMC10942443 DOI: 10.1101/2024.03.06.583770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Ergosterol is essential for fungal cell membrane integrity and growth, and numerous antifungal drugs target ergosterol. Inactivation or modification of ergosterol biosynthetic genes can lead to changes in antifungal drug susceptibility, filamentation and stress response. Here, we found that the ergosterol biosynthesis gene ERG251 is a hotspot for point mutations during adaptation to antifungal drug stress within two distinct genetic backgrounds of Candida albicans. Heterozygous point mutations led to single allele dysfunction of ERG251 and resulted in azole tolerance in both genetic backgrounds. This is the first known example of point mutations causing azole tolerance in C. albicans. Importantly, single allele dysfunction of ERG251 in combination with recurrent chromosome aneuploidies resulted in bona fide azole resistance. Homozygous deletions of ERG251 caused increased fitness in low concentrations of fluconazole and decreased fitness in rich medium, especially at low initial cell density. Dysfunction of ERG251 resulted in transcriptional upregulation of the alternate sterol biosynthesis pathway and ZRT2, a Zinc transporter. Notably, we determined that overexpression of ZRT2 is sufficient to increase azole tolerance in C. albicans. Our combined transcriptional and phenotypic analyses revealed the pleiotropic effects of ERG251 on stress responses including cell wall, osmotic and oxidative stress. Interestingly, while loss of either allele of ERG251 resulted in similar antifungal drug responses, we observed functional divergence in filamentation regulation between the two alleles of ERG251 (ERG251-A and ERG251-B) with ERG251-A exhibiting a dominant role in the SC5314 genetic background. Finally, in a murine model of systemic infection, homozygous deletion of ERG251 resulted in decreased virulence while the heterozygous deletion mutants maintain their pathogenicity. Overall, this study provides extensive genetic, transcriptional and phenotypic analysis for the effects of ERG251 on drug susceptibility, fitness, filamentation and stress responses.
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Affiliation(s)
- Xin Zhou
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Audrey Hilk
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Norma V. Solis
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Bode M. Hogan
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Tessa A. Bierbaum
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Scott G. Filler
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Laura S. Burrack
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
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11
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Li J, Aubry L, Brandalise D, Coste AT, Sanglard D, Lamoth F. Upc2-mediated mechanisms of azole resistance in Candida auris. Microbiol Spectr 2024; 12:e0352623. [PMID: 38206035 PMCID: PMC10845950 DOI: 10.1128/spectrum.03526-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Candida auris is an emerging yeast pathogen of major concern because of its ability to cause hospital outbreaks of invasive candidiasis and to develop resistance to antifungal drugs. A majority of C. auris isolates are resistant to fluconazole, an azole drug used for the treatment of invasive candidiasis. Mechanisms of azole resistance are multiple, including mutations in the target gene ERG11 and activation of the transcription factors Tac1b and Mrr1, which control the drug transporters Cdr1 and Mdr1, respectively. We investigated the role of the transcription factor Upc2, which is known to regulate the ergosterol biosynthesis pathway and azole resistance in other Candida spp. Genetic deletion and hyperactivation of Upc2 by epitope tagging in C. auris resulted in drastic increases and decreases in susceptibility to azoles, respectively. This effect was conserved in strains with genetic hyperactivation of Tac1b or Mrr1. Reverse transcription PCR analyses showed that Upc2 regulates ERG11 expression and also activates the Mrr1/Mdr1 pathway. We showed that upregulation of MDR1 by Upc2 could occur independently from Mrr1. The impact of UPC2 deletion on MDR1 expression and azole susceptibility in a hyperactive Mrr1 background was stronger than that of MRR1 deletion in a hyperactive Upc2 background. While Upc2 hyperactivation resulted in a significant increase in the expression of TAC1b, CDR1 expression remained unchanged. Taken together, our results showed that Upc2 is crucial for azole resistance in C. auris, via regulation of the ergosterol biosynthesis pathway and activation of the Mrr1/Mdr1 pathway. Notably, Upc2 is a very potent and direct activator of Mdr1.IMPORTANCECandida auris is a yeast of major medical importance causing nosocomial outbreaks of invasive candidiasis. Its ability to develop resistance to antifungal drugs, in particular to azoles (e.g., fluconazole), is concerning. Understanding the mechanisms of azole resistance in C. auris is important and may help in identifying novel antifungal targets. This study shows the key role of the transcription factor Upc2 in azole resistance of C. auris and shows that this effect is mediated via different pathways, including the regulation of ergosterol biosynthesis and also the direct upregulation of the drug transporter Mdr1.
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Affiliation(s)
- Jizhou Li
- Department of Laboratory Medicine and Pathology, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Lola Aubry
- Department of Laboratory Medicine and Pathology, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Danielle Brandalise
- Department of Laboratory Medicine and Pathology, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alix T. Coste
- Department of Laboratory Medicine and Pathology, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Dominique Sanglard
- Department of Laboratory Medicine and Pathology, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Frederic Lamoth
- Department of Laboratory Medicine and Pathology, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- Infectious Diseases Service, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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12
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Acosta-Zaldívar M, Qi W, Mishra A, Roy U, King WR, Patton-Vogt J, Anderson MZ, Köhler JR. Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577887. [PMID: 38352318 PMCID: PMC10862840 DOI: 10.1101/2024.01.29.577887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Phosphorus is essential in all cells' structural, metabolic and regulatory functions. For fungal cells that import inorganic phosphate (Pi) up a steep concentration gradient, surface Pi transporters are critical capacitators of growth. Fungi must deploy Pi transporters that enable optimal Pi uptake in pH and Pi concentration ranges prevalent in their environments. Single, triple and quadruple mutants were used to characterize the four Pi transporters we identified for the human fungal pathogen Candida albicans, which must adapt to alkaline conditions during invasion of the host bloodstream and deep organs. A high-affinity Pi transporter, Pho84, was most efficient across the widest pH range while another, Pho89, showed high-affinity characteristics only within one pH unit of neutral. Two low-affinity Pi transporters, Pho87 and Fgr2, were active only in acidic conditions. Only Pho84 among the Pi transporters was clearly required in previously identified Pi-related functions including Target of Rapamycin Complex 1 signaling and hyphal growth. We used in vitro evolution and whole genome sequencing as an unbiased forward genetic approach to probe adaptation to prolonged Pi scarcity of two quadruple mutant lineages lacking all 4 Pi transporters. Lineage-specific genomic changes corresponded to divergent success of the two lineages in fitness recovery during Pi limitation. In this process, initial, large-scale genomic alterations like aneuploidies and loss of heterozygosity were eventually lost as populations presumably gained small-scale mutations. Severity of some phenotypes linked to Pi starvation, like cell wall stress hypersensitivity, decreased in parallel to evolving populations' fitness recovery in Pi scarcity, while that of others like membrane stress responses diverged from these fitness phenotypes. C. albicans therefore has diverse options to reconfigure Pi management during prolonged scarcity. Since Pi homeostasis differs substantially between fungi and humans, adaptive processes to Pi deprivation may harbor small-molecule targets that impact fungal growth and virulence.
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Affiliation(s)
- Maikel Acosta-Zaldívar
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
- Current affiliation: Planasa, Valladolid, Spain
| | - Wanjun Qi
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
| | - Abhishek Mishra
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
| | - Udita Roy
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
| | - William R. King
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Matthew Z. Anderson
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI
- Department of Medical Genetics, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
| | - Julia R. Köhler
- Division of Infectious Diseases, Boston Children’s Hospital/Harvard Medical School, Boston, MA 02115, USA
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13
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Zheng L, Xu Y, Wang C, Yang F, Dong Y, Guo L. Susceptibility to caspofungin is regulated by temperature and is dependent on calcineurin in Candida albicans. Microbiol Spectr 2023; 11:e0179023. [PMID: 37966204 PMCID: PMC10715083 DOI: 10.1128/spectrum.01790-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Echinocandins are the newest antifungal drugs and are first-line treatment option for life-threatening systemic infections. Due to lack of consensus regarding what temperature should be used when evaluating susceptibility of yeasts to echinocandins, typically either 30°C, 35°C, or 37°C is used. However, the impact of temperature on antifungal efficacy of echinocandins is unexplored. In the current study, we demonstrated that Candida albicans laboratory strain SC5314 was more susceptible to caspofungin at 37°C than at 30°C. We also found that calcineurin was required for temperature-modulated caspofungin susceptibility. Surprisingly, the altered caspofungin susceptibility was not due to differential expression of some canonical genes such as FKS, CHS, or CHT genes. The molecular mechanism of temperature-modulated caspofungin susceptibility is undetermined and deserves further investigations.
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Affiliation(s)
- Lijun Zheng
- Department of Ultrasound Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi Xu
- Department of Pharmacy, The 960 Hospital of PLA, Jinan, China
| | - Chen Wang
- Department of Pharmacy, The 960 Hospital of PLA, Jinan, China
| | - Feng Yang
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yubo Dong
- Department of Pharmacy, The 960 Hospital of PLA, Jinan, China
| | - Liangsheng Guo
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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14
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Giuraniuc CV, Parkin C, Almeida MC, Fricker M, Shadmani P, Nye S, Wehmeier S, Chawla S, Bedekovic T, Lehtovirta-Morley L, Richards DM, Gow NA, Brand AC. Dynamic calcium-mediated stress response and recovery signatures in the fungal pathogen, Candida albicans. mBio 2023; 14:e0115723. [PMID: 37750683 PMCID: PMC10653887 DOI: 10.1128/mbio.01157-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Intracellular calcium signaling plays an important role in the resistance and adaptation to stresses encountered by fungal pathogens within the host. This study reports the optimization of the GCaMP fluorescent calcium reporter for live-cell imaging of dynamic calcium responses in single cells of the pathogen, Candida albicans, for the first time. Exposure to membrane, osmotic or oxidative stress generated both specific changes in single cell intracellular calcium spiking and longer calcium transients across the population. Repeated treatments showed that calcium dynamics become unaffected by some stresses but not others, consistent with known cell adaptation mechanisms. By expressing GCaMP in mutant strains and tracking the viability of individual cells over time, the relative contributions of key signaling pathways to calcium flux, stress adaptation, and cell death were demonstrated. This reporter, therefore, permits the study of calcium dynamics, homeostasis, and signaling in C. albicans at a previously unattainable level of detail.
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Affiliation(s)
- C. V. Giuraniuc
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - C. Parkin
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - M. C. Almeida
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - M. Fricker
- School of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - P. Shadmani
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - S. Nye
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - S. Wehmeier
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - S. Chawla
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - T. Bedekovic
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - L. Lehtovirta-Morley
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - D. M. Richards
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Department of Physics and Astronomy, University of Exeter, Exeter, United Kingdom
| | - N. A. Gow
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
| | - A. C. Brand
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- MRC Centre for Medical Mycology at the University of Exeter, Exeter, United Kingdom
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
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15
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Wang YL, Chang CY, Hsu NS, Lo IW, Lin KH, Chen CL, Chang CF, Wang ZC, Ogasawara Y, Dairi T, Maruyama C, Hamano Y, Li TL. N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry. Nat Commun 2023; 14:2528. [PMID: 37137912 PMCID: PMC10156733 DOI: 10.1038/s41467-023-38218-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
Oxidized cysteine residues are highly reactive and can form functional covalent conjugates, of which the allosteric redox switch formed by the lysine-cysteine NOS bridge is an example. Here, we report a noncanonical FAD-dependent enzyme Orf1 that adds a glycine-derived N-formimidoyl group to glycinothricin to form the antibiotic BD-12. X-ray crystallography was used to investigate this complex enzymatic process, which showed Orf1 has two substrate-binding sites that sit 13.5 Å apart unlike canonical FAD-dependent oxidoreductases. One site could accommodate glycine and the other glycinothricin or glycylthricin. Moreover, an intermediate-enzyme adduct with a NOS-covalent linkage was observed in the later site, where it acts as a two-scissile-bond linkage facilitating nucleophilic addition and cofactor-free decarboxylation. The chain length of nucleophilic acceptors vies with bond cleavage sites at either N-O or O-S accounting for N-formimidoylation or N-iminoacetylation. The resultant product is no longer sensitive to aminoglycoside-modifying enzymes, a strategy that antibiotic-producing species employ to counter drug resistance in competing species.
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Affiliation(s)
- Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chin-Yuan Chang
- Department of Biology Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - I-Wen Lo
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Liang Chen
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Zhe-Chong Wang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Chitose Maruyama
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan
- Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan
| | - Yoshimitsu Hamano
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan.
- Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan.
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
- Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.
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16
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Anderson FM, Visser ND, Amses KR, Hodgins-Davis A, Weber AM, Metzner KM, McFadden MJ, Mills RE, O’Meara MJ, James TY, O’Meara TR. Candida albicans selection for human commensalism results in substantial within-host diversity without decreasing fitness for invasive disease. PLoS Biol 2023; 21:e3001822. [PMID: 37205709 PMCID: PMC10234564 DOI: 10.1371/journal.pbio.3001822] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 06/01/2023] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
Candida albicans is a frequent colonizer of human mucosal surfaces as well as an opportunistic pathogen. C. albicans is remarkably versatile in its ability to colonize diverse host sites with differences in oxygen and nutrient availability, pH, immune responses, and resident microbes, among other cues. It is unclear how the genetic background of a commensal colonizing population can influence the shift to pathogenicity. Therefore, we examined 910 commensal isolates from 35 healthy donors to identify host niche-specific adaptations. We demonstrate that healthy people are reservoirs for genotypically and phenotypically diverse C. albicans strains. Using limited diversity exploitation, we identified a single nucleotide change in the uncharacterized ZMS1 transcription factor that was sufficient to drive hyper invasion into agar. We found that SC5314 was significantly different from the majority of both commensal and bloodstream isolates in its ability to induce host cell death. However, our commensal strains retained the capacity to cause disease in the Galleria model of systemic infection, including outcompeting the SC5314 reference strain during systemic competition assays. This study provides a global view of commensal strain variation and within-host strain diversity of C. albicans and suggests that selection for commensalism in humans does not result in a fitness cost for invasive disease.
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Affiliation(s)
- Faith M. Anderson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Noelle D. Visser
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Kevin R. Amses
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea Hodgins-Davis
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Alexandra M. Weber
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Katura M. Metzner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Michael J. McFadden
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ryan E. Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Matthew J. O’Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Timothy Y. James
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Teresa R. O’Meara
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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17
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Application of the Mutant Libraries for Candida albicans Functional Genomics. Int J Mol Sci 2022; 23:ijms232012307. [PMID: 36293157 PMCID: PMC9603287 DOI: 10.3390/ijms232012307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Candida albicans is a typical opportunistic pathogen in humans that causes serious health risks in clinical fungal infections. The construction of mutant libraries has made remarkable developments in the study of C. albicans molecular and cellular biology with the ongoing advancements of gene editing, which include the application of CRISPR-Cas9 and novel high-efficient transposon. Large-scale genetic screens and genome-wide functional analysis accelerated the investigation of new genetic regulatory mechanisms associated with the pathogenicity and resistance to environmental stress in C. albicans. More importantly, sensitivity screening based on C. albicans mutant libraries is critical for the target identification of novel antifungal compounds, which leads to the discovery of Sec7p, Tfp1p, Gwt1p, Gln4p, and Erg11p. This review summarizes the main types of C. albicans mutant libraries and interprets their applications in morphogenesis, biofilm formation, fungus-host interactions, antifungal drug resistance, and target identification.
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18
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An Adjuvant-Based Approach Enables the Use of Dominant HYG and KAN Selectable Markers in Candida albicans. mSphere 2022; 7:e0034722. [PMID: 35968963 PMCID: PMC9429937 DOI: 10.1128/msphere.00347-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida albicans is a pathobiont fungus that can colonize multiple niches in the human body but is also a frequent cause of both mucosal and systemic disease. Despite its clinical importance, a paucity of dominant selectable markers has hindered the development of tools for genetic manipulation of the species. One factor limiting the utilization of dominant selectable markers is that C. albicans is inherently more resistant to antibiotics used for selection in other species. Here, we showed that the inclusion of suitable adjuvants can enable the use of two aminoglycoside antibiotics, hygromycin B and G418, for positive selection in C. albicans. Combining these antibiotics with an adjuvant, such as quinine or molybdate, substantially suppressed the background growth of C. albicans, thereby enabling transformants expressing CaHygB or CaKan markers to be readily identified. We verified that these adjuvants were not mutagenic to C. albicans and that CaHygB and CaKan markers were orthogonal to the existing marker NAT1/SAT1, and so provide complementary tools for the genetic manipulation of C. albicans strains. Our study also established that adjuvant-based approaches can enable the use of selectable markers that would otherwise be limited by high background growth from susceptible cells. IMPORTANCE Only a single dominant selectable marker has been widely adopted for use in the opportunistic fungal pathogen Candida albicans. This is in stark contrast to model fungi where a repertoire of dominant markers is readily available. A limiting factor for C. albicans has been the high levels of background growth obtained with multiple antibiotics, thereby limiting their use for distinguishing cells that carry an antibiotic-resistance gene from those that do not. Here, we demonstrated that the inclusion of adjuvants can reduce background growth and enable the robust use of both CaHygB and CaKan markers for genetic selection in C. albicans.
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19
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D’Spain S, Andrade PI, Brockman NE, Fu J, Wickes BL. Agrobacterium tumefaciens-Mediated Transformation of Candida glabrata. J Fungi (Basel) 2022; 8:596. [PMID: 35736079 PMCID: PMC9225417 DOI: 10.3390/jof8060596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
The use of broad-spectrum antimycotic therapy, immunosuppressive therapy, and indwelling medical devices has contributed to the increased frequency of mucosal and systemic infections caused by Candida glabrata. A major concern for C. glabrata and other Candida spp. infections is the increase in drug resistance. To address these issues, additional molecular tools for the study of C. glabrata are needed. In this investigation, we developed an Agrobacterium tumefaciens transformation system for C. glabrata. A number of parameters were investigated to determine their effect on transformation frequency, and then an optimized protocol was developed. The optimal conditions for the transformation of C. glabrata were found to be an infection incubation temperature of 26 °C, 0.2 mM acetosyringone in both induction media and co-culture media, 0.7% agar concentration, and a multiplicity of infection of 50:1 A. tumefaciens to C. glabrata. Importantly, the frequency of multiple integrations was low (5%), demonstrating that A. tumefaciens generally integrates at single sites in C. glabrata, which is consistent with other fungal A. tumefaciens transformation systems. The development of this system in C. glabrata adds another tool for the molecular manipulation of this increasingly important fungal pathogen.
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Affiliation(s)
| | | | | | | | - Brian L. Wickes
- The Department of Microbiology, Immunology, and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA; (S.D.); (P.I.A.); (N.E.B.); (J.F.)
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20
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Rapid Hypothesis Testing in Candida albicans Clinical Isolates Using a Cloning-Free, Modular, and Recyclable System for CRISPR-Cas9 Mediated Mutant and Revertant Construction. Microbiol Spectr 2022; 10:e0263021. [PMID: 35612314 PMCID: PMC9241802 DOI: 10.1128/spectrum.02630-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As increasing evidence emerges that interstrain genetic diversity among Candida albicans clinical isolates underpins phenotypic variation compared to the reference isolate SC5314, new genetic tools are required to interrogate gene function across strain backgrounds. Here, the SAT1-flipper plasmid was reengineered to contain a C. albicans codon optimized hygromycin B resistance gene (CaHygB). Cassettes were PCR-amplified from both SAT1-flipper and CaHygB-flipper plasmids using primers with homologous sequences flanking target genes of interest to serve as repair templates. Ribonucleoprotein (RNP) complexes containing proprietary CRISPR RNAs (crRNAs), universal transactivating CRISPR RNA (tracrRNA), and Cas9 protein were assembled in vitro and transformed, along with both repair templates, by electroporation into C. albicans. Homozygous deletion of the ADE2 gene results in red-pigmented colonies and this gene was used to validate our approach. Both in SC5314 and a variety of clinical isolates (529L, JS15, SJCA1, TW1), homozygous gene targeting was nearly 100% when plating on media containing nourseothricin and hygromycin B with transformation efficiencies exceeding 104 homozygous deletion mutants per μg of DNA. A gene reversion system was also employed with plasmids pDUP3 and pDIS3 engineered to contain the ADH1 terminator and an overlap extension PCR-mediated approach combined with CRISPR-Cas9 targeting at the NEUT5 neutral locus. A variety of single or compound mutants (Δ/Δals3, Δ/Δcph1 Δ/Δefg1, Δ/Δece1) and their revertant strains were constructed and phenotypically validated by a variety of assays, including biofilm formation, hyphal growth, and macrophage IL-1β response. Thus, we have established a cloning-free, modular system for highly efficient homozygous gene deletion and reversion in diverse isolates. IMPORTANCE Recently, phenotypic heterogeneity in Candida albicans isolates has been recognized as an underappreciated factor contributing to gene diversification and broadly impacts strain-to-strain antifungal resistance, fitness, and pathogenicity. We have designed a cloning-free genetic system for rapid gene deletion and reversion in C. albicans clinical isolates that interlaces established recyclable genetic systems with CRISPR-Cas9 technology. The SAT1-flipper was reengineered to contain CaHygB encoding resistance to hygromycin B. Using a modular PCR-mediated approach coupled with in vitro ribonucleoprotein assembly with commercial reagents, both SAT1- and CaHygB-flipper cassettes were simultaneously integrated at loci with high efficiency (104 transformants per μg DNA) and upward of 99% homozygous gene targeting across a collection of diverse isolates of various anatomical origin. Revertant strains were constructed by overlap extension PCR with CRISPR-Cas9 targeted integration at the NEUT5 locus. Thus, this facile system will aid in unraveling the genetic factors contributing to the complexity of intraspecies diversity.
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21
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Lemberg C, Martinez de San Vicente K, Fróis-Martins R, Altmeier S, Tran VDT, Mertens S, Amorim-Vaz S, Rai LS, d’Enfert C, Pagni M, Sanglard D, LeibundGut-Landmann S. Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation. PLoS Pathog 2022; 18:e1010012. [PMID: 35404986 PMCID: PMC9041809 DOI: 10.1371/journal.ppat.1010012] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 04/26/2022] [Accepted: 03/17/2022] [Indexed: 12/19/2022] Open
Abstract
As part of the human microbiota, the fungus Candida albicans colonizes the oral cavity and other mucosal surfaces of the human body. Commensalism is tightly controlled by complex interactions of the fungus and the host to preclude fungal elimination but also fungal overgrowth and invasion, which can result in disease. As such, defects in antifungal T cell immunity render individuals susceptible to oral thrush due to interrupted immunosurveillance of the oral mucosa. The factors that promote commensalism and ensure persistence of C. albicans in a fully immunocompetent host remain less clear. Using an experimental model of C. albicans oral colonization in mice we explored fungal determinants of commensalism in the oral cavity. Transcript profiling of the oral isolate 101 in the murine tongue tissue revealed a characteristic metabolic profile tailored to the nutrient poor conditions in the stratum corneum of the epithelium where the fungus resides. Metabolic adaptation of isolate 101 was also reflected in enhanced nutrient acquisition when grown on oral mucosa substrates. Persistent colonization of the oral mucosa by C. albicans also correlated inversely with the capacity of the fungus to induce epithelial cell damage and to elicit an inflammatory response. Here we show that these immune evasive properties of isolate 101 are explained by a strong attenuation of a number of virulence genes, including those linked to filamentation. De-repression of the hyphal program by deletion or conditional repression of NRG1 abolished the commensal behaviour of isolate 101, thereby establishing a central role of this factor in the commensal lifestyle of C. albicans in the oral niche of the host. The oral microbiota represents an important part of the human microbiota and includes several hundreds to several thousands of bacterial and fungal species. One of the most prominent fungus colonizing the oral cavity is the yeast Candida albicans. While the presence of C. albicans usually remains unnoticed, the fungus can under certain circumstances cause lesions on the lining of the mouth referred to as oral thrush or contribute to other common oral diseases such as caries. Maintaining C. albicans commensalism in the oral mucosa is therefore of utmost importance for oral health and overall wellbeing. While overt fungal growth and disease is limited by immunosurveillance mechanisms during homeostasis, C. albicans strives to survive and evades elimination from the host. Here, we show that while commensalism in the oral cavity is characterized by a restricted fungal virulence and hyphal program, enforcing filamentation in a commensal isolate is sufficient for driving pathogenicity and fungus-induced inflammation in the oral mucosa thwarting persistent colonization. Our results further support a critical role for specialized nutrient acquisition allowing the fungus to thrive in the nutrient poor environment of the squamous epithelium. Together, this work revealed key determinants of C. albicans commensalism in the oral niche.
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Affiliation(s)
- Christina Lemberg
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Kontxi Martinez de San Vicente
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Ricardo Fróis-Martins
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Simon Altmeier
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Van Du T. Tran
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sarah Mertens
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Sara Amorim-Vaz
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Laxmi Shanker Rai
- Institut Pasteur, Université de Paris, INRAE, USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Christophe d’Enfert
- Institut Pasteur, Université de Paris, INRAE, USC2019, Unité Biologie et Pathogénicité Fongiques, Paris, France
| | - Marco Pagni
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Salomé LeibundGut-Landmann
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
- * E-mail:
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22
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Deciphering the Mrr1/Mdr1 Pathway in Azole Resistance of Candida auris. Antimicrob Agents Chemother 2022; 66:e0006722. [PMID: 35343781 DOI: 10.1128/aac.00067-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Candida auris is an emerging yeast pathogen with a remarkable ability to develop antifungal resistance, in particular to fluconazole and other azoles. Azole resistance in C. auris was shown to result from different mechanisms, such as mutations in the target gene ERG11 or gain-of-function (GOF) mutations in the transcription factor TAC1b and overexpression of the drug transporter Cdr1. The roles of the transcription factor Mrr1 and of the drug transporter Mdr1 in azole resistance is still unclear. Previous works showed that deletion of MRR1 or MDR1 had no or little impact on azole susceptibility of C. auris. However, an amino acid substitution in Mrr1 (N647T) was identified in most C. auris isolates of clade III that were fluconazole resistant. This study aimed at investigating the role of the transcription factor Mrr1 in azole resistance of C. auris. While the MRR1N647T mutation was always concomitant to hot spot ERG11 mutations, MRR1 deletion in one of these isolates only resulted in a modest decrease of azole MICs. However, introduction of the MRR1N647T mutation in an azole-susceptible C. auris isolate from another clade with wild-type MRR1 and ERG11 alleles resulted in significant increase of fluconazole and voriconazole MICs. We demonstrated that this MRR1 mutation resulted in reduced azole susceptibility via upregulation of the drug transporter MDR1 and not CDR1. In conclusion, this work demonstrates that the Mrr1-Mdr1 axis may contribute to C. auris azole resistance by mechanisms that are independent from ERG11 mutations and from CDR1 upregulation.
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23
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Wang Y, Zhou J, Zou Y, Chen X, Liu L, Qi W, Huang X, Chen C, Liu NN. Fungal commensalism modulated by a dual-action phosphate transceptor. Cell Rep 2022; 38:110293. [PMID: 35081357 DOI: 10.1016/j.celrep.2021.110293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/01/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023] Open
Abstract
Successful host colonization by fungi in fluctuating niches requires response and adaptation to multiple environmental stresses. However, our understanding about how fungal species thrive in the gastrointestinal (GI) ecosystem by combing multifaceted nutritional stress with respect to homeostatic host-commensal interactions is still in its infancy. Here, we discover that depletion of the phosphate transceptor Pho84 across multiple fungal species encountered a substantial cost in gastrointestinal colonization. Mechanistically, Pho84 enhances the gastrointestinal commensalism via a dual-action activity, coordinating both phosphate uptake and TOR activation by induction of the transcriptional regulator Try4 and downstream commensalism-related transcription. As such, Pho84 promotes Candida albicans commensalism, but this does not translate into enhanced pathogenicity. Thus, our study uncovers a specific nutrient-dependent dual-action regulatory pathway for Pho84 on fungal commensalism.
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Affiliation(s)
- Yuanyuan Wang
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China; The University of Chinese Academy of Sciences, Beijing, China; The Nanjing Unicorn Academy of Innovation, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Nanjing 211135, China
| | - Jia Zhou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yun Zou
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China; The University of Chinese Academy of Sciences, Beijing, China; The Nanjing Unicorn Academy of Innovation, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Nanjing 211135, China
| | - Xiaoqing Chen
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China; The University of Chinese Academy of Sciences, Beijing, China
| | - Lin Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wanjun Qi
- Division of Infectious Diseases, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA
| | - Xinhua Huang
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Changbin Chen
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China; The Nanjing Unicorn Academy of Innovation, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Nanjing 211135, China.
| | - Ning-Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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24
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Bravo Ruiz G, Lorenz A. Genetic Transformation of Candida auris via Homology-Directed Repair Using a Standard Lithium Acetate Protocol. Methods Mol Biol 2022; 2517:95-110. [PMID: 35674948 DOI: 10.1007/978-1-0716-2417-3_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Reverse genetics is a particularly powerful tool in non-model organisms with known whole-genome sequences enabling the characterization of gene and, thus, protein function via a mutant phenotype. Reverse genetic approaches require genetic manipulation techniques which often need to be specifically developed for non-model organisms; this can be fraught with difficulties. Here, we describe a genetic transformation protocol for the recently emerged human pathogen Candida auris to target the integration of DNA constructs into genomic locations via homology-directed repair using long flanking homologous sequences (>1 kb). We detail the generation of DNA constructs for gene deletion with dominant drug resistance markers via fusion PCR, the transformation of these constructs into chemically competent C. auris cells, and the confirmation of correct integration by PCR. This strategy can be adapted to deliver DNA constructs other than deletion cassettes, including promoter exchanges and protein tags.
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Affiliation(s)
- Gustavo Bravo Ruiz
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK.
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25
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Forward and reverse genetic dissection of morphogenesis identifies filament-competent Candida auris strains. Nat Commun 2021; 12:7197. [PMID: 34893621 PMCID: PMC8664941 DOI: 10.1038/s41467-021-27545-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022] Open
Abstract
Candida auris is an emerging healthcare-associated pathogen of global concern. Recent reports have identified C. auris isolates that grow in cellular aggregates or filaments, often without a clear genetic explanation. To investigate the regulation of C. auris morphogenesis, we applied an Agrobacterium-mediated transformation system to all four C. auris clades. We identified aggregating mutants associated with disruption of chitin regulation, while disruption of ELM1 produced a polarized, filamentous growth morphology. We developed a transiently expressed Cas9 and sgRNA system for C. auris that significantly increased targeted transformation efficiency across the four C. auris clades. Using this system, we confirmed the roles of C. auris morphogenesis regulators. Morphogenic mutants showed dysregulated chitinase expression, attenuated virulence, and altered antifungal susceptibility. Our findings provide insights into the genetic regulation of aggregating and filamentous morphogenesis in C. auris. Furthermore, the genetic tools described here will allow for efficient manipulation of the C. auris genome. Some isolates of the emerging fungal pathogen Candida auris can form cellular aggregates or filaments. Here, Santana and O’Meara use Agrobacterium-mediated transformation and a CRISPR-Cas9 system to identify several genes that regulate C. auris morphogenesis.
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26
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Crunden JL, Diezmann S. Hsp90 interaction networks in fungi-tools and techniques. FEMS Yeast Res 2021; 21:6413543. [PMID: 34718512 PMCID: PMC8599792 DOI: 10.1093/femsyr/foab054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 10/26/2021] [Indexed: 01/01/2023] Open
Abstract
Heat-shock protein 90 (Hsp90) is a central regulator of cellular proteostasis. It stabilizes numerous proteins that are involved in fundamental processes of life, including cell growth, cell-cycle progression and the environmental response. In addition to stabilizing proteins, Hsp90 governs gene expression and controls the release of cryptic genetic variation. Given its central role in evolution and development, it is important to identify proteins and genes that interact with Hsp90. This requires sophisticated genetic and biochemical tools, including extensive mutant collections, suitable epitope tags, proteomics approaches and Hsp90-specific pharmacological inhibitors for chemogenomic screens. These usually only exist in model organisms, such as the yeast Saccharomyces cerevisiae. Yet, the importance of other fungal species, such as Candida albicans and Cryptococcus neoformans, as serious human pathogens accelerated the development of genetic tools to study their virulence and stress response pathways. These tools can also be exploited to map Hsp90 interaction networks. Here, we review tools and techniques for Hsp90 network mapping available in different fungi and provide a summary of existing mapping efforts. Mapping Hsp90 networks in fungal species spanning >500 million years of evolution provides a unique vantage point, allowing tracking of the evolutionary history of eukaryotic Hsp90 networks.
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Affiliation(s)
- Julia L Crunden
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stephanie Diezmann
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
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27
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Uthayakumar D, Sharma J, Wensing L, Shapiro RS. CRISPR-Based Genetic Manipulation of Candida Species: Historical Perspectives and Current Approaches. Front Genome Ed 2021; 2:606281. [PMID: 34713231 PMCID: PMC8525362 DOI: 10.3389/fgeed.2020.606281] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/09/2020] [Indexed: 12/26/2022] Open
Abstract
The Candida genus encompasses a diverse group of ascomycete fungi that have captured the attention of the scientific community, due to both their role in pathogenesis and emerging applications in biotechnology; the development of gene editing tools such as CRISPR, to analyze fungal genetics and perform functional genomic studies in these organisms, is essential to fully understand and exploit this genus, to further advance antifungal drug discovery and industrial value. However, genetic manipulation of Candida species has been met with several distinctive barriers to progress, such as unconventional codon usage in some species, as well as the absence of a complete sexual cycle in its diploid members. Despite these challenges, the last few decades have witnessed an expansion of the Candida genetic toolbox, allowing for diverse genome editing applications that range from introducing a single point mutation to generating large-scale mutant libraries for functional genomic studies. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology is among the most recent of these advancements, bringing unparalleled versatility and precision to genetic manipulation of Candida species. Since its initial applications in Candida albicans, CRISPR-Cas9 platforms are rapidly evolving to permit efficient gene editing in other members of the genus. The technology has proven useful in elucidating the pathogenesis and host-pathogen interactions of medically relevant Candida species, and has led to novel insights on antifungal drug susceptibility and resistance, as well as innovative treatment strategies. CRISPR-Cas9 tools have also been exploited to uncover potential applications of Candida species in industrial contexts. This review is intended to provide a historical overview of genetic approaches used to study the Candida genus and to discuss the state of the art of CRISPR-based genetic manipulation of Candida species, highlighting its contributions to deciphering the biology of this genus, as well as providing perspectives for the future of Candida genetics.
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Affiliation(s)
- Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Jehoshua Sharma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Lauren Wensing
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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28
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Xu Y, Lu H, Zhu S, Li WQ, Jiang YY, Berman J, Yang F. Multifactorial Mechanisms of Tolerance to Ketoconazole in Candida albicans. Microbiol Spectr 2021; 9:e0032121. [PMID: 34160280 PMCID: PMC8552639 DOI: 10.1128/spectrum.00321-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/20/2022] Open
Abstract
Candida albicans is a prevalent opportunistic human fungal pathogen for which treatment is limited to only four main classes of antifungal drugs, with the azole and echinocandin classes being used most frequently. Drug tolerance, the ability of some cells to grow slowly in supra-MIC drug concentrations, decreases the number of available treatment options. Here, we investigated factors affecting tolerance and resistance to ketoconazole in C. albicans. We found both temperature and the composition of growth medium significantly affected tolerance with little effect on resistance. In deletion analysis of known efflux pump genes, CDR1 was partially required for azole tolerance, while CDR2 and MDR1 were dispensable. Tolerance also required Hsp90 and calcineurin components; CRZ1, which encodes a transcription factor downstream of calcineurin, was required only partially. Deletion of VMA11, which encodes a vacuolar ATPase subunit, and concanamycin A, a V-ATPase inhibitor, abolished tolerance, indicating the importance of vacuolar energy transactions in tolerance. Thus, tolerance to ketoconazole is regulated by multiple factors, including physiological and genetic mechanisms. IMPORTANCE Due to the ever-expanding range of invasive medical procedures and treatments, invasive fungal infections now pose a serious global threat to many people living in an immunocompromised status. Like humans, fungi are eukaryotic, which significantly limits the number of unique antifungal targets; the current arsenal of antifungal agents is limited to just three frontline drug classes. Additional treatment complexities result from the development of drug tolerance and resistance, which further narrows therapeutic options; however, the difference between tolerance and resistance remains largely unknown. This study demonstrates that tolerance and resistance are regulated by multiple genetic and physiological factors. It is prudent to note that some factors affect tolerance only, while other factors affect both tolerance and resistance. The complex underlying mechanisms of these drug responses are highlighted by the fact that there are both shared and distinct mechanisms that regulate tolerance and resistance.
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Affiliation(s)
- Yi Xu
- Department of Pharmacy, The 960 Hospital of PLA, Jinan, China
| | - Hui Lu
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shuo Zhu
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wan-Qian Li
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuan-ying Jiang
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Feng Yang
- Department of Pharmacology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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29
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Novel ERG11 and TAC1b mutations associated with azole resistance in Candida auris. Antimicrob Agents Chemother 2021; 65:AAC.02663-20. [PMID: 33619054 PMCID: PMC8092887 DOI: 10.1128/aac.02663-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Candida auris is a novel Candida species that has spread in all continents causing nosocomial outbreaks of invasive candidiasis. C. auris has the ability to develop resistance to all antifungal drug classes. Notably, many C. auris isolates are resistant to the azole drug fluconazole, a standard therapy of invasive candidiasis.Azole resistance in C. auris can result from mutations in the azole target gene ERG11 and/or overexpression of the efflux pump Cdr1. TAC1 is a transcription factor controlling CDR1 expression in C. albicans The role of TAC1 homologs in C. auris (TAC1a and TAC1b) remains to be better defined.In this study, we compared sequences of ERG11, TAC1a and TAC1b between a fluconazole-susceptible and five fluconazole-resistant C. auris isolates of clade IV. Among four of the resistant isolates, we identified a similar genotype with concomitant mutations in ERG11 (F444L) and TAC1b (S611P). The simultaneous deletion of tandemly arranged TAC1a/TAC1b resulted in a decrease of minimal inhibitory concentration (MIC) for fluconazole. Introduction of the ERG11 and TAC1b mutations separately and/or combined in the wild-type azole susceptible isolate resulted in a significant increase of azole resistance with a cumulative effect of the two combined mutations. Interestingly, CDR1 expression was not significantly affected by TAC1a/TAC1b deletion or by the presence of the TAC1b S611P mutation, suggesting the existence of Tac1-dependent and Cdr1-independent azole resistance mechanisms.We demonstrated the role of two previously unreported mutations responsible for azole resistance in C. auris, which were a common signature among four azole-resistant isolates of clade IV.
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30
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Demers EG, Stajich JE, Ashare A, Occhipinti P, Hogan DA. Balancing Positive and Negative Selection: In Vivo Evolution of Candida lusitaniae MRR1. mBio 2021; 12:e03328-20. [PMID: 33785623 PMCID: PMC8092287 DOI: 10.1128/mbio.03328-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
The evolution of pathogens in response to selective pressures present during chronic infections can influence their persistence and virulence and the outcomes of antimicrobial therapy. Because subpopulations within an infection can be spatially separated and the host environment can fluctuate, an appreciation of the pathways under selection may be most easily revealed through the analysis of numerous isolates from single infections. Here, we continued our analysis of a set of clonally derived Clavispora (Candida) lusitaniae isolates from a single chronic lung infection with a striking enrichment in the number of alleles of MRR1 Genetic and genomic analyses found evidence for repeated acquisition of gain-of-function mutations that conferred constitutive Mrr1 activity. In the same population, there were multiple alleles with both gain-of-function mutations and secondary suppressor mutations that either attenuated or abolished the constitutive activity, suggesting the presence of counteracting selective pressures. Our studies demonstrated trade-offs between high Mrr1 activity, which confers resistance to the antifungal fluconazole, host factors, and bacterial products through its regulation of MDR1, and resistance to hydrogen peroxide, a reactive oxygen species produced in the neutrophilic environment associated with this infection. This inverse correlation between high Mrr1 activity and hydrogen peroxide resistance was observed in multiple Candida species and in serially collected populations from this individual over 3 years. These data lead us to propose that dynamic or variable selective pressures can be reflected in population genomics and that these dynamics can complicate the drug resistance profile of the population.IMPORTANCE Understanding microbial evolution within patients is critical for managing chronic infections and understanding host-pathogen interactions. Here, our analysis of multiple MRR1 alleles in isolates from a single Clavispora (Candida) lusitaniae infection revealed the selection for both high and low Mrr1 activity. Our studies reveal trade-offs between high Mrr1 activity, which confers resistance to the commonly used antifungal fluconazole, host antimicrobial peptides, and bacterial products, and resistance to hydrogen peroxide. This work suggests that spatial or temporal differences within chronic infections can support a large amount of dynamic and parallel evolution and that Mrr1 activity is under both positive and negative selective pressure to balance different traits that are important for microbial survival.
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Affiliation(s)
- Elora G Demers
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Alix Ashare
- Dartmouth-Hitchcock Medical Center, Section of Pulmonary and Critical Care Medicine, Lebanon, New Hampshire, USA
| | - Patricia Occhipinti
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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31
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Douchi D, Mosey M, Astling DP, Knoshaug EP, Nag A, McGowen J, Laurens LM. Nuclear and chloroplast genome engineering of a productive non-model alga Desmodesmus armatus: Insights into unusual and selective acquisition mechanisms for foreign DNA. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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32
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A conserved regulator controls asexual sporulation in the fungal pathogen Candida albicans. Nat Commun 2020; 11:6224. [PMID: 33277479 PMCID: PMC7718266 DOI: 10.1038/s41467-020-20010-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 11/03/2020] [Indexed: 12/16/2022] Open
Abstract
Transcription factor Rme1 is conserved among ascomycetes and regulates meiosis and pseudohyphal growth in Saccharomyces cerevisiae. The genome of the meiosis-defective pathogen Candida albicans encodes an Rme1 homolog that is part of a transcriptional circuitry controlling hyphal growth. Here, we use chromatin immunoprecipitation and genome-wide expression analyses to study a possible role of Rme1 in C. albicans morphogenesis. We find that Rme1 binds upstream and activates the expression of genes that are upregulated during chlamydosporulation, an asexual process leading to formation of large, spherical, thick-walled cells during nutrient starvation. RME1 deletion abolishes chlamydosporulation in three Candida species, whereas its overexpression bypasses the requirement for chlamydosporulation cues and regulators. RME1 expression levels correlate with chlamydosporulation efficiency across clinical isolates. Interestingly, RME1 displays a biphasic pattern of expression, with a first phase independent of Rme1 function and dependent on chlamydospore-inducing cues, and a second phase dependent on Rme1 function and independent of chlamydospore-inducing cues. Our results indicate that Rme1 plays a central role in chlamydospore development in Candida species.
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33
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Weissman Z, Pinsky M, Donegan RK, Reddi AR, Kornitzer D. Using genetically encoded heme sensors to probe the mechanisms of heme uptake and homeostasis in Candida albicans. Cell Microbiol 2020; 23:e13282. [PMID: 33104284 DOI: 10.1111/cmi.13282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/22/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022]
Abstract
Candida albicans is a major fungal pathogen that can utilise hemin and haemoglobin as iron sources in the iron-scarce host environment. While C. albicans is a heme prototroph, we show here that it can also efficiently utilise external heme as a cellular heme source. Using genetically encoded ratiometric fluorescent heme sensors, we show that heme extracted from haemoglobin and free hemin enter the cells with different kinetics. Heme supplied as haemoglobin is taken up via the Common in Fungal Extracellular Membrane (CFEM) hemophore cascade, and reaches the cytoplasm over several hours, whereas entry of free hemin via CFEM-dependent and independent pathways is much faster, less than an hour. To prevent an influx of extracellular heme from reaching toxic levels in the cytoplasm, the cells deploy Hmx1, a heme oxygenase. Hmx1 was previously suggested to be involved in utilisation of haemoglobin and hemin as iron sources, but we find that it is primarily required to prevent heme toxicity. Taken together, the combination of novel heme sensors with genetic analysis revealed new details of the fungal mechanisms of heme import and homeostasis, necessary to balance the uses of heme as essential cofactor and potential iron source against its toxicity.
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Affiliation(s)
- Ziva Weissman
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine, Technion-I.I.T., Haifa, Israel
| | - Mariel Pinsky
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine, Technion-I.I.T., Haifa, Israel
| | - Rebecca K Donegan
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amit R Reddi
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Daniel Kornitzer
- Department of Molecular Microbiology, B. Rappaport Faculty of Medicine, Technion-I.I.T., Haifa, Israel
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Nemeth T, Papp C, Vagvolgyi C, Chakraborty T, Gacser A. Identification and Characterization of a Neutral Locus for Knock-in Purposes in C. parapsilosis. Front Microbiol 2020; 11:1194. [PMID: 32582114 PMCID: PMC7289963 DOI: 10.3389/fmicb.2020.01194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
Invasive fungal infections caused by Candida species affect approximately 700,000 people worldwide resulting in 300,000 deaths annually. Besides Candida albicans, other members of the genus have gained relevance in the last two decades, including C. parapsilosis whose incidence is particularly high amongst low birth weight neonates. To investigate the virulence properties of this pathogen several techniques have been developed for generating knock-out mutants, however, no target locus for knock-in approaches have been published so far. Here we report CpNEUT5L (N5L), an intergenic locus in C. parapsilosis, and introduce an integrative GatewayTM and a classical ligation based replacement plasmid to target it with. As a proof of principle, we fluorescently tagged laboratory and prototroph strains and established that this locus is also suitable for reintegration purposes. We concluded that GFP-expressing constructs integrated into this region provide strong, homogenous fluorescent signals while alteration of this locus affects neither the growth of the mutants in liquid or on solid media, even in the presence of different stressors, nor their basic virulence properties. Hence, our findings demonstrate that N5L is a highly effective neutral locus for knock-in approaches in C. parapsilosis.
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Affiliation(s)
- Tibor Nemeth
- Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Csaba Papp
- Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Csaba Vagvolgyi
- Department of Microbiology, University of Szeged, Szeged, Hungary
| | | | - Attila Gacser
- Department of Microbiology, University of Szeged, Szeged, Hungary.,MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
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Wang Q, Verma J, Vidan N, Wang Y, Tucey TM, Lo TL, Harrison PF, See M, Swaminathan A, Kuchler K, Tscherner M, Song J, Powell DR, Sopta M, Beilharz TH, Traven A. The YEATS Domain Histone Crotonylation Readers Control Virulence-Related Biology of a Major Human Pathogen. Cell Rep 2020; 31:107528. [PMID: 32320659 DOI: 10.1016/j.celrep.2020.107528] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/31/2020] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
Identification of multiple histone acylations diversifies transcriptional control by metabolism, but their functions are incompletely defined. Here we report evidence of histone crotonylation in the human fungal pathogen Candida albicans. We define the enzymes that regulate crotonylation and show its dynamic control by environmental signals: carbon sources, the short-chain fatty acids butyrate and crotonate, and cell wall stress. Crotonate regulates stress-responsive transcription and rescues C. albicans from cell wall stress, indicating broad impact on cell biology. The YEATS domain crotonylation readers Taf14 and Yaf9 are required for C. albicans virulence, and Taf14 controls gene expression, stress resistance, and invasive growth via its chromatin reader function. Blocking the Taf14 C terminus with a tag reduced virulence, suggesting that inhibiting Taf14 interactions with chromatin regulators impairs function. Our findings shed light on the regulation of histone crotonylation and the functions of the YEATS proteins in eukaryotic pathogen biology and fungal infections.
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Affiliation(s)
- Qi Wang
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Jiyoti Verma
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Nikolina Vidan
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia; Department of Molecular Biology, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Yanan Wang
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Timothy M Tucey
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Tricia L Lo
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Paul F Harrison
- Bioinformatics Platform, Monash University, Clayton 3800 VIC, Australia
| | - Michael See
- Bioinformatics Platform, Monash University, Clayton 3800 VIC, Australia
| | - Angavai Swaminathan
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Karl Kuchler
- Medical University of Vienna, Center for Medical Biochemistry, Max Perutz Labs, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/2, Vienna, Austria
| | - Michael Tscherner
- Medical University of Vienna, Center for Medical Biochemistry, Max Perutz Labs, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/2, Vienna, Austria
| | - Jiangning Song
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Clayton 3800 VIC, Australia
| | - Mary Sopta
- Department of Molecular Biology, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - Traude H Beilharz
- Development and Stem Cells Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia
| | - Ana Traven
- Infection and Immunity Program and the Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 VIC, Australia.
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Two dominant selectable markers for genetic manipulation in Neurospora crassa. Curr Genet 2020; 66:835-847. [PMID: 32152733 DOI: 10.1007/s00294-020-01063-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/11/2022]
Abstract
Neurospora crassa is an excellent model fungus for studies on molecular genetics, biochemistry, physiology, and molecular cell biology. Along with the rapid progress of Neurospora research, new tools facilitating more efficient and accurate genetic analysis are in high demand. Here, we tested whether the dominant selective makers widely used in yeasts are applicable in N. crassa. Among them, we found that the strains of N. crassa are sensitive to the aminoglycoside antibiotics, G418 and nourseothricin. 1000 μg/mL of G418 or 50 μg/mL of nourseothricin is sufficient to inhibit Neurospora growth completely. When the neomycin phosphotransferase gene (neo) used in mammalian cells is expressed, N. crassa shows potent resistance to G418. This establishes G418-resistant marker as a dominant selectable marker to use in N. crassa. Similarly, when the nourseothricin acetyltransferase gene (nat) from Streptomyces noursei is induced by qa-2 promoter in the presence of quinic acid (QA), N. crassa shows potent resistance to nourseothricin. When nat is constitutively expressed by full-length or truncated versions of the promoter from the N. crassa cfp gene (NCU02193), or by the trpC promoter of Aspergillus nidulans, the growth of N. crassa in the presence of nourseothricin is proportional to the expression levels of Nat. Finally, these two markers are used to knock-out wc-2 or al-1 gene from the N. crassa genome. The successful development of these two markers in this study expands the toolbox for N. crassa and very likely for other filamentous fungi as well.
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Yang F, Teoh F, Tan ASM, Cao Y, Pavelka N, Berman J. Aneuploidy Enables Cross-Adaptation to Unrelated Drugs. Mol Biol Evol 2020; 36:1768-1782. [PMID: 31028698 PMCID: PMC6657732 DOI: 10.1093/molbev/msz104] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aneuploidy is common both in tumor cells responding to chemotherapeutic agents and in fungal cells adapting to antifungal drugs. Because aneuploidy simultaneously affects many genes, it has the potential to confer multiple phenotypes to the same cells. Here, we analyzed the mechanisms by which Candida albicans, the most prevalent human fungal pathogen, acquires the ability to survive both chemotherapeutic agents and antifungal drugs. Strikingly, adaptation to both types of drugs was accompanied by the acquisition of specific whole-chromosome aneuploidies, with some aneuploid karyotypes recovered independently and repeatedly from very different drug conditions. Specifically, strains selected for survival in hydroxyurea, an anticancer drug, acquired cross-adaptation to caspofungin, a first-line antifungal drug, and both acquired traits were attributable to trisomy of the same chromosome: loss of trisomy was accompanied by loss of adaptation to both drugs. Mechanistically, aneuploidy simultaneously altered the copy number of most genes on chromosome 2, yet survival in hydroxyurea or caspofungin required different genes and stress response pathways. Similarly, chromosome 5 monosomy conferred increased tolerance to both fluconazole and to caspofungin, antifungals with different mechanisms of action. Thus, the potential for cross-adaptation is not a feature of aneuploidy per se; rather, it is dependent on specific genes harbored on given aneuploid chromosomes. Furthermore, pre-exposure to hydroxyurea increased the frequency of appearance of caspofungin survivors, and hydroxyurea-adapted C. albicans cells were refractory to antifungal drug treatment in a mouse model of systemic candidiasis. This highlights the potential clinical consequences for the management of cancer chemotherapy patients at risk of fungal infections.
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Affiliation(s)
- Feng Yang
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Flora Teoh
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Alrina Shin Min Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yongbing Cao
- Department of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Shanghai TCM-Integrated Institute of Vascular Disease, Shanghai, China
| | - Norman Pavelka
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Judith Berman
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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Caplan T, Lorente-Macías Á, Stogios PJ, Evdokimova E, Hyde S, Wellington MA, Liston S, Iyer KR, Puumala E, Shekhar-Guturja T, Robbins N, Savchenko A, Krysan DJ, Whitesell L, Zuercher WJ, Cowen LE. Overcoming Fungal Echinocandin Resistance through Inhibition of the Non-essential Stress Kinase Yck2. Cell Chem Biol 2020; 27:269-282.e5. [PMID: 31924499 DOI: 10.1016/j.chembiol.2019.12.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 01/12/2023]
Abstract
New strategies are urgently needed to counter the threat to human health posed by drug-resistant fungi. To explore an as-yet unexploited target space for antifungals, we screened a library of protein kinase inhibitors for the ability to reverse resistance of the most common human fungal pathogen, Candida albicans, to caspofungin, a widely used antifungal. This screen identified multiple 2,3-aryl-pyrazolopyridine scaffold compounds capable of restoring caspofungin sensitivity. Using chemical genomic, biochemical, and structural approaches, we established the target for our most potent compound as Yck2, a casein kinase 1 family member. Combination of this compound with caspofungin eradicated drug-resistant C. albicans infection while sparing co-cultured human cells. In mice, genetic depletion of YCK2 caused an ∼3-log10 decline in fungal burden in a model of systemic caspofungin-resistant C. albicans infection. Structural insights and our tool compound's profile in culture support targeting the Yck2 kinase function as a broadly active antifungal strategy.
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Affiliation(s)
- Tavia Caplan
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Álvaro Lorente-Macías
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry Applied to Biomedicine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain
| | - Peter J Stogios
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Center for Structural Genomics of Infectious Diseases (CSGID), Toronto, ON, M5G 1M1, Canada
| | - Elena Evdokimova
- Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Center for Structural Genomics of Infectious Diseases (CSGID), Toronto, ON, M5G 1M1, Canada
| | - Sabrina Hyde
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Melanie A Wellington
- Departments of Pediatrics and Microbiology/Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Sean Liston
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Kali R Iyer
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Emily Puumala
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Tanvi Shekhar-Guturja
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID), Toronto, ON, M5G 1M1, Canada; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Damian J Krysan
- Departments of Pediatrics and Microbiology/Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - William J Zuercher
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.
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Abstract
Antifungal resistance is an inevitable phenomenon when fungal pathogens are exposed to antifungal drugs. These drugs can be grouped in four distinct classes (azoles, candins, polyenes, and pyrimidine analogs) and are used in different clinical settings. Failures in therapy implicate the sequential or combined use of these different drug classes, which can result in some cases in the development of multidrug resistance (MDR). MDR is particularly challenging in the clinic since it drastically reduces possible treatment alternatives. In this study, we report the rapid development of MDR in Candida lusitaniae in a patient, which became resistant to all known antifungal agents used until now in medicine. To understand how MDR developed in C. lusitaniae, whole-genome sequencing followed by comparative genome analysis was undertaken in sequential MDR isolates. This helped to detect all specific mutations linked to drug resistance and explained the different MDR patterns exhibited by the clinical isolates. Multidrug resistance (MDR) has emerged in hospitals due to the use of several agents administered in combination or sequentially to the same individual. We reported earlier MDR in Candida lusitaniae during therapy with amphotericin B (AmB), azoles, and candins. Here, we used comparative genomic approaches between the initial susceptible isolate and 4 other isolates with different MDR profiles. From a total of 18 nonsynonymous single nucleotide polymorphisms (NSS) in genome comparisons with the initial isolate, six could be associated with MDR. One of the single nucleotide polymorphisms (SNPs) occurred in a putative transcriptional activator (MRR1) resulting in a V668G substitution in isolates resistant to azoles and 5-fluorocytosine (5-FC). We demonstrated by genome editing that MRR1 acted by upregulation of MFS7 (a multidrug transporter) in the presence of the V668G substitution. MFS7 itself mediated not only azole resistance but also 5-FC resistance, which represents a novel resistance mechanism for this drug class. Three other distinct NSS occurred in FKS1 (a glucan synthase gene that is targeted by candins) in three candin-resistant isolates. Last, two other NSS in ERG3 and ERG4 (ergosterol biosynthesis) resulting in nonsense mutations were revealed in AmB-resistant isolates, one of which accumulated the two ERG NSS. AmB-resistant isolates lacked ergosterol and exhibited sterol profiles, consistent with ERG3 and ERG4 defects. In conclusion, this genome analysis combined with genetics and metabolomics helped decipher the resistance profiles identified in this clinical case. MDR isolates accumulated six different mutations conferring resistance to all antifungal agents used in medicine. This case study illustrates the capacity of C. lusitaniae to rapidly adapt under drug pressure within the host.
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A new toolkit for gene tagging in Candida albicans containing recyclable markers. PLoS One 2019; 14:e0219715. [PMID: 31295309 PMCID: PMC6622542 DOI: 10.1371/journal.pone.0219715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
Gene manipulation and epitope tagging are essential tools for understanding the molecular function of specific genes. The opportunistic human pathogen Candida albicans is a diploid fungus that utilizes a non-canonical genetic code. Since selection markers available in this organism are scarce, several tools based on recyclable markers have been developed for gene disruption, such as the Clox system. This system relies on the Cre recombinase, which recycles selection markers flanked by loxP sites with high efficiency, facilitating single marker or multi-marker recycling. However, PCR-based modules for epitope tagging, such the pFA-modules, mainly use limited non-recyclable auxotrophic markers. To solve this problem, we have used a Gibson assembly strategy to construct a set of new plasmids where the auxotrophic markers of the pFA vectors were swapped with five recyclable marker modules of the Clox system, enhancing the versatility of the pFA plasmids. This new toolkit, named pFA-Clox, is composed of 36 new vectors for gene disruption and epitope tagging (GFP, 3xGFP, mCherry, 3xHA, 5xmyc and TAP). These plasmids contain the dominant NAT1 marker, as well as URA3, HIS1 and ARG4 cassettes, thereby permitting functional analysis of laboratory strains as well as clinical isolates of C. albicans. In summary, we have adapted the Clox system to the pFA-backbone vectors. Thus, the set of primers used for the amplification of previously published pFA modules can also be utilized in this new pFA-Clox system. Therefore, this new toolkit harbors the advantages of both systems, allowing accelerated gene modification strategies that could reduce time and costs in strain construction for C. albicans.
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Monitoring of Fluconazole and Caspofungin Activity against In Vivo Candida glabrata Biofilms by Bioluminescence Imaging. Antimicrob Agents Chemother 2019; 63:AAC.01555-18. [PMID: 30420485 DOI: 10.1128/aac.01555-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/27/2018] [Indexed: 12/25/2022] Open
Abstract
Candida glabrata can attach to various medical implants and forms thick biofilms despite its inability to switch from yeast to hyphae. The current in vivo C. glabrata biofilm models only provide limited information about colonization and infection and usually require animal sacrifice. To gain real-time information from individual BALB/c mice, we developed a noninvasive imaging technique to visualize C. glabrata biofilms in catheter fragments that were subcutaneously implanted on the back of mice. Bioluminescent C. glabrata reporter strains (luc OPT 7/2/4 and luc OPT 8/1/4), free of auxotrophic markers, expressing a codon-optimized firefly luciferase were generated. A murine subcutaneous model was used to follow real-time in vivo biofilm formation in the presence and absence of fluconazole and caspofungin. The fungal load in biofilms was quantified by CFU counts and by bioluminescence imaging (BLI). C. glabrata biofilms formed within the first 24 h, as documented by the increased number of device-associated cells and elevated bioluminescent signal compared with adhesion at the time of implant. The in vivo model allowed monitoring of the antibiofilm activity of caspofungin against C. glabrata biofilms through bioluminescent imaging from day four after the initiation of treatment. Contrarily, signals emitted from biofilms implanted in fluconazole-treated mice were similar to the light emitted from control-treated mice. This study gives insights into the real-time development of C. glabrata biofilms under in vivo conditions. BLI proved to be a dynamic, noninvasive, and sensitive tool to monitor continuous biofilm formation and activity of antifungal agents against C. glabrata biofilms formed on abiotic surfaces in vivo.
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Development of a Transformation Method for Metschnikowia borealis and other CUG-Serine Yeasts. Genes (Basel) 2019; 10:genes10020078. [PMID: 30678093 PMCID: PMC6409616 DOI: 10.3390/genes10020078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/09/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022] Open
Abstract
Yeasts belonging to the Metschnikowia genus are particularly interesting for the unusual formation of only two needle-shaped ascospores during their mating cycle. Presently, the meiotic process that can lead to only two spores from a diploid zygote is poorly understood. The expression of fluorescent nuclear proteins should allow the meiotic process to be visualized in vivo; however, no large-spored species of Metschnikowia has ever been transformed. Accordingly, we aimed to develop a transformation method for Metschnikowia borealis, a particularly large-spored species of Metschnikowia, with the goal of enabling the genetic manipulations required to study biological processes in detail. Genetic analyses confirmed that M. borealis, and many other Metschnikowia species, are CUG-Ser yeasts. Codon-optimized selectable markers lacking CUG codons were used to successfully transform M. borealis by electroporation and lithium acetate, and transformants appeared to be the result of random integration. Mating experiments confirmed that transformed-strains were capable of generating large asci and undergoing recombination. Finally, random integration was used to transform an additional 21 yeast strains, and all attempts successfully generated transformants. The results provide a simple method to transform many yeasts from an array of different clades and can be used to study or develop many species for various applications.
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Polvi EJ, Veri AO, Liu Z, Hossain S, Hyde S, Kim SH, Tebbji F, Sellam A, Todd RT, Xie JL, Lin ZY, Wong CJ, Shapiro RS, Whiteway M, Robbins N, Gingras AC, Selmecki A, Cowen LE. Functional divergence of a global regulatory complex governing fungal filamentation. PLoS Genet 2019; 15:e1007901. [PMID: 30615616 PMCID: PMC6336345 DOI: 10.1371/journal.pgen.1007901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 01/17/2019] [Accepted: 12/16/2018] [Indexed: 01/17/2023] Open
Abstract
Morphogenetic transitions are prevalent in the fungal kingdom. For a leading human fungal pathogen, Candida albicans, the capacity to transition between yeast and filaments is key for virulence. For the model yeast Saccharomyces cerevisiae, filamentation enables nutrient acquisition. A recent functional genomic screen in S. cerevisiae identified Mfg1 as a regulator of morphogenesis that acts in complex with Flo8 and Mss11 to mediate transcriptional responses crucial for filamentation. In C. albicans, Mfg1 also interacts physically with Flo8 and Mss11 and is critical for filamentation in response to diverse cues, but the mechanisms through which it regulates morphogenesis remained elusive. Here, we explored the consequences of perturbation of Mfg1, Flo8, and Mss11 on C. albicans morphogenesis, and identified functional divergence of complex members. We observed that C. albicans Mss11 was dispensable for filamentation, and that overexpression of FLO8 caused constitutive filamentation even in the absence of Mfg1. Harnessing transcriptional profiling and chromatin immunoprecipitation coupled to microarray analysis, we identified divergence between transcriptional targets of Flo8 and Mfg1 in C. albicans. We also established that Flo8 and Mfg1 cooperatively bind to promoters of key regulators of filamentation, including TEC1, for which overexpression was sufficient to restore filamentation in the absence of Flo8 or Mfg1. To further explore the circuitry through which Mfg1 regulates morphogenesis, we employed a novel strategy to select for mutations that restore filamentation in the absence of Mfg1. Whole genome sequencing of filamentation-competent mutants revealed chromosome 6 amplification as a conserved adaptive mechanism. A key determinant of the chromosome 6 amplification is FLO8, as deletion of one allele blocked morphogenesis, and chromosome 6 was not amplified in evolved lineages for which FLO8 was re-located to a different chromosome. Thus, this work highlights rewiring of key morphogenetic regulators over evolutionary time and aneuploidy as an adaptive mechanism driving fungal morphogenesis. Fungal infections pose a severe burden to human health worldwide. Candida albicans is a leading cause of systemic fungal infections, with mortality rates approaching 40%. One of the key virulence traits of this fungus is its ability to transition between yeast and filamentous forms in response to diverse host-relevant cues. The model yeast Saccharomyces cerevisiae is also capable of filamentous growth in certain conditions, and previous work has identified a key transcriptional complex required for filamentation in both species. However, here we discover that the circuitry governed by this complex in C. albicans is largely distinct from that in the non-pathogenic S. cerevisiae. We also employ a novel selection strategy to perform experimental evolution, identifying chromosome triplication as a mechanism to restore filamentation in a non-filamentous mutant. This work reveals unique circuitry governing a key virulence trait in a leading fungal pathogen, identifying potential therapeutic targets to combat these life-threatening infections.
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Affiliation(s)
- Elizabeth J. Polvi
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Amanda O. Veri
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Zhongle Liu
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Saif Hossain
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Sabrina Hyde
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Sang Hu Kim
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Faiza Tebbji
- Infectious Disease Research Centre, Université Laval, Quebec, Canada
| | - Adnane Sellam
- Infectious Disease Research Centre, Université Laval, Quebec, Canada
| | - Robert T. Todd
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Jinglin L. Xie
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Ontario, Canada
| | - Cassandra J. Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Ontario, Canada
| | - Rebecca S. Shapiro
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | | | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Ontario, Canada
| | - Anna Selmecki
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- * E-mail:
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Lee H, Han C, Lee HW, Park G, Jeon W, Ahn J, Lee H. Development of a promising microbial platform for the production of dicarboxylic acids from biorenewable resources. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:310. [PMID: 30455739 PMCID: PMC6225622 DOI: 10.1186/s13068-018-1310-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND As a sustainable industrial process, the production of dicarboxylic acids (DCAs), used as precursors of polyamides, polyesters, perfumes, plasticizers, lubricants, and adhesives, from vegetable oil has continuously garnered interest. Although the yeast Candida tropicalis has been used as a host for DCA production, additional strains are continually investigated to meet productivity thresholds and industrial needs. In this regard, the yeast Wickerhamiella sorbophila, a potential candidate strain, has been screened. However, the lack of genetic and physiological information for this uncommon strain is an obstacle that merits further research. To overcome this limitation, we attempted to develop a method to facilitate genetic recombination in this strain and produce high amounts of DCAs from methyl laurate using engineered W. sorbophila. RESULTS In the current study, we first developed efficient genetic engineering tools for the industrial application of W. sorbophila. To increase homologous recombination (HR) efficiency during transformation, the cell cycle of the yeast was synchronized to the S/G2 phase using hydroxyurea. The HR efficiency at POX1 and POX2 loci increased from 56.3% and 41.7%, respectively, to 97.9% in both cases. The original HR efficiency at URA3 and ADE2 loci was nearly 0% during the early stationary and logarithmic phases of growth, and increased to 4.8% and 25.6%, respectively. We used the developed tools to construct W. sorbophila UHP4, in which β-oxidation was completely blocked. The strain produced 92.5 g/l of dodecanedioic acid (DDDA) from methyl laurate over 126 h in 5-l fed-batch fermentation, with a productivity of 0.83 g/l/h. CONCLUSIONS Wickerhamiella sorbophila UHP4 produced more DDDA methyl laurate than C. tropicalis. Hence, we demonstrated that W. sorbophila is a powerful microbial platform for vegetable oil-based DCA production. In addition, by using the developed genetic engineering tools, this emerging yeast could be used for the production of a variety of fatty acid derivatives, such as fatty alcohols, fatty aldehydes, and ω-hydroxy fatty acids.
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Affiliation(s)
- Heeseok Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113 Republic of Korea
| | - Changpyo Han
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Hyeok-Won Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Gyuyeon Park
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113 Republic of Korea
| | - Wooyoung Jeon
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
| | - Hongweon Lee
- Biotechnology Process Engineering Center, Korean Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do 28116 Republic of Korea
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Veri AO, Miao Z, Shapiro RS, Tebbji F, O’Meara TR, Kim SH, Colazo J, Tan K, Vyas VK, Whiteway M, Robbins N, Wong KH, Cowen LE. Tuning Hsf1 levels drives distinct fungal morphogenetic programs with depletion impairing Hsp90 function and overexpression expanding the target space. PLoS Genet 2018; 14:e1007270. [PMID: 29590106 PMCID: PMC5873724 DOI: 10.1371/journal.pgen.1007270] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/22/2018] [Indexed: 12/24/2022] Open
Abstract
The capacity to respond to temperature fluctuations is critical for microorganisms to survive within mammalian hosts, and temperature modulates virulence traits of diverse pathogens. One key temperature-dependent virulence trait of the fungal pathogen Candida albicans is its ability to transition from yeast to filamentous growth, which is induced by environmental cues at host physiological temperature. A key regulator of temperature-dependent morphogenesis is the molecular chaperone Hsp90, which has complex functional relationships with the transcription factor Hsf1. Although Hsf1 controls global transcriptional remodeling in response to heat shock, its impact on morphogenesis remains unknown. Here, we establish an intriguing paradigm whereby overexpression or depletion of C. albicans HSF1 induces morphogenesis in the absence of external cues. HSF1 depletion compromises Hsp90 function, thereby driving filamentation. HSF1 overexpression does not impact Hsp90 function, but rather induces a dose-dependent expansion of Hsf1 direct targets that drives overexpression of positive regulators of filamentation, including Brg1 and Ume6, thereby bypassing the requirement for elevated temperature during morphogenesis. This work provides new insight into Hsf1-mediated environmentally contingent transcriptional control, implicates Hsf1 in regulation of a key virulence trait, and highlights fascinating biology whereby either overexpression or depletion of a single cellular regulator induces a profound developmental transition. For human pathogens, the capacity to respond to elevated temperature is required for survival, with elevated temperature in the form of fever as a conserved host response to defend against infection. One of the leading fungal pathogens of humans in Candida albicans, which is capable of growing in both a yeast and filamentous state. The ability to transition between these forms is a key virulence trait, and one that is highly temperature-dependent. A pivotal regulator of filamentous growth is the temperature-responsive molecular chaperone Hsp90, which has complex relationships with the transcription factor Hsf1. Although Hsf1 regulates changes in gene expression in response to heat shock, its impact on morphogenesis remains unknown. Here, we uncover an intriguing phenomenon whereby overexpression or depletion of C. albicans HSF1 induces morphogenesis. We observe that HSF1 depletion compromises Hsp90 function, thereby driving filamentation. In contrast, HSF1 overexpression induces a dose-dependent expansion of its transcriptional targets that drives overexpression of positive regulators of filamentous growth. This work illuminates novel mechanisms through which tuning the levels of an environmentally contingent transcription factor drives a key developmental program.
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Affiliation(s)
- Amanda O. Veri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Zhengqiang Miao
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Rebecca S. Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Faiza Tebbji
- Infectious Disease Research Centre, Université Laval, Quebec City, Quebec, Canada
| | - Teresa R. O’Meara
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sang Hu Kim
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Juan Colazo
- Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Valmik K. Vyas
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Malcolm Whiteway
- Department of Biology, Concordia University, Montréal, Quebec, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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46
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FKS2 and FKS3 Genes of Opportunistic Human Pathogen Candida albicans Influence Echinocandin Susceptibility. Antimicrob Agents Chemother 2018; 62:AAC.02299-17. [PMID: 29358288 DOI: 10.1128/aac.02299-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/09/2018] [Indexed: 12/27/2022] Open
Abstract
Candida albicans, a prevailing opportunistic fungal pathogen of humans, has a diploid genome containing three homologous FKS genes that are evolutionarily conserved. One of these, the essential gene FKS1, encodes the catalytic subunit of glucan synthase, which is the target of echinocandin drugs and also serves as a site of drug resistance. The other two glucan synthase-encoding genes, FKS2 and FKS3, are also expressed, but their roles in resistance are considered unimportant. However, we report here that expression of FKS1 is upregulated in strains lacking either FKS2 or FKS3 Furthermore, in contrast to what is observed in heterozygous FKS1 deletion strains, cells lacking FKS2 or FKS3 contain increased amounts of cell wall glucan, are more resistant to echinocandin drugs, and consistently are tolerant to cell wall-damaging agents. Our data indicate that C. albicansFKS2 and FKS3 can act as negative regulators of FKS1, thereby influencing echinocandin susceptibility.
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Kim S, Nguyen QB, Wolyniak MJ, Frechette G, Lehman CR, Fox BK, Sundstrom P. Release of transcriptional repression through the HCR promoter region confers uniform expression of HWP1 on surfaces of Candida albicans germ tubes. PLoS One 2018; 13:e0192260. [PMID: 29438403 PMCID: PMC5810986 DOI: 10.1371/journal.pone.0192260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/19/2018] [Indexed: 12/31/2022] Open
Abstract
The mechanisms that fungi use to co-regulate subsets of genes specifically associated with morphogenic states represent a basic unsolved problem in fungal biology. Candida albicans is an important model of fungal differentiation both for rapid interconversion between yeast and hyphal growth forms and for white/opaque switching mechanisms. The Sundstrom lab is interested in mechanisms regulating hypha-specific expression of adhesin genes that are critical for C. albicans hyphal growth phenotypes and pathogenicity. Early studies on hypha-specific genes such as HWP1 and ALS3 reported 5’ intergenic regions that are larger than those typically found in an average promoter and are associated with hypha-specific expression. In the case of HWP1, activation and repression involves a 368 bp region, denoted the HWP1 control region (HCR), located 1410 bp upstream of its transcription start site. In previous work we showed that HCR confers developmental regulation to a heterologous ENO1 promoter, indicating that HCR by itself contains sufficient information to couple gene expression to morphology. Here we show that the activation and repression mediated by HCR are localized to distinct HCR regions that are targeted by the transcription factors Nrg1p and Efg1p. The finding that Efg1p mediates both repression via HCR under yeast morphological conditions and activation conditions positions Efg1p as playing a central role in coupling HWP1 expression to morphogenesis through the HCR region. These localization studies revealed that the 120 terminal base pairs of HCR confer Efg1p-dependent repressive activity in addition to the Nrg1p repressive activity mediated by DNA upstream of this subregion. The 120 terminal base pair subregion of HCR also contained an initiation site for an HWP1 transcript that is specific to yeast growth conditions (HCR-Y) and may function in the repression of downstream DNA. The detection of an HWP1 mRNA isoform specific to hyphal growth conditions (HWP1-H) showed that morphology-specific mRNA isoforms occur under both yeast and hyphal growth conditions. Similar results were found at the ALS3 locus. Taken together, these results, suggest that the long 5’ intergenic regions upstream of hypha-specific genes function in generating mRNA isoforms that are important for morphology-specific gene expression. Additional complexity in the HWP1 promoter involving HCR-independent activation was discovered by creating a strain lacking HCR that exhibited variable HWP1 expression during hyphal growth conditions. These results show that while HCR is important for ensuring uniform HWP1 expression in cell populations, HCR independent expression also exists. Overall, these results elucidate HCR-dependent mechanisms for coupling HWP1-dependent gene expression to morphology uniformly in cell populations and prompt the hypothesis that mRNA isoforms may play a role in coupling gene expression to morphology in C. albicans.
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Affiliation(s)
- Samin Kim
- Department of Microbiology and Immunology, Microbiology and Molecular Pathogenesis Program, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Quoc Bao Nguyen
- Department of Microbiology and Immunology, Microbiology and Molecular Pathogenesis Program, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Michael J. Wolyniak
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, Virginia, United States of America
| | - Gregory Frechette
- Department of Microbiology and Immunology, Microbiology and Molecular Pathogenesis Program, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Christian R. Lehman
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, Virginia, United States of America
| | - Brandon K. Fox
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, Virginia, United States of America
| | - Paula Sundstrom
- Department of Microbiology and Immunology, Microbiology and Molecular Pathogenesis Program, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail:
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Shapiro RS, Chavez A, Porter CBM, Hamblin M, Kaas CS, DiCarlo JE, Zeng G, Xu X, Revtovich AV, Kirienko NV, Wang Y, Church GM, Collins JJ. A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nat Microbiol 2018; 3:73-82. [PMID: 29062088 PMCID: PMC5832965 DOI: 10.1038/s41564-017-0043-0] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/15/2017] [Indexed: 11/09/2022]
Abstract
Candida albicans is the leading cause of fungal infections; yet, complex genetic interaction analysis remains cumbersome in this diploid pathogen. Here, we developed a CRISPR-Cas9-based 'gene drive array' platform to facilitate efficient genetic analysis in C. albicans. In our system, a modified DNA donor molecule acts as a selfish genetic element, replaces the targeted site and propagates to replace additional wild-type loci. Using mating-competent C. albicans haploids, each carrying a different gene drive disabling a gene of interest, we are able to create diploid strains that are homozygous double-deletion mutants. We generate double-gene deletion libraries to demonstrate this technology, targeting antifungal efflux and biofilm adhesion factors. We screen these libraries to identify virulence regulators and determine how genetic networks shift under diverse conditions. This platform transforms our ability to perform genetic interaction analysis in C. albicans and is readily extended to other fungal pathogens.
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Affiliation(s)
- Rebecca S Shapiro
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Alejandro Chavez
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, 10032, NY, USA
| | - Caroline B M Porter
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Meagan Hamblin
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Christian S Kaas
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Expression Technologies 2, Novo Nordisk A/S, Maaloev, 2760, Denmark
| | - James E DiCarlo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA
| | - Guisheng Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology & Research, 61 Biopolis Drive (Proteos), Singapore, 138673, Singapore
| | - Xiaoli Xu
- Institute of Molecular and Cell Biology, Agency for Science, Technology & Research, 61 Biopolis Drive (Proteos), Singapore, 138673, Singapore
| | | | | | - Yue Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology & Research, 61 Biopolis Drive (Proteos), Singapore, 138673, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117549, Singapore
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA.
| | - James J Collins
- Department of Biological Engineering, Institute for Medical Engineering and Science, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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49
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Niikura H, Maruyama C, Ogasawara Y, Shin-Ya K, Dairi T, Hamano Y. Functional analysis of methyltransferases participating in streptothricin-related antibiotic biosynthesis. J Biosci Bioeng 2017; 125:148-154. [PMID: 29029816 DOI: 10.1016/j.jbiosc.2017.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/05/2017] [Accepted: 09/14/2017] [Indexed: 10/18/2022]
Abstract
Streptothricin (ST) and its related compounds produced by Streptomyces strains are broad-spectrum antibiotics that consist of carbamoylated d-gulosamine, amino-acid side chain, and streptolidine lactam moieties. BD-12, a streptothricin-related antibiotic, has a glycine-derived side chain and two N-methyl groups, whereas ST-F carrying the l-β-lysine side chain has no methyl group. In our previous studies, we identified and characterized the BD-12 and ST biosynthetic gene clusters. Here we report the functional analysis of two methyltransferase genes (orf 6 and orf 13) in the BD-12 biosynthetic gene cluster. Combinatorial biosynthesis using these two methyltransferase genes and the ST biosynthetic gene cluster resulted in the production of three methylated forms of ST-F. Among them, N,N'-dimethyl-ST-F, a novel compound generated in the present study, showed bacteria-specific antibiotic activities, although ST-F exhibits antibiotic activities against both prokaryotes and eukaryotes. Our findings also demonstrated that the orf 6 and orf 13 genes are responsible for the N-methylations of the amide bonds in the streptolidine lactam and in the amino-acid side chain linkage, respectively, and that N-methyl modification of the streptolidine lactam confers resistance in part against an ST hydrolase, SttH.
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Affiliation(s)
- Haruka Niikura
- Department of Bioscience, Fukui Prefectural University, Yoshida-Gun, Fukui 910-1195, Japan
| | - Chitose Maruyama
- Department of Bioscience, Fukui Prefectural University, Yoshida-Gun, Fukui 910-1195, Japan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan; The Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience, Fukui Prefectural University, Yoshida-Gun, Fukui 910-1195, Japan.
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50
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Xie JL, Bohovych I, Wong EOY, Lambert JP, Gingras AC, Khalimonchuk O, Cowen LE, Leach MD. Ydj1 governs fungal morphogenesis and stress response, and facilitates mitochondrial protein import via Mas1 and Mas2. MICROBIAL CELL 2017; 4:342-361. [PMID: 29082232 PMCID: PMC5657825 DOI: 10.15698/mic2017.10.594] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mitochondria underpin metabolism, bioenergetics, signalling, development and cell death in eukaryotes. Most of the ~1,000 yeast mitochondrial proteins are encoded in the nucleus and synthesised as precursors in the cytosol, with mitochondrial import facilitated by molecular chaperones. Here, we focus on the Hsp40 chaperone Ydj1 in the fungal pathogen Candida albicans, finding that it is localised to both the cytosol and outer mitochondrial membrane, and is required for cellular stress responses and for filamentation, a key virulence trait. Mapping the Ydj1 protein interaction network highlighted connections with co-chaperones and regulators of filamentation. Furthermore, the mitochondrial processing peptidases Mas1 and Mas2 were highly enriched for interaction with Ydj1. Additional analysis demonstrated that loss of MAS1, MAS2 or YDJ1 perturbs mitochondrial morphology and function. Deletion of YDJ1 impairs import of Su9, a protein that is cleaved to a mature form by Mas1 and Mas2. Thus, we highlight a novel role for Ydj1 in cellular morphogenesis, stress responses, and mitochondrial import in the fungal kingdom.
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Affiliation(s)
- Jinglin L Xie
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Iryna Bohovych
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Erin O Y Wong
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA.,Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA.,Fred & Pamela Buffett Cancer Center, Omaha, NE 68198, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Michelle D Leach
- Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
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