scholarly journals CRISPR/Cas9 mediated editing of the Quorn fungus Fusarium venenatum A3/5 by transient expression of Cas9 and sgRNAs targeting endogenous marker gene PKS12

2021 ◽  
Author(s):  
Fiona M Wilson ◽  
Richard J Harrison
Keyword(s):  
Gene Expression ◽  
Transient Expression ◽  
Gene Editing ◽  
Polyketide Synthase ◽  
Marker Gene ◽  
Constitutive Expression ◽  
Cost Effective ◽  
Editing Efficiency ◽  
Base Editing ◽  
Fusarium Venenatum

AbstractBackgroundGene editing using CRISPR/Cas9 is a widely used tool for precise gene modification, modulating gene expression and introducing novel proteins, and its use has been reported in a number of filamentous fungi including the genus Fusarium. The aim of this study was to optimise gene editing efficiency using AMA1 replicator vectors for transient expression of CRISPR constituents in Fusarium venenatum (A3/5), used commercially in the production of mycoprotein (Quorn™).ResultsWe present evidence of CRISPR/Cas9 mediated gene editing in Fusarium venenatum, by targeting the endogenous visible marker gene PKS12, which encodes a polyketide synthase responsible for the synthesis of the pigment aurofusarin. Constructs for expression of single guide RNAs (sgRNAs) were cloned into an AMA1 replicator vector incorporating a construct for constitutive expression of cas9 codon-optimised for Aspergillus niger or F. venenatum. Vectors were maintained under selection for transient expression of sgRNAs and cas9 in transformed protoplasts. 100% gene editing efficiency of protoplast-derived isolates was obtained using A. niger cas9 when sgRNA transcription was regulated by the F. venenatum 5SrRNA promoter. In comparison, expression of sgRNAs using a PgdpA-ribozyme construct was much less effective, generating mutant phenotypes in 0-40% of isolates, with evidence of off-target editing. Viable isolates were not obtained from protoplasts transformed with an AMA1 vector expressing cas9 codon-optimised for F. venenatum.ConclusionsUsing an AMA1 replicator vector for transient expression of A. niger cas9 and sgRNAs transcribed from the native 5SrRNA promoter, we demonstrate efficient gene editing of an endogenous marker gene in F. venenatum, resulting in knockout of gene function and a visible mutant phenotype in 100% of isolates. This establishes a platform for further development of CRISPR/Cas technology in F. venenatum, such as modulation of gene expression, gene insertion, base editing and prime editing. These tools will facilitate an understanding of the controls of secondary metabolism and hyphal development during fermentation of F. venenatum for mycoprotein production and may be used to validate prototypes of strains for improvement using classical means, enabling more cost-effective and sustainable production of this industrially important fungus.

scholarly journals CRISPR/Cas9 mediated editing of the Quorn fungus Fusarium venenatum A3/5 by transient expression of Cas9 and sgRNAs targeting endogenous marker gene PKS12

2021 ◽  
Author(s):  
Fiona Wilson ◽  
Richard J Harrison
Keyword(s):  
Gene Expression ◽  
Transient Expression ◽  
Gene Editing ◽  
Polyketide Synthase ◽  
Marker Gene ◽  
Constitutive Expression ◽  
Cost Effective ◽  
Editing Efficiency ◽  
Base Editing ◽  
Fusarium Venenatum

Abstract Background Gene editing using CRISPR/Cas9 is a widely used tool for precise gene modification, modulating gene expression and introducing novel proteins, and its use has been reported in a number of filamentous fungi including the genus Fusarium. The aim of this study was to optimise gene editing efficiency using AMA1 replicator vectors for transient expression of CRISPR constituents in Fusarium venenatum (A3/5), used commercially in the production of mycoprotein (Quorn™). Results We present evidence of CRISPR/Cas9 mediated gene editing in Fusarium venenatum, by targeting the endogenous visible marker gene PKS12, which encodes a polyketide synthase responsible for the synthesis of the pigment aurofusarin. Constructs for expression of single guide RNAs (sgRNAs) were cloned into an AMA1 replicator vector incorporating a construct for constitutive expression of cas9 codon-optimised for Aspergillus niger or F. venenatum. Vectors were maintained under selection for transient expression of sgRNAs and cas9 in transformed protoplasts. 100% gene editing efficiency of protoplast-derived isolates was obtained using A. niger cas9 when sgRNA transcription was regulated by the F. venenatum 5SrRNA promoter. In comparison, expression of sgRNAs using a PgdpA-ribozyme construct was much less effective, generating mutant phenotypes in 0–40% of isolates, with evidence of off-target editing. Viable isolates were not obtained from protoplasts transformed with an AMA1 vector expressing cas9 codon-optimised for F. venenatum. Conclusions Using an AMA1 replicator vector for transient expression of A. niger cas9 and sgRNAs transcribed from the native 5SrRNA promoter, we demonstrate efficient gene editing of an endogenous marker gene in F. venenatum, resulting in knockout of gene function and a visible mutant phenotype in 100% of isolates. This establishes a platform for further development of CRISPR/Cas technology in F. venenatum, such as modulation of gene expression, gene insertion, base editing and prime editing. These tools will facilitate an understanding of the controls of secondary metabolism and hyphal development during fermentation of F. venenatum for mycoprotein production and may be used to validate prototypes of strains for improvement using classical means, enabling more cost-effective and sustainable production of this industrially important fungus.

scholarly journals CRISPR/Cas9 mediated editing of the Quorn fungus Fusarium venenatum A3/5 by transient expression of Cas9 and sgRNAs targeting endogenous marker gene PKS12

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Fiona M. Wilson ◽  
Richard J. Harrison
Keyword(s):  
Transient Expression ◽  
Gene Editing ◽  
Polyketide Synthase ◽  
Marker Gene ◽  
Constitutive Expression ◽  
Strain Improvement ◽  
Editing Efficiency ◽  
Efficient Gene ◽  
Fusarium Venenatum ◽  
Mutant Phenotypes

Abstract Background Gene editing using CRISPR/Cas9 is a widely used tool for precise gene modification, modulating gene expression and introducing novel proteins, and its use has been reported in various filamentous fungi including the genus Fusarium. The aim of this study was to optimise gene editing efficiency using AMA1 replicator vectors for transient expression of CRISPR constituents in Fusarium venenatum (A3/5), used commercially in the production of mycoprotein (Quorn™). Results We present evidence of CRISPR/Cas9 mediated gene editing in Fusarium venenatum, by targeting the endogenous visible marker gene PKS12, which encodes a polyketide synthase responsible for the synthesis of the pigment aurofusarin. Constructs for expression of single guide RNAs (sgRNAs) were cloned into an AMA1 replicator vector incorporating a construct for constitutive expression of cas9 codon-optimised for Aspergillus niger or F. venenatum. Vectors were maintained under selection for transient expression of sgRNAs and cas9 in transformed protoplasts. 100% gene editing efficiency of protoplast-derived isolates was obtained using A. niger cas9 when sgRNA transcription was regulated by the F. venenatum 5SrRNA promoter. In comparison, expression of sgRNAs using a PgdpA-ribozyme construct was much less effective, generating mutant phenotypes in 0–40% of isolates. Viable isolates were not obtained from protoplasts transformed with an AMA1 vector expressing cas9 codon-optimised for F. venenatum. Conclusions Using an AMA1 replicator vector for transient expression of A. niger cas9 and sgRNAs transcribed from the native 5SrRNA promoter, we demonstrate efficient gene editing of an endogenous marker gene in F. venenatum, resulting in knockout of gene function and a visible mutant phenotype in 100% of isolates. This establishes a platform for further development of CRISPR/Cas technology in F. venenatum for use as a research tool, for understanding the controls of secondary metabolism and hyphal development and validating prototypes of strains produced using traditional methods for strain improvement.

scholarly journals Massively parallel quantification of CRISPR editing in cells by TRAP-seq enables better design of Cas9, ABE, CBE gRNAs of high efficiency and accuracy

2020 ◽  
Author(s):  
Xi Xiang ◽  
Kunli Qu ◽  
Xue Liang ◽  
Xiaoguang Pan ◽  
Jun Wang ◽  
...  
Keyword(s):  
High Throughput ◽  
Gene Editing ◽  
High Efficiency ◽  
Outcome Data ◽  
Massively Parallel ◽  
Human Embryonic Kidney Cells ◽  
Editing Efficiency ◽  
Base Editing ◽  
Target Sites ◽  
In Cells

AbstractThe CRISPR RNA-guided endonucleases Cas9, and Cas9-derived adenine/cytosine base editors (ABE/CBE), have been used in both research and therapeutic applications. However, broader use of this gene editing toolbox is hampered by the great variability of efficiency among different target sites. Here we present TRAP-seq, a versatile and scalable approach in which the CRISPR gRNA expression cassette and the corresponding surrogate site are captured by Targeted Reporter Anchored Positional Sequencing in cells. TRAP-seq can faithfully recapitulate the CRISPR gene editing outcomes introduced to the corresponding endogenous genome site and most importantly enables massively parallel quantification of CRISPR gene editing in cells. We demonstrate the utility of this technology for high-throughput quantification of SpCas9 editing efficiency and indel outcomes for 12,000 gRNAs in human embryonic kidney cells. Using this approach, we also showed that TRAP-seq enables high throughput quantification of both ABE and CBE efficiency at 12,000 sites in cells. This rich amount of ABE/CBE outcome data enable us to reveal several novel nucleotide features (e.g. preference of flanking bases, nucleotide motifs, STOP recoding types) affecting base editing efficiency, as well as designing improved machine learning-based prediction tools for designing SpCas9, ABE and CBE gRNAs of high efficiency and accuracy (>70%). We have integrated all the 12,000 CRISPR gene editing outcomes for SpCas9, ABE and CBE into a CRISPR-centered portal: The Human CRISPR Atlas. This study extends our knowledge on CRISPR gene and base editing, and will facilitate the application and development of CRISPR in both research and therapy.

Presence of transcription regulatory elements within an intron of the virus-inducible murine TIMP gene

1988 ◽  
Vol 8 (8) ◽  
pp. 3227-3234
Author(s):  
B Coulombe ◽  
A Ponton ◽  
L Daigneault ◽  
B R Williams ◽  
D Skup
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Phorbol Esters ◽  
Marker Gene ◽  
Constitutive Expression ◽  
Regulatory Elements ◽  
Functional Assay ◽  
Rnase Protection ◽  
Intron 1 ◽  
Timp Gene

The expression of the gene for the murine tissue inhibitor of metalloproteinases (TIMP) is induced in response to viruses, growth factors, and phorbol esters. In this report we show that the accumulation of TIMP mRNA after Newcastle disease virus induction is caused by transcriptional activation of the gene. Comparison of the sequences of cDNA and genomic clones along with RNase protection and primer extension analyses revealed that the murine TIMP gene possesses multiple cap sites and that the exon 1 consists exclusively of 5'-noncoding sequences. We observed that DNA regions analogous to those found upstream of the virus-inducible interferon genes are present within intron 1 of the TIMP gene. To investigate the possible role of TIMP intron 1 in gene expression, we used a functional assay based on the transfection of plasmids in which the DNA segment to be tested is placed in proximity to a marker gene driven by the heterologous herpes simplex virus thymidine kinase promoter. Our results indicate that TIMP intron 1 contains DNA sequence elements capable of modulating the activity of a heterologous promoter in two different ways: (i) by enhancing constitutive expression and (ii) by conferring virus inducibility. These results suggest that intron 1 may be involved in the transcriptional regulation of TIMP gene expression.

scholarly journals Plant-based biosensors for detecting CRISPR-mediated genome engineering

2021 ◽  
Author(s):  
Guoliang Yuan ◽  
Md Mahmudul Hassan ◽  
Tao Yao ◽  
Haiwei Lu ◽  
Michael Melesse Vergara ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Genome Editing ◽  
Transient Expression ◽  
Gene Editing ◽  
Genome Engineering ◽  
Protoplast Transformation ◽  
Reliable System ◽  
Base Editing ◽  
Detection Systems ◽  
Cas9 Nuclease

CRISPR/Cas has recently emerged as the most reliable system for genome engineering in various species. However, concerns about risks associated with CRISPR/Cas9 technology are increasing on potential unintended DNA changes that might accidentally arise from CRISPR gene editing. Developing a system that can detect and report the presence of active CRIPSR/Cas tools in biological systems is therefore very necessary. Here, we developed the real-time detection systems that can spontaneously indicate CRISPR-Cas tools for genome editing and gene regulation including CRISPR/Cas9 nuclease, base editing, prime editing and CRISPRa in plants. Using the fluorescence-based molecular biosensors, we demonstrated that the activities of CRISPR/Cas9 nuclease, base editing, prime editing and CRIPSRa can be effectively detected in transient expression via protoplast transformation and leaf infiltration (in Arabidopsis, poplar, and tobacco) and stable transformation in Arabidopsis.

scholarly journals Presence of transcription regulatory elements within an intron of the virus-inducible murine TIMP gene.

1988 ◽  
Vol 8 (8) ◽  
pp. 3227-3234 ◽  
Author(s):  
B Coulombe ◽  
A Ponton ◽  
L Daigneault ◽  
B R Williams ◽  
D Skup
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Phorbol Esters ◽  
Marker Gene ◽  
Constitutive Expression ◽  
Regulatory Elements ◽  
Functional Assay ◽  
Rnase Protection ◽  
Intron 1 ◽  
Timp Gene

The expression of the gene for the murine tissue inhibitor of metalloproteinases (TIMP) is induced in response to viruses, growth factors, and phorbol esters. In this report we show that the accumulation of TIMP mRNA after Newcastle disease virus induction is caused by transcriptional activation of the gene. Comparison of the sequences of cDNA and genomic clones along with RNase protection and primer extension analyses revealed that the murine TIMP gene possesses multiple cap sites and that the exon 1 consists exclusively of 5'-noncoding sequences. We observed that DNA regions analogous to those found upstream of the virus-inducible interferon genes are present within intron 1 of the TIMP gene. To investigate the possible role of TIMP intron 1 in gene expression, we used a functional assay based on the transfection of plasmids in which the DNA segment to be tested is placed in proximity to a marker gene driven by the heterologous herpes simplex virus thymidine kinase promoter. Our results indicate that TIMP intron 1 contains DNA sequence elements capable of modulating the activity of a heterologous promoter in two different ways: (i) by enhancing constitutive expression and (ii) by conferring virus inducibility. These results suggest that intron 1 may be involved in the transcriptional regulation of TIMP gene expression.

scholarly journals CRISPR/dCas9 (D10A) -Mediated Hb CS Gene Editing and Identification of Genetically Modified Fibroblasts

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 5754-5754
Author(s):  
Lian Yu ◽  
Wei Hao Wu ◽  
WANG Shunqing ◽  
Ken H. Young ◽  
Funeng Jiang
Keyword(s):  
Gene Therapy ◽  
Gene Editing ◽  
Conflicts Of Interest ◽  
Transfection Efficiency ◽  
Target Sequence ◽  
Gene Repair ◽  
Single Base ◽  
Editing Efficiency ◽  
Base Editing ◽  
Alpha Thalassemia

Background: Alpha-thalassemia (α-thalassemia) is an inherited hemolytic disease caused by complete or absent synthesis of α-globin chains due to alpha-globin chain synthesis disorders and is one of the most common genetic diseases in the world. At present, the most commonly used strategies in the gene therapy research of thalassemia, the nonhomologous end joining (NHEJ) apparatus, is only suitable for the study of beta thalassemia and sickle-type anemia. The DNA double strand breaks have a high risk to induce frameshift mutations, leading to more serious clinical consequences. Therefore, it is still necessary to study a safer genetic repair program for alpha-thalassemia. Methods: The donor we chose to repair was from a patient with a genotype of -SEA/αCSα, whose mutation is one of the most common thalassemia alleles in Longyan city, and the HBA1 gene is normal. Due to the deletion of a copy of the HBA2 gene, only one copy of the mutation needs to be repaired, making it a suitable candidate for the study of alpha thalassemia gene therapy. To minimize the risk of non-specific mutations introduced into the locus of interest, we used the single-base editing apparatus, dCas9 (dead Cas9), which only cleaves one strand of DNA and precisely modifies one base, effectively improve the specificity of target cleavage and reduce the risk of off-target. The recognition sequence on the homologous arm in the template was lengthened to reduce the risk of off-target.(see Figure 1 ) Result We used the pmaxGFP plasmid as a positive control for optimizing electroporation conditions. More than 80% transfection efficiency was obtained (see Figure 2 ) Fig 2 pmaxGFP transfection to verify the transfection efficiency of fibroblasts ( 100x ) To investigate the effectiveness of sgRNA and donor plasmids for mutated gene repair, we analyzed the repair efficiency of fibroblasts. Primers were designed near the repair site and PCR sequences were amplified by PCR . After amplification of the genomic fragments, BamH1 digestion assay was performed. Fig 3 PCR and Bam HI digested results using primers for the gene of interest, showed the gene editing efficiency was 4~10%. The sequencing results showed that three clonals of α- thalassaemia mutations were successfully repaired. Fig 4 Hb CS gene mutation target sequence repair and sequencing results The sequencing results of Fig. 5 show that no mutation was detected at the six potential off-target sites. Fig 5 off-target effect detection The use of base editing is limited by off-target activity and DNA delivery efficiency to cells. Filtration into fibroblasts by plasmid electroporation, CRISPR/Cas9-mediated editing efficiency is usually 3~10%, and we achieve a gene editing efficiency of 4~10% (Figure 4). Conclusions Our data show that the gene transfer of normal HBA2 gene by electroporation the single-base editor CRISPR/dCas9 (D10A) and donor into cells can successfully repair Hb CS mutations. Disclosures No relevant conflicts of interest to declare.

scholarly journals Harnessing a Transient Gene Expression System in Nicotiana benthamiana to Explore Plant Agrochemical Transporters

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 524
Author(s):  
Bingqi Wu ◽  
Zhiting Chen ◽  
Xiaohui Xu ◽  
Ronghua Chen ◽  
Siwei Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transient Expression ◽  
Nicotiana Benthamiana ◽  
Heterologous Gene Expression ◽  
Expression System ◽  
Functional Characterization ◽  
Transient Gene Expression ◽  
High Mobility ◽  
Gene Expression System

Functional characterization of plant agrichemical transporters provided an opportunity to discover molecules that have a high mobility in plants and have the potential to increase the amount of pesticides reaching damage sites. Agrobacterium-mediated transient expression in tobacco is simple and fast, and its protein expression efficiency is high; this system is generally used to mediate heterologous gene expression. In this article, transient expression of tobacco nicotine uptake permease (NtNUP1) and rice polyamine uptake transporter 1 (OsPUT1) in Nicotiana benthamiana was performed to investigate whether this system is useful as a platform for studying the interactions between plant transporters and pesticides. The results showed that NtNUP1 increases nicotine uptake in N. benthamiana foliar discs and protoplasts, indicating that this transient gene expression system is feasible for studying gene function. Moreover, yeast expression of OsPUT1 apparently increases methomyl uptake. Overall, this method of constructing a transient gene expression system is useful for improving the efficiency of analyzing the functions of plant heterologous transporter-encoding genes and revealed that this system can be further used to study the functions of transporters and pesticides, especially their interactions.

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