Multiple gene substitution by Target-AID base-editing technology in tomato

Hunziker, Johan; Nishida, Keiji; Kondo, Akihiko; Kishimoto, Sanae; Ariizumi, Tohru; Ezura, Hiroshi

doi:10.1038/s41598-020-77379-2

Cited by 47 publications

(38 citation statements)

References 44 publications

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“…Since then, base editing has been applied to different fields of life science including plants ( Molla et al, 2021 ). Base editors have been adopted in different plant species, including Arabidopsis ( Kang et al, 2018 ; Xue et al, 2018 ; Bastet et al, 2019 ; Zhenxiang Li et al, 2019 ), rice ( Li et al, 2017 ; Lu and Zhu, 2017 ; Shimatani et al, 2017 ; Hua et al, 2018 ; Li et al, 2018 ; Xue et al, 2018 ; Yan et al, 2018 ; Zong et al, 2018 ; Hao Li et al, 2019 ; Hua et al, 2019 ; Juan Li et al, 2020 ; Zeng et al, 2020 ; Ren et al, 2021 ), maize ( Zong et al, 2017 ), wheat ( Zong et al, 2017 ; Li et al, 2018 ; Zhang et al, 2019 ), tomato ( Shimatani et al, 2017 ; Veillet et al, 2019a ; Hunziker et al, 2020 ; Veillet et al, 2020 ), potato ( Zong et al, 2018 ; Veillet et al, 2019a ; Veillet et al, 2019b ; Veillet et al, 2020 ), Nicotiana benthamiana ( Wang et al, 2021 ), soybean ( Cai et al, 2020 ), rapeseed ( Kang et al, 2018 ; Wu et al, 2020 ; Cheng et al, 2021 ), cotton ( Qin et al, 2020 ), watermelon ( Tian et al, 2018 ), strawberry ( Xing et al, 2020 ), apple ( Malabarba et al, 2021 ), pear ( Malabarba et al, 2021 ), and poplar tree ( Gen Li et al, 2021 ). Base editors have not been reported in citrus.…”

Section: Introductionmentioning

confidence: 99%

Base Editors for Citrus Gene Editing

Huang

Wang

2022

Front. Genome Ed.

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Base editors, such as adenine base editors (ABE) and cytosine base editors (CBE), provide alternatives for precise genome editing without generating double-strand breaks (DSBs), thus avoiding the risk of genome instability and unpredictable outcomes caused by DNA repair. Precise gene editing mediated by base editors in citrus has not been reported. Here, we have successfully adapted the ABE to edit the TATA box in the promoter region of the canker susceptibility gene LOB1 from TATA to CACA in grapefruit (Citrus paradise) and sweet orange (Citrus sinensis). TATA-edited plants are resistant to the canker pathogen Xanthomonas citri subsp. citri (Xcc). In addition, CBE was successfully used to edit the acetolactate synthase (ALS) gene in citrus. ALS-edited plants were resistant to the herbicide chlorsulfuron. Two ALS-edited plants did not show green fluorescence although the starting construct for transformation contains a GFP expression cassette. The Cas9 gene was undetectable in the herbicide-resistant citrus plants. This indicates that the ALS edited plants are transgene-free, representing the first transgene-free gene-edited citrus using the CRISPR technology. In summary, we have successfully adapted the base editors for precise citrus gene editing. The CBE base editor has been used to generate transgene-free citrus via transient expression.

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Section: Introductionmentioning

confidence: 99%

Base Editors for Citrus Gene Editing

Huang

Wang

2022

Front. Genome Ed.

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“…By targeting genes associated with GABA metabolism, including GABA‐TP1 , GABA‐TP2 , GABA‐TP3 , CAT9 ,and SSADH , Li et al (2018b) obtained CRISPR genome-edited tomatoes with GABA content up to 19-fold higher than that of the wild type. Hunziker et al (2020) used the CRISPR/Cas9 system fused with target activation-induced cytidine deaminase (Target-AID) base-editing technology to knock out the SlDDB1 , SlDET1 , and SlCYC-B genes to alter carotenoid accumulation. Lycopene is a plant nutrient with antioxidant properties which have been linked to beneficial effects on several diseases, including heart and cardiovascular diseases and certain cancers.…”

Section: Crispr/cas Is a Robust And Powerful Tool For Precision Brementioning

confidence: 99%

CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement

Brant

Budak

et al. 2021

J. Zhejiang Univ. Sci. B

123

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Since it was first recognized in bacteria and archaea as a mechanism for innate viral immunity in the early 2010s, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) has rapidly been developed into a robust, multifunctional genome editing tool with many uses. Following the discovery of the initial CRISPR/Cas-based system, the technology has been advanced to facilitate a multitude of different functions. These include development as a base editor, prime editor, epigenetic editor, and CRISPR interference (CRISPRi) and CRISPR activator (CRISPRa) gene regulators. It can also be used for chromatin and RNA targeting and imaging. Its applications have proved revolutionary across numerous biological fields, especially in biomedical and agricultural improvement. As a diagnostic tool, CRISPR has been developed to aid the detection and screening of both human and plant diseases, and has even been applied during the current coronavirus disease 2019 (COVID-19) pandemic. CRISPR/Cas is also being trialed as a new form of gene therapy for treating various human diseases, including cancers, and has aided drug development. In terms of agricultural breeding, precise targeting of biological pathways via CRISPR/Cas has been key to regulating molecular biosynthesis and allowing modification of proteins, starch, oil, and other functional components for crop improvement. Adding to this, CRISPR/Cas has been shown capable of significantly enhancing both plant tolerance to environmental stresses and overall crop yield via the targeting of various agronomically important gene regulators. Looking to the future, increasing the efficiency and precision of CRISPR/Cas delivery systems and limiting off-target activity are two major challenges for wider application of the technology. This review provides an in-depth overview of current CRISPR development, including the advantages and disadvantages of the technology, recent applications, and future considerations.

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“…Multiplex editing of five genes associated with the carotenoid metabolic pathway of tomato, including stay-green 1 ( SGR1 ), lycopene ɛ-cyclase ( LCY-E ), beta-lycopene cyclase ( Blc ), lycopene β-cyclase 1 ( LCY-B1 ), and LCY-B2 , was engineered by CRISPR/Cas9, and the multiplex-edited tomato fruit showed an approximately 5.1-fold increase in the lycopene content (Li et al 2018d ). CBE-mediated nucleotide substitutions in three other tomato genes responsible for carotenoid accumulation, including DNA Damage UV Binding protein 1 ( SlDDB1 ), deetiolated1 ( SlDET1 ), and Lycopene beta cyclase ( SlCYC-B ), also showed a significant increase in total carotenoid, lycopene, and β-carotene (Hunziker et al 2020 ). Tomato fruit contains a large amount of gamma-aminobutyric acid (GABA) (Takayama and Ezura 2015 ), which is a non-protein amino acid and a health-promoting functional compound as an inhibitory neurotransmitter (Bachtiar et al 2015 ).…”

Section: Applications Of Genome Editing In Tomato Improvementmentioning

confidence: 99%

Advances in application of genome editing in tomato and recent development of genome editing technology

Xia

Cheng

et al. 2021

Theor Appl Genet

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Genome editing, a revolutionary technology in molecular biology and represented by the CRISPR/Cas9 system, has become widely used in plants for characterizing gene function and crop improvement. Tomato, serving as an excellent model plant for fruit biology research and making a substantial nutritional contribution to the human diet, is one of the most important applied plants for genome editing. Using CRISPR/Cas9-mediated targeted mutagenesis, the re-evaluation of tomato genes essential for fruit ripening highlights that several aspects of fruit ripening should be reconsidered. Genome editing has also been applied in tomato breeding for improving fruit yield and quality, increasing stress resistance, accelerating the domestication of wild tomato, and recently customizing tomato cultivars for urban agriculture. In addition, genome editing is continuously innovating, and several new genome editing systems such as the recent prime editing, a breakthrough in precise genome editing, have recently been applied in plants. In this review, these advances in application of genome editing in tomato and recent development of genome editing technology are summarized, and their leaving important enlightenment to plant research and precision plant breeding is also discussed.

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Multiple gene substitution by Target-AID base-editing technology in tomato

Cited by 47 publications

References 44 publications

Base Editors for Citrus Gene Editing

Base Editors for Citrus Gene Editing

CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement

Advances in application of genome editing in tomato and recent development of genome editing technology

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