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Chauvel M, Bachellier-Bassi S, Guérout AM, Lee KK, Maufrais C, Permal E, Da Fonseca JP, Znaidi S, Mazel D, Munro CA, d'Enfert C, Legrand M. High-throughput functional profiling of the human fungal pathogen Candida albicans genome. Res Microbiol 2023; 174:104025. [PMID: 36587858 DOI: 10.1016/j.resmic.2022.104025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
Candida albicans is a major fungal pathogen of humans. Although its genome has been sequenced more than two decades ago, there are still over 4300 uncharacterized C. albicans genes. We previously generated an ORFeome as well as a collection of destination vectors to facilitate overexpression of C. albicans ORFs. Here, we report the construction of ∼2500 overexpression mutants and their evaluation by in vitro spotting on rich medium and in a liquid pool experiment in rich medium, allowing the identification of genes whose overexpression has a fitness cost. The candidates were further validated at the individual strain level. This new resource allows large-scale screens in different growth conditions to be performed routinely. Altogether, based on the concept of identifying functionally related genes by cluster analysis, the availability of this overexpression mutant collection will facilitate the characterization of gene functions in C. albicans.
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Affiliation(s)
- Murielle Chauvel
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
| | - Sophie Bachellier-Bassi
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
| | - Anne-Marie Guérout
- Institut Pasteur, Université Paris Cité, UMR3525 CNRS, Unité Plasticité du Génome Bactérien, F-75015 Paris, France.
| | - Keunsook K Lee
- Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK; NGeneBio, 307 Daerung Post-tower 1, 288 Digital-ro, Guro-gu, Seoul 08390, Republic of Korea.
| | - Corinne Maufrais
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France; Institut Pasteur, Université Paris Cité, Hub de Bioinformatique, F-75015 Paris, France.
| | - Emmanuelle Permal
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France; Institut Pasteur, Université Paris Cité, UMR3525 CNRS, Unité Plasticité du Génome Bactérien, F-75015 Paris, France; Institut Pasteur, Université Paris Cité, Hub de Bioinformatique, F-75015 Paris, France.
| | - Juliana Pipoli Da Fonseca
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques (C2RT), F-75015 Paris, France.
| | - Sadri Znaidi
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France; Laboratoire de Microbiologie Moléculaire, Vaccinologie et Développement Biotechnologique, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis-Belvédère, Tunisia.
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, UMR3525 CNRS, Unité Plasticité du Génome Bactérien, F-75015 Paris, France.
| | - Carol A Munro
- Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK.
| | - Christophe d'Enfert
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
| | - Melanie Legrand
- Institut Pasteur, Université Paris Cité, INRAE USC2019, Unité Biologie et Pathogénicité Fongiques, F-75015 Paris, France.
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Gervais NC, La Bella AA, Wensing LF, Sharma J, Acquaviva V, Best M, Cadena López RO, Fogal M, Uthayakumar D, Chavez A, Santiago-Tirado F, Flores-Mireles AL, Shapiro RS. Development and applications of a CRISPR activation system for facile genetic overexpression in Candida albicans. G3 (BETHESDA, MD.) 2023; 13:jkac301. [PMID: 36450451 PMCID: PMC9911074 DOI: 10.1093/g3journal/jkac301] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/02/2021] [Accepted: 11/04/2022] [Indexed: 12/02/2022]
Abstract
For the fungal pathogen Candida albicans, genetic overexpression readily occurs via a diversity of genomic alterations, such as aneuploidy and gain-of-function mutations, with important consequences for host adaptation, virulence, and evolution of antifungal drug resistance. Given the important role of overexpression on C. albicans biology, it is critical to develop and harness tools that enable the analysis of genes expressed at high levels in the fungal cell. Here, we describe the development, optimization, and application of a novel, single-plasmid-based CRISPR activation (CRISPRa) platform for targeted genetic overexpression in C. albicans, which employs a guide RNA to target an activator complex to the promoter region of a gene of interest, thus driving transcriptional expression of that gene. Using this system, we demonstrate the ability of CRISPRa to drive high levels of gene expression in C. albicans, and we assess optimal guide RNA targeting for robust and constitutive overexpression. We further demonstrate the specificity of the system via RNA sequencing. We highlight the application of CRISPR activation to overexpress genes involved in pathogenesis and drug susceptibility, and contribute toward the identification of novel phenotypes. Consequently, this tool will facilitate a broad range of applications for the study of C. albicans genetic overexpression.
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Affiliation(s)
- Nicholas C Gervais
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | - Alyssa A La Bella
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Lauren F Wensing
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | - Jehoshua Sharma
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | - Victoria Acquaviva
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | - Madison Best
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | | | - Meea Fogal
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
| | - Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
- Present address: Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | | | - Ana L Flores-Mireles
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1H 5N4, Canada
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