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Huang L, Li N, Song Y, Gao J, Nian L, Zhou J, Zhang B, Liu Z, Zheng Y. Development of a marker recyclable CRISPR/Cas9 system for scarless and multigene editing in Fusarium fujikuroi. Biotechnol J 2024; 19:e2400164. [PMID: 39014928 DOI: 10.1002/biot.202400164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024]
Abstract
Iterative metabolic engineering of Fusarium fujikuroi has traditionally been hampered by its low homologous recombination efficiency and scarcity of genetic markers. Thus, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas9) system has emerged as a promising tool for precise genome editing in this organism. Some integrated CRISPR/Cas9 strategies have been used to engineer F. fujikuroi to improve GA3 production capabilities, but low editing efficiency and possible genomic instability became the major obstacle. Herein, we developed a marker recyclable CRISPR/Cas9 system for scarless and multigene editing in F. fujikuroi. This system, based on an autonomously replicating sequence, demonstrated the capability of a single plasmid harboring all editing components to achieve 100%, 75%, and 37.5% editing efficiency for single, double, and triple gene targets, respectively. Remarkably, even with a reduction in homologous arms to 50 bp, we achieved a 12.5% gene editing efficiency. By employing this system, we successfully achieved multicopy integration of the truncated 3-hydroxy-3-methyl glutaryl coenzyme A reductase gene (tHMGR), leading to enhanced GA3 production. A key advantage of our plasmid-based gene editing approach was the ability to recycle selective markers through a simplified protoplast preparation and recovery process, which eliminated the need for additional genetic markers. These findings demonstrated that the single-plasmid CRISPR/Cas9 system enables rapid and precise multiple gene deletions/integrations, laying a solid foundation for future metabolic engineering efforts aimed at industrial GA3 production.
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Affiliation(s)
- Lianggang Huang
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ningning Li
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yixin Song
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Jie Gao
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Lu Nian
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Junping Zhou
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Bo Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Zhiqiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yuguo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China
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Hervay NT, Elias D, Habova M, Jacko J, Morvova M, Gbelska Y. Catechin potentiates the antifungal effect of miconazole in Candida glabrata. Folia Microbiol (Praha) 2023; 68:835-842. [PMID: 37145224 PMCID: PMC10689516 DOI: 10.1007/s12223-023-01061-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023]
Abstract
The rising number of invasive fungal infections caused by drug-resistant Candida strains is one of the greatest challenges for the development of novel antifungal strategies. The scarcity of available antifungals has drawn attention to the potential of natural products as antifungals and in combinational therapies. One of these is catechins-polyphenolic compounds-flavanols, found in a variety of plants. In this work, we evaluated the changes in the susceptibility of Candida glabrata strain characterized at the laboratory level and clinical isolates using the combination of catechin and antifungal azoles. Catechin alone had no antifungal activity within the concentration range tested. Its use in combination with miconazole resulted in complete inhibition of growth in the sensitive C. glabrata isolate and a significant growth reduction in the azole resistant C. glabrata clinical isolate. Simultaneous use of catechin and miconazole leads to increased intracellular ROS generation. The enhanced susceptibility of C. glabrata clinical isolates to miconazole by catechin was accompanied with the intracellular accumulation of ROS and changes in the plasma membrane permeability, as measured using fluorescence anisotropy, affecting the function of plasma membrane proteins.
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Affiliation(s)
- Nora Tóth Hervay
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, Bratislava, 842 15, Slovak Republic
| | - Daniel Elias
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, Bratislava, 842 15, Slovak Republic
| | - Marcela Habova
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, Bratislava, 842 15, Slovak Republic
| | - Juraj Jacko
- Faculty of Mathematics, Physics and Informatics, Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, Mlynska Dolina, Bratislava, 842 48, Slovak Republic
| | - Marcela Morvova
- Faculty of Mathematics, Physics and Informatics, Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, Mlynska Dolina, Bratislava, 842 48, Slovak Republic
| | - Yvetta Gbelska
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, Bratislava, 842 15, Slovak Republic.
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Elias D, Tóth Hervay N, Bujdos M, Gbelska Y. Essential Role of CgErg6p in Maintaining Oxidative Stress Tolerance and Iron Homeostasis in Candida glabrata. J Fungi (Basel) 2023; 9:jof9050579. [PMID: 37233290 DOI: 10.3390/jof9050579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
The human pathogenic fungus Candida glabrata is the second leading cause of candidemia, a life-threatening invasive mycosis. Clinical outcomes are complicated by reduced susceptibility of C. glabrata to azoles together with its ability to evolve stable resistance to both azoles and echinocandins following drug exposure. Compared to other Candida spp., C. glabrata displays robust oxidative stress resistance. In this study, we investigated the impact of CgERG6 gene deletion on the oxidative stress response in C. glabrata. CgERG6 gene encodes sterol-24-C-methyltransferase, which is involved in the final steps of ergosterol biosynthesis. Our previous results showed that the Cgerg6Δ mutant has a lower ergosterol content in its membranes. Here, we show that the Cgerg6Δ mutant displays increased susceptibility to oxidative stress inducing agents, such as menadione, hydrogen peroxide and diamide, accompanied with increased intracellular ROS production. The Cgerg6Δ mutant is not able to tolerate higher concentrations of iron in the growth media. We observed increased expression of transcription factors, CgYap1p, CgMsn4p and CgYap5p, together with increased expression of catalase encoding the CgCTA1 gene and vacuolar iron transporter CgCCC1 in the Cgerg6Δ mutant cells. However, it seems that the CgERG6 gene deletion does not influence the function of mitochondria.
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Affiliation(s)
- Daniel Elias
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Nora Tóth Hervay
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Marek Bujdos
- Faculty of Natural Sciences, Institute of Laboratory Research on Geomaterials, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Yvetta Gbelska
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovakia
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Acs-Szabo L, Papp LA, Takacs S, Miklos I. Disruption of the Schizosaccharomyces japonicus lig4 Disturbs Several Cellular Processes and Leads to a Pleiotropic Phenotype. J Fungi (Basel) 2023; 9:jof9050550. [PMID: 37233261 DOI: 10.3390/jof9050550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/15/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Gene targeting is a commonly used method to reveal the function of genes. Although it is an attractive tool for molecular studies, it can frequently be a challenge because its efficiency can be low and it requires the screening of a large number of transformants. Generally, these problems originate from the elevated level of ectopic integration caused by non-homologous DNA end joining (NHEJ). To eliminate this problem, NHEJ-related genes are frequently deleted or disrupted. Although these manipulations can improve gene targeting, the phenotype of the mutant strains raised the question of whether mutations have side effects. The aim of this study was to disrupt the lig4 gene in the dimorphic fission yeast, S. japonicus, and investigate the phenotypic changes of the mutant strain. The mutant cells have shown various phenotypic changes, such as increased sporulation on complete medium, decreased hyphal growth, faster chronological aging, and higher sensitivity to heat shock, UV light, and caffeine. In addition, higher flocculation capacity has been observed, especially at lower sugar concentrations. These changes were supported by transcriptional profiling. Many genes belonging to metabolic and transport processes, cell division, or signaling had altered mRNA levels compared to the control strain. Although the disruption improved the gene targeting, we assume that the lig4 inactivation can cause unexpected physiological side effects, and we have to be very careful with the manipulations of the NHEJ-related genes. To reveal the exact mechanisms behind these changes, further investigations are required.
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Affiliation(s)
- Lajos Acs-Szabo
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Laszlo Attila Papp
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Szonja Takacs
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Ida Miklos
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
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Elias D, Hervay NT, Jacko J, Morvova M, Valachovic M, Gbelska Y. Erg6p is essential for antifungal drug resistance, plasma membrane properties and cell wall integrity in Candida glabrata. FEMS Yeast Res 2022; 21:6680247. [PMID: 36047961 DOI: 10.1093/femsyr/foac045] [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: 05/30/2022] [Revised: 07/18/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
ERG6 gene encodes C-24 methyltransferase, one of the specific enzymes that differ in mammalian and yeast sterol biosynthesis. To explore the function of CgErg6p in the yeast pathogen Candida glabrata, we have constructed the Cgerg6Δ deletion mutant. We found that C. glabrata cells lacking CgErg6p exhibit reduced susceptibility to both antifungal azoles and polyenes. The reduced content of ergosterol in the Cgerg6 deletion mutant was accompanied by increased expression of genes encoding the last steps of the ergosterol biosynthetic pathway. The absence of CgErg6p leads to plasma membrane hyperpolarization and decrease in its fluidity compared to the parental C. glabrata strain. The absence of sterols containing C-24 alkyls influenced the susceptibility of Cgerg6Δ mutant cells to alkali metal cations and several other metabolic inhibitors. Our results thus show that sterols lacking C-24 alkyls are not sufficient substitutes for maintaining yeast plasma membrane function. The absence of CgErg6p influences also the cell wall integrity and calcineurin signaling in C. glabrata.
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Affiliation(s)
- Daniel Elias
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovak Republic
| | - Nora Toth Hervay
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovak Republic
| | - Juraj Jacko
- Faculty of Mathematics, Physics and Informatics, Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, Mlynska dolina, 842 48 Bratislava, Slovak Republic
| | - Marcela Morvova
- Faculty of Mathematics, Physics and Informatics, Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, Mlynska dolina, 842 48 Bratislava, Slovak Republic
| | - Martin Valachovic
- Institute of Animal Biochemistry and Genetics CBS SAS, Dubravska cesta 9, 840 05 BratislavaSlovak Republic
| | - Yvetta Gbelska
- Faculty of Natural Sciences, Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovicova 6, 842 15 Bratislava, Slovak Republic
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Epigenetic Regulation of Antifungal Drug Resistance. J Fungi (Basel) 2022; 8:jof8080875. [PMID: 36012862 PMCID: PMC9409733 DOI: 10.3390/jof8080875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Abstract
In medical mycology, epigenetic mechanisms are emerging as key regulators of multiple aspects of fungal biology ranging from development, phenotypic and morphological plasticity to antifungal drug resistance. Emerging resistance to the limited therapeutic options for the treatment of invasive fungal infections is a growing concern. Human fungal pathogens develop drug resistance via multiple mechanisms, with recent studies highlighting the role of epigenetic changes involving the acetylation and methylation of histones, remodeling of chromatin and heterochromatin-based gene silencing, in the acquisition of antifungal resistance. A comprehensive understanding of how pathogens acquire drug resistance will aid the development of new antifungal therapies as well as increase the efficacy of current antifungals by blocking common drug-resistance mechanisms. In this article, we describe the epigenetic mechanisms that affect resistance towards widely used systemic antifungal drugs: azoles, echinocandins and polyenes. Additionally, we review the literature on the possible links between DNA mismatch repair, gene silencing and drug-resistance mechanisms.
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What do we know about the biology of the emerging fungal pathogen of humans Candida auris? Microbiol Res 2020; 242:126621. [PMID: 33096325 DOI: 10.1016/j.micres.2020.126621] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/25/2020] [Accepted: 10/04/2020] [Indexed: 02/07/2023]
Abstract
Candida auris is a worrisome fungal pathogen of humans which emerged merely about a decade ago. Ever since then the scientific community worked hard to understand clinically relevant traits, such as virulence factors, antifungal resistance mechanisms, and its ability to adhere to human skin and medical devices. Whole-genome sequencing of clinical isolates and epidemiological studies outlining the path of nosocomial outbreaks have been the focus of research into this pathogenic and multidrug-resistant yeast since its first description in 2009. More recently, work was started by several laboratories to explore the biology of C. auris. Here, we review the insights of studies characterizing the mechanisms underpinning antifungal drug resistance, biofilm formation, morphogenetic switching, cell aggregation, virulence, and pathogenicity of C. auris. We conclude that, although some progress has been made, there is still a long journey ahead of us, before we fully understand this novel pathogen. Critically important is the development of molecular tools for C. auris to make this fungus genetically tractable and traceable. This will allow an in-depth molecular dissection of the life cycle of C. auris, of its characteristics while interacting with the human host, and the mechanisms it employs to avoid being killed by antifungals and the immune system.
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Cen YK, Lin JG, Wang YL, Wang JY, Liu ZQ, Zheng YG. The Gibberellin Producer Fusarium fujikuroi: Methods and Technologies in the Current Toolkit. Front Bioeng Biotechnol 2020; 8:232. [PMID: 32292777 PMCID: PMC7118215 DOI: 10.3389/fbioe.2020.00232] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/06/2020] [Indexed: 12/18/2022] Open
Abstract
In recent years, there has been a noticeable increase in research interests on the Fusarium species, which includes prevalent plant pathogens and human pathogens, common microbial food contaminants and industrial microbes. Taken the advantage of gibberellin synthesis, Fusarium fujikuroi succeed in being a prevalent plant pathogen. At the meanwhile, F. fujikuroi was utilized for industrial production of gibberellins, a group of extensively applied phytohormone. F. fujikuroi has been known for its outstanding performance in gibberellin production for almost 100 years. Research activities relate to this species has lasted for a very long period. The slow development in biological investigation of F. fujikuroi is largely due to the lack of efficient research technologies and molecular tools. During the past decade, technologies to analyze the molecular basis of host-pathogen interactions and metabolic regulations have been developed rapidly, especially on the aspects of genetic manipulation. At the meanwhile, the industrial fermentation technologies kept sustained development. In this article, we reviewed the currently available research tools/methods for F. fujikuroi research, focusing on the topics about genetic engineering and gibberellin production.
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Affiliation(s)
- Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jian-Guang Lin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - You-Liang Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jun-You Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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Cen Y, Timmermans B, Souffriau B, Thevelein JM, Van Dijck P. Comparison of genome engineering using the CRISPR-Cas9 system in C. glabrata wild-type and lig4 strains. Fungal Genet Biol 2017; 107:44-50. [PMID: 28822858 DOI: 10.1016/j.fgb.2017.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 08/09/2017] [Accepted: 08/15/2017] [Indexed: 10/19/2022]
Abstract
Candida glabrata is reported as the second most prevalent human opportunistic fungal pathogen in North America and is threatening patients all over the world. Its incidence is rising, while it has developed resistance to the most widely used antifungal drugs, necessitating new approaches based on better insight into the biology of the organism. Despite its close phylogenetic relationship with Saccharomyces cerevisiae, generating precise genomic alterations in this species is problematic. Previously we have shown that deletion of LIG4, which encodes an enzyme involved in Non-Homologous End Joining (NHEJ), strongly enhances the probability of obtaining correctly modified transformants. In this work we used the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated protein 9 (Cas9) system to genetically engineer the C. glabrata genome, targeting the genes ADE2, MET15 and SOK2, located on different chromosomes. We used the CRISPR-Cas9 technology to replace the open reading frame (ORF) by the SAT1 selective marker or introduced a premature stop codon in ADE2 and MET15, as they are easily scored by their adenine or methionine auxotrophy, respectively. The SOK2 gene was modified by insertion of a triple HA-tag sequence and the transformants were verified in a western blot. The CRISPR-Cas9 mediated targeting efficiency varies depending on the gene targeted and the genetic modification performed. We show that CRISPR-Cas9 mediated genome editing is more efficient than the conventional method in the wild-type strain, moreover it has the big advantage being marker-free. In previous work, we showed that the targeting efficiency is highly increased in the lig4Δ strain using the conventional way to delete genes in C. glabrata. Using the CRISPR-Cas9 system in this strain, the percentage of correct transformants is consistently higher compared to the wild-type strain. This indicates that using the lig4 mutant as such is already a strong improvement, while the CRISPR-Cas9 gives the additional advantage of not leaving a scar or marker and that it therefore can be used to generate multiple modifications.
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Affiliation(s)
- Yuke Cen
- KU Leuven, Laboratory of Molecular Cell Biology, Kasteelpark Arenberg 31, bus 2438, 3001 Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Bea Timmermans
- KU Leuven, Laboratory of Molecular Cell Biology, Kasteelpark Arenberg 31, bus 2438, 3001 Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Ben Souffriau
- KU Leuven, Laboratory of Molecular Cell Biology, Kasteelpark Arenberg 31, bus 2438, 3001 Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Johan M Thevelein
- KU Leuven, Laboratory of Molecular Cell Biology, Kasteelpark Arenberg 31, bus 2438, 3001 Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Patrick Van Dijck
- KU Leuven, Laboratory of Molecular Cell Biology, Kasteelpark Arenberg 31, bus 2438, 3001 Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
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Oguro Y, Yamazaki H, Ara S, Shida Y, Ogasawara W, Takagi M, Takaku H. Efficient gene targeting in non-homologous end-joining-deficient Lipomyces starkeyi strains. Curr Genet 2017; 63:751-763. [DOI: 10.1007/s00294-017-0679-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/21/2017] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
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Abstract
Adaptation to alternating CO2 concentrations is crucial for all organisms. Carbonic anhydrases—metalloenzymes that have been found in all domains of life—enable fixation of scarce CO2 by accelerating its conversion to bicarbonate and ensure maintenance of cellular metabolism. In fungi and other eukaryotes, the carbonic anhydrase Nce103 has been shown to be essential for growth in air (~0.04% CO2). Expression of NCE103 is regulated in response to CO2 availability. In Saccharomyces cerevisiae, NCE103 is activated by the transcription factor ScCst6, and in Candida albicans and Candida glabrata, it is activated by its homologues CaRca1 and CgRca1, respectively. To identify the kinase controlling Cst6/Rca1, we screened an S. cerevisiae kinase/phosphatase mutant library for the ability to regulate NCE103 in a CO2-dependent manner. We identified ScSch9 as a potential ScCst6-specific kinase, as the sch9Δ mutant strain showed deregulated NCE103 expression on the RNA and protein levels. Immunoprecipitation revealed the binding capabilities of both proteins, and detection of ScCst6 phosphorylation by ScSch9 in vitro confirmed Sch9 as the Cst6 kinase. We could show that CO2-dependent activation of Sch9, which is part of a kinase cascade, is mediated by lipid/Pkh1/2 signaling but not TORC1. Finally, we tested conservation of the identified regulatory cascade in the pathogenic yeast species C. albicans and C. glabrata. Deletion of SCH9 homologues of both species impaired CO2-dependent regulation of NCE103 expression, which indicates a conservation of the CO2 adaptation mechanism among yeasts. Thus, Sch9 is a Cst6/Rca1 kinase that links CO2 adaptation to lipid signaling via Pkh1/2 in fungi. All living organisms have to cope with alternating CO2 concentrations as CO2 levels range from very low in the atmosphere (0.04%) to high (5% and more) in other niches, including the human body. In fungi, CO2 is sensed via two pathways. The first regulates virulence in pathogenic yeast by direct activation of adenylyl cyclase. The second pathway, although playing a fundamental role in fungal metabolism, is much less understood. Here the transcription factor Cst6/Rca1 controls carbon homeostasis by regulating carbonic anhydrase expression. Upstream signaling in this pathway remains elusive. We identify Sch9 as the kinase controlling Cst6/Rca1 activity in yeast and demonstrate that this pathway is conserved in pathogenic yeast species, which highlights identified key players as potential pharmacological targets. Furthermore, we provide a direct link between adaptation to changing CO2 conditions and lipid/Pkh1/2 signaling in yeast, thus establishing a new signaling cascade central to metabolic adaptation.
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Ho HL, Haynes K. Candida glabrata: new tools and technologies-expanding the toolkit. FEMS Yeast Res 2015; 15:fov066. [PMID: 26205243 PMCID: PMC4629792 DOI: 10.1093/femsyr/fov066] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/29/2015] [Accepted: 07/15/2015] [Indexed: 12/11/2022] Open
Abstract
In recent years, there has been a noticeable rise in fungal infections related to non-albicans Candida species, including Candida glabrata which has both intrinsic resistance to and commonly acquired resistance to azole antifungals. Phylogenetically, C. glabrata is more closely related to the mostly non-pathogenic model organism Saccharomyces cerevisiae than to other Candida species. Despite C. glabrata's designation as a pathogen by Wickham in 1957, relatively little is known about its mechanism of virulence. Over the past few years, technology to analyse the molecular basis of infection has developed rapidly, and here we briefly review the major advances in tools and technologies available to explore and investigate the virulence of C. glabrata that have occurred over the past decade.
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Affiliation(s)
- Hsueh-lui Ho
- Biosciences, University of Exeter, Stocker Road, Exeter, Devon EX4 4QD, UK
| | - Ken Haynes
- Biosciences, University of Exeter, Stocker Road, Exeter, Devon EX4 4QD, UK
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