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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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Mao Y, Solis NV, Sharma A, Cravener MV, Filler SG, Mitchell AP. Use of the Iron-Responsive RBT5 Promoter for Regulated Expression in Candida albicans. mSphere 2022; 7:e0030522. [PMID: 35862800 PMCID: PMC9429880 DOI: 10.1128/msphere.00305-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/03/2022] [Indexed: 11/20/2022] Open
Abstract
Engineered conditional gene expression is used in appraisal of gene function and pathway relationships. For pathogens like the fungus Candida albicans, conditional expression systems are most useful if they are active in the infection environment and if they can be utilized in multiple clinical isolates. Here, we describe such a system. It employs the RBT5 promoter and can be implemented with a few PCRs. We validated the system with RBT5 promoter fusions to two genes that promote filamentation and polarized growth, UME6 and HGC1, and with efg1Δ/Δ mutants, which are defective in an activator of filamentous growth. An RBT5 promoter fusion to either gene enabled filamentous growth of an efg1Δ/Δ mutant of strain SC5314 in iron-limited media, including RPMI with serum and yeast extract-peptone-dextrose with bathophenanthrolinedisulfonic acid. The RBT5-UME6 fusion promoted filamentation of efg1Δ/Δ mutants in RPMI with serum of four other clinical C. albicans isolates as well. In a mouse model of disseminated candidiasis, the RBT5-UME6 fusion promoted filamentation of the SC5314 efg1Δ/Δ mutant in kidney tissue, an indication that the RBT5 promoter is active in the iron-limited host environment. The RBT5 promoter expands the conditional expression toolkit for C. albicans genetics. IMPORTANCE Genetic strategies have been vital for mechanistic analysis of biological processes. Here, we describe a genetic tool for the fungal pathogen Candida albicans.
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Affiliation(s)
- Yinhe Mao
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Norma V. Solis
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Anupam Sharma
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Max V. Cravener
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Scott G. Filler
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Aaron P. Mitchell
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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Rai LS, van Wijlick L, Chauvel M, d'Enfert C, Legrand M, Bachellier-Bassi S. Overexpression approaches to advance understanding of Candida albicans. Mol Microbiol 2021; 117:589-599. [PMID: 34569668 PMCID: PMC9298300 DOI: 10.1111/mmi.14818] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/15/2022]
Abstract
Candida albicans is an opportunistic fungal pathogen that is responsible for infections linked to high mortality. Loss‐of‐function approaches, taking advantage of gene knockouts or inducible down‐regulation, have been successfully used in this species in order to understand gene function. However, overexpression of a gene provides an alternative, powerful tool to elucidate gene function and identify novel phenotypes. Notably, overexpression can identify pathway components that might remain undetected using loss‐of‐function approaches. Several repressible or inducible promoters have been developed which allow to shut off or turn on the expression of a gene in C. albicans upon growth in the presence of a repressor or inducer. In this review, we summarize recent overexpression approaches used to study different aspects of C. albicans biology, including morphogenesis, biofilm formation, drug tolerance, and commensalism.
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Affiliation(s)
- Laxmi Shanker Rai
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
| | - Lasse van Wijlick
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
| | - Murielle Chauvel
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
| | - Christophe d'Enfert
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
| | - Mélanie Legrand
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
| | - Sophie Bachellier-Bassi
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
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Shabbir Hussain M, Wheeldon I, Blenner MA. A Strong Hybrid Fatty Acid Inducible Transcriptional Sensor Built From Yarrowia lipolytica Upstream Activating and Regulatory Sequences. Biotechnol J 2017; 12. [PMID: 28731568 DOI: 10.1002/biot.201700248] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/21/2017] [Indexed: 01/24/2023]
Abstract
The engineering of Yarrowia lipolytica to accumulate lipids with high titers and productivities has been enabled with a handful of constitutive promoters for pathway engineering. However, the development of promoters that are both strong and lipid responsive could greatly benefit the bioproduction efficiency of lipid-derived oleochemicals in oleaginous yeast. In this study, a fatty acid regulated hybrid promoter for use in Y. lipolytica is engineered. A 200 bp upstream regulatory sequence in the peroxisomal acyl CoA oxidase 2 (POX2) promoter is identified. Further analysis of the promoter sequence reveal a regulatory sequence, that when used in tandem repeats, lead to a 48-fold induction of gene expression relative to glucose and fourfold higher than the native POX2 promoter. To date, this is the strongest inducible promoter reported in Y. lipolytica. Taken together, the results show that it is possible to engineer strong promoters that retain strong inducibility. These types of promoters will be useful in controlling metabolism and as fatty acid sensors.
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Affiliation(s)
| | - Ian Wheeldon
- Chemical & Environmental Engineering, University of California Riverside, Riverside, CA, USA
| | - Mark A Blenner
- Chemical & Biomolecular Engineering, Clemson University, Clemson, SC, USA
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Cassilly CD, Farmer AT, Montedonico AE, Smith TK, Campagna SR, Reynolds TB. Role of phosphatidylserine synthase in shaping the phospholipidome of Candida albicans. FEMS Yeast Res 2017; 17:2966860. [PMID: 28158422 DOI: 10.1093/femsyr/fox007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 01/31/2017] [Indexed: 01/06/2023] Open
Abstract
Phosphatidylserine (PS) synthase (Cho1p) and the PS decarboxylase enzymes (Psd1p and Psd2p), which synthesize PS and phosphatidylethanolamine (PE), respectively, are crucial for Candida albicans virulence. Mutations that disrupt these enzymes compromise virulence. These enzymes are part of the cytidine diphosphate-diacylglycerol pathway (i.e. de novo pathway) for phospholipid synthesis. Understanding how losses of PS and/or PE synthesis pathways affect the phospholipidome of Candida is important for fully understanding how these enzymes impact virulence. The cho1Δ/Δ and psd1Δ/Δ psd2Δ/Δ mutations cause similar changes in levels of phosphatidic acid, phosphatidylglycerol, phosphatidylinositol and PS. However, only slight changes were seen in PE and phosphatidylcholine (PC). This finding suggests that the alternative mechanism for making PE and PC, the Kennedy pathway, can compensate for loss of the de novo synthesis pathway. Candida albicans Cho1p, the lipid biosynthetic enzyme with the most potential as a drug target, has been biochemically characterized, and analysis of its substrate specificity and kinetics reveal that these are similar to those previously published for Saccharomyces cerevisiae Cho1p.
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Affiliation(s)
- Chelsi D Cassilly
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Abigail T Farmer
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
| | | | - Terry K Smith
- Biomedical Sciences Research Complex, Schools of Biology and Chemistry, The North Haugh, The University St. Andrews, Fife KY16 9ST, UK
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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Bijlani S, Nahar AS, Ganesan K. Improved Tet-On and Tet-Off systems for tetracycline-regulated expression of genes in Candida. Curr Genet 2017; 64:303-316. [DOI: 10.1007/s00294-017-0720-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/27/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
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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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Bortezomib inhibits bacterial and fungal β-carbonic anhydrases. Bioorg Med Chem 2016; 24:4406-4409. [PMID: 27469982 DOI: 10.1016/j.bmc.2016.07.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 07/16/2016] [Indexed: 12/28/2022]
Abstract
Inhibition of the β-carbonic anhydrases (CAs, EC 4.2.1.1) from pathogenic fungi (Cryptococcus neoformans, Candida albicans, Candida glabrata, Malassezia globosa) and bacteria (three isoforms from Mycobacterium tuberculosis, Rv3273, Rv1284 and Rv3588), as well from the insect Drosophila melanogaster (DmeCA) and the plant Flaveria bidentis (FbiCA1) with the boronic acid peptidomimetic proteosome inhibitor bortezomib was investigated. Bortezomib was a micromolar inhibitor of all these enzymes, with KIs ranging between 1.12 and 11.30μM. Based on recent crystallographic data it is hypothesized that the B(OH)2 moiety of the inhibitor is directly coordinated to the zinc ion from the enzyme active site. The class of boronic acids, an under-investigated type of CA inhibitors, may lead to the development of anti-infectives with a novel mechanism of action, based on the pathogenic organisms CA inhibition.
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Defosse TA, Melin C, Obando Montoya EJ, Lanoue A, Foureau E, Glévarec G, Oudin A, Simkin AJ, Crèche J, Atehortùa L, Giglioli-Guivarc’h N, Clastre M, Courdavault V, Papon N. A new series of vectors for constitutive, inducible or repressible gene expression in Candida guilliermondii. J Biotechnol 2014; 180:37-42. [DOI: 10.1016/j.jbiotec.2014.03.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 12/11/2022]
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10
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Natural and synthetic small boron-containing molecules as potential inhibitors of bacterial and fungal quorum sensing. Chem Rev 2010; 111:209-37. [PMID: 21171664 DOI: 10.1021/cr100093b] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Innocenti A, Hall RA, Schlicker C, Scozzafava A, Steegborn C, Mühlschlegel FA, Supuran CT. Carbonic anhydrase inhibitors. Inhibition and homology modeling studies of the fungal β-carbonic anhydrase from Candida albicans with sulfonamides. Bioorg Med Chem 2009; 17:4503-9. [DOI: 10.1016/j.bmc.2009.05.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 04/29/2009] [Accepted: 05/04/2009] [Indexed: 10/20/2022]
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13
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Carbonic anhydrase inhibitors. Inhibition of the fungal β-carbonic anhydrases from Candida albicans and Cryptococcus neoformans with boronic acids. Bioorg Med Chem Lett 2009; 19:2642-5. [DOI: 10.1016/j.bmcl.2009.03.147] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 03/30/2009] [Accepted: 03/30/2009] [Indexed: 01/22/2023]
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