Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system

Liu, Rui; Chen, Ling; Jiang, Yanping; Zhou, Zhihua; Zou, Gen

doi:10.1038/celldisc.2015.7

Cited by 368 publications

(356 citation statements)

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“…For the CRISPR/ Cas9 system in yeast it has been reported that through short NHEJmediated indels, there is a 469-fold increase in mutation frequency for target gene disruption after cas9 gene induction (24). Moreover, the simultaneous targeting of multiple loci can be achieved by introducing multiple and unique gRNA sequences (18,26).…”

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confidence: 99%

“…CRISPR/Cas9 originates as a prokaryotic adaptive defense system against invading viruses and DNA (15,16). Remarkably, and in just the past 2 years, the system derived from Streptococcus pyogenes (17) has been simplified as a genomic engineering tool in diverse eukaryotes, such as mice and rats (18)(19)(20)(21), plants (22,23), and even fungi, including Saccharomyces cerevisiae (24), Candida albicans (25), Trichoderma reesei (26), and other Aspergillus spp. (27).…”

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Development of the CRISPR/Cas9 System for Targeted Gene Disruption in Aspergillus fumigatus

et al. 2015

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bLow rates of homologous recombination have broadly encumbered genetic studies in the fungal pathogen Aspergillus fumigatus. The CRISPR/Cas9 system of bacteria has recently been developed for targeted mutagenesis of eukaryotic genomes with high efficiency and, importantly, through a mechanism independent of homologous repair machinery. As this new technology has not been developed for use in A. fumigatus, we sought to test its feasibility for targeted gene disruption in this organism. As a proof of principle, we first demonstrated that CRISPR/Cas9 can indeed be used for high-efficiency (25 to 53%) targeting of the A. fumigatus polyketide synthase gene (pksP), as evidenced by the generation of colorless (albino) mutants harboring the expected genomic alteration. We further demonstrated that the constitutive expression of the Cas9 nuclease by itself is not deleterious to A. fumigatus growth or virulence, thus making the CRISPR system compatible with studies involved in pathogenesis. Taken together, these data demonstrate that CRISPR can be utilized for loss-of-function studies in A. fumigatus and has the potential to bolster the genetic toolbox for this important pathogen.

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Development of the CRISPR/Cas9 System for Targeted Gene Disruption in Aspergillus fumigatus

et al. 2015

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“…Many new approaches are becoming available for functional characterization. For example, the CRISPR-Cas9 system appears to be a good alternative to T-DNA knock-outs in fungi and its feasibility was recently demonstrated in Trichoderma reesei (Liu et al, 2015) and Pyricularia oryzae (Arazoe et al, 2015) following codon usage optimization of the Cas9 for use in filamentous fungi. This method may be favoured over conventional knock-out and knock-down systems due to its efficiency and the ability to produce knockdowns using a less efficient Cas9 nuclease (Doudna and Charpentier, 2014).…”

Section: Box 84 Differential Expression Analysismentioning

confidence: 99%

Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel

Naidoo¹,

Visser²,

Zwart³

et al. 2018

Current Issues in Molecular Biology

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RNA-sequencing technology has been widely adopted to investigate host responses during infection with pathogens. Dual RNA-sequencing (RNA-seq) allows the simultaneous capture of pathogen-specific transcripts during infection, providing a more complete view of the interaction. In this review, we focus on the design of dual RNAseq experiments and the application of downstream data analysis to gain biological insight into both sides of the interaction. Recent literature in this area demonstrates the power of the dual RNA-seq approach and shows that it is not limited to model systems where genomic resources are available. Sequencing costs continue to decrease and single cell transcriptomics is becoming more feasible. In combination with proteomics and metabolomics studies, these technological advances are likely to contribute to our understanding of the temporal and spatial aspects of dynamic plant-pathogen interactions. A dual approach in plantaThe interaction between plants and pathogens is an active and dynamic process that can be likened to a duel. Plants have complex defence mechanisms that can be rendered ineffective when pathogens interfere with one of the various processes required for host defence. These processes include penetration resistance, recognition by Pattern Recognition Receptors (PRRs), phytohormone signalling pathways, secretory pathways, secondary metabolite production, and plant cell death (Dou and Zhou, 2012). Until recently, transcriptomic approaches have been applied in the host and pathogen separately to obtain the gene expression profile of each organism and gain insight into infection biology or host defence mechanisms.RNA sequencing (RNA-seq) is a powerful technology that does not rely on any prior knowledge of transcripts and can generate vast quantities of data with much smaller costs involved than for older techniques such as microarrays (Pareek et al., 2011;Wilhelm and Landry, 2009). An advantage of RNA-seq in the field of plant-pathogen interactions is that both plant and pathogen transcripts can be detected simultaneously and accurately in the same sample. This tactic, known as dual RNAseq, in planta RNA-seq, simultaneous RNA-seq, or comparative RNA-seq, is a relatively new technique both in the plant and medical fields. In plants, it allows for the study of plant-pathogen interactions in herbaceous crops Kunjeti et al., 2012;Lowe et al., 2014) as well as trees (Hayden et al., 2014;Liang et al., 2014;Teixeira et al., 2014). This review outlines technical considerations for dual RNA-seq experiments, summarizes recent insights drawn from such approaches in plant-pathogen interactions, and provides an

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“…The efficient CRISPR/Cas9 system in another filamentous fungus Trichoderma reesei confirmed itself as a powerful genome-manipulating tool other filamentous fungal species. In T. reesei, it was shown that the CRISPR/Cas9 system was controllable and conditional through inducible Cas9 expression (Liu et al, 2015).…”

Section: Gene Editing With Crispr Technology In Cells and Model Organmentioning

confidence: 99%

CRISPR/Cas in genome defense and gene editing

Kryštofová

2016

Acta Chimica Slovaca

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Targeted genome editing using engineered nucleases such as ZFNs and TALENs has been rapidly replaced by the CRISPR/Cas9 (clustered, regulatory interspaced, short palindromic/ CRISPR-associated nuclease) system. CRISPR/Cas9 technology represents a significant improvement enabling a new level of targeting, efficiency and simplicity. Gene editing mediated by CRISPR/Cas9 has been recently used not only in bacteria but in many eukaryotic cells and organisms, from yeasts to mammals. Other modifications of the CRISPR-Cas9 system have been used to introduce heterologous domains to regulate gene expressions or label specific loci in various cell types. The review focuses not only on native CRISPR/Cas systems which evolved in prokaryotes as an endogenous adaptive defense mechanism against foreign DNA attacks, but also on the CRISPR/Cas9 adoption as a powerful tool for site-specific gene modifications in fungi, plants and mammals.

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Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system

Cited by 368 publications

References 44 publications

Development of the CRISPR/Cas9 System for Targeted Gene Disruption in Aspergillus fumigatus

Development of the CRISPR/Cas9 System for Targeted Gene Disruption in Aspergillus fumigatus

Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel

CRISPR/Cas in genome defense and gene editing

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