scholarly journals Exploiting Type I-B CRISPR Genome Editing System in Thermoanaerobacterium Aotearoense SCUT27 And Engineering The Strain For High-Level Ethanol Production

2021 ◽  
Author(s):  
Kaiqun Dai ◽  
Hongxin Fu ◽  
Xiaolong Guo ◽  
Chunyun Qu ◽  
Jufang Wang
Keyword(s):  
Ethanol Production ◽  
Genome Editing ◽  
Gene Editing ◽  
Selection Marker ◽  
Type I ◽  
Lignocellulosic Hydrolysates ◽  
Editing Efficiency ◽  
Negative Selection Marker ◽  
Wide Range ◽  
High Level

Abstract Background: Thermophilic microbes for biofuels and chemicals have attracted great attention due to their tolerance of high temperature and wide range of substrate utilization. Thermoanaerobacterium aotearoense SCUT27 has the ability of glucose and xylose co-utilization in lignocellulosic biomass. Polygene manipulation was a bottleneck since it was hindered by available markers for selection. In this study, the endogenous Type I-B CRISPR/Cas system was developed for multiplex genome editing in SCUT27. Results: The protospacer-adjacent motif (PAM) was identified by in silico and orotidine-5’-phosphate decarboxylase (pyrF) and then lactate dehydrogenase (ldh) were chosen as the editing target to assess the toxicity of this immune system and gene editing efficiency. The mutants could be repeatedly obtained with an editing efficiency of 58.3-100%. Higher transformation efficiency was observed after optimization of some editing strategies. Furthermore, a new method was performed for screening mutants of plasmid curing (recycling of the editing plasmid) for multiplex genome editing based on the negative selection marker tdk, and then ldh and arginine repressor (argR) were knocked out successively. The mutant SCUT27/Δldh/ΔargR had the prominent advantages over SCUT27 for ethanol production with enhanced ability to metabolize xylose. When cultured under various lignocellulosic hydrolysates, the mutant showed a satisfactory performance with the ethanol titer and yield improved by 147.42–739.40% and 112.67–267.89%, respectively, compared with SCUT27, as well as the enhanced tolerance to inhibitors.Conclusion: The multi-gene editing by native CRISPR/Cas system is a promising strategy to engineer SCUT27 for higher ethanol production with lignocellulosic hydrolysates.

scholarly journals 230 Genome editing applications in plants: high-throughput CRISPR/Cas editing for crop improvement

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 56-56
Author(s):  
Michael Thomson
Keyword(s):  
Genome Editing ◽  
High Throughput ◽  
Positional Cloning ◽  
Gene Editing ◽  
Crop Improvement ◽  
Cost Effective ◽  
Gene Families ◽  
Ease Of Use ◽  
Plant Genome ◽  
Wide Range

Abstract The precision and ease of use of CRISPR nucleases, such as Cas9 and Cpf1, for plant genome editing has the potential to accelerate a wide range of applications for crop improvement. For upstream research on gene discovery and validation, rapid gene knock-outs can enable testing of single genes and multi-gene families for functional effects. Large chromosomal deletions can test the function of tandem gene arrays and assist with positional cloning of QTLs by helping to narrow down the target region. Nuclease-deactivated Cas9 fusion proteins with transcriptional activators and repressors can be used to up and down-regulate gene expression. Even more promising, gene insertions and allele replacements can provide the opportunity to rapidly test the effects of different alleles at key loci in the same genetic background, providing a more precise alternative to marker-assisted backcrossing. Recently, Texas A&M AgriLife Research has supported the development of a Crop Genome Editing Lab at Texas A&M working towards optimizing a high-throughput gene editing pipeline and providing an efficient and cost-effective gene editing service for research and breeding groups. The lab is using rice as a model to test and optimize new approaches aimed towards overcoming current bottlenecks. For example, a wealth of genomics data from the rice community enables the development of novel approaches to predict which genes and target modifications may be most beneficial for crop improvement, taking advantage of known major genes, high-resolution GWAS data, multiple high-quality reference genomes, transcriptomics data, and resequencing data from the 3,000 Rice Genomes Project. Current projects have now expanded to work across multiple crops to provide breeding and research groups with a rapid gene editing pipeline to test candidate genes in their programs, with the ultimate goal of developing nutritious, high-yielding, stress-tolerant crops for the future.

scholarly journals CRISPR-Cas9 System for Plant Genome Editing: Current Approaches and Emerging Developments

Agronomy ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1033 ◽  
Author(s):  
Jake Adolf V. Montecillo ◽  
Luan Luong Chu ◽  
Hanhong Bae
Keyword(s):  
Genetic Engineering ◽  
Genome Editing ◽  
Gene Editing ◽  
Fine Tuning ◽  
Plant Genome ◽  
Detection Methods ◽  
Editing Efficiency ◽  
Targeted Gene Editing ◽  
Transgene Detection ◽  
Selection Of

Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. This editing technology has been in the limelight due to its simplicity and versatility compared to other previously known genome editing platforms. Several modifications of this editing system have been established for adoption in a variety of plants, as well as for its improved efficiency and portability, bringing new opportunities for the development of transgene-free improved varieties of economically important crops. This review presents an overview of CRISPR-Cas9 and its application in plant genome editing. A catalog of the current and emerging approaches for the implementation of the system in plants is also presented with details on the existing gaps and limitations. Strategies for the establishment of the CRISPR-Cas9 molecular construct such as the selection of sgRNAs, PAM compatibility, choice of promoters, vector architecture, and multiplexing approaches are emphasized. Progress in the delivery and transgene detection methods, together with optimization approaches for improved on-target efficiency are also detailed in this review. The information laid out here will provide options useful for the effective and efficient exploitation of the system for plant genome editing and will serve as a baseline for further developments of the system. Future combinations and fine-tuning of the known parameters or factors that contribute to the editing efficiency, fidelity, and portability of CRISPR-Cas9 will indeed open avenues for new technological advancements of the system for targeted gene editing in plants.

scholarly journals Advances in Genome Editing With CRISPR Systems and Transformation Technologies for Plant DNA Manipulation

2021 ◽  
Vol 11 ◽  
Author(s):  
Satya Swathi Nadakuduti ◽  
Felix Enciso-Rodríguez
Keyword(s):  
Genome Editing ◽  
Viral Vectors ◽  
Gene Editing ◽  
De Novo ◽  
Alternative Methods ◽  
Zinc Finger Nucleases ◽  
Target Range ◽  
Homing Endonucleases ◽  
Plant Gene ◽  
Wide Range

The year 2020 marks a decade since the first gene-edited plants were generated using homing endonucleases and zinc finger nucleases. The advent of CRISPR/Cas9 for gene-editing in 2012 was a major science breakthrough that revolutionized both basic and applied research in various organisms including plants and consequently honored with “The Nobel Prize in Chemistry, 2020.” CRISPR technology is a rapidly evolving field and multiple CRISPR-Cas derived reagents collectively offer a wide range of applications for gene-editing and beyond. While most of these technological advances are successfully adopted in plants to advance functional genomics research and development of innovative crops, others await optimization. One of the biggest bottlenecks in plant gene-editing has been the delivery of gene-editing reagents, since genetic transformation methods are only established in a limited number of species. Recently, alternative methods of delivering CRISPR reagents to plants are being explored. This review mainly focuses on the most recent advances in plant gene-editing including (1) the current Cas effectors and Cas variants with a wide target range, reduced size and increased specificity along with tissue specific genome editing tool kit (2) cytosine, adenine, and glycosylase base editors that can precisely install all possible transition and transversion mutations in target sites (3) prime editing that can directly copy the desired edit into target DNA by search and replace method and (4) CRISPR delivery mechanisms for plant gene-editing that bypass tissue culture and regeneration procedures including de novo meristem induction, delivery using viral vectors and prospects of nanotechnology-based approaches.

scholarly journals Efficient Gene Editing Through an Intronic Selection Marker in Cells

2021 ◽  
Author(s):  
Shang Wang ◽  
Yuqing Li ◽  
Li Zhong ◽  
Kai Wu ◽  
Ruhua Zhang ◽  
...  
Keyword(s):  
Gene Editing ◽  
Selection Marker ◽  
End Joining ◽  
Dna Variation ◽  
Editing Efficiency ◽  
Endogenous Gene ◽  
Positive Effects ◽  
Efficient Gene ◽  
Almost All ◽  
In Cells

Abstract Background Gene editing technology has provided researchers with the ability to modify genome sequences in almost all eukaryotes. Gene-edited cell lines are being used with increasing frequency in both bench research and targeted therapy. Despite the great importance and universality of gene editing, however, precision and efficiency are hard to achieve with the prevailing editing strategies, such as homology-directed DNA repair (HDR) and the use of base editors (BEs). Results & Discussion Our group has developed a novel gene editing technology to indicate DNA variation with an independent selection marker using an HDR strategy, which we named Gene Editing through an Intronic Selection marker (GEIS). GEIS uses a simple process to avoid nonhomologous end joining (NHEJ)-mediated false-positive effects and achieves editing efficiency as high as 91% without disturbing endogenous gene splicing and expression. We re-examined the correlation of the conversion tract and editing efficiency, and our data suggest that GEIS has the potential to edit approximately 99% of gene editing targets in human and mouse cells. The results of further comprehensive analysis suggest that the strategy may be useful for introducing multiple DNA variations in cells.

Characterization and applications of Type I CRISPR-Cas systems

2020 ◽  
Vol 48 (1) ◽  
pp. 15-23 ◽  
Author(s):  
Claudio Hidalgo-Cantabrana ◽  
Rodolphe Barrangou
Keyword(s):  
Transcriptional Regulation ◽  
Genome Editing ◽  
Adaptive Immune System ◽  
Type I ◽  
Research Areas ◽  
Wide Range ◽  
Class 1 ◽  
Compact Class ◽  
Molecular Machinery ◽  
Repair Template

CRISPR-Cas constitutes the adaptive immune system of bacteria and archaea. This RNA-mediated sequence-specific recognition and targeting machinery has been used broadly for diverse applications in a wide range of organisms across the tree of life. The compact class 2 systems, that hinge on a single Cas effector nuclease have been harnessed for genome editing, transcriptional regulation, detection, imaging and other applications, in different research areas. However, most of the CRISPR-Cas systems belong to class 1, and the molecular machinery of the most widespread and diverse Type I systems afford tremendous opportunities for a broad range of applications. These highly abundant systems rely on a multi-protein effector complex, the CRISPR associated complex for antiviral defense (Cascade), which drives DNA targeting and cleavage. The complexity of these systems has somewhat hindered their widespread usage, but the pool of thousands of diverse Type I CRISPR-Cas systems opens new avenues for CRISPR-based applications in bacteria, archaea and eukaryotes. Here, we describe the features and mechanism of action of Type I CRISPR-Cas systems, illustrate how endogenous systems can be reprogrammed to target the host genome and perform genome editing and transcriptional regulation by co-delivering a minimal CRISPR array together with a repair template. Moreover, we discuss how these systems can also be used in eukaryotes. This review provides a framework for expanding the CRISPR toolbox, and repurposing the most abundant CRISPR-Cas systems for a wide range of applications.

scholarly journals CRISPR/Cas12a mediated genome engineering in photosynthetic bacteria

2020 ◽  
Author(s):  
Yang Zhang ◽  
Jifeng Yuan
Keyword(s):  
Genome Editing ◽  
Transcriptional Repression ◽  
Gene Editing ◽  
Photosynthetic Bacteria ◽  
Genome Engineering ◽  
Biotechnological Applications ◽  
End Joining ◽  
Editing Efficiency ◽  
Francisella Novicida ◽  
Non Homologous End Joining

ABSTRACTPurple non-sulfur photosynthetic bacteria (PNSB) such as R. capsulatus serve as a versatile platform for fundamental studies and various biotechnological applications. In this study, we sought to develop the class II RNA-guided CRISPR/Cas12a system from Francisella novicida for both genome editing and gene down-regulation in R. capsulatus. About 90% editing efficiency was achieved by using CRISPR/Cas12a driven by a strong promoter Ppuc when targeting ccoO or nifH gene. When both genes were simultaneously targeted, the multiplex gene editing efficiency reached >63%. In addition, CRISPR interference using deactivated Cas12a was also evaluated using reporter genes gfp and lacZ, and the repression efficiency reached >80%. In summary, our work represents the first report to develop CRISPR/Cas12a mediated genome editing/transcriptional repression in R. capsulatus, which would greatly accelerate PNSB-related researches.IMPORTANCEPurple non-sulfur photosynthetic bacteria (PNSB) such as R. capsulatus serve as a versatile platform for fundamental studies and various biotechnological applications. However, lack of efficient gene editing tools remains a main obstacle for progressing in PNSB-related researches. Here, we developed CRISPR/Cas12a for genome editing via the non-homologous end joining (NHEJ) repair machinery in R. capsulatus. In addition, DNase-deactivated Cas12a was found to simultaneously suppress multiple targeted genes. Taken together, our work offers a new set of tools for efficient genome engineering in PNSB such as R. capsulatus.

scholarly journals Optimized Cas9 expression improves performance of large-scale CRISPR screening

2021 ◽  
Author(s):  
Joao M. Fernandes Neto ◽  
Katarzyna Jastrzebski ◽  
Cor Lieftink ◽  
Lenno Krenning ◽  
Matheus Dias ◽  
...  
Keyword(s):  
Genome Editing ◽  
Large Scale ◽  
Gene Editing ◽  
Functional Genomic ◽  
Editing Efficiency ◽  
Expression Levels ◽  
Genomic Screening ◽  
Invaluable Tool ◽  
Improved Performance

CRISPR technology is an invaluable tool for large-scale functional genomic screening. Genome editing efficiency and timing are important parameters impacting the performance of pooled CRISPR screens. Here we show that by optimizing Cas9 expression levels, the time necessary for gene editing can be reduced contributing to improved performance of CRISPR based screening.

Semiquantitative analysis of integrated genomes of human T-lymphotropic virus type I in asymptomatic virus carriers

Blood ◽  
1991 ◽  
Vol 78 (8) ◽  
pp. 2082-2088 ◽  
Author(s):  
O Shinzato ◽  
S Ikeda ◽  
S Momita ◽  
Y Nagata ◽  
S Kamihira ◽  
...  
Keyword(s):  
Virus Type ◽  
Mononuclear Cells ◽  
Imaging System ◽  
Type I ◽  
Peripheral Blood Mononuclear ◽  
T Lymphotropic Virus ◽  
Standard Curve ◽  
Dot Hybridization ◽  
Wide Range ◽  
High Level

Abstract A semiquantitative estimation of human T-lymphotropic virus type I (HTLV-I) integration by peripheral blood mononuclear cells (PBMC) was performed. Genomic DNA samples derived from 134 HTLV-I carriers were subjected to 40 or 60 cycles of the polymerase chain reaction to amplify the pol region of HTLV-I. The HTLV-I genome was detected by dot hybridization using a 32P-labeled oligonucleotide probe for the pol region. The radioactivity of hybridized dot membranes was then counted with an RI Imaging System (Ambis Inc, San Diego, CA) and the HTLV-I genome dose was determined by comparison with standard curve for serially diluted HTLV-I genome-positive DNA. A wide range of variation of HTLV-I genome integration was observed. When the integrated genome dose was calculated as the number of HTLV-I copies per 100 PBMC, 7 carriers (5%) had more than 10 copies, 56 (42%) had 1 to 10 copies, 46 (34%) had 0.1 to 1 copy, and 24 (18%) had less than 0.1 copy. In one sample, the HTLV-I genome was undetectable, which may indicate that the integrated genome was present at less than 0.01 copies per 100 PBMC. Age- or sex-related variations in the distribution of individuals with different HTLV-I genome were rather limited. However, carriers with a high level of the HTLV-I genome were always more than 30 years old and were predominantly male (six of seven).

scholarly journals Single-Cell-State Culture of Human Pluripotent Stem Cells Increases Transfection Efficiency

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2037-2037
Author(s):  
Takenobu Nii ◽  
Hiroshi Kohara ◽  
Tomotoshi Marumoto ◽  
Tetsushi Sakuma ◽  
Takashi Yamamoto ◽  
...  
Keyword(s):  
Stem Cells ◽  
Gene Transfer ◽  
Single Cell ◽  
Genome Editing ◽  
Pluripotent Stem Cells ◽  
Gene Editing ◽  
Transfection Efficiency ◽  
Editing Efficiency ◽  
Cell State ◽  
Transfection Method

Abstract Human pluripotent stem cells (hPSCs), such as human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), have the potential to self-renew indefinitely and differentiate into various cell types. hPSCs can differentiate into various stem or progenitor cell populations used for regenerative medicine and drug development. Newly developed genome editing technology has advanced the use of hPSCs for such purposes. However, to fully utilize hPSCs to achieve this goal, more efficient gene transfer methods under defined conditions are required. Development of efficient genome editing methods, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9), for use in hPSCs holds great promise in the fields of basic and clinical research. Among these methods, TALENs are more efficient and safer for use in hPSCs to achieve specific gene editing, as ZFNs had a low gene editing efficiency and CRISPR/Cas9 was accompanied by more severe off-target effects than TALENs. Electroporation is a widely used transfection method for hPSC genome editing; however, this method results in reduced cell viability and gene editing efficiency. In the past decade, various methods were developed for gene transfer into hPSCs; however, hPSCs form tightly packed colonies, making gene transfer difficult. In this study, we established a culture method of hPSCs at a single-cell-state to reduce cell density, and investigated gene transfection efficiency followed by gene editing efficiency. hPSCs cultured in a single-cell-state were transfected using non-liposomal transfection reagents with plasmid DNA driven by the human elongation factor 1-alpha 1 (EF1α) promoter or mRNA encoding enhanced green fluorescent protein (eGFP). The proportion of eGFP+ cells considerably increased in single-cell-state cultures (DNA: 95.80 ± 2.51%, mRNA: 99.70 ± 0.10%). Moreover, most of the cells were viable (control: 93.10 ± 0.40%, DNA: 83.40 ± 2.03%, mRNA: 86.71 ± 0.19%). The mean fluorescence intensity (MFI) was approximately three-fold higher than that in cells transfected by electroporation (electroporation (EPN): 6631 ± 992; transfection (TFN): 17933 ± 1595). eGFP expression was detected by fluorescence microscopy until day seven post-transfection. Our results also demonstrate an inverse correlation between cell density and transfection efficiency. To test whether transfection using this method affected the "stemness" of hPSCs, we examined SSEA4 and NANOG expression in eGFP-transfected cells by flow cytometry analysis. The percentage of both SSEA4+ and NANOG+ cells was greater than 90%. Moreover, transplantation of eGFP-transfected cells into immunodeficient mice led to the formation of teratomas. These results strongly suggested that single-cell-state hPSC culture improved transfection efficiency without inducing differentiation or loss of pluripotency. Moreover, we used our efficient transfection method to edit the hPSC genome using TALENs. We constructed a Platinum TALEN driven by the EF1α promoter targeting the adenomatous polyposis coli (APC) gene and analyzed the efficiency of gene editing using the Cel-1 assay. Our efficient transfection method induced mutations more efficiently than electroporation (Transfection: 11.1 ± 1.38%, Electroporation: 3.2 ± 0.89). These results showed that TALENs increased gene editing efficiency in single-cell-state hPSC cultures. Overall, our efficient hPSC transfection method using single-cell-state culture provides an excellent experimental system to investigate the full potential of hPSCs. We expect that this method may contribute to the fields of hPSC-based regenerative medicine and drug discovery. Disclosures No relevant conflicts of interest to declare.

CRISPR/ Cas9 Off-Targets: Computational Analysis of Causes, Prediction, Detection and Overcoming Strategies

2021 ◽  
Vol 16 ◽  
Author(s):  
Roshan Kumar Roy ◽  
Ipsita Debashree ◽  
Sonal Srivastava ◽  
Narayan Rishi ◽  
Ashish Srivastava
Keyword(s):  
Machine Learning ◽  
Gene Therapy ◽  
Genome Editing ◽  
Gene Editing ◽  
Computational Analysis ◽  
Regulatory Mechanisms ◽  
Learning Approaches ◽  
Cellular Mechanisms ◽  
Wide Range ◽  
Target Activity

: CRISPR/Cas9 technology is a highly flexible RNA-guided endonuclease (RGEN) based gene-editing tool that has transformed the field of genomics, gene therapy, and genome/epigenome imaging. Its wide range of applications provides immense scope for understanding as well as manipulating genetic/epigenetic elements. However, the RGEN is prone to off-target mutagenesis that leads to deleterious effects. This review details the molecular and cellular mechanisms underlying the off-target activity, various available detection and prediction methodology ranging from sequencing to machine learning approaches, and the strategies to overcome/minimise off-targets. A coherent and concise method increasing target precision would prove indispensable to concrete manipulation and interpretation of genome editing results that can revolutionise therapeutics, including clarity in genome regulatory mechanisms during development.

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