Recent Advances in Genome Editing Tools in Medical Mycology Research
Abstract
:1. Introduction
2. Genome Editing Technologies
2.1. RNA Interference (RNAi)
2.2. Restriction Enzymes
2.3. Zinc-Finger Nucleases (ZFNs)
2.4. Transcription Activator-Like Effector Nucleases (TALENs)
2.5. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR Associated Protein 9 (CRISPR-Cas9)
3. Mechanism of Action of CRISPR-Cas9
4. Applications of CRISPR-Cas9 Genome Editing Tool in Medically Important Fungi
4.1. Clinically Relevant Yeasts
4.2. Filamentous Fungi
5. Conclusions and Future Prospects
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
Ago | Argonaute |
AIDS | acquired immunodeficiency syndrome |
CRISPR | clustered regularly interspaced short palindromic repeats |
CRISPR-Cas9 | clustered regularly interspaced short palindromic repeats associated protein 9 |
Cas9-NLS | cas9 with a nuclear localization signal |
crRNA | CRISPR RNA |
dCas9 | dead version of Cas9 |
DSB | double stranded break |
dsRNA | double-stranded RNA |
HR | homologous recombination |
HDR | homology directed repair |
IDT | integrated DNA technologies |
MIC | minimum inhibitory concentration |
mRNA | messenger RNA |
NHEJ | non-homologous end joining |
NGG | nucleotide- guanine-guanine |
PAM | protospacer adjacent motif |
PKS | polyketide synthase |
REMI | restriction enzyme mediated integration |
RISC | RNA- induced silencing complex |
RVD | repeat variable di-residues |
SAT1-FLP | SAT1 flipper |
siRNA | small interfering RNA |
sgRNA | single guide RNA |
SNP | single nucleotide polymorphism |
TALEN | transcription activator-like effector nucleases |
tracrRNA | trans-activating crRNA |
ZFN | zinc-finger nuclease |
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Organism | CAS9 Expression Module | GRNA Expression Module | Target Gene (S) | Purpose of Application | Editing Rate and Result | References |
---|---|---|---|---|---|---|
C. albicans | Candida/Saccharomyces codon–optimized version of Cas9 (CaCas9)/the ENO1 promoter | The RNA polymerase III (Pol III) promoter SNR52 | ADE2, CDR1/CDR2 | To generate homozygous mutations in one transformation by Duet and Solo system | Duet system showed 20–40% mutagenesis efficiency, and Solo system enabled 60–80% targeting | Vyas et al. (2015) [57] |
C. albicans | Transient CRISPR-Cas9 system by using a SAT1-FLP system | SNR52P/TENO1 | NDT80, REP1, and RON1 | To better understand role of target genes (single or in combination) in virulence | Single, double, and triple deletion strains were successfully constructed | Min et al. (2018) [60] |
C. albicans | US-pENO1 ˃ Cas9-NAT | NAT-pSNR52-gRNA-DS | ADE2, URA3, WOR1,WOR, and CZF1 | To develop a marker less system without need for molecular cloning step | 80% single gene deletion, 20% double genes deletion and ˃50% integration efficiency | Nguyen et al. (2017) [58] |
C. albicans | CIp-ARG4-PTEF CaCAS9 | PADH1-tRNA-driven gRNA expression | RFP | To optimize gRNA intracellular expression | Increase the gene editing efficiency by 10-fold | Ng et al. (2017) [64] |
C. albicans | CaCas9 into the C. albicans genome at the NEUT5L locus | 5′ homology arm–SNR52 promoter–gRNA1–gRNA2-3′ homology arm | antifungal efflux and biofilm adhesion factors | To develop a gene drive array system for the generation of combinatorial deletion mutants | Two larges pairwise gene deletion mutants were successfully generated | Shapiro et al. (2018) [63] |
C. albicans | the ENO1 promoter/Cas9 (CaCas9)/TCYC1 | SNR52P/TENO1 | ADE2 | To describe a transient CRISPR-Cas9 system for efficient gene deletion | Homozygous deletions by introduction of CaCas9 transiently | Min et al. (2016) [59] |
C. parapsilosis | TEF1p-CAS9-TEF1t | pCpSNR52-sgRNA-SUP4t and cpGAPDHp-HH-sgRNA-HDV-GAPDHt | ADE2, CPAR2_101060 and URA3 | To apply gene manipulation in single transformation step which can be used for editing of any number of target genes | The system yielded up to 100% efficiency across a panel of 20 clinical isolates | Lombardi et al. (2017) [66] |
C. glabrata | pTEF1-Cas9-tCYC1/pCYC1-Cas9-tCYC1 | pSNR52-sgRNA-tTY2/pRNAH1-sgRNA-tTY2 | ADE2, VPK1 and YPS11 | To establish a loss-of-function mutation through the NHEJ repair pathway | High | Enkler et al. (2016) [61] |
C. glabrata | pTEF-Cas9-KanMX | pSNR52-sgRNA-CYC1t | ADE2, MET15 and SOK2 | To compare genome modifications in C. glabrata wild type and lig4 strains | Targeting efficiency in the lig4Δ mutant was higher than in the wild type strain | Cen et al. (2017) [62] |
C. albicans | Codon-optimized version of Cas9(CaCas9)-SV40NLS | SNR52 RNA polymerase III promoter | CDR1 and CDR2 | To present a modified gene-drive-based assay for gene manipulation | − | Halder et al. (2019) [65] |
C. albicans | ACT1p-dCAS9-ACT1t | SNR52p-gRNA tail | ADE2 | To demonstrate a functional CRISPRi system for transcriptional repression | 20-fold repression of target gene achieved | Wensing et al. (2019) [68] |
C. parapsilosis, C. orthopsilosis, C. metapsilosis and C. tropicalis | MgTEF1p-CAS9-MgTRP1t | pAgTEF1-sgRNA-HDV-ScCYC1t | ADE2 and CPAR2_101060 | To construct an autonomously replicating plasmid for markerless ediing in Candida spp. | Single gene distribution efficiency observed in C. parapsilosis (approximately 80%), C. meta psilosis (100%), C. tropicalis (88–100%) | Lombardi et al. (2019) [67] |
Cryptococcus neoformance | TEF1p-Cas9-SV40NLS-TEF1t | pACT1-HH-gRNA-HDV-TRPt | ADE2 | To demonstrate the first proof of principle study | 70% | Arras et al. (2016) [71] |
C. neoformans | ACT1P-SV40NLS-Cas9-NLS-bGHpAt | pCnU6-GN19-gRNA-6Ts | ADE2 and Tsp2-1 | To develop a system for gene alterations by subsequent complementation and off-target effects reduction | Frequency of gene deletion was over 80%, indel efficiency and HR rates were 40–90% and 20–90%, respectively | Wang et al. (2016) [72] |
C. neoformans | GPD1p–Cas9-GPD1 t | pCnU6-sgRNA-6-Tt | ADE2 | To generate a TRACE system as an cost-effective and efficient strategy for genetic modifications | Up to 90% gene disruption rate | Fan et al. (2018) [73] |
C. neoformans | pTEF-Cas9-FLAG-NLS | ptRNA-sgRNA-NLS | GIB2 | To deliver a preassembled RNP via electroporation to accelerate of gene editing | Approach is sufficient to induce gene modification | Wang P. (2018) [74] |
Organism | CAS9 Expression Module | GRNA Expression Module | Target Gene (S) | Purpose of Application | Editing Rate and Result | References |
---|---|---|---|---|---|---|
A. fumigatus | p-hph-Ptef1-cas9 | p426-SNR52p-gRNA.CAN1.Y-SUP4t | PKSP | To test CRISPR-CAS9 method in this organism | High gene targeting efficiency reached 25–53% | Fuller et al. (2015) [83] |
A. fumigatus | Gpdap-3xFLAG-NLS-Cas9-NLS-TRPCt | U6-3-gRNA | pksP and cnaA genes | To establish the system for mutagenesis using MMEJ process | Approximately 95–100% rate of mutagenesis obtained | Zhang et al. (2016) [84] |
A. fumigatus | Alt-R-CRISPR-Cas9 components from integrated DNA technologies (IDT) | cr5 = pksP and cr3 = pksP | PKSP | An in vitro assembly of RNP demonstrated to eliminate the strain construction step | Gene deletion efficiency was close to 100% | Al-Abdallah et al. (2017) [48] |
A. fumigatus | Cas9-NLS | T7-sgRNA | CYP51A | To investigate the mechanisms of azole resistance via cyp51A alteration | Site-directed mutagenesis successfully performed using CRISPR-CAS9 system | Umeyama et al. (2018) [46] |
Mucor circinelloides | Alt-R CRISPR-Cas9 tracrRNA | Alt-R CRISPR crRNA | CARB and HMGR2 | To obtain mitotically stable mutants, a plasmid free CRISPR-Cas9 approach demonstrated | Targeting efficiency of NHEJ and HR reach to 100% | Nagy et al. (2017) [85] |
Rhizopus delemar | pmCas9: tRNA-gRNA | pmCas9: tRNA-gRNA | PYRF | For investigating molecular pathogenesis mechanisms, point mutation introduced | Efficiency of 36% to 59% | Bruni et al. (2019) [86] |
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Nargesi, S.; Kaboli, S.; Thekkiniath, J.; Heidari, S.; Keramati, F.; Seyedmousavi, S.; Hedayati, M.T. Recent Advances in Genome Editing Tools in Medical Mycology Research. J. Fungi 2021, 7, 257. https://doi.org/10.3390/jof7040257
Nargesi S, Kaboli S, Thekkiniath J, Heidari S, Keramati F, Seyedmousavi S, Hedayati MT. Recent Advances in Genome Editing Tools in Medical Mycology Research. Journal of Fungi. 2021; 7(4):257. https://doi.org/10.3390/jof7040257
Chicago/Turabian StyleNargesi, Sanaz, Saeed Kaboli, Jose Thekkiniath, Somayeh Heidari, Fatemeh Keramati, Seyedmojtaba Seyedmousavi, and Mohammad Taghi Hedayati. 2021. "Recent Advances in Genome Editing Tools in Medical Mycology Research" Journal of Fungi 7, no. 4: 257. https://doi.org/10.3390/jof7040257