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Znaidi S, van Wijlick L, Hernández‐Cervantes A, Sertour N, Desseyn J, Vincent F, Atanassova R, Gouyer V, Munro CA, Bachellier‐Bassi S, Dalle F, Jouault T, Bougnoux M, d'Enfert C. Systematic gene overexpression in Candida albicans identifies a regulator of early adaptation to the mammalian gut. Cell Microbiol 2018; 20:e12890. [PMID: 29998470 PMCID: PMC6220992 DOI: 10.1111/cmi.12890] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/28/2018] [Accepted: 06/28/2018] [Indexed: 12/12/2022]
Abstract
Candida albicans is part of the human gastrointestinal (GI) microbiota. To better understand how C. albicans efficiently establishes GI colonisation, we competitively challenged growth of 572 signature-tagged strains (~10% genome coverage), each conditionally overexpressing a single gene, in the murine gut. We identified CRZ2, a transcription factor whose overexpression and deletion respectively increased and decreased early GI colonisation. Using clues from genome-wide expression and gene-set enrichment analyses, we found that the optimal activity of Crz2p occurs under hypoxia at 37°C, as evidenced by both phenotypic and transcriptomic analyses following CRZ2 genetic perturbation. Consistent with early colonisation of the GI tract, we show that CRZ2 overexpression confers resistance to acidic pH and bile salts, suggesting an adaptation to the upper sections of the gut. Genome-wide location analyses revealed that Crz2p directly modulates the expression of many mannosyltransferase- and cell-wall protein-encoding genes, suggesting a link with cell-wall function. We show that CRZ2 overexpression alters cell-wall phosphomannan abundance and increases sensitivity to tunicamycin, suggesting a role in protein glycosylation. Our study reflects the powerful use of gene overexpression as a complementary approach to gene deletion to identify relevant biological pathways involved in C. albicans interaction with the host environment.
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Affiliation(s)
- Sadri Znaidi
- Institut Pasteur, INRAUnité Biologie et Pathogénicité FongiquesParisFrance
- Institut Pasteur de Tunis, University of Tunis El ManarLaboratoire de Microbiologie Moléculaire, Vaccinologie et Développement BiotechnologiqueTunisTunisia
| | - Lasse van Wijlick
- Institut Pasteur, INRAUnité Biologie et Pathogénicité FongiquesParisFrance
| | | | - Natacha Sertour
- Institut Pasteur, INRAUnité Biologie et Pathogénicité FongiquesParisFrance
| | - Jean‐Luc Desseyn
- Lille Inflammation Research International Center, UMR 995 InsermUniversité Lille 2, Faculté de MédecineLilleFrance
| | | | | | - Valérie Gouyer
- Lille Inflammation Research International Center, UMR 995 InsermUniversité Lille 2, Faculté de MédecineLilleFrance
| | - Carol A. Munro
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical SciencesUniversity of AberdeenAberdeenUK
| | | | - Frédéric Dalle
- UMR 1347Université de BourgogneDijonFrance
- Centre Hospitalier UniversitaireService de Parasitologie MycologieDijonFrance
| | - Thierry Jouault
- Lille Inflammation Research International Center, UMR 995 InsermUniversité Lille 2, Faculté de MédecineLilleFrance
| | - Marie‐Elisabeth Bougnoux
- Institut Pasteur, INRAUnité Biologie et Pathogénicité FongiquesParisFrance
- Laboratoire de Parasitologie‐Mycologie, Service de Microbiologie, Hôpital Necker‐Enfants MaladesUniversité Paris Descartes, Faculté de MédecineParisFrance
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152
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Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans. mBio 2018; 9:mBio.02048-18. [PMID: 30377286 PMCID: PMC6212825 DOI: 10.1128/mbio.02048-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Comprehensive understanding of an organism requires that we understand the contributions of most, if not all, of its genes. Classical genetic approaches to this issue have involved systematic deletion of each gene in the genome, with comprehensive sets of mutants available only for very-well-studied model organisms. We took a different approach, harnessing the power of in vivo transposition coupled with deep sequencing to identify >500,000 different mutations, one per cell, in the prevalent human fungal pathogen Candida albicans and to map their positions across the genome. The transposition approach is efficient and less labor-intensive than classic approaches. Here, we describe the production and analysis (aided by machine learning) of a large collection of mutants and the comprehensive identification of 1,610 C. albicans genes that are essential for growth under standard laboratory conditions. Among these C. albicans essential genes, we identify those that are also essential in two distantly related model yeasts as well as those that are conserved in all four major human fungal pathogens and that are not conserved in the human genome. This list of genes with functions important for the survival of the pathogen provides a good starting point for the development of new antifungal drugs, which are greatly needed because of the emergence of fungal pathogens with elevated resistance and/or tolerance of the currently limited set of available antifungal drugs. Knowing the full set of essential genes for a given organism provides important information about ways to promote, and to limit, its growth and survival. For many non-model organisms, the lack of a stable haploid state and low transformation efficiencies impede the use of conventional approaches to generate a genome-wide comprehensive set of mutant strains and the identification of the genes essential for growth. Here we report on the isolation and utilization of a highly stable haploid derivative of the human pathogenic fungus Candida albicans, together with a modified heterologous transposon and machine learning (ML) analysis method, to predict the degree to which all of the open reading frames are required for growth under standard laboratory conditions. We identified 1,610 C. albicans essential genes, including 1,195 with high “essentiality confidence” scores, thereby increasing the number of essential genes (currently 66 in the Candida Genome Database) by >20-fold and providing an unbiased approach to determine the degree of confidence in the determination of essentiality. Among the genes essential in C. albicans were 602 genes also essential in the model budding and fission yeasts analyzed by both deletion and transposon mutagenesis. We also identified essential genes conserved among the four major human pathogens C. albicans, Aspergillus fumigatus, Cryptococcus neoformans, and Histoplasma capsulatum and highlight those that lack homologs in humans and that thus could serve as potential targets for the design of antifungal therapies.
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153
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Candida albicans gains azole resistance by altering sphingolipid composition. Nat Commun 2018; 9:4495. [PMID: 30374049 PMCID: PMC6206040 DOI: 10.1038/s41467-018-06944-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/03/2018] [Indexed: 12/31/2022] Open
Abstract
Fungal infections by drug-resistant Candida albicans pose a global public health threat. However, the pathogen’s diploid genome greatly hinders genome-wide investigations of resistance mechanisms. Here, we develop an efficient piggyBac transposon-mediated mutagenesis system using stable haploid C. albicans to conduct genome-wide genetic screens. We find that null mutants in either gene FEN1 or FEN12 (encoding enzymes for the synthesis of very-long-chain fatty acids as precursors of sphingolipids) exhibit resistance to fluconazole, a first-line antifungal drug. Mass-spectrometry analyses demonstrate changes in cellular sphingolipid composition in both mutants, including substantially increased levels of several mannosylinositolphosphoceramides with shorter fatty-acid chains. Treatment with fluconazole induces similar changes in wild-type cells, suggesting a natural response mechanism. Furthermore, the resistance relies on a robust upregulation of sphingolipid biosynthesis genes. Our results shed light into the mechanisms underlying azole resistance, and the new transposon-mediated mutagenesis system should facilitate future genome-wide studies of C. albicans. The fungal pathogen Candida albicans is diploid, which hinders genome-wide studies. Here, Gao et al. present a piggyBac transposon-mediated mutagenesis system using stable haploid C. albicans strains, and use it to identify genes and mechanisms underlying azole resistance.
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154
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Abstract
Aspergillus nidulans has long-been used as a model organism to gain insights into the genetic basis of asexual and sexual developmental processes both in other members of the genus Aspergillus, and filamentous fungi in general. Paradigms have been established concerning the regulatory mechanisms of conidial development. However, recent studies have shown considerable genome divergence in the fungal kingdom, questioning the general applicability of findings from Aspergillus, and certain longstanding evolutionary theories have been questioned. The phylogenetic distribution of key regulatory elements of asexual reproduction in A. nidulans was investigated in a broad taxonomic range of fungi. This revealed that some proteins were well conserved in the Pezizomycotina (e.g. AbaA, FlbA, FluG, NsdD, MedA, and some velvet proteins), suggesting similar developmental roles. However, other elements (e.g. BrlA) had a more restricted distribution solely in the Eurotiomycetes, and it appears that the genetic control of sporulation seems to be more complex in the aspergilli than in some other taxonomic groups of the Pezizomycotina. The evolution of the velvet protein family is discussed based on the history of expansion and contraction events in the early divergent fungi. Heterologous expression of the A. nidulans abaA gene in Monascus ruber failed to induce development of complete conidiophores as seen in the aspergilli, but did result in increased conidial production. The absence of many components of the asexual developmental pathway from members of the Saccharomycotina supports the hypothesis that differences in the complexity of their spore formation is due in part to the increased diversity of the sporulation machinery evident in the Pezizomycotina. Investigations were also made into the evolution of sex and sexuality in the aspergilli. MAT loci were identified from the heterothallic Aspergillus (Emericella) heterothallicus and Aspergillus (Neosartorya) fennelliae and the homothallic Aspergillus pseudoglaucus (=Eurotium repens). A consistent architecture of the MAT locus was seen in these and other heterothallic aspergilli whereas much variation was seen in the arrangement of MAT loci in homothallic aspergilli. This suggested that it is most likely that the common ancestor of the aspergilli exhibited a heterothallic breeding system. Finally, the supposed prevalence of asexuality in the aspergilli was examined. Investigations were made using A. clavatus as a representative 'asexual' species. It was possible to induce a sexual cycle in A. clavatus given the correct MAT1-1 and MAT1-2 partners and environmental conditions, with recombination confirmed utilising molecular markers. This indicated that sexual reproduction might be possible in many supposedly asexual aspergilli and beyond, providing general insights into the nature of asexuality in fungi.
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155
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Schoeters F, Munro CA, d'Enfert C, Van Dijck P. A High-Throughput Candida albicans Two-Hybrid System. mSphere 2018; 3:e00391-18. [PMID: 30135223 PMCID: PMC6106057 DOI: 10.1128/msphere.00391-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 07/24/2018] [Indexed: 12/18/2022] Open
Abstract
Candida albicans is a human fungal pathogen that does not follow the universal codon usage, as it translates the CUG codon into serine rather than leucine. This makes it difficult to study protein-protein interactions using the standard yeast two-hybrid (Y2H) system in the model organism Saccharomyces cerevisiae Due to the lack of adapted tools, only a small number of protein-protein interactions (PPIs) have been detected or studied using C. albicans-optimized tools despite the importance of PPIs to understand cell biology. However, with the sequencing of the whole genome of C. albicans, the availability of an ORFeome collection containing 5,099 open reading frames (ORFs) in Gateway-adapted donor vectors, and the creation of a Gateway-compatible C. albicans-specific two-hybrid (C2H) system, it became possible to study protein-protein interactions on a larger scale using C. albicans itself as the model organism. Erroneous translations are hereby eliminated compared to using the S. cerevisiae Y2H system. Here, we describe the technical adaptations and the first application of the C2H system for a high-throughput screen, thus making it possible to screen thousands of PPIs at once in C. albicans itself. This first, small-scale high-throughput screen, using Pho85 as a bait protein against 1,646 random prey proteins, yielded one interacting partner (Pcl5). The interaction found with the high-throughput setup was further confirmed with a low-throughput C2H experiment and with a coimmunoprecipitation (co-IP) experiment.IMPORTANCECandida albicans is a major fungal pathogen, and due to the rise of fungal infections and emerging resistance to the limited antifungals available, it is important to develop novel and more specific antifungals. Protein-protein interactions (PPIs) can be applied as very specific drug targets. However, because of the aberrant codon usage of C. albicans, the traditional yeast two-hybrid system in Saccharomyces cerevisiae is difficult to use, and only a limited number of PPIs have been described in C. albicans To overcome this, a C. albicans two-hybrid (C2H) system was developed in 2010. The current work describes, for the first time, the application of the C2H system in a high-throughput setup. We hereby show the usefulness of the C2H system to investigate and detect PPIs in C. albicans, making it possible to further elucidate protein networks in C. albicans, which has the potential to lead to the development of novel antifungals which specifically disrupt PPIs important for virulence.
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Affiliation(s)
- Floris Schoeters
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- KU Leuven Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Leuven, Belgium
| | - Carol A Munro
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Aberdeen, United Kingdom
| | - Christophe d'Enfert
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris, France
| | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- KU Leuven Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Leuven, Belgium
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156
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Legrand M, Bachellier-Bassi S, Lee KK, Chaudhari Y, Tournu H, Arbogast L, Boyer H, Chauvel M, Cabral V, Maufrais C, Nesseir A, Maslanka I, Permal E, Rossignol T, Walker LA, Zeidler U, Znaidi S, Schoeters F, Majgier C, Julien RA, Ma L, Tichit M, Bouchier C, Van Dijck P, Munro CA, d’Enfert C. Generating genomic platforms to study Candida albicans pathogenesis. Nucleic Acids Res 2018; 46:6935-6949. [PMID: 29982705 PMCID: PMC6101633 DOI: 10.1093/nar/gky594] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/19/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
The advent of the genomic era has made elucidating gene function on a large scale a pressing challenge. ORFeome collections, whereby almost all ORFs of a given species are cloned and can be subsequently leveraged in multiple functional genomic approaches, represent valuable resources toward this endeavor. Here we provide novel, genome-scale tools for the study of Candida albicans, a commensal yeast that is also responsible for frequent superficial and disseminated infections in humans. We have generated an ORFeome collection composed of 5099 ORFs cloned in a Gateway™ donor vector, representing 83% of the currently annotated coding sequences of C. albicans. Sequencing data of the cloned ORFs are available in the CandidaOrfDB database at http://candidaorfeome.eu. We also engineered 49 expression vectors with a choice of promoters, tags and selection markers and demonstrated their applicability to the study of target ORFs transferred from the C. albicans ORFeome. In addition, the use of the ORFeome in the detection of protein-protein interaction was demonstrated. Mating-compatible strains as well as Gateway™-compatible two-hybrid vectors were engineered, validated and used in a proof of concept experiment. These unique and valuable resources should greatly facilitate future functional studies in C. albicans and the elucidation of mechanisms that underlie its pathogenicity.
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Affiliation(s)
- Mélanie Legrand
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Sophie Bachellier-Bassi
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Keunsook K Lee
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Yogesh Chaudhari
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Hélène Tournu
- VIB-KU Leuven Center for Microbiology, Leuven 3001, Belgium
- Laboratory of Molecular Cell Biology, KU Leuven, Leuven 3001, Belgium
| | - Laurence Arbogast
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Hélène Boyer
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Murielle Chauvel
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Vitor Cabral
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris 75015, France
| | - Corinne Maufrais
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP CNRS-Paris 75015, France
| | - Audrey Nesseir
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris 75015, France
| | - Irena Maslanka
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Emmanuelle Permal
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Tristan Rossignol
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Louise A Walker
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Ute Zeidler
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Sadri Znaidi
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Floris Schoeters
- VIB-KU Leuven Center for Microbiology, Leuven 3001, Belgium
- Laboratory of Molecular Cell Biology, KU Leuven, Leuven 3001, Belgium
| | - Charlotte Majgier
- Modul-Bio, Parc Scientifique Luminy Biotech II, Marseille 13009, France
| | - Renaud A Julien
- Modul-Bio, Parc Scientifique Luminy Biotech II, Marseille 13009, France
| | - Laurence Ma
- Institut Pasteur-Biomics Pole-CITECH-Paris 75015, France
| | - Magali Tichit
- Institut Pasteur-Biomics Pole-CITECH-Paris 75015, France
| | | | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Leuven 3001, Belgium
- Laboratory of Molecular Cell Biology, KU Leuven, Leuven 3001, Belgium
| | - Carol A Munro
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Christophe d’Enfert
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
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157
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Allert S, Förster TM, Svensson CM, Richardson JP, Pawlik T, Hebecker B, Rudolphi S, Juraschitz M, Schaller M, Blagojevic M, Morschhäuser J, Figge MT, Jacobsen ID, Naglik JR, Kasper L, Mogavero S, Hube B. Candida albicans-Induced Epithelial Damage Mediates Translocation through Intestinal Barriers. mBio 2018; 9:e00915-18. [PMID: 29871918 PMCID: PMC5989070 DOI: 10.1128/mbio.00915-18] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 01/31/2023] Open
Abstract
Life-threatening systemic infections often occur due to the translocation of pathogens across the gut barrier and into the bloodstream. While the microbial and host mechanisms permitting bacterial gut translocation are well characterized, these mechanisms are still unclear for fungal pathogens such as Candida albicans, a leading cause of nosocomial fungal bloodstream infections. In this study, we dissected the cellular mechanisms of translocation of C. albicans across intestinal epithelia in vitro and identified fungal genes associated with this process. We show that fungal translocation is a dynamic process initiated by invasion and followed by cellular damage and loss of epithelial integrity. A screen of >2,000 C. albicans deletion mutants identified genes required for cellular damage of and translocation across enterocytes. Correlation analysis suggests that hypha formation, barrier damage above a minimum threshold level, and a decreased epithelial integrity are required for efficient fungal translocation. Translocation occurs predominantly via a transcellular route, which is associated with fungus-induced necrotic epithelial damage, but not apoptotic cell death. The cytolytic peptide toxin of C. albicans, candidalysin, was found to be essential for damage of enterocytes and was a key factor in subsequent fungal translocation, suggesting that transcellular translocation of C. albicans through intestinal layers is mediated by candidalysin. However, fungal invasion and low-level translocation can also occur via non-transcellular routes in a candidalysin-independent manner. This is the first study showing translocation of a human-pathogenic fungus across the intestinal barrier being mediated by a peptide toxin.IMPORTANCECandida albicans, usually a harmless fungus colonizing human mucosae, can cause lethal bloodstream infections when it manages to translocate across the intestinal epithelium. This can result from antibiotic treatment, immune dysfunction, or intestinal damage (e.g., during surgery). However, fungal processes may also contribute. In this study, we investigated the translocation process of C. albicans using in vitro cell culture models. Translocation occurs as a stepwise process starting with invasion, followed by epithelial damage and loss of epithelial integrity. The ability to secrete candidalysin, a peptide toxin deriving from the hyphal protein Ece1, is key: C. albicans hyphae, secreting candidalysin, take advantage of a necrotic weakened epithelium to translocate through the intestinal layer.
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Affiliation(s)
- Stefanie Allert
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
| | - Toni M Förster
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
| | | | - Jonathan P Richardson
- Mucosal & Salivary Biology Division, Dental Institute, King's College London, London, United Kingdom
| | - Tony Pawlik
- Research Group Microbial Immunology, Hans-Knöll-Institute, Jena, Germany
| | - Betty Hebecker
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
- Research Group Microbial Immunology, Hans-Knöll-Institute, Jena, Germany
- Aberdeen Fungal Group, MRC Centre for Medical Mycology, University of Aberdeen, Aberdeen, United Kingdom
| | - Sven Rudolphi
- Research Group Microbial Immunology, Hans-Knöll-Institute, Jena, Germany
| | - Marc Juraschitz
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
| | - Martin Schaller
- Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Mariana Blagojevic
- Mucosal & Salivary Biology Division, Dental Institute, King's College London, London, United Kingdom
| | - Joachim Morschhäuser
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Marc Thilo Figge
- Research Group Applied Systems Biology, Hans-Knöll-Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller-University Jena, Jena, Germany
| | - Ilse D Jacobsen
- Research Group Microbial Immunology, Hans-Knöll-Institute, Jena, Germany
- Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Julian R Naglik
- Mucosal & Salivary Biology Division, Dental Institute, King's College London, London, United Kingdom
| | - Lydia Kasper
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
| | - Selene Mogavero
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Hans-Knöll-Institute, Jena, Germany
- Institute of Microbiology, Friedrich-Schiller-University Jena, Jena, Germany
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158
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Motaung TE. Cryptococcus neoformans mutant screening: a genome-scale's worth of function discovery. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2018.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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159
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Su C, Yu J, Lu Y. Hyphal development in Candida albicans from different cell states. Curr Genet 2018; 64:1239-1243. [PMID: 29796903 DOI: 10.1007/s00294-018-0845-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 01/01/2023]
Abstract
Candida albicans is an important opportunistic fungal pathogen of immunocompromised individuals. The ability to switch between yeast, pseudohyphal, and hyphal growth forms (polymorphism) is one of the most investigated virulence attributes of C. albicans. The usual method for inducing hypha formation in the lab is by diluting cells from a saturated culture into fresh medium at 37 °C. The molecular mechanism at action under these conditions has been previously investigated. C. albicans can also form hyphae in growing cells without dilution. The ability of C. albicans to form hyphae in different cell states facilitates the fungus to adapt varied host environments during infection. A recent study by Su et al. uncovered the molecular mechanism for how C. albicans develops hyphae under the condition without inoculation. N-Acetylglucosamine (GlcNAc) stimulates filamentation in log phase cells through transcriptional down-regulation of NRG1, the major repressor of hyphal development. Instead of cAMP-PKA pathway, GlcNAc sensor Ngs1 is responsible for this process. Ngs1 binds to GlcNAc to activate its N-acetyltransferase activity, leading to the induction of BRG1 expression. The increased level of BRG1 could repress NRG1 transcripts, resulting in hyphal growth. Hyphal development in log phase cells induced by serum or neutral pH also requires activation of BRG1 to down-regulate NRG1 transcription. Therefore, hyphal induction under the condition without inoculation is trigged by Brg1-mediated removal of Nrg1 inhibition. This review describes our current understanding of the molecular mechanism underlying hyphal development, the best studied virulence factor in C. albicans. These will expand the number of potential drug targets with novel modes of action for anti-virulence therapeutics.
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Affiliation(s)
- Chang Su
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Yu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yang Lu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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160
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Mount HO, Revie NM, Todd RT, Anstett K, Collins C, Costanzo M, Boone C, Robbins N, Selmecki A, Cowen LE. Global analysis of genetic circuitry and adaptive mechanisms enabling resistance to the azole antifungal drugs. PLoS Genet 2018; 14:e1007319. [PMID: 29702647 PMCID: PMC5922528 DOI: 10.1371/journal.pgen.1007319] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/19/2018] [Indexed: 12/20/2022] Open
Abstract
Invasive fungal infections caused by the pathogen Candida albicans have transitioned from a rare curiosity to a major cause of human mortality. This is in part due to the emergence of resistance to the limited number of antifungals available to treat fungal infections. Azoles function by targeting the biosynthesis of ergosterol, a key component of the fungal cell membrane. Loss-of-function mutations in the ergosterol biosynthetic gene ERG3 mitigate azole toxicity and enable resistance that depends upon fungal stress responses. Here, we performed a genome-wide synthetic genetic array screen in Saccharomyces cerevisiae to map ERG3 genetic interactors and uncover novel circuitry important for azole resistance. We identified nine genes that enabled erg3-mediated azole resistance in the model yeast and found that only two of these genes had a conserved impact on resistance in C. albicans. Further, we screened a C. albicans homozygous deletion mutant library and identified 13 genes for which deletion enhances azole susceptibility. Two of the genes, RGD1 and PEP8, were also important for azole resistance acquired by diverse mechanisms. We discovered that loss of function of retrograde transport protein Pep8 overwhelms the functional capacity of the stress response regulator calcineurin, thereby abrogating azole resistance. To identify the mechanism through which the GTPase activator protein Rgd1 enables azole resistance, we selected for mutations that restore resistance in strains lacking Rgd1. Whole genome sequencing uncovered parallel adaptive mechanisms involving amplification of both chromosome 7 and a large segment of chromosome 3. Overexpression of a transporter gene on the right portion of chromosome 3, NPR2, was sufficient to enable azole resistance in the absence of Rgd1. Thus, we establish a novel mechanism of adaptation to drug-induced stress, define genetic circuitry underpinning azole resistance, and illustrate divergence in resistance circuitry over evolutionary time. Fungal infections caused by the pathogen Candida albicans pose a serious threat to human health. Treating these infections relies heavily on the azole antifungals, however, resistance to these drugs develops readily demanding novel therapeutic strategies. We performed large-scale systematic screens in both C. albicans and the model yeast Saccharomyces cerevisiae to identify genes that enable azole resistance. Our genome-wide screen in S. cerevisiae identified nine determinants of azole resistance, only two of which were important for resistance in C. albicans. Our screen of C. albicans mutants identified 13 genes for which deletion enhances susceptibility to azoles, including RGD1 and PEP8. We found that loss of Pep8 overwhelms the functional capacity of a key stress response regulator, calcineurin. In contrast, amplification of chromosome 7 and the right portion of chromosome 3 can restore resistance in strains lacking Rgd1, suggesting that Rgd1 may enable azole resistance by inducing genes in these amplified regions. Specifically, overexpression of a gene involved in transport on chromosome 3, NPR2, was sufficient to restore azole resistance in the absence of Rgd1. Thus, we establish novel circuitry important for antifungal drug resistance, and uncover adaptive mechanisms involving genomic plasticity that occur in response to drug induced stress.
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Affiliation(s)
| | - Nicole M. Revie
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Robert T. Todd
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Kaitlin Anstett
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Cathy Collins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, 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, Toronto, Ontario, Canada
- * E-mail:
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161
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Meir J, Hartmann E, Eckstein MT, Guiducci E, Kirchner F, Rosenwald A, LeibundGut-Landmann S, Pérez JC. Identification of Candida albicans regulatory genes governing mucosal infection. Cell Microbiol 2018; 20:e12841. [PMID: 29575428 DOI: 10.1111/cmi.12841] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 12/19/2022]
Abstract
The fungus Candida albicans thrives on a variety of human mucosae, yet the fungal determinants that contribute to fitness on these surfaces remain underexplored. Here, by screening a collection of C. albicans deletion strains in a mouse model of oral infection (oropharyngeal candidiasis), we identify several novel regulatory genes that modulate the fitness of the fungus in this locale. We investigate in detail the interplay between the host mucosa and one of the identified mutants and establish that the C. albicans transcription regulator CUP9 is a key determinant of mucosal colonisation. Deletion of cup9 resulted in the formation of more foci of colonisation and heightened persistence in infected tongues. Furthermore, the cup9 mutant produced longer and denser filaments in the oral mucosa without eliciting an enhanced local immune response. Consistent with its role in oral colonisation, we show that CUP9's top target of regulation is a major effector of Candida's adherence to buccal cells. Finally, we establish that CUP9 also governs the interplay of the fungus with vaginal epithelial cells and has a role in vaginal infections, another common mucosal disease associated with Candida. Thus, our findings reveal a mechanism whereby C. albicans can regulate proliferation on mucosal surfaces.
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Affiliation(s)
- Juliane Meir
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany.,Institute for Molecular Infection Biology, University Würzburg, Würzburg, Germany
| | - Elena Hartmann
- Institute for Pathology, University Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Marie-Therese Eckstein
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany.,Institute for Molecular Infection Biology, University Würzburg, Würzburg, Germany
| | - Eva Guiducci
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Florian Kirchner
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Andreas Rosenwald
- Institute for Pathology, University Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | | | - J Christian Pérez
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany.,Institute for Molecular Infection Biology, University Würzburg, Würzburg, Germany
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162
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Systematic Complex Haploinsufficiency-Based Genetic Analysis of Candida albicans Transcription Factors: Tools and Applications to Virulence-Associated Phenotypes. G3-GENES GENOMES GENETICS 2018; 8:1299-1314. [PMID: 29472308 PMCID: PMC5873919 DOI: 10.1534/g3.117.300515] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genetic interaction analysis is a powerful approach to the study of complex biological processes that are dependent on multiple genes. Because of the largely diploid nature of the human fungal pathogen Candida albicans, genetic interaction analysis has been limited to a small number of large-scale screens and a handful for gene-by-gene studies. Complex haploinsufficiency, which occurs when a strain containing two heterozygous mutations at distinct loci shows a phenotype that is distinct from either of the corresponding single heterozygous mutants, is an expedient approach to genetic interactions analysis in diploid organisms. Here, we describe the construction of a barcoded-library of 133 heterozygous TF deletion mutants and deletion cassettes for designed to facilitate complex haploinsufficiency-based genetic interaction studies of the TF networks in C. albicans. We have characterized the phenotypes of these heterozygous mutants under a broad range of in vitro conditions using both agar-plate and pooled signature tag-based assays. Consistent with previous studies, haploinsufficiency is relative uncommon. In contrast, a set of 12 TFs enriched in mutants with a role in adhesion were found to have altered competitive fitness at early time points in a murine model of disseminated candidiasis. Finally, we characterized the genetic interactions of a set of biofilm related TFs in the first two steps of biofilm formation, adherence and filamentation of adherent cells. The genetic interaction networks at each stage of biofilm formation are significantly different indicating that the network is not static but dynamic.
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163
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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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164
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Su C, Yu J, Sun Q, Liu Q, Lu Y. Hyphal induction under the condition without inoculation in Candida albicans is triggered by Brg1-mediated removal of NRG1 inhibition. Mol Microbiol 2018; 108:410-423. [PMID: 29485686 DOI: 10.1111/mmi.13944] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2018] [Indexed: 12/28/2022]
Abstract
Candida albicans can switch between yeast and hyphae growth forms, which is critical for its pathogenesis. Diluting from saturated cells into fresh medium at 37°C is routinely used to induce hyphae, which depends on the cAMP-PKA pathway-activated transcriptional down-regulation of NRG1 and degradation of Nrg1 protein triggered by inoculation. It is reported that N-acetylglucosamine (GlcNAc), serum or neutral pH could stimulate filamentation in log phase cells, whereas how C. albicans develops hyphae without inoculation remains unknown. Here, we show that NRG1 down-regulation is necessary for hyphal growth under this condition. Instead of cAMP-PKA pathway, GlcNAc sensor Ngs1 is responsible for the down-regulation of NRG1 upon GlcNAc induction in log phase cells through its N-acetyltransferase activity. From a genetic screen, Brg1 is found to be essential for hyphal development without inoculation. Ngs1 binds to BRG1 promoter to induce its expression in GlcNAc. Importantly, constitutively expressed BRG1 induces NRG1 down-regulation even in the absence of GlcNAc or Ngs1. Serum or neutral pH-induced filamentation in log phase cells is also through Brg1-mediated NRG1 down-regulation. Our study provides a molecular mechanism for how C. albicans forms hyphae in different cell states. This flexibility may facilitate C. albicans to adapt varied host environment during infection.
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Affiliation(s)
- Chang Su
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Yu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qiangqiang Sun
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qian Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Lu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
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165
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Dal81 Regulates Expression of Arginine Metabolism Genes in Candida parapsilosis. mSphere 2018; 3:3/2/e00028-18. [PMID: 29564399 PMCID: PMC5853489 DOI: 10.1128/msphere.00028-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 02/08/2018] [Indexed: 01/26/2023] Open
Abstract
Fungi can use a wide variety of nitrogen sources. In the absence of preferred sources such as ammonium, glutamate, and glutamine, secondary sources, including most other amino acids, are used. Expression of the nitrogen utilization pathways is very strongly controlled at the transcriptional level. Here, we investigated the regulation of nitrogen utilization in the pathogenic yeast Candida parapsilosis. We found that the functions of many regulators are conserved with respect to Saccharomyces cerevisiae and other fungi. For example, the core GATA activators GAT1 and GLN3 have a conserved role in nitrogen catabolite repression (NCR). There is one ortholog of GZF3 and DAL80, which represses expression of genes in preferred nitrogen sources. The regulators PUT3 and UGA3 are required for metabolism of proline and γ-aminobutyric acid (GABA), respectively. However, the role of the Dal81 transcription factor is distinctly different. In S. cerevisiae, Dal81 is a positive regulator of acquisition of nitrogen from GABA, allantoin, urea, and leucine, and it is required for maximal induction of expression of the relevant pathway genes. In C. parapsilosis, induction of GABA genes is independent of Dal81, and deleting DAL81 has no effect on acquisition of nitrogen from GABA or allantoin. Instead, Dal81 represses arginine synthesis during growth under preferred nitrogen conditions. IMPORTANCE Utilization of nitrogen by fungi is controlled by nitrogen catabolite repression (NCR). Expression of many genes is switched off during growth on nonpreferred nitrogen sources. Gene expression is regulated through a combination of activation and repression. Nitrogen regulation has been studied best in the model yeast Saccharomyces cerevisiae. We found that although many nitrogen regulators have a conserved function in Saccharomyces species, some do not. The Dal81 transcriptional regulator has distinctly different functions in S. cerevisiae and C. parapsilosis. In the former, it regulates utilization of nitrogen from GABA and allantoin, whereas in the latter, it regulates expression of arginine synthesis genes. Our findings make an important contribution to our understanding of nitrogen regulation in a human-pathogenic fungus.
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166
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Transcription factor network efficiency in the regulation of Candida albicans biofilms: it is a small world. Curr Genet 2018; 64:883-888. [PMID: 29318385 DOI: 10.1007/s00294-018-0804-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 12/29/2017] [Accepted: 01/02/2018] [Indexed: 10/18/2022]
Abstract
Complex biological processes are frequently regulated through networks comprised of multiple signaling pathways, transcription factors, and effector molecules. The identity of specific genes carrying out these functions is usually determined by single mutant genetic analysis. However, to understand how the individual genes/gene products function, it is necessary to determine how they interact with other components of the larger network; one approach to this is to use genetic interaction analysis. The human fungal pathogen Candida albicans regulates biofilm formation through an interconnected set of transcription factor hubs and is, therefore, an example of this type of complex network. Here, we describe experiments and analyses designed to understand how the C. albicans biofilm transcription factor hubs interact and to explore the role of network structure in its overall function. To do so, we analyzed published binding and genetic interaction data to characterize the topology of the network. The hubs are best characterized as a small world network that functions with high efficiency and low robustness (high fragility). Highly efficient networks rapidly transmit perturbations at given nodes to the rest of the network. Consistent with this model, we have found that relatively modest perturbations, such as reduction in the gene dosage of hub transcription factors by one-half, lead to significant alterations in target gene expression and biofilm fitness. C. albicans biofilm formation occurs under very specific environmental conditions and we propose that the fragile, small world structure of the genetic network is part of the mechanism that imposes this stringency.
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167
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Ries LNA, Beattie S, Cramer RA, Goldman GH. Overview of carbon and nitrogen catabolite metabolism in the virulence of human pathogenic fungi. Mol Microbiol 2017; 107:277-297. [PMID: 29197127 DOI: 10.1111/mmi.13887] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 12/12/2022]
Abstract
It is estimated that fungal infections, caused most commonly by Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans, result in more deaths annually than malaria or tuberculosis. It has long been hypothesized the fungal metabolism plays a critical role in virulence though specific nutrient sources utilized by human pathogenic fungi in vivo has remained enigmatic. However, the metabolic utilisation of preferred carbon and nitrogen sources, encountered in a host niche-dependent manner, is known as carbon catabolite and nitrogen catabolite repression (CCR, NCR), and has been shown to be important for virulence. Several sensory and uptake systems exist, including carbon and nitrogen source-specific sensors and transporters, that allow scavenging of preferred nutrient sources. Subsequent metabolic utilisation is governed by transcription factors, whose functions and essentiality differ between fungal species. Furthermore, additional factors exist that contribute to the implementation of CCR and NCR. The role of the CCR and NCR-related factors in virulence varies greatly between fungal species and a substantial gap in knowledge exists regarding specific pathways. Further elucidation of carbon and nitrogen metabolism mechanisms is therefore required in a fungal species- and animal model-specific manner in order to screen for targets that are potential candidates for anti-fungal drug development.
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Affiliation(s)
- Laure Nicolas Annick Ries
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, Ribeirão Preto, São Paulo, 3900, CEP 14049-900, Brazil
| | - Sarah Beattie
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, 74 College Street Remsen 213, Hanover, NH 03755, USA
| | - Robert A Cramer
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, 74 College Street Remsen 213, Hanover, NH 03755, USA
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n°, Ribeirão Preto, São Paulo, CEP 14040903, Brazil
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168
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Romo JA, Pierce CG, Chaturvedi AK, Lazzell AL, McHardy SF, Saville SP, Lopez-Ribot JL. Development of Anti-Virulence Approaches for Candidiasis via a Novel Series of Small-Molecule Inhibitors of Candida albicans Filamentation. mBio 2017; 8:e01991-17. [PMID: 29208749 PMCID: PMC5717394 DOI: 10.1128/mbio.01991-17] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 12/14/2022] Open
Abstract
Candida albicans remains the main etiologic agent of candidiasis, the most common fungal infection and now the third most frequent infection in U.S. hospitals. The scarcity of antifungal agents and their limited efficacy contribute to the unacceptably high morbidity and mortality rates associated with these infections. The yeast-to-hypha transition represents the main virulence factor associated with the pathogenesis of C. albicans infections. In addition, filamentation is pivotal for robust biofilm development, which represents another major virulence factor for candidiasis and further complicates treatment. Targeting pathogenic mechanisms rather than growth represents an attractive yet clinically unexploited approach in the development of novel antifungal agents. Here, we performed large-scale phenotypic screening assays with 30,000 drug-like small-molecule compounds within ChemBridge's DIVERSet chemical library in order to identify small-molecule inhibitors of C. albicans filamentation, and our efforts led to the identification of a novel series of bioactive compounds with a common biaryl amide core structure. The leading compound of this series, N-[3-(allyloxy)-phenyl]-4-methoxybenzamide, was able to prevent filamentation under all liquid and solid medium conditions tested, suggesting that it impacts a common core component of the cellular machinery that mediates hypha formation under different environmental conditions. In addition to filamentation, this compound also inhibited C. albicans biofilm formation. This leading compound also demonstrated in vivo activity in clinically relevant murine models of invasive and oral candidiasis. Overall, our results indicate that compounds within this series represent promising candidates for the development of novel anti-virulence approaches to combat C. albicans infections.IMPORTANCE Since fungi are eukaryotes, there is a limited number of fungus-specific targets and, as a result, the antifungal arsenal is exceedingly small. Furthermore, the efficacy of antifungal treatment is compromised by toxicity and development of resistance. As a consequence, fungal infections carry high morbidity and mortality rates, and there is an urgent but unmet need for novel antifungal agents. One appealing strategy for antifungal drug development is to target pathogenetic mechanisms associated with infection. In Candida albicans, one of the most common pathogenic fungi, morphogenetic transitions between yeast cells and filamentous hyphae represent a key virulence factor associated with the ability of fungal cells to invade tissues, cause damage, and form biofilms. Here, we describe and characterize a novel small-molecule compound capable of inhibiting C. albicans filamentation both in vitro and in vivo; as such, this compound represents a leading candidate for the development of anti-virulence therapies against candidiasis.
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Affiliation(s)
- Jesus A Romo
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Christopher G Pierce
- Department of Biology, University of the Incarnate Word, San Antonio, Texas, USA
| | - Ashok K Chaturvedi
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna L Lazzell
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Stanton F McHardy
- Department of Chemistry and Center for Innovation in Drug Discovery, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Stephen P Saville
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Jose L Lopez-Ribot
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, Texas, USA
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169
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Caspofungin on ARGET-ATRP grafted PHEMA polymers: Enhancement and selectivity of prevention of attachment ofCandida albicans. Biointerphases 2017; 12:05G602. [DOI: 10.1116/1.4986054] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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170
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Rehman L, Su X, Li X, Qi X, Guo H, Cheng H. FreB is involved in the ferric metabolism and multiple pathogenicity-related traits of Verticillium dahliae. Curr Genet 2017; 64:645-659. [PMID: 29177887 DOI: 10.1007/s00294-017-0780-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 10/25/2017] [Accepted: 11/08/2017] [Indexed: 01/31/2023]
Abstract
Ferric reductases are integral membrane proteins involved in the reduction of environmental ferric iron into the biologically available ferrous iron. In the most overwhelming phytopathogenic fungus, Verticillium dahliae, these ferric reductase are not studied in details. In this study we explored the role of FreB gene (VDAG_06616) in the ferric reduction and virulence of V. dahliae by generating the knockout mutants (ΔFreB) and complementary strains (ΔFreB-C) using protoplast transformation. When cultured on media supplemented with FeSO4, FeCl3 and no iron, ΔFreB exhibited significantly reduced growth and spore production especially on media with no iron. Transmembrane ferric reductase activity of ΔFreB was decreased up to 50% than wild type strains (Vd-wt). The activity was fully restored in ΔFreB-C. Meanwhile, the expression levels of other related genes (Frect-4, Frect-5, Frect-6 and Met) were obviously increased in ΔFreB. Compared with the Vd-wt and ΔFreB-C, ΔFreB-1 and ΔFreB-2 were impaired in colony diameter and spore number on different carbon sources (starch, sucrose, galactose and xylose). ΔFreB-1 and ΔFreB-2 were also highly sensitive to oxidative stress as revealed by the plate diffusion assay when 100 µM H2O2 was applied to the fungal culture. When Nicotiana benthamiana plants were inoculated, ΔFreB exhibited less disease symptoms than Vd-wt and ΔFreB-C. In conclusion, the present findings not only indicate that FreB mediates the ferric metabolism and is required for the full virulence in V. dahliae, but would also accelerate future investigation to uncover the pathogenic mechanism of this fungus.
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Affiliation(s)
- Latifur Rehman
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaokang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiliang Qi
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huiming Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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171
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Wofford JD, Park J, McCormick SP, Chakrabarti M, Lindahl PA. Ferric ions accumulate in the walls of metabolically inactivating Saccharomyces cerevisiae cells and are reductively mobilized during reactivation. Metallomics 2017; 8:692-708. [PMID: 27188213 DOI: 10.1039/c6mt00070c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mössbauer and EPR spectra of fermenting yeast cells before and after cell wall (CW) digestion revealed that CWs accumulated iron as cells transitioned from exponential to post-exponential growth. Most CW iron was mononuclear nonheme high-spin (NHHS) Fe(III), some was diamagnetic and some was superparamagnetic. A significant portion of CW Fe was removable by EDTA. Simulations using an ordinary-differential-equations-based model suggested that cells accumulate Fe as they become metabolically inactive. When dormant Fe-loaded cells were metabolically reactivated in Fe-deficient bathophenanthroline disulfonate (BPS)-treated medium, they grew using Fe that had been mobilized from their CWs AND using trace amounts of Fe in the Fe-deficient medium. When grown in Fe-deficient medium, Fe-starved cells contained the lowest cellular Fe concentrations reported for a eukaryotic cell. During metabolic reactivation of Fe-loaded dormant cells, Fe(III) ions in the CWs of these cells were mobilized by reduction to Fe(II), followed by release from the CW and reimport into the cell. BPS short-circuited this process by chelating mobilized and released Fe(II) ions before reimport; the resulting Fe(II)(BPS)3 complex adsorbed on the cell surface. NHHS Fe(II) ions appeared transiently during mobilization, suggesting that these ions were intermediates in this process. In the presence of chelators and at high pH, metabolically inactive cells leached CW Fe; this phenomenon probably differs from metabolic mobilization. The iron regulon, as reported by Fet3p levels, was not expressed during post-exponential conditions; Fet3p was maximally expressed in exponentially growing cells. Decreased expression of the iron regulon and metabolic decline combine to promote CW Fe accumulation.
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Affiliation(s)
- Joshua D Wofford
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA.
| | - Jinkyu Park
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA.
| | - Sean P McCormick
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA.
| | - Mrinmoy Chakrabarti
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA.
| | - Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA. and Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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172
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The Candida albicans TOR-Activating GTPases Gtr1 and Rhb1 Coregulate Starvation Responses and Biofilm Formation. mSphere 2017; 2:mSphere00477-17. [PMID: 29152581 PMCID: PMC5687921 DOI: 10.1128/msphere.00477-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/20/2017] [Indexed: 01/09/2023] Open
Abstract
Candida albicans is the major fungal pathogen of humans and is responsible for a wide range of infections, including life-threatening systemic infections in susceptible hosts. Target of rapamycin complex 1 (TORC1) is an essential regulator of metabolism in this fungus, and components of this complex are under increased investigation as targets for new antifungal drugs. The present study characterized the role of GTR1, encoding a putative GTPase, in TORC1 activation. This study shows that GTR1 encodes a protein required for activation of TORC1 activity in response to amino acids and regulation of nitrogen starvation responses. GTR1 mutants show increased cell-cell adhesion and biofilm formation and increased expression of genes involved in these processes. This study demonstrates that starvation responses and biofilm formation are coregulated by GTR1 and suggests that these responses are linked to compete with the microbiome for space and nutrients. Target of rapamycin complex 1 (TORC1) is an essential regulator of metabolism in eukaryotic cells and in the fungal pathogen Candida albicans regulates morphogenesis and nitrogen acquisition. Gtr1 encodes a highly conserved GTPase that in Saccharomyces cerevisiae regulates nitrogen sensing and TORC1 activation. Here, we characterize the role of C. albicans GTR1 in TORC1 activation and compare it with the previously characterized GTPase Rhb1. A homozygous gtr1/gtr1 mutant exhibited impaired TORC1-mediated phosphorylation of ribosomal protein S6 and increased susceptibility to rapamycin. Overexpression of GTR1 impaired nitrogen starvation-induced filamentous growth, MEP2 expression, and growth in bovine serum albumin as the sole nitrogen source. Both GTR1 and RHB1 were shown to regulate genes involved in ribosome biogenesis, amino acid biosynthesis, and expression of biofilm growth-induced genes. The rhb1/rhb1 mutant exhibited a different pattern of expression of Sko1-regulated genes and increased susceptibility to Congo red and calcofluor white. The homozygous gtr1/gtr1 mutant exhibited enhanced flocculation phenotypes and, similar to the rhb1/rhb1 mutant, exhibited enhanced biofilm formation on plastic surfaces. In summary, Gtr1 and Rhb1 link nutrient sensing and biofilm formation and this connectivity may have evolved to enhance the competitiveness of C. albicans in niches where there is intense competition with other microbes for space and nutrients. IMPORTANCECandida albicans is the major fungal pathogen of humans and is responsible for a wide range of infections, including life-threatening systemic infections in susceptible hosts. Target of rapamycin complex 1 (TORC1) is an essential regulator of metabolism in this fungus, and components of this complex are under increased investigation as targets for new antifungal drugs. The present study characterized the role of GTR1, encoding a putative GTPase, in TORC1 activation. This study shows that GTR1 encodes a protein required for activation of TORC1 activity in response to amino acids and regulation of nitrogen starvation responses. GTR1 mutants show increased cell-cell adhesion and biofilm formation and increased expression of genes involved in these processes. This study demonstrates that starvation responses and biofilm formation are coregulated by GTR1 and suggests that these responses are linked to compete with the microbiome for space and nutrients.
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173
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Böhm L, Torsin S, Tint SH, Eckstein MT, Ludwig T, Pérez JC. The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice. PLoS Pathog 2017; 13:e1006699. [PMID: 29069103 PMCID: PMC5673237 DOI: 10.1371/journal.ppat.1006699] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/06/2017] [Accepted: 10/17/2017] [Indexed: 12/18/2022] Open
Abstract
Many microorganisms that cause systemic, life-threatening infections in humans reside as harmless commensals in our digestive tract. Yet little is known about the biology of these microbes in the gut. Here, we visualize the interface between the human commensal and pathogenic fungus Candida albicans and the intestine of mice, a surrogate host. Because the indigenous mouse microbiota restricts C. albicans settlement, we compared the patterns of colonization in the gut of germ free and antibiotic-treated conventionally raised mice. In contrast to the heterogeneous morphologies found in the latter, we establish that in germ free animals the fungus almost uniformly adopts the yeast cell form, a proxy of its commensal state. By screening a collection of C. albicans transcription regulator deletion mutants in gnotobiotic mice, we identify several genes previously unknown to contribute to in vivo fitness. We investigate three of these regulators—ZCF8, ZFU2 and TRY4—and show that indeed they favor the yeast form over other morphologies. Consistent with this finding, we demonstrate that genetically inducing non-yeast cell morphologies is detrimental to the fitness of C. albicans in the gut. Furthermore, the identified regulators promote adherence of the fungus to a surface covered with mucin and to mucus-producing intestinal epithelial cells. In agreement with this result, histology sections indicate that C. albicans dwells in the murine gut in close proximity to the mucus layer. Thus, our findings reveal a set of regulators that endows C. albicans with the ability to endure in the intestine through multiple mechanisms. The very same microbes that cause life-threatening human diseases are often harmless inhabitants on our mucosal surfaces. Yet the hallmarks of this so-called ‘commensal’ state remain underexplored. In this report we investigate the case of Candida albicans, the most prominent fungal species living in the human intestine but also a common cause of deep-seated, fatal infections. Mice carrying their own natural intact flora are not readily colonized by C. albicans implying a fundamental incompatibility between the indigenous mouse microbiota and this fungus. We explore the patterns of colonization of C. albicans in mice completely devoid of other microbes. We show that the fungus adopts its normal commensal morphology in these animals indicating that this experimental system is a suitable proxy to clearly dissect its commensal lifestyle in vivo. Gaining insights into the mechanisms that sustain the commensal features of C. albicans and other microbes is key to understand—and be able to prevent—what goes awry when these microorganisms invade other tissues and cause disease.
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Affiliation(s)
- Lena Böhm
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany.,Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Sanda Torsin
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany
| | - Su Hlaing Tint
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany
| | - Marie Therese Eckstein
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany.,Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Tobias Ludwig
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany.,Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - J Christian Pérez
- Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany.,Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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174
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Chaillot J, Tebbji F, García C, Wurtele H, Pelletier R, Sellam A. pH-Dependant Antifungal Activity of Valproic Acid against the Human Fungal Pathogen Candida albicans. Front Microbiol 2017; 8:1956. [PMID: 29062309 PMCID: PMC5640775 DOI: 10.3389/fmicb.2017.01956] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/22/2017] [Indexed: 11/20/2022] Open
Abstract
Current antifungal drugs suffer from limitations including toxicity, the emergence of resistance and decreased efficacy at low pH that are typical of human vaginal surfaces. Here, we have shown that the antipsychotic drug valproic acid (VPA) exhibited a strong antifungal activity against both sensitive and resistant Candida albicans in pH condition similar to that encountered in vagina. VPA exerted a strong anti-biofilm activity and attenuated damage of vaginal epithelial cells caused by C. albicans. We also showed that VPA synergizes with the allylamine antifungal, Terbinafine. We undertook a chemogenetic screen to delineate biological processes that underlies VPA-sensitivity in C. albicans and found that vacuole-related genes were required to tolerate VPA. Confocal fluorescence live-cell imaging revealed that VPA alters vacuole integrity and support a model where alteration of vacuoles contributes to the antifungal activity. Taken together, this study suggests that VPA could be used as an effective antifungal against vulvovaginal candidiasis.
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Affiliation(s)
- Julien Chaillot
- Infectious Diseases Research Centre-CRI, Research Center of the CHU de Québec, Université Laval, Quebec, QC, Canada
| | - Faiza Tebbji
- Infectious Diseases Research Centre-CRI, Research Center of the CHU de Québec, Université Laval, Quebec, QC, Canada
| | - Carlos García
- Infectious Diseases Research Centre-CRI, Research Center of the CHU de Québec, Université Laval, Quebec, QC, Canada
| | - Hugo Wurtele
- Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - René Pelletier
- Medical Microbiology and Infectious Diseases, Research Center of the CHU de Québec, Quebec, QC, Canada
| | - Adnane Sellam
- Infectious Diseases Research Centre-CRI, Research Center of the CHU de Québec, Université Laval, Quebec, QC, Canada.,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, QC, Canada
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175
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Basso V, Znaidi S, Lagage V, Cabral V, Schoenherr F, LeibundGut-Landmann S, d'Enfert C, Bachellier-Bassi S. The two-component response regulator Skn7 belongs to a network of transcription factors regulating morphogenesis in Candida albicans and independently limits morphogenesis-induced ROS accumulation. Mol Microbiol 2017; 106:157-182. [PMID: 28752552 DOI: 10.1111/mmi.13758] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2017] [Indexed: 01/01/2023]
Abstract
Skn7 is a conserved fungal heat shock factor-type transcriptional regulator. It participates in maintaining cell wall integrity and regulates the osmotic/oxidative stress response (OSR) in S. cerevisiae, where it is part of a two-component signal transduction system. Here, we comprehensively address the function of Skn7 in the human fungal pathogen Candida albicans. We provide evidence reinforcing functional divergence, with loss of the cell wall/osmotic stress-protective roles and acquisition of the ability to regulate morphogenesis on solid medium. Mapping of the Skn7 transcriptional circuitry, through combination of genome-wide expression and location technologies, pointed to a dual regulatory role encompassing OSR and filamentous growth. Genetic interaction analyses revealed close functional interactions between Skn7 and master regulators of morphogenesis, including Efg1, Cph1 and Ume6. Intracellular biochemical assays revealed that Skn7 is crucial for limiting the accumulation of reactive oxygen species (ROS) in filament-inducing conditions on solid medium. Interestingly, functional domain mapping using site-directed mutagenesis allowed decoupling of Skn7 function in morphogenesis from protection against intracellular ROS. Our work identifies Skn7 as an integral part of the transcriptional circuitry controlling C. albicans filamentous growth and illuminates how C. albicans relies on an evolutionarily-conserved regulator to protect itself from intracellular ROS during morphological development.
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Affiliation(s)
- Virginia Basso
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, 25 rue du Docteur Roux, Paris, France.,Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Dr. Roux, Paris, France
| | - Sadri Znaidi
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, 25 rue du Docteur Roux, Paris, France.,Institut Pasteur de Tunis, Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique, 13 Place Pasteur, Tunis-Belvédère, B.P. 74, 1002, Tunisia.,University of Tunis El Manar, Tunis 1036, Tunisia
| | - Valentine Lagage
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, 25 rue du Docteur Roux, Paris, France
| | - Vitor Cabral
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, 25 rue du Docteur Roux, Paris, France.,Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Dr. Roux, Paris, France
| | - Franziska Schoenherr
- Institute of Virology, Winterthurerstr. 266a, Zürich, Switzerland.,SUPSI, Laboratorio Microbiologia Applicata, via Mirasole 22a, Bellinzona, Switzerland
| | | | - Christophe d'Enfert
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, 25 rue du Docteur Roux, Paris, France
| | - Sophie Bachellier-Bassi
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, 25 rue du Docteur Roux, Paris, France
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176
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Phosphate Acquisition and Virulence in Human Fungal Pathogens. Microorganisms 2017; 5:microorganisms5030048. [PMID: 28829379 PMCID: PMC5620639 DOI: 10.3390/microorganisms5030048] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 01/23/2023] Open
Abstract
The ability of pathogenic fungi to acquire essential macro and micronutrients during infection is a well-established virulence trait. Recent studies in the major human fungal pathogens Candida albicans and Cryptococcus neoformans have revealed that acquisition of the essential macronutrient, phosphate, is essential for virulence. The phosphate sensing and acquisition pathway in fungi, known as the PHO pathway, has been extensively characterized in the model yeast Saccharomyces cerevisiae. In this review, we highlight recent advances in phosphate sensing and signaling mechanisms, and use the S. cerevisiae PHO pathway as a platform from which to compare the phosphate acquisition and storage strategies employed by several human pathogenic fungi. We also explore the multi-layered roles of phosphate acquisition in promoting fungal stress resistance to pH, cationic, and oxidative stresses, and describe emerging roles for the phosphate storage molecule polyphosphate (polyP). Finally, we summarize the recent studies supporting the necessity of phosphate acquisition in mediating the virulence of human fungal pathogens, highlighting the concept that this requirement is intimately linked to promoting resistance to host-imposed stresses.
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177
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Genetic analysis of the Candida albicans biofilm transcription factor network using simple and complex haploinsufficiency. PLoS Genet 2017; 13:e1006948. [PMID: 28793308 PMCID: PMC5565191 DOI: 10.1371/journal.pgen.1006948] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/21/2017] [Accepted: 07/28/2017] [Indexed: 11/19/2022] Open
Abstract
Biofilm formation by Candida albicans is a key aspect of its pathobiology and is regulated by an integrated network of transcription factors (Bcr1, Brg1, Efg1, Ndt80, Rob1, and Tec1). To understand the details of how the transcription factors function together to regulate biofilm formation, we used a systematic genetic interaction approach based on generating all possible double heterozygous mutants of the network genes and quantitatively analyzing the genetic interactions between them. Overall, the network is highly susceptible to genetic perturbation with the six network heterozygous mutants all showing alterations in biofilm formation (haploinsufficiency). In addition, many double heterozygous mutants are as severely affected as homozygous deletions. As a result, the network shows properties of a highly interdependent ‘small-world’ network that is highly efficient but not robust. In addition, these genetic interaction data indicate that TEC1 represents a network component whose expression is highly sensitive to small perturbations in the function of other networks TFs. We have also found that expression of ROB1 is dependent on both auto-regulation and cooperative interactions with other network TFs. Finally, the heterozygous NDT80 deletion mutant is hyperfilamentous under both biofilm and hyphae-inducing conditions in a TEC1-dependent manner. Taken together, genetic interaction analysis of this network has provided new insights into the functions of individual TFs as well as into the role of the overall network topology in its function. Biofilm formation is part and parcel of the ability of Candida albicans, a normal component of the human gastrointestinal microbial community, to cause disease. Recent work by many investigators has provided detailed information regarding how C. albicans converts to the biofilm stage of growth. The vast majority of these studies have involved the study of strains lacking a single gene that affects biofilm formation. Using this genetic approach in combination with other genome-wide techniques, a network of transcription factors was identified that play a crucial role in regulating biofilm-related processes. Here, we have systematically generated and characterized strains with mutations in two biofilm network transcription factors in order to determine how these genes interact. This represents the first systematic quantitative genetic interaction study in C. albicans and, by combining our results with that of previous labs, provides a new level of detail regarding the integrated functions of these transcription factors. In addition, our data indicate that the biofilm transcription factor network is very sensitive to genetic perturbation and propose that this fragility is a function of its small-world topography which, in turn, promotes network efficiency at the expense of robustness.
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178
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Wangsanut T, Ghosh AK, Metzger PG, Fonzi WA, Rolfes RJ. Grf10 and Bas1 Regulate Transcription of Adenylate and One-Carbon Biosynthesis Genes and Affect Virulence in the Human Fungal Pathogen Candida albicans. mSphere 2017; 2:e00161-17. [PMID: 28776040 PMCID: PMC5541157 DOI: 10.1128/msphere.00161-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 11/21/2022] Open
Abstract
Candida albicans is an opportunistic human fungal pathogen that causes superficial fungal infections and lethal systemic infections. To colonize and establish infections, C. albicans coordinates the expression of virulence and metabolic genes. Previous work showed that the homeodomain transcription factor Grf10 is required for formation of hyphae, a virulence factor. Here we report global gene expression analysis of a grf10Δ strain using a DNA microarray and identify genes for de novo adenylate biosynthesis (ADE genes), one-carbon metabolism, and a nucleoside permease (NUP). Upregulation of these genes in response to adenine limitation required both Grf10 and the myb protein Bas1, as shown by quantitative real-time PCR (qRT-PCR). Phenotypic analysis showed that both mutants exhibited growth defects when grown in the absence of adenine, and the doubling time was slower for the bas1Δ mutant. Bas1 is required for basal expression of these genes, whereas NUP expression is more dependent upon Grf10. Disruption of BAS1 led to only modest defects in hypha formation and weak attenuation of virulence in a systemic mouse model of infection, as opposed to the previously reported strong effects found in the grf10Δ mutant. Our data are consistent with a model in which Grf10 coordinates metabolic effects on nucleotide metabolism by interaction with Bas1 and indicate that AMP biosynthesis and its regulation are important for C. albicans growth and virulence. IMPORTANCECandida albicans is a commensal and a common constituent of the human microbiota; however, it can become pathogenic and cause infections in both immunocompetent and immunocompromised people. C. albicans exhibits remarkable metabolic versatility as it can colonize multiple body sites as a commensal or pathogen. Understanding how C. albicans adapts metabolically to each ecological niche is essential for developing novel therapeutic approaches. Purine metabolism has been targeted pharmaceutically in several diseases; however, the regulation of this pathway has not been fully elucidated in C. albicans. Here, we report how C. albicans controls the AMP de novo biosynthesis pathway in response to purine availability. We show that the lack of the transcription factors Grf10 and Bas1 leads to purine metabolic dysfunction, and this dysfunction affects the ability of C. albicans to establish infections.
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Affiliation(s)
| | - Anup K. Ghosh
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Peter G. Metzger
- Department of Biology, Georgetown University, Washington, DC, USA
| | - William A. Fonzi
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
| | - Ronda J. Rolfes
- Department of Biology, Georgetown University, Washington, DC, USA
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179
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The CCAAT-Binding Complex Controls Respiratory Gene Expression and Iron Homeostasis in Candida Glabrata. Sci Rep 2017; 7:3531. [PMID: 28615656 PMCID: PMC5471220 DOI: 10.1038/s41598-017-03750-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/20/2017] [Indexed: 12/04/2022] Open
Abstract
The CCAAT-binding complex (CBC) is a heterotrimeric transcription factor which is widely conserved in eukaryotes. In the model yeast S. cerevisiae, CBC positively controls the expression of respiratory pathway genes. This role involves interactions with the regulatory subunit Hap4. In many pathogenic fungi, CBC interacts with the HapX regulatory subunit to control iron homeostasis. HapX is a bZIP protein which only shares with Hap4 the Hap4Like domain (Hap4L) required for its interaction with CBC. Here, we show that CBC has a dual role in the pathogenic yeast C. glabrata. It is required, along with Hap4, for the constitutive expression of respiratory genes and it is also essential for the iron stress response, which is mediated by the Yap5 bZIP transcription factor. Interestingly, Yap5 contains a vestigial Hap4L domain. The mutagenesis of this domain severely reduced Yap5 binding to its targets and compromised its interaction with Hap5. Hence, Yap5, like HapX in other species, acts as a CBC regulatory subunit in the regulation of iron stress response. This work reveals new aspects of iron homeostasis in C. glabrata and of the evolution of the role of CBC and Hap4L-bZIP proteins in this process.
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180
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Affiliation(s)
- Thabiso E Motaung
- a Variety Improvement, South African Sugarcane Research Institute - Crop Biology Resource Center, Mount Edgecombe , Durban , South Africa.,b Germplasm Development, Agricultural Research Council - Small Grain Institute , Bethlehem , South Africa
| | - Toi J Tsilo
- b Germplasm Development, Agricultural Research Council - Small Grain Institute , Bethlehem , South Africa.,c Department of Life and Consumer Sciences , University of South Africa , Pretoria , South Africa
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181
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Phosphate is the third nutrient monitored by TOR in Candida albicans and provides a target for fungal-specific indirect TOR inhibition. Proc Natl Acad Sci U S A 2017; 114:6346-6351. [PMID: 28566496 DOI: 10.1073/pnas.1617799114] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Target of Rapamycin (TOR) pathway regulates morphogenesis and responses to host cells in the fungal pathogen Candida albicans Eukaryotic Target of Rapamycin complex 1 (TORC1) induces growth and proliferation in response to nitrogen and carbon source availability. Our unbiased genetic approach seeking unknown components of TORC1 signaling in C. albicans revealed that the phosphate transporter Pho84 is required for normal TORC1 activity. We found that mutants in PHO84 are hypersensitive to rapamycin and in response to phosphate feeding, generate less phosphorylated ribosomal protein S6 (P-S6) than the WT. The small GTPase Gtr1, a component of the TORC1-activating EGO complex, links Pho84 to TORC1. Mutants in Gtr1 but not in another TORC1-activating GTPase, Rhb1, are defective in the P-S6 response to phosphate. Overexpression of Gtr1 and a constitutively active Gtr1Q67L mutant suppresses TORC1-related defects. In Saccharomyces cerevisiae pho84 mutants, constitutively active Gtr1 suppresses a TORC1 signaling defect but does not rescue rapamycin hypersensitivity. Hence, connections from phosphate homeostasis (PHO) to TORC1 may differ between C. albicans and S. cerevisiae The converse direction of signaling from TORC1 to the PHO regulon previously observed in S. cerevisiae was genetically shown in C. albicans using conditional TOR1 alleles. A small molecule inhibitor of Pho84, a Food and Drug Administration-approved drug, inhibits TORC1 signaling and potentiates the activity of the antifungals amphotericin B and micafungin. Anabolic TORC1-dependent processes require significant amounts of phosphate. Our study shows that phosphate availability is monitored and also controlled by TORC1 and that TORC1 can be indirectly targeted by inhibiting Pho84.
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182
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Koch C, Konieczka J, Delorey T, Lyons A, Socha A, Davis K, Knaack SA, Thompson D, O'Shea EK, Regev A, Roy S. Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies. Cell Syst 2017; 4:543-558.e8. [PMID: 28544882 PMCID: PMC5515301 DOI: 10.1016/j.cels.2017.04.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/20/2017] [Accepted: 04/26/2017] [Indexed: 11/22/2022]
Abstract
Changes in transcriptional regulatory networks can significantly contribute to species evolution and adaptation. However, identification of genome-scale regulatory networks is an open challenge, especially in non-model organisms. Here, we introduce multi-species regulatory network learning (MRTLE), a computational approach that uses phylogenetic structure, sequence-specific motifs, and transcriptomic data, to infer the regulatory networks in different species. Using simulated data from known networks and transcriptomic data from six divergent yeasts, we demonstrate that MRTLE predicts networks with greater accuracy than existing methods because it incorporates phylogenetic information. We used MRTLE to infer the structure of the transcriptional networks that control the osmotic stress responses of divergent, non-model yeast species and then validated our predictions experimentally. Interrogating these networks reveals that gene duplication promotes network divergence across evolution. Taken together, our approach facilitates study of regulatory network evolutionary dynamics across multiple poorly studied species.
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Affiliation(s)
- Christopher Koch
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wl, USA
| | - Jay Konieczka
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Toni Delorey
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ana Lyons
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amanda Socha
- Dartmouth College, Biology department, Hanover, NH 03755, USA
| | - Kathleen Davis
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Sara A Knaack
- Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, Wl, USA
| | - Dawn Thompson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Erin K O'Shea
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard University, Northwest Laboratory, Cambridge, Massachusetts, USA
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Northwest Laboratory, Cambridge, Massachusetts, USA
- Department of Molecular and Cellular Biology, Harvard University, Northwest Laboratory, Cambridge, Massachusetts, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, Wl, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wl, USA
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183
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He BZ, Zhou X, O'Shea EK. Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway. eLife 2017; 6:25157. [PMID: 28485712 PMCID: PMC5446240 DOI: 10.7554/elife.25157] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 04/29/2017] [Indexed: 01/23/2023] Open
Abstract
Although combinatorial regulation is a common feature in gene regulatory networks, how it evolves and affects network structure and function is not well understood. In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are required for gene induction and survival during phosphate starvation. In the related human commensal C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate starvation and is only partially required for inducing PHO genes. Phylogenetic survey suggests that reduced dependence on Pho2 evolved in C. glabrata and closely related species. In S. cerevisiae, less Pho2-dependent Pho4 orthologs induce more genes. In C. glabrata, its Pho4 binds to more locations and induces three times as many genes as Pho4 in S. cerevisiae does. Our work shows how evolution of combinatorial regulation allows for rapid expansion of a gene regulatory network’s targets, possibly extending its physiological functions. The diversity of life on Earth has intrigued generations of scientists and nature lovers alike. Research over recent decades has revealed that much of the diversity we can see did not require the invention of new genes. Instead, living forms diversified mostly by using old genes in new ways – for example, by changing when or where an existing gene became active. This kind of change is referred to as “regulatory evolution”. A class of proteins called transcription factors are hot spots in regulatory evolution. These proteins recognize specific sequences of DNA to control the activity of other genes, and so represent the “readers” of the genetic information. Small changes to how a transcription factor is regulated, or the genes it targets, can lead to dramatic changes in an organism. Before we can understand how life on Earth evolved to be so diverse, scientists must first answer how transcription factors evolve and what consequences this has on their target genes. So far, most studies of regulatory evolution have focused on networks of transcription factors and genes that control how an organism develops. He et al. have now studied a regulatory network that is behind a different process, namely how an organism responds to stress or starvation. These two types of regulatory networks are structured differently and work in different ways. These differences made He et al. wonder if the networks evolved differently too. The chemical phosphate is an essential nutrient for all living things, and He et al. compared how two different species of yeast responded to a lack of phosphate. The key difference was how much a major transcription factor known as Pho4 depended on a so-called co-activator protein named Pho2 to carry out its role. Baker’s yeast (Saccharomyces cerevisiae), which is commonly used in laboratory experiments, requires both Pho4 and Pho2 to activate about 20 genes when inorganic phosphate is not available in its environment. However, in a related yeast species called Candida glabrata, Pho4 has evolved to depend less on Pho2. He et al. went on to show that, as well as being less dependent on Pho2, Pho4 in C. glabrata activates more than three times as many genes as Pho4 in S. cerevisiae does in the absence of phosphate. These additional gene targets for Pho4 in C. glabrata are predicted to extend the network’s activities, and allow it to regulate new process including the yeast’s responses to other types of stress and the building of the yeast’s cell wall. Together these findings show a new way that regulatory networks can evolve, that is, by reducing its dependence on the co-activator, a transcription factor can expand the number of genes it targets. This has not been seen for regulatory networks related to development, suggesting that different networks can indeed evolve in different ways. Lastly, because disease-causing microbes are often stressed inside their hosts and C. glabrata sometimes infects humans, understanding how this yeast’s response to stress has evolved may lead to new ways to prevent and treat this infection.
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Affiliation(s)
- Bin Z He
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Xu Zhou
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Erin K O'Shea
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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184
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Ramírez-Zavala B, Mottola A, Haubenreißer J, Schneider S, Allert S, Brunke S, Ohlsen K, Hube B, Morschhäuser J. The Snf1-activating kinase Sak1 is a key regulator of metabolic adaptation and in vivo fitness of Candida albicans. Mol Microbiol 2017; 104:989-1007. [PMID: 28337802 DOI: 10.1111/mmi.13674] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2017] [Indexed: 01/06/2023]
Abstract
The metabolic flexibility of the opportunistic fungal pathogen Candida albicans is important for colonisation and infection of different host niches. Complex regulatory networks, in which protein kinases play central roles, link metabolism and other virulence-associated traits, such as filamentous growth and stress resistance, and thereby control commensalism and pathogenicity. By screening a protein kinase deletion mutant library that was generated in the present work using an improved SAT1 flipper cassette, we found that the previously uncharacterised kinase Sak1 is a key upstream activator of the protein kinase Snf1, a highly conserved regulator of nutrient stress responses that is essential for viability in C. albicans. The sak1Δ mutants failed to grow on many alternative carbon sources and were hypersensitive to cell wall/membrane stress. These phenotypes were mirrored in mutants lacking other subunits of the SNF1 complex and partially compensated by a hyperactive form of Snf1. Transcriptional profiling of sak1Δ mutants showed that Sak1 ensures basal expression of glyoxylate cycle and gluconeogenesis genes even in glucose-rich media and thereby contributes to the metabolic plasticity of C. albicans. In a mouse model of gastrointestinal colonisation, sak1Δ mutants were rapidly outcompeted by wild-type cells, demonstrating that Sak1 is essential for the in vivo fitness of C. albicans.
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Affiliation(s)
| | - Austin Mottola
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Julia Haubenreißer
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Sabrina Schneider
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Stefanie Allert
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany.,Friedrich Schiller University, Jena, Germany.,Center for Sepsis Control and Care (CSCC), Jena, Germany
| | - Joachim Morschhäuser
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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185
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Pataki E, Sipiczki M, Miklos I. Schizosaccharomyces pombe rsv1 Transcription Factor and its Putative Homologues Preserved their Functional Homology and are Evolutionarily Conserved. Curr Microbiol 2017; 74:710-717. [PMID: 28342076 DOI: 10.1007/s00284-017-1227-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/02/2017] [Indexed: 11/24/2022]
Abstract
Environmental glucose is an important regulator of biological processes, as it can launch different cell processes depending on its concentration. Thus, low glucose concentration can induce entry into quiescence, which ensures long-term viability for the cells or in other cases mycelial growth in the dimorphic species, which, in turn, provides the cells with fresh nutrients. Several genes, such as the genes of cAMP cascade, are involved in glucose sensing and response. Since this signal transduction pathway seemed to be an evolutionarily conserved process, we assumed that its genes were also conserved and preserved their functional homology. To obtain evidence, Schizosaccharomyces pombe rsv1 and its orthologous genes were investigated using in silico and experimental approaches. Our results supported that the Rsv1 zinc-finger transcription factors of Schizosaccharomyces japonicus and Schizosaccharomyces octosporus and the Candida albicans cas5p were really functional homologues of the S. pombe Rsv1. Namely, the homologous proteins were able to restore mutant phenotype of the S. pombe rsv1-deleted cells. Bioinformatic anaysis revealed that the most conserved parts of the proteins always contained the C2H2 domains and the complementation abilities of the counterpart genes were not uniform regarding the investigated features, which can be in connection with the conserved regions outside C2H2.
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Affiliation(s)
- Emese Pataki
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Matthias Sipiczki
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Ida Miklos
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
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186
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Gerstein AC, Lim H, Berman J, Hickman MA. Ploidy tug-of-war: Evolutionary and genetic environments influence the rate of ploidy drive in a human fungal pathogen. Evolution 2017; 71:1025-1038. [PMID: 28195309 DOI: 10.1111/evo.13205] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 01/27/2017] [Indexed: 12/18/2022]
Abstract
Variation in baseline ploidy is seen throughout the tree of life, yet the factors that determine why one ploidy level is maintained over another remain poorly understood. Experimental evolution studies using asexual fungal microbes with manipulated ploidy levels intriguingly reveals a propensity to return to the historical baseline ploidy, a phenomenon that we term "ploidy drive." We evolved haploid, diploid, and polyploid strains of the human fungal pathogen Candida albicans under three different nutrient limitation environments to test whether these conditions, hypothesized to select for low ploidy levels, could counteract ploidy drive. Strains generally maintained or acquired smaller genome sizes (measured as total nuclear DNA through flow cytometry) in minimal medium and under phosphorus depletion compared to in a complete medium, while mostly maintained or acquired increased genome sizes under nitrogen depletion. Improvements in fitness often ran counter to changes in genome size; in a number of scenarios lines that maintained their original genome size often increased in fitness more than lines that converged toward diploidy (the baseline ploidy of C. albicans). Combined, this work demonstrates a role for both the environment and genotype in determination of the rate of ploidy drive, and highlights questions that remain about the force(s) that cause genome size variation.
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Affiliation(s)
- Aleeza C Gerstein
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota.,Department of Microbiology & Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota
| | - Heekyung Lim
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota
| | - Judith Berman
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota.,Department of Microbiology & Immunology, Medical School, University of Minnesota, Minneapolis, Minnesota.,Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Meleah A Hickman
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota.,Department of Biology, O. Wayne Rollins Research Center, Emory University, Atlanta, Georgia
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187
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Abstract
Candida albicans is an important etiological agent of superficial and life-threatening infections in individuals with compromised immune systems. To date, we know of several overlapping genetic networks that govern virulence attributes in this fungal pathogen. Classical use of deletion mutants has led to the discovery of numerous virulence factors over the years, and genome-wide functional analysis has propelled gene discovery at an even faster pace. Indeed, a number of recent studies using large-scale genetic screens followed by genome-wide functional analysis has allowed for the unbiased discovery of many new genes involved in C. albicans biology. Here we share our perspectives on the role of these studies in analyzing fundamental aspects of C. albicans virulence properties.
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Affiliation(s)
- Thabiso E Motaung
- a Agricultural Research Council - Small Grain Institute , Bethlehem , South Africa
| | - Ruan Ells
- b University of the Free Sate , Bloemfontein , South Africa
| | | | | | - Toi J Tsilo
- a Agricultural Research Council - Small Grain Institute , Bethlehem , South Africa.,c Department of Life and Consumer Sciences , University of South Africa , Pretoria , South Africa
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188
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Kelliher CM, Haase SB. Connecting virulence pathways to cell-cycle progression in the fungal pathogen Cryptococcus neoformans. Curr Genet 2017; 63:803-811. [PMID: 28265742 PMCID: PMC5605583 DOI: 10.1007/s00294-017-0688-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 11/01/2022]
Abstract
Proliferation and host evasion are critical processes to understand at a basic biological level for improving infectious disease treatment options. The human fungal pathogen Cryptococcus neoformans causes fungal meningitis in immunocompromised individuals by proliferating in cerebrospinal fluid. Current antifungal drugs target "virulence factors" for disease, such as components of the cell wall and polysaccharide capsule in C. neoformans. However, mechanistic links between virulence pathways and the cell cycle are not as well studied. Recently, cell-cycle synchronized C. neoformans cells were profiled over time to identify gene expression dynamics (Kelliher et al., PLoS Genet 12(12):e1006453, 2016). Almost 20% of all genes in the C. neoformans genome were periodically activated during the cell cycle in rich media, including 40 genes that have previously been implicated in virulence pathways. Here, we review important findings about cell-cycle-regulated genes in C. neoformans and provide two examples of virulence pathways-chitin synthesis and G-protein coupled receptor signaling-with their putative connections to cell division. We propose that a "comparative functional genomics" approach, leveraging gene expression timing during the cell cycle, orthology to genes in other fungal species, and previous experimental findings, can lead to mechanistic hypotheses connecting the cell cycle to fungal virulence.
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Affiliation(s)
- Christina M Kelliher
- Department of Biology, Duke University, Box 90338, 130 Science Drive, Durham, NC, 27708-0338, USA
| | - Steven B Haase
- Department of Biology, Duke University, Box 90338, 130 Science Drive, Durham, NC, 27708-0338, USA.
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189
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Adaptation of Candida albicans to Reactive Sulfur Species. Genetics 2017; 206:151-162. [PMID: 28235888 DOI: 10.1534/genetics.116.199679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 02/20/2017] [Indexed: 12/28/2022] Open
Abstract
Candida albicans is an opportunistic fungal pathogen that is highly resistant to different oxidative stresses. How reactive sulfur species (RSS) such as sulfite regulate gene expression and the role of the transcription factor Zcf2 and the sulfite exporter Ssu1 in such responses are not known. Here, we show that C. albicans specifically adapts to sulfite stress and that Zcf2 is required for that response as well as induction of genes predicted to remove sulfite from cells and to increase the intracellular amount of a subset of nitrogen metabolites. Analysis of mutants in the sulfate assimilation pathway show that sulfite conversion to sulfide accounts for part of sulfite toxicity and that Zcf2-dependent expression of the SSU1 sulfite exporter is induced by both sulfite and sulfide. Mutations in the SSU1 promoter that selectively inhibit induction by the reactive nitrogen species (RNS) nitrite, a previously reported activator of SSU1, support a model for C. albicans in which Cta4-dependent RNS induction and Zcf2-dependent RSS induction are mediated by parallel pathways, different from S. cerevisiae in which the transcription factor Fzf1 mediates responses to both RNS and RSS. Lastly, we found that endogenous sulfite production leads to an increase in resistance to exogenously added sulfite. These results demonstrate that C. albicans has a unique response to sulfite that differs from the general oxidative stress response, and that adaptation to internal and external sulfite is largely mediated by one transcription factor and one effector gene.
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190
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A tool named Iris for versatile high-throughput phenotyping in microorganisms. Nat Microbiol 2017; 2:17014. [PMID: 28211844 PMCID: PMC5464397 DOI: 10.1038/nmicrobiol.2017.14] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/10/2017] [Indexed: 12/14/2022]
Abstract
Advances in our ability to systematically introduce and track controlled genetic variance in microbes have fueled high-throughput reverse genetics approaches in the past decade. When coupled to quantitative readouts, such approaches are extremely powerful at elucidating gene function and providing insights into the underlying pathways and the overall cellular network organization. Yet, until now all efforts for quantifying microbial macroscopic phenotypes have been restricted to monitoring growth in a small number of model microbes. We developed an image analysis software named Iris, which allows for systematic exploration of a number of orthogonal-to-growth processes, including biofilm formation, colony morphogenesis, envelope biogenesis, sporulation and reporter activity. In addition, Iris provides more sensitive growth measurements than current available software, and is compatible with a variety of different microbes, as well as with endpoint or kinetic data. We used Iris to reanalyze existing chemical genomics data in Escherichia coli and to perform proof-of-principle screens on colony biofilm formation and morphogenesis of different bacterial species and the pathogenic fungus, Candida albicans. Thereby we recapitulated existing knowledge but also identified a plethora of additional genes and pathways involved in both processes.
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191
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Genome-Wide Screen for Haploinsufficient Cell Size Genes in the Opportunistic Yeast Candida albicans. G3-GENES GENOMES GENETICS 2017; 7:355-360. [PMID: 28040776 PMCID: PMC5295585 DOI: 10.1534/g3.116.037986] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
One of the most critical but still poorly understood aspects of eukaryotic cell proliferation is the basis for commitment to cell division in late G1 phase, called Start in yeast and the Restriction Point in metazoans. In all species, a critical cell size threshold coordinates cell growth with cell division and thereby establishes a homeostatic cell size. While a comprehensive survey of cell size genetic determinism has been performed in the saprophytic yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, very little is known in pathogenic fungi. As a number of critical Start regulators are haploinsufficient for cell size, we applied a quantitative analysis of the size phenome, using elutriation-barcode sequencing methodology, to 5639 barcoded heterozygous deletion strains of the opportunistic yeast Candida albicans. Our screen identified conserved known regulators and biological processes required to maintain size homeostasis in the opportunistic yeast C. albicans. We also identified novel C. albicans-specific size genes and provided a conceptual framework for future mechanistic studies. Interestingly, some of the size genes identified were required for fungal pathogenicity suggesting that cell size homeostasis may be elemental to C. albicans fitness or virulence inside the host.
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192
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Hsieh SH, Brunke S, Brock M. Encapsulation of Antifungals in Micelles Protects Candida albicans during Gall-Bladder Infection. Front Microbiol 2017; 8:117. [PMID: 28203228 PMCID: PMC5285334 DOI: 10.3389/fmicb.2017.00117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/17/2017] [Indexed: 12/12/2022] Open
Abstract
Candida albicans is a dimorphic fungus that colonizes human mucosal surfaces with the potential to cause life-threatening invasive candidiasis. Studies on systemic candidiasis in a murine infection model using in vivo real-time bioluminescence imaging revealed persistence of C. albicans in the gall bladder under antifungal therapy. Preliminary analyses showed that bile conferred resistance against a wide variety of antifungals enabling survival in this cryptic host niche. Here, bile and its components were studied for their ability to reduce antifungal efficacy in order to elucidate the underlying mechanism of protection. While unconjugated bile salts were toxic to C. albicans, taurine, or glycine conjugated bile salts were well tolerated and protective against caspofungin and amphotericin B when exceeding their critical micellar concentration. Microarray experiments indicated that upregulation of genes generally known to mediate antifungal protection is not involved in the protection process. In contrast, rhodamine 6G and crystal violet in- and efflux experiments indicated encapsulation of antifungals in micelles, thereby reducing their bioavailability. Furthermore, farnesol sensing was abolished in the presence of conjugated bile salts trapping C. albicans cells in the hyphal morphology. This suggests that bioavailability of amphiphilic and hydrophobic compounds is reduced in the presence of bile. In contrast, small and hydrophilic molecules, such as cycloheximide, flucytosine, or sodium azide kept their antifungal properties. We therefore conclude that treatment of gall bladder and bile duct infections is hampered by the ability of bile salts to encapsulate antifungals in micelles. As a consequence, treatment of gall bladder or bile duct infections should favor the use of small hydrophilic drugs that are not solubilised in micelles.
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Affiliation(s)
- Shih-Hung Hsieh
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell InstituteJena, Germany; Fungal Genetics and Biology Group, School of Life Sciences, University of NottinghamNottingham, UK
| | - Sascha Brunke
- Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute Jena, Germany
| | - Matthias Brock
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell InstituteJena, Germany; Fungal Genetics and Biology Group, School of Life Sciences, University of NottinghamNottingham, UK
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193
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Phagosomal Neutralization by the Fungal Pathogen Candida albicans Induces Macrophage Pyroptosis. Infect Immun 2017; 85:IAI.00832-16. [PMID: 27872238 DOI: 10.1128/iai.00832-16] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/15/2016] [Indexed: 02/04/2023] Open
Abstract
The interaction of Candida albicans with the innate immune system is the key determinant of the pathogen/commensal balance and has selected for adaptations that facilitate the utilization of nutrients commonly found within the host, including proteins and amino acids; many of the catabolic pathways needed to assimilate these compounds are required for persistence in the host. We have shown that C. albicans co-opts amino acid catabolism to generate and excrete ammonia, which raises the extracellular pH, both in vitro and in vivo and induces hyphal morphogenesis. Mutants defective in the uptake or utilization of amino acids, such as those lacking STP2, a transcription factor that regulates the expression of amino acid permeases, are impaired in multiple aspects of fungus-macrophage interactions resulting from an inability to neutralize the phagosome. Here we identified a novel role in amino acid utilization for Ahr1p, a transcription factor previously implicated in regulation of adherence and hyphal morphogenesis. Mutants lacking AHR1 were defective in growth, alkalinization, and ammonia release on amino acid-rich media, similar to stp2Δ and ahr1Δ stp2Δ cells, and occupied more acidic phagosomes. Notably, ahr1Δ and stp2Δ strains did not induce pyroptosis, as measured by caspase-1-dependent interleukin-1β release, though this phenotype could be suppressed by pharmacological neutralization of the phagosome. Altogether, we show that C. albicans-driven neutralization of the phagosome promotes hyphal morphogenesis, sufficient for induction of caspase-1-mediated macrophage lysis.
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194
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Chakravarti A, Camp K, McNabb DS, Pinto I. The Iron-Dependent Regulation of the Candida albicans Oxidative Stress Response by the CCAAT-Binding Factor. PLoS One 2017; 12:e0170649. [PMID: 28122000 PMCID: PMC5266298 DOI: 10.1371/journal.pone.0170649] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 01/09/2017] [Indexed: 11/18/2022] Open
Abstract
Candida albicans is the most frequently encountered fungal pathogen in humans, capable of causing mucocutaneous and systemic infections in immunocompromised individuals. C. albicans virulence is influenced by multiple factors. Importantly, iron acquisition and avoidance of the immune oxidative burst are two critical barriers for survival in the host. Prior studies using whole genome microarray expression data indicated that the CCAAT-binding factor is involved in the regulation of iron uptake/utilization and the oxidative stress response. This study examines directly the role of the CCAAT-binding factor in regulating the expression of oxidative stress genes in response to iron availability. The CCAAT-binding factor is a heterooligomeric transcription factor previously shown to regulate genes involved in respiration and iron uptake/utilization in C. albicans. Since these pathways directly influence the level of free radicals, it seemed plausible the CCAAT-binding factor regulates genes necessary for the oxidative stress response. In this study, we show the CCAAT-binding factor is involved in regulating some oxidative stress genes in response to iron availability, including CAT1, SOD4, GRX5, and TRX1. We also show that CAT1 expression and catalase activity correlate with the survival of C. albicans to oxidative stress, providing a connection between iron obtainability and the oxidative stress response. We further explore the role of the various CCAAT-binding factor subunits in the formation of distinct protein complexes that modulate the transcription of CAT1 in response to iron. We find that Hap31 and Hap32 can compensate for each other in the formation of an active transcriptional complex; however, they play distinct roles in the oxidative stress response during iron limitation. Moreover, Hap43 was found to be solely responsible for the repression observed under iron deprivation.
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Affiliation(s)
- Ananya Chakravarti
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Kyle Camp
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - David S. McNabb
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Inés Pinto
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas, United States of America
- * E-mail:
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195
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Zinc Cluster Transcription Factors Alter Virulence in Candida albicans. Genetics 2016; 205:559-576. [PMID: 27932543 DOI: 10.1534/genetics.116.195024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/16/2016] [Indexed: 11/18/2022] Open
Abstract
Almost all humans are colonized with Candida albicans However, in immunocompromised individuals, this benign commensal organism becomes a serious, life-threatening pathogen. Here, we describe and analyze the regulatory networks that modulate innate responses in the host niches. We identified Zcf15 and Zcf29, two Zinc Cluster transcription Factors (ZCF) that are required for C. albicans virulence. Previous sequence analysis of clinical C. albicans isolates from immunocompromised patients indicates that both ZCF genes diverged during clonal evolution. Using in vivo animal models, ex vivo cell culture methods, and in vitro sensitivity assays, we demonstrate that knockout mutants of both ZCF15 and ZCF29 are hypersensitive to reactive oxygen species (ROS), suggesting they help neutralize the host-derived ROS produced by phagocytes, as well as establish a sustained infection in vivo Transcriptomic analysis of mutants under resting conditions where cells were not experiencing oxidative stress revealed a large network that control macro and micronutrient homeostasis, which likely contributes to overall pathogen fitness in host niches. Under oxidative stress, both transcription factors regulate a separate set of genes involved in detoxification of ROS and down-regulating ribosome biogenesis. ChIP-seq analysis, which reveals vastly different binding partners for each transcription factor (TF) before and after oxidative stress, further confirms these results. Furthermore, the absence of a dominant binding motif likely facilitates their mobility, and supports the notion that they represent a recent expansion of the ZCF family in the pathogenic Candida species. Our analyses provide a framework for understanding new aspects of the interface between C. albicans and host defense response, and extends our understanding of how complex cell behaviors are linked to the evolution of TFs.
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196
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Phenotypic Profiling Reveals that Candida albicans Opaque Cells Represent a Metabolically Specialized Cell State Compared to Default White Cells. mBio 2016; 7:mBio.01269-16. [PMID: 27879329 PMCID: PMC5120136 DOI: 10.1128/mbio.01269-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The white-opaque switch is a bistable, epigenetic transition affecting multiple traits in Candida albicans including mating, immunogenicity, and niche specificity. To compare how the two cell states respond to external cues, we examined the fitness, phenotypic switching, and filamentation properties of white cells and opaque cells under 1,440 different conditions at 25°C and 37°C. We demonstrate that white and opaque cells display striking differences in their integration of metabolic and thermal cues, so that the two states exhibit optimal fitness under distinct conditions. White cells were fitter than opaque cells under a wide range of environmental conditions, including growth at various pHs and in the presence of chemical stresses or antifungal drugs. This difference was exacerbated at 37°C, consistent with white cells being the default state of C. albicans in the mammalian host. In contrast, opaque cells showed greater fitness than white cells under select nutritional conditions, including growth on diverse peptides at 25°C. We further demonstrate that filamentation is significantly rewired between the two states, with white and opaque cells undergoing filamentous growth in response to distinct external cues. Genetic analysis was used to identify signaling pathways impacting the white-opaque transition both in vitro and in a murine model of commensal colonization, and three sugar sensing pathways are revealed as regulators of the switch. Together, these findings establish that white and opaque cells are programmed for differential integration of metabolic and thermal cues and that opaque cells represent a more metabolically specialized cell state than the default white state. IMPORTANCE Epigenetic transitions are an important mechanism by which microbes adapt to external stimuli. For Candida albicans, such transitions are crucial for adaptation to complex, fluctuating environments, and therefore contribute to its success as a human pathogen. The white-opaque switch modulates multiple C. albicans attributes, from sexual competency to niche specificity. Here, we demonstrate that metabolic circuits are extensively rewired between white and opaque states, so that the two cell types exhibit optimal fitness under different nutritional conditions and at different temperatures. We thereby establish that epigenetic events can profoundly alter the metabolism of fungal cells. We also demonstrate that epigenetic switching regulates filamentation and biofilm formation, two phenotypes closely associated with pathogenesis. These experiments reveal that white cells, considered the most clinically relevant form of C. albicans, are a "general-purpose" state suited to many environments, whereas opaque cells appear to represent a more metabolically specialized form of the species.
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Danhof HA, Vylkova S, Vesely EM, Ford AE, Gonzalez-Garay M, Lorenz MC. Robust Extracellular pH Modulation by Candida albicans during Growth in Carboxylic Acids. mBio 2016; 7:e01646-16. [PMID: 27935835 PMCID: PMC5111404 DOI: 10.1128/mbio.01646-16] [Citation(s) in RCA: 51] [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: 09/06/2016] [Accepted: 10/24/2016] [Indexed: 12/25/2022] Open
Abstract
The opportunistic fungal pathogen Candida albicans thrives within diverse niches in the mammalian host. Among the adaptations that underlie this fitness is an ability to utilize a wide array of nutrients, especially sources of carbon that are disfavored by many other fungi; this contributes to its ability to survive interactions with the phagocytes that serve as key barriers against disseminated infections. We have reported that C. albicans generates ammonia as a byproduct of amino acid catabolism to neutralize the acidic phagolysosome and promote hyphal morphogenesis in a manner dependent on the Stp2 transcription factor. Here, we report that this species rapidly neutralizes acidic environments when utilizing carboxylic acids like pyruvate, α-ketoglutarate (αKG), or lactate as the primary carbon source. Unlike in cells growing in amino acid-rich medium, this does not result in ammonia release, does not induce hyphal differentiation, and is genetically distinct. While transcript profiling revealed significant similarities in gene expression in cells grown on either carboxylic or amino acids, genetic screens for mutants that fail to neutralize αKG medium identified a nonoverlapping set of genes, including CWT1, encoding a transcription factor responsive to cell wall and nitrosative stresses. Strains lacking CWT1 exhibit retarded αKG-mediated neutralization in vitro, exist in a more acidic phagolysosome, and are more susceptible to macrophage killing, while double cwt1Δ stp2Δ mutants are more impaired than either single mutant. Together, our observations indicate that C. albicans has evolved multiple ways to modulate the pH of host-relevant environments to promote its fitness as a pathogen. IMPORTANCE The fungal pathogen Candida albicans is a ubiquitous and usually benign constituent of the human microbial ecosystem. In individuals with weakened immune systems, this organism can cause potentially life-threatening infections and is one of the most common causes of hospital-acquired infections. Understanding the interactions between C. albicans and immune phagocytic cells, such as macrophages and neutrophils, will define the mechanisms of pathogenesis in this species. One such adaptation is an ability to make use of nonstandard nutrients that we predict are plentiful in certain niches within the host, including within these phagocytic cells. We show here that the metabolism of certain organic acids enables C. albicans to neutralize acidic environments, such as those within macrophages. This phenomenon is distinct in several significant ways from previous reports of similar processes, indicating that C. albicans has evolved multiple mechanisms to combat the harmful acidity of phagocytic cells.
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Affiliation(s)
- Heather A Danhof
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
- The Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Slavena Vylkova
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Elisa M Vesely
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
- The Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Amy E Ford
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
- The Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Manuel Gonzalez-Garay
- The Brown Foundation Institute for Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Michael C Lorenz
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
- The Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, Texas, USA
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Bultman KM, Kowalski CH, Cramer RA. Aspergillus fumigatus virulence through the lens of transcription factors. Med Mycol 2016; 55:24-38. [PMID: 27816905 DOI: 10.1093/mmy/myw120] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 08/19/2016] [Accepted: 10/17/2016] [Indexed: 02/07/2023] Open
Abstract
Invasive aspergillosis (IA), most commonly caused by the filamentous fungus Aspergillus fumigatus, occurs in immune compromised individuals. The ability of A. fumigatus to proliferate in a multitude of environments is hypothesized to contribute to its pathogenicity and virulence. Transcription factors (TF) have long been recognized as critical proteins for fungal pathogenicity, as many are known to play important roles in the transcriptional regulation of pathways implicated in virulence. Such pathways include regulation of conidiation and development, adhesion, nutrient acquisition, adaptation to environmental stress, and interactions with the host immune system among others. In both murine and insect models of IA, TF loss of function in A. fumigatus results in cases of hyper- and hypovirulence as determined through host survival, fungal burden, and immune response analyses. Consequently, the study of specific TFs in A. fumigatus has revealed important insights into mechanisms of pathogenicity and virulence. Although in vitro studies have identified virulence-related functions of specific TFs, the full picture of their in vivo functions remain largely enigmatic and an exciting area of current research. Moreover, the vast majority of TFs remain to be characterized and studied in this important human pathogen. Here in this mini-review we provide an overview of selected TFs in A. fumigatus and their contribution to our understanding of this important human pathogen's pathogenicity and virulence.
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Affiliation(s)
- Katherine M Bultman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Caitlin H Kowalski
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Robert A Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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Abstract
Candida albicans is an important human fungal pathogen, in terms of both its clinical significance and its use as an experimental model for scientific investigation. Although this opportunistic pathogen is a natural component of the human flora, it can cause life-threatening infections in immunosuppressed patients. There are currently a limited number of antifungal molecules and drug targets, and increasing resistance to the front-line therapeutics, demonstrating a clear need for new antifungal drugs. Understanding the biology of this pathogen is an important prerequisite for identifying new drug targets for antifungal therapeutics. In this review, we highlight some recent developments that help us to understand how virulence traits are regulated at the molecular level, in addition to technical advances that improve the ability of genome editing in C. albicans.
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Affiliation(s)
- Adnane Sellam
- Infectious Diseases Research Centre-CRI, CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, Quebec, Canada; Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Malcolm Whiteway
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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Pais P, Costa C, Cavalheiro M, Romão D, Teixeira MC. Transcriptional Control of Drug Resistance, Virulence and Immune System Evasion in Pathogenic Fungi: A Cross-Species Comparison. Front Cell Infect Microbiol 2016; 6:131. [PMID: 27812511 PMCID: PMC5072224 DOI: 10.3389/fcimb.2016.00131] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/29/2016] [Indexed: 12/26/2022] Open
Abstract
Transcription factors are key players in the control of the activation or repression of gene expression programs in response to environmental stimuli. The study of regulatory networks taking place in fungal pathogens is a promising research topic that can help in the fight against these pathogens by targeting specific fungal pathways as a whole, instead of targeting more specific effectors of virulence or drug resistance. This review is focused on the analysis of regulatory networks playing a central role in the referred mechanisms in the human fungal pathogens Aspergillus fumigatus, Cryptococcus neoformans, Candida albicans, Candida glabrata, Candida parapsilosis, and Candida tropicalis. Current knowledge on the activity of the transcription factors characterized in each of these pathogenic fungal species will be addressed. Particular focus is given to their mechanisms of activation, regulatory targets and phenotypic outcome. The review further provides an evaluation on the conservation of transcriptional circuits among different fungal pathogens, highlighting the pathways that translate common or divergent traits among these species in what concerns their drug resistance, virulence and host immune evasion features. It becomes evident that the regulation of transcriptional networks is complex and presents significant variations among different fungal pathogens. Only the oxidative stress regulators Yap1 and Skn7 are conserved among all studied species; while some transcription factors, involved in nutrient homeostasis, pH adaptation, drug resistance and morphological switching are present in several, though not all species. Interestingly, in some cases not very homologous transcription factors display orthologous functions, whereas some homologous proteins have diverged in terms of their function in different species. A few cases of species specific transcription factors are also observed.
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Affiliation(s)
- Pedro Pais
- Biological Sciences Research Group, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal; Biological Sciences Research Group, Institute for Bioengineering and Biosciences, Instituto Superior TécnicoLisboa, Portugal
| | - Catarina Costa
- Biological Sciences Research Group, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal; Biological Sciences Research Group, Institute for Bioengineering and Biosciences, Instituto Superior TécnicoLisboa, Portugal
| | - Mafalda Cavalheiro
- Biological Sciences Research Group, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal; Biological Sciences Research Group, Institute for Bioengineering and Biosciences, Instituto Superior TécnicoLisboa, Portugal
| | - Daniela Romão
- Biological Sciences Research Group, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal; Biological Sciences Research Group, Institute for Bioengineering and Biosciences, Instituto Superior TécnicoLisboa, Portugal
| | - Miguel C Teixeira
- Biological Sciences Research Group, Department of Bioengineering, Instituto Superior Técnico, Universidade de LisboaLisbon, Portugal; Biological Sciences Research Group, Institute for Bioengineering and Biosciences, Instituto Superior TécnicoLisboa, Portugal
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