1
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Wang X, Fang T, Lu J, Tripathi L, Qi Y. Broad range plastid genome editing with monomeric TALE-linked cytosine and dual base editors. Plant Biotechnol J 2024. [PMID: 38709858 DOI: 10.1111/pbi.14358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/19/2024] [Accepted: 04/03/2024] [Indexed: 05/08/2024]
Affiliation(s)
- Xiaoyu Wang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Tyson Fang
- University of Michigan, Ann Arbor, Michigan, USA
| | - Jason Lu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
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2
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Niu Q, Xie H, Cao X, Song M, Wang X, Li S, Pang K, Zhang Y, Zhu JK, Zhu J. Engineering soybean with high levels of herbicide resistance with a Cas12-SF01-based cytosine base editor. Plant Biotechnol J 2024. [PMID: 38643514 DOI: 10.1111/pbi.14356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/07/2024] [Accepted: 03/29/2024] [Indexed: 04/23/2024]
Affiliation(s)
- Qingfeng Niu
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
- Research Center for Biological Breeding Technology, Research Institute of Frontier Science, Anhui Agricultural University, Hefei, Anhui, China
| | - Hongtao Xie
- Bellagen Biotechnology Co., Ltd, Jinan, Shandong, China
| | - Xuesong Cao
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Minglei Song
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xin Wang
- Shandong Normal University, Jinan, Shandong, China
| | - Shasha Li
- Shandong Normal University, Jinan, Shandong, China
| | - Kang Pang
- Bellagen Biotechnology Co., Ltd, Jinan, Shandong, China
| | | | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jianhua Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
- Research Center for Biological Breeding Technology, Research Institute of Frontier Science, Anhui Agricultural University, Hefei, Anhui, China
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3
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Ren CY, Liu YS, He YS, Zhang LP, Rao JH, Rao Y, Chen JH. Engineered CBEs based on Macaca fascicularis A3A with improved properties for precise genome editing. Cell Rep 2024; 43:113878. [PMID: 38431844 DOI: 10.1016/j.celrep.2024.113878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/20/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
Cytidine deaminase defines the properties of cytosine base editors (CBEs) for C-to-T conversion. Replacing the cytidine deaminase rat APOBEC1 (rA1) in CBEs with a human APOBEC3A (hA3A) improves CBE properties. However, the potential CBE application of macaque A3A orthologs remains undetermined. Our current study develops and evaluates engineered CBEs based on Macaca fascicularis A3A (mA3A). Here, we demonstrate that BE4-mA3A and its RNA-editing-derived variants exhibit improved CBE properties, except for DNA off-target activity, compared to BE3-rA1 and BE4-rA1. Unexpectedly, deleting Ser-Val-Arg (SVR) in BE4-mA3A dramatically reduces DNA and RNA off-target activities and improves editing accuracy, with on-target efficiency unaffected. In contrast, a chimeric BE4-hA3A-SVR+ shows editing efficiency increased by about 50%, with other properties unaffected. Our findings demonstrate that mA3A-based CBEs could provide prototype options with advantages over rA1- and hA3A-based CBEs for further optimization, highlighting the importance of the SVR motif in defining CBE intrinsic properties.
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Affiliation(s)
- Chun-Yan Ren
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan-Shan Liu
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China
| | - Yu-Shan He
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Lin-Pei Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jun-Hua Rao
- Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China; Joint Primate Research Center for Chronic Diseases, Jiangnan University and Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China; Jiangnan University-Xinshijie Eye Hospital Joint Ophthalmic Research Center, Xinshijie Eye Hospital, Wuxi, China.
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4
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Ganesan V, Monteiro L, Pedada D, Stohr A, Blenner M. High-Efficiency Multiplexed Cytosine Base Editors for Natural Product Synthesis in Yarrowia lipolytica. ACS Synth Biol 2023; 12:3082-3091. [PMID: 37768786 DOI: 10.1021/acssynbio.3c00435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Yarrowia lipolytica is an industrial host with a high fatty acid flux. Even though CRISPR-based tools have accelerated its metabolic engineering, there remains a need to develop tools for rapid multiplexed strain engineering to accelerate the design-build-test-learn cycle. Base editors have the potential to perform high-efficiency multiplexed gene editing because they do not depend upon double-stranded DNA breaks. Here, we identified that base editors are less toxic than CRISPR-Cas9 for multiplexed gene editing. We increased the editing efficiency by removing the extra nucleotides between tRNA and gRNA and increasing the base editor and gRNA copy number in a Ku70 deficient strain. We achieved five multiplexed gene editing in the ΔKu70 strain at 42% efficiency. Initially, we were unsuccessful at performing multiplexed base editing in NHEJ competent strain; however, we increased the editing efficiency by using a co-selection approach to enrich base editing events. Base editor-mediated canavanine gene (CAN1) knockout provided resistance to the import of canavanine, which enriched the base editing in other unrelated genetic loci. We performed multiplexed editing of up to three genes at 40% efficiency in the Po1f strain through the CAN1 co-selection approach. Finally, we demonstrated the application of multiplexed cytosine base editor for rapid multigene knockout to increase naringenin production by 2-fold from glucose or glycerol as a carbon source.
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Affiliation(s)
- Vijaydev Ganesan
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Lummy Monteiro
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Dheeraj Pedada
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Anthony Stohr
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Mark Blenner
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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5
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Westberg I, Carlsen FM, Johansen IE, Petersen BL. Cytosine base editors optimized for genome editing in potato protoplasts. Front Genome Ed 2023; 5:1247702. [PMID: 37719877 PMCID: PMC10502308 DOI: 10.3389/fgeed.2023.1247702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023] Open
Abstract
In this study, we generated and compared three cytidine base editors (CBEs) tailor-made for potato (Solanum tuberosum), which conferred up to 43% C-to-T conversion of all alleles in the protoplast pool. Earlier, gene-edited potato plants were successfully generated by polyethylene glycol-mediated CRISPR/Cas9 transformation of protoplasts followed by explant regeneration. In one study, a 3-4-fold increase in editing efficiency was obtained by replacing the standard Arabidopsis thaliana AtU6-1 promotor with endogenous potato StU6 promotors driving the expression of the gRNA. Here, we used this optimized construct (SpCas9/StU6-1::gRNA1, target gRNA sequence GGTC4C5TTGGAGC12AAAAC17TGG) for the generation of CBEs tailor-made for potato and tested for C-to-T base editing in the granule-bound starch synthase 1 gene in the cultivar Desiree. First, the Streptococcus pyogenes Cas9 was converted into a (D10A) nickase (nCas9). Next, one of three cytosine deaminases from human hAPOBEC3A (A3A), rat (evo_rAPOBEC1) (rA1), or sea lamprey (evo_PmCDA1) (CDA1) was C-terminally fused to nCas9 and a uracil-DNA glycosylase inhibitor, with each module interspaced with flexible linkers. The CBEs were overall highly efficient, with A3A having the best overall base editing activity, with an average 34.5%, 34.5%, and 27% C-to-T conversion at C4, C5, and C12, respectively, whereas CDA1 showed an average base editing activity of 34.5%, 34%, and 14.25% C-to-T conversion at C4, C5, and C12, respectively. rA1 exhibited an average base editing activity of 18.75% and 19% at C4 and C5 and was the only base editor to show no C-to-T conversion at C12.
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Affiliation(s)
| | | | | | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Frederiksberg, Denmark
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6
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Engstler M, Beneke T. Gene editing and scalable functional genomic screening in Leishmania species using the CRISPR/Cas9 cytosine base editor toolbox LeishBASEedit. eLife 2023; 12:85605. [PMID: 37222701 DOI: 10.7554/elife.85605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/28/2023] [Indexed: 05/25/2023] Open
Abstract
CRISPR/Cas9 gene editing has revolutionised loss-of-function experiments in Leishmania, the causative agent of leishmaniasis. As Leishmania lack a functional non-homologous DNA end joining pathway however, obtaining null mutants typically requires additional donor DNA, selection of drug resistance-associated edits or time-consuming isolation of clones. Genome-wide loss-of-function screens across different conditions and across multiple Leishmania species are therefore unfeasible at present. Here, we report a CRISPR/Cas9 cytosine base editor (CBE) toolbox that overcomes these limitations. We employed CBEs in Leishmania to introduce STOP codons by converting cytosine into thymine and created http://www.leishbaseedit.net/ for CBE primer design in kinetoplastids. Through reporter assays and by targeting single- and multi-copy genes in L. mexicana, L. major, L. donovani, and L. infantum, we demonstrate how this tool can efficiently generate functional null mutants by expressing just one single-guide RNA, reaching up to 100% editing rate in non-clonal populations. We then generated a Leishmania-optimised CBE and successfully targeted an essential gene in a plasmid library delivered loss-of-function screen in L. mexicana. Since our method does not require DNA double-strand breaks, homologous recombination, donor DNA, or isolation of clones, we believe that this enables for the first time functional genetic screens in Leishmania via delivery of plasmid libraries.
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Affiliation(s)
- Markus Engstler
- Department of Cell and Developmental Biology, Biocentre, University of Würzburg, Wuerzburg, Germany
| | - Tom Beneke
- Department of Cell and Developmental Biology, Biocentre, University of Würzburg, Wuerzburg, Germany
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7
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Lee M, Heo YB, Woo HM. Cytosine base editing in cyanobacteria by repressing archaic Type IV uracil-DNA glycosylase. Plant J 2023; 113:610-625. [PMID: 36565011 DOI: 10.1111/tpj.16074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Base editing enables precise gene editing without requiring donor DNA or double-stranded breaks. To facilitate base editing tools, a uracil DNA glycosylase inhibitor (UGI) was fused to cytidine deaminase-Cas nickase to inhibit uracil DNA glycosylase (UDG). Herein, we revealed that the bacteriophage PBS2-derived UGI of the cytosine base editor (CBE) could not inhibit archaic Type IV UDG in oligoploid cyanobacteria. To overcome the limitation of the CBE, dCas12a-assisted gene repression of the udg allowed base editing at the desired targets with up to 100% mutation frequencies, and yielded correct phenotypes of desired mutants in cyanobacteria. Compared with the original CBE (BE3), base editing was analyzed within a broader C4-C16 window with a strong TC-motif preference. Using multiplexed CyanoCBE, while udg was repressed, simultaneous base editing at two different sites was achieved with lower mutation frequencies than single CBE. Our discovery of a Type IV UDG that is not inhibited by the UGI of the CBE in cyanobacteria and the development of dCas12a-mediated base editing should facilitate the application of base editing not only in cyanobacteria, but also in archaea and green algae that possess Type IV UDGs. We revealed the bacteriophage-derived UGI of the base editor did not repress Type IV UDG in cyanobacteria. To overcome the limitation, orthogonal dCas12a interference was successfully applied to repress the UDG gene expression in cyanobacteria during base editing occurred, yielding a premature translational termination at desired targets. This study will open a new opportunity to perform base editing with Type IV UDGs in archaea and green algae.
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Affiliation(s)
- Mieun Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Yu Been Heo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
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8
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Liu H, Zhu Y, Li M, Gu Z. Precise genome editing with base editors. Med Rev (2021) 2023; 3:75-84. [PMID: 37724105 PMCID: PMC10471085 DOI: 10.1515/mr-2022-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/01/2023] [Indexed: 09/20/2023]
Abstract
Single-nucleotide variants account for about half of known pathogenic genetic variants in human. Genome editing strategies by reversing pathogenic point mutations with minimum side effects have great therapeutic potential and are now being actively pursued. The emerge of precise and efficient genome editing strategies such as base editing and prime editing provide powerful tools for nucleotide conversion without inducing double-stranded DNA breaks (DSBs), which have shown great potential for curing genetic disorders. A diverse toolkit of base editors has been developed to improve the editing efficiency and accuracy in different context of application. Here, we summarized the evolving of base editors (BEs), their limitations and future perspective of base editing-based therapeutic strategies.
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Affiliation(s)
- Hongcai Liu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu Province, China
| | - Yao Zhu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu Province, China
| | - Minjie Li
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu Province, China
| | - Zhimin Gu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu Province, China
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Heo YB, Hwang GH, Kang SW, Bae S, Woo HM. High-Fidelity Cytosine Base Editing in a GC-Rich Corynebacterium glutamicum with Reduced DNA Off-Target Editing Effects. Microbiol Spectr 2022; 10:e0376022. [PMID: 36374037 PMCID: PMC9769817 DOI: 10.1128/spectrum.03760-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Genome editing technology is a powerful tool for programming microbial cell factories. However, rat APOBEC1-derived cytosine base editor (CBE) that converts C•G to T•A at target genes induced DNA off-targets, regardless of single-guide RNA (sgRNA) sequences. Although the high efficiencies of the bacterial CBEs have been developed, a risk of unidentified off-targets impeded genome editing for microbial cell factories. To address the issues, we demonstrate the genome engineering of Corynebacterium glutamicum as a GC-rich model industrial bacterium by generating premature termination codons (PTCs) in desired genes using high-fidelity cytosine base editors (CBEs). Through this CBE-STOP approach of introducing specific cytosine conversions, we constructed several single-gene-inactivated strains for three genes (ldh, idsA, and pyc) with high base editing efficiencies of average 95.6% (n = 45, C6 position) and the highest success rate of up to 100% for PTCs and ultimately developed a strain with five genes (ldh, actA, ackA, pqo, and pta) that were inactivated sequentially for enhancing succinate production. Although these mutant strains showed the desired phenotypes, whole-genome sequencing (WGS) data revealed that genome-wide point mutations occurred in each strain and further accumulated according to the duration of CBE plasmids. To lower the undesirable mutations, high-fidelity CBEs (pCoryne-YE1-BE3 and pCoryne-BE3-R132E) was employed for single or multiplexed genome editing in C. glutamicum, resulting in drastically reduced sgRNA-independent off-targets. Thus, we provide a CRISPR-assisted bacterial genome engineering tool with an average high efficiency of 90.5% (n = 76, C5 or C6 position) at the desired targets. IMPORTANCE Rat APOBEC1-derived cytosine base editor (CBE) that converts C•G to T•A at target genes induced DNA off-targets, regardless of single-guide RNA (sgRNA) sequences. Although the high efficiencies of bacterial CBEs have been developed, a risk of unidentified off-targets impeded genome editing for microbial cell factories. To address the issues, we identified the DNA off-targets for single and multiple genome engineering of the industrial bacterium Corynebacterium glutamicum using whole-genome sequencing. Further, we developed the high-fidelity (HF)-CBE with significantly reduced off-targets with comparable efficiency and precision. We believe that our DNA off-target analysis and the HF-CBE can promote CRISPR-assisted genome engineering over conventional gene manipulation tools by providing a markerless genetic tool without need for a foreign DNA donor.
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Affiliation(s)
- Yu Been Heo
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Gue-Ho Hwang
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, Republic of Korea
| | - Seok Won Kang
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sangsu Bae
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Jongno-gu, Seoul, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
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Wu Y, Ren Q, Zhong Z, Liu G, Han Y, Bao Y, Liu L, Xiang S, Liu S, Tang X, Zhou J, Zheng X, Sretenovic S, Zhang T, Qi Y, Zhang Y. Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice. Plant Biotechnol J 2022; 20:1670-1682. [PMID: 35524459 PMCID: PMC9398351 DOI: 10.1111/pbi.13838] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/28/2022] [Indexed: 05/04/2023]
Abstract
PAM-relaxed Cas9 nucleases, cytosine base editors and adenine base editors are promising tools for precise genome editing in plants. However, their genome-wide off-target effects are largely unexplored. Here, we conduct whole-genome sequencing (WGS) analyses of transgenic plants edited by xCas9, Cas9-NGv1, Cas9-NG, SpRY, nCas9-NG-PmCDA1, nSpRY-PmCDA1 and nSpRY-ABE8e in rice. Our results reveal that Cas9 nuclease and base editors, when coupled with the same guide RNA (gRNA), prefer distinct gRNA-dependent off-target sites. De novo generated gRNAs by SpRY editors lead to additional, but insubstantial, off-target mutations. Strikingly, ABE8e results in ~500 genome-wide A-to-G off-target mutations at TA motif sites per transgenic plant. ABE8e's preference for the TA motif is also observed at the target sites. Finally, we investigate the timeline and mechanism of somaclonal variation due to tissue culture, which chiefly contributes to the background mutations. This study provides a comprehensive understanding on the scale and mechanisms of off-target and background mutations occurring during PAM-relaxed genome editing in plants.
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Affiliation(s)
- Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri‐Product SafetyThe Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Qiurong Ren
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Zhaohui Zhong
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri‐Product SafetyThe Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri‐Product SafetyThe Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri‐Product SafetyThe Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Li Liu
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Shuyue Xiang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Shuo Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri‐Product SafetyThe Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Xu Tang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Jianping Zhou
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xuelian Zheng
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Simon Sretenovic
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri‐Product SafetyThe Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Yong Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
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11
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Zhou J, Liu Y, Wei Y, Zheng S, Gou S, Chen T, Yang Y, Lan T, Chen M, Liao Y, Zhang Q, Tang C, Liu Y, Wu Y, Peng X, Gao M, Wang J, Zhang K, Lai L, Zou Q. Eliminating predictable DNA off-target effects of cytosine base editor by using dual guiders including sgRNA and TALE. Mol Ther 2022; 30:2443-2451. [PMID: 35443934 PMCID: PMC9263286 DOI: 10.1016/j.ymthe.2022.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/07/2022] [Accepted: 04/16/2022] [Indexed: 11/30/2022] Open
Abstract
Predictable DNA off-target effect is one of the major safety concerns for the application of cytosine base editors (CBEs). To eliminate Cas9-dependent DNA off-target effects, we designed a novel effective CBE system with dual guiders by combining CRISPR with transcription activator-like effector (TALE). In this system, Cas9 nickase (nCas9) and cytosine deaminase are guided to the same target site to conduct base editing by single-guide RNA (sgRNA) and TALE, respectively. However, if nCas9 is guided to a wrong site by sgRNA, it will not generate base editing due to the absence of deaminase. Similarly, when deaminase is guided to a wrong site by TALE, base editing will not occur due to the absence of single-stranded DNA. In this way, Cas9- and TALE-dependent DNA off-target effects could be completely eliminated. Furthermore, by fusing TALE with YE1, a cytidine deaminase with minimal Cas9-independent off-target effect, we established a novel CBE that could induce efficient C-to-T conversion without detectable Cas9- or TALE-dependent DNA off-target mutations.
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Affiliation(s)
- Jizeng Zhou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China; School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Yang Liu
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yuhui Wei
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shuwen Zheng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Shixue Gou
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yang Yang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Ting Lan
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Min Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yuan Liao
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Quanjun Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China
| | - Chengcheng Tang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yu Liu
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yunqin Wu
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Xiaohua Peng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Minghui Gao
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Junwei Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kun Zhang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China; School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China.
| | - Liangxue Lai
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China; CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.
| | - Qingjian Zou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China.
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12
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Zhang C, Li N, Rao L, Li J, Liu Q, Tian C. Development of an Efficient C-to-T Base-Editing System and Its Application to Cellulase Transcription Factor Precise Engineering in Thermophilic Fungus Myceliophthora thermophila. Microbiol Spectr 2022;:e0232121. [PMID: 35608343 DOI: 10.1128/spectrum.02321-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Myceliophthora thermophila is a thermophilic fungus with great potential in biorefineries and biotechnology. The base editor is an upgraded version of the clustered regularly interspaced short palindromic repeats (CRISPR)-dependent genome-editing tool that introduces precise point mutations without causing DNA double-strand breaks (DSBs) and has been used in various organisms but rarely in filamentous fungi, especially thermophilic filamentous fungi. Here, for the first time, we constructed three cytosine base editors (CBEs) in M. thermophila, namely, evolved apolipoprotein B mRNA-editing enzyme catalytic subunit 1 (APOBEC1) cytosine base editor 4 max (Mtevo-BE4max), bacteriophage Mu Gam protein cytosine base editor 4 max (MtGAM-BE4max), and evolved CDA1 deaminase cytosine base editor (Mtevo-CDA1), and efficiently inactivated genes by precisely converting three codons (CAA, CAG, and CGA) into stop codons without DSB formation. The Mtevo-CDA1 editor with up to 92.6% editing efficiency is a more suitable tool for cytosine base editing in thermophilic fungi. To investigate the function of each motif of the cellulase transcription factor M. thermophila CLR-2 (MtCLR-2), we used the Mtevo-CDA1 editor. The fungal-specific motif of MtCLR-2 was found to be strongly involved in cellulase secretion, conidium formation, hyphal branching, and colony formation. Mutation of the fungus-specific motif caused significant defects in these characteristics. Thus, we developed an efficient thermophilic fungus-compatible base-editing system that could also be used for genetic engineering in other relevant filamentous fungi. IMPORTANCE A CRISPR/Cas-based base-editing approach has been developed to introduce point mutations without inducing double-strand breaks (DSBs) and attracted substantial academic and industrial interest. Our study developed the deaminase-cytosine base-editing system to efficiently edit three target genes, amdS, cre-1, and the essential cellulase regulator gene Mtclr-2, in Myceliophthora thermophila. A variety of point mutations in the target loci of the DNA-binding domain and fungus-specific motif of M. thermophila CLR-2 (MtCLR-2) were successfully generated via our base editor Mtevo-CDA1 to elucidate its function. Here, we show that the DNA-binding domain of MtCLR-2 is important for the fungal response to cellulose conditions, while its fungus-specific motif is involved in fungal growth. These findings indicate that our base editor can be an effective tool for elucidating the functions of motifs of target genes in filamentous fungi and for metabolic engineering in the field of synthetic biology.
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13
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Jeong DE, Kim MS, Kim HR, Choi SK. Cell Factory Engineering of Undomesticated Bacillus Strains Using a Modified Integrative and Conjugative Element for Efficient Plasmid Delivery. Front Microbiol 2022; 13:802040. [PMID: 35558120 PMCID: PMC9086855 DOI: 10.3389/fmicb.2022.802040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/14/2022] [Indexed: 11/29/2022] Open
Abstract
A large number of Bacillus strains have been isolated from various environments and many of them have great potential as cell factories. However, they have been rarely developed as cell factories due to their poor transformation efficiency. In this study, we developed a highly efficient plasmid delivery system for undomesticated Bacillus strains using a modified integrative and conjugative element (MICE), which was designed to be activated by an inducer, prevent self-transfer, and deliver desired plasmids to the recipient cells. The MICE system was demonstrated to successfully introduce a gfp-containing plasmid into all 41 undomesticated Bacillus subtilis strains tested and eight other Bacillus species. The MICE was used to deliver a cytosine base editor (CBE)-based multiplex genome-editing tool for the cell factory engineering of the Bacillus species. The introduced CBE enabled one-step inactivation of the major extracellular protease genes of the tested strains. The engineered strains were used as hosts for heterologous expression of nattokinase, which resulted in various enzyme expression levels. The results suggested that the MICE and CBE systems can be powerful tools for genetic engineering of undomesticated Bacillus strains, and greatly contribute to the expansion of the Bacillus cell factory.
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Affiliation(s)
- Da-Eun Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Man Su Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, South Korea
| | - Ha-Rim Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, South Korea
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14
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Wu S, Li L, Li M, Sun S, Zhao Y, Xue X, Chen F, Zhong J, Guo J, Qu Q, Wang X, Liu Z, Qiao Y. Two Compact Cas9 Ortholog-Based Cytosine Base Editors Expand the DNA Targeting Scope and Applications In Vitro and In Vivo. Front Cell Dev Biol 2022; 10:809922. [PMID: 35300420 PMCID: PMC8921874 DOI: 10.3389/fcell.2022.809922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/17/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9-based base editing tools enable precise genomic installation and hold great promise for gene therapy, whereas the big size of Cas9 nucleases and its reliability on specific protospacer adjacent motif (PAM) sequences as well as target site preferences restrict the extensive applications of base editing tools. Here, we generate two cytosine base editors (CBEs) by fusing cytidine deaminases with two compact codon-optimized Cas9 orthologs from Streptococcus_gordonii_str._Challis_substr._CH1 (ancSgo-BE4) and Streptococcus_thermophilus_LMG_18311 (ancSth1a-BE4), which are much smaller than Streptococcus pyogenes (SpCas9) and recognize NNAAAG and NHGYRAA PAM sequences, respectively. Both CBEs display high activity, high fidelity, a different editing window, and low by-products for cytosine base editing with minimal DNA and RNA off-targeting activities in mammalian cells. Moreover, both editors show comparable or higher editing efficiencies than two engineered SpCas9 variant (SpCas9-NG and SpRY)-based CBEs in our tested target sites, which perfectly match the PAM sequences for ancSgo-BE4 or ancSth1a-BE4. In addition, we successfully generate two mouse models harboring clinically relevant mutations at the Ar gene via ancSgo-BE4 and ancSth1a-BE4, which display androgen insensitivity syndrome and/or developmental lethality in founder mice. Thus, the two novel CBEs broaden the base editing tool kits with expanded targeting scope and window for efficient gene modification and applications, respectively.
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Affiliation(s)
- Susu Wu
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Liping Li
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Min Li
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Shiyu Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuting Zhao
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaowen Xue
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Feiyu Chen
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jingli Zhong
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Junfan Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qianhui Qu
- Shanghai Stomatological Hospital, Institutes of Biomedical Science, Department of Systems Biology for Medicine, Fudan University, Shanghai, China
| | - Xiongjun Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yunbo Qiao
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, China
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15
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Zhang C, Kang G, Liu X, Zhao S, Yuan S, Li L, Yang Y, Wang F, Zhang X, Yang J. Genome Engineering in Plant Using an Efficient CRISPR-xCas9 Toolset With an Expanded PAM Compatibility. Front Genome Ed 2021; 2:618385. [PMID: 34713242 PMCID: PMC8525348 DOI: 10.3389/fgeed.2020.618385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/24/2020] [Indexed: 12/02/2022] Open
Abstract
The CRISPR-Cas9 system enables simple, rapid, and effective genome editing in many species. Nevertheless, the requirement of an NGG protospacer adjacent motif (PAM) for the widely used canonical Streptococcus pyogenes Cas9 (SpCas9) limits the potential target sites. The xCas9, an engineered SpCas9 variant, was developed to broaden the PAM compatibility to NG, GAA, and GAT PAMs in human cells. However, no knockout rice plants were generated for GAA PAM sites, and only one edited target with a GAT PAM was reported. In this study, we used tRNA and enhanced sgRNA (esgRNA) to develop an efficient CRISPR-xCas9 genome editing system able to mutate genes at NG, GAA, GAT, and even GAG PAM sites in rice. We also developed the corresponding xCas9-based cytosine base editor (CBE) that can edit the NG and GA PAM sites. These new editing tools will be useful for future rice research or breeding, and may also be applicable for other related plant species.
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Affiliation(s)
- Chengwei Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Guiting Kang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Xinxiang Liu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Si Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Shuang Yuan
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Lu Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Yongxing Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Feipeng Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Xiang Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Jinxiao Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
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16
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Park ME, Yun JY, Kim HU. C-to-G Base Editing Enhances Oleic Acid Production by Generating Novel Alleles of FATTY ACID DESATURASE 2 in Plants. Front Plant Sci 2021; 12:748529. [PMID: 34764970 PMCID: PMC8576475 DOI: 10.3389/fpls.2021.748529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/30/2021] [Indexed: 06/01/2023]
Abstract
The demand for vegetable oil, which is mainly used for dietary purposes and cooking, is steadily increasing worldwide. It is often desirable to reduce unsaturation levels of fatty acids in order to increase storage stability and reduce trans-fat generation during cooking. Functional disruption of FATTY ACID DESATURASE 2 (FAD2) prevents the conversion of monounsaturated oleic acid to polyunsaturated linoleic acid, thereby enhancing the production of the desirable oleic acid. However, FAD2 null alleles, due to growth defects under stress conditions, are impractical for agronomical purposes. Here, we aimed to attenuate FAD2 activity in planta while avoiding adverse growth effects by introducing amino-acid substitutions using CRISPR base editors. In Arabidopsis, we applied the adenine base editor (ABE) and cytosine base editor (CBE) to induce semi-random base substitutions within several selected FAD2 coding regions. Isolation of base-edited fad2 alleles with higher oleic acid revealed that the CBE application induced C-to-T and/or C-to-G base substitutions within the targeted sequences, resulting in an alteration of the FAD2 enzyme activities; for example, fad2-144 with multiple C-to-G base substitutions showed less growth defects but with a significant increase in oleic acids by 3-fold higher than wild type. Our "proof-of-concept" approach suggests that equivalent alleles may be generated in vegetable oil crops via precision genome editing for practical cultivation. Our targeted semi-random strategy may serve as a new complementary platform for planta engineering of useful agronomic traits.
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Affiliation(s)
- Mid-Eum Park
- Department of Molecular Biology, Graduate School, Sejong University, Seoul, South Korea
| | - Jae-Young Yun
- Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, South Korea
| | - Hyun Uk Kim
- Department of Molecular Biology, Graduate School, Sejong University, Seoul, South Korea
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, South Korea
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17
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Li G, Sretenovic S, Eisenstein E, Coleman G, Qi Y. Highly efficient C-to-T and A-to-G base editing in a Populus hybrid. Plant Biotechnol J 2021; 19:1086-1088. [PMID: 33742755 PMCID: PMC8196628 DOI: 10.1111/pbi.13581] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 05/03/2023]
Affiliation(s)
- Gen Li
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
| | - Simon Sretenovic
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
| | - Edward Eisenstein
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
- Fischell Department of BioengineeringUniversity of MarylandCollege ParkMarylandUSA
| | - Gary Coleman
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
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18
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Abstract
Life science has been in pursuit of precise and efficient genome editing in living cells since the very beginning of the first restriction cloning attempt. The introduction of RNA-guided CRISPR-associated (Cas) nucleases contributed to this ultimate goal through their ability to deliver a double-strand break (DSB) to a precise target location in various species, obsoleting the preceding editing tools, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). The derivative technology, base editing, combines the catalytically inactivated Cas nuclease and nucleotide deaminase and mediates the genetic modifications at single-nucleotide precision without introducing a DSB. Moreover, the cytosine base editors (CBEs) are able to transform multiple codons into stop codons, rapidly inactivating a gene of interest and enabling loss-of-function study in some recombination-deficient species. Here, we present the CRISPR-CBEI tool kit to assist the design of sgRNAs for CBE-mediated gene inactivation. Base editing is a promising technique, allowing precise single-base mutagenesis in genomes without double-strand DNA breaks or donor templates. Cytosine base editors (CBEs) convert cytosine to thymidine. In particular, CBEs can transform four codons, CAA, CAG, CGA, and TGG, into stop codons, providing a new means to rapidly inactivate a gene of interest and enabling loss-of-function study in recombination-deficient species and the construction of gene-inactivation libraries. However, designing single guide RNAs (sgRNAs) for gene inactivation is more complicated and more restricted in applicability than using the lustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (CRISPR/Cas9) system only, especially for researchers who do not specialize in the bioinformatics skills needed to design and evaluate sgRNAs. Here, we present a new user-friendly designing tool kit, namely, CRISPR-CBEI (cytosine base editor-mediated gene inactivation), including a Web tool and a command-line tool. The Web tool is dedicated to the design of sgRNAs for CBE-mediated gene inactivation and integrates various functions, including open reading frame (ORF) identification, CBE customization, sgRNA designing, summarizing, and front-end off-target searching against user-defined unlimited-file-size local genome files without the necessity of uploading to the server. The command-line version serves the same purpose but for a larger number of coding DNA sequences (CDSs), for instance, for designing a CBE-inactivation library in a target species which provides comprehensive evaluations of CBEs and target genomes. We envision that this tool would contribute to CBE-inactivation design. IMPORTANCE Life science has been in pursuit of precise and efficient genome editing in living cells since the very beginning of the first restriction cloning attempt. The introduction of RNA-guided CRISPR-associated (Cas) nucleases contributed to this ultimate goal through their ability to deliver a double-strand break (DSB) to a precise target location in various species, obsoleting the preceding editing tools, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). The derivative technology, base editing, combines the catalytically inactivated Cas nuclease and nucleotide deaminase and mediates the genetic modifications at single-nucleotide precision without introducing a DSB. Moreover, the cytosine base editors (CBEs) are able to transform multiple codons into stop codons, rapidly inactivating a gene of interest and enabling loss-of-function study in some recombination-deficient species. Here, we present the CRISPR-CBEI tool kit to assist the design of sgRNAs for CBE-mediated gene inactivation.
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19
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Abstract
CRISPR-mediated DNA base editors, which include cytosine base editors (CBEs) and adenine base editors (ABEs), are promising tools that can induce point mutations at desired sites in a targeted manner to correct or disrupt gene expression. Their high editing efficiency, coupled with their ability to generate a targeted mutation without generating a DNA double-strand break (DSB) or requiring a donor DNA template, suggests that DNA base editors will be useful for treating genetic diseases, among other applications. However, this hope has recently been challenged by the discovery of DNA base editor shortcomings, including off-target DNA editing, the generation of bystander mutations, and promiscuous deamination effects in both DNA and RNA, which arise from the main DNA base editor constituents, a Cas nuclease variant and a deaminase. In this review, we summarize information about the DNA base editors that have been developed to date, introduce their associated potential challenges, and describe current efforts to minimize or mitigate those issues of DNA base editors.
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Affiliation(s)
- You Kyeong Jeong
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, South Korea
| | - Beomjong Song
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sangsu Bae
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, South Korea.
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20
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Su X, Chen W, Cai Q, Liang P, Chen Y, Cong P, Huang J. Effective generation of maternal genome point mutated porcine embryos by injection of cytosine base editor into germinal vesicle oocytes. Sci China Life Sci 2020; 63:996-1005. [PMID: 31974864 DOI: 10.1007/s11427-019-1611-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/23/2019] [Indexed: 01/19/2023]
Abstract
Cytosine and adenine base editors are promising new tools for introducing precise genetic modifications that are required to generate disease models and to improve traits in pigs. Base editors can catalyze the conversion of C→T (C>T) or A→G (A>G) in the target site through a single guide RNA. Injection of base editors into the zygote cytoplasm can result in the production of offspring with precise point mutations, but most F0 are mosaic, and breeding of F1 heterozygous pigs is time-intensive. Here, we developed a method called germinal vesicle oocyte base editing (GVBE) to produce point mutant F0 porcine embryos by editing the maternal alleles during the GV to MII transition. Injection of cytosine base editor 3 (BE3) mRNA and X-linked Dmd-specific guide RNAs into GVoocytes efficiently edited maternal Dmd during in vitro maturation and did not affect the maturation potential of the oocytes. The edited MII oocytes developed into blastocysts after parthenogenetic activation (PA) or in vitro fertilization (IVF). However, BE3 may reduce the developmental potential of IVF blastocysts from 31.5%±0.8% to 20.4% ±2.1%. There 40%-78.3% diploid PA blastocysts had no more than two different alleles, including up to 10% embryos that had only C>T mutation alleles. Genotyping of IVF blastocysts indicated that over 70% of the edited embryos had one allele or two different alleles of Dmd. Since the male embryos had only a copy of Dmd allele, all five (5/19) F0 male embryos are homozygous and three of them were Dmd precise C>T mutation. Nine (9/19) female IVF embryos had two different alleles including a WT and a C>T mutation. DNA sequencing showed that some of them might be heterozygous embryos. In conclusion, the GVBE method is a valuable method for generating F0 embryos with maternal point mutated alleles in a single step.
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Affiliation(s)
- Xiaohu Su
- Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wei Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qingqing Cai
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Puping Liang
- Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yaosheng Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Peiqing Cong
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Junjiu Huang
- Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Key Laboratory of Reproductive Medicine of Guangdong Province, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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Zhang C, Xu W, Wang F, Kang G, Yuan S, Lv X, Li L, Liu Y, Yang J. Expanding the base editing scope to GA and relaxed NG PAM sites by improved xCas9 system. Plant Biotechnol J 2020; 18:884-886. [PMID: 31545544 PMCID: PMC7061872 DOI: 10.1111/pbi.13259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/02/2019] [Accepted: 09/05/2019] [Indexed: 05/13/2023]
Affiliation(s)
- Chengwei Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingBeijing Academy of Agriculture & Forestry SciencesBeijingChina
| | - Wen Xu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingBeijing Academy of Agriculture & Forestry SciencesBeijingChina
| | - Feipeng Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingBeijing Academy of Agriculture & Forestry SciencesBeijingChina
| | - Guiting Kang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingBeijing Academy of Agriculture & Forestry SciencesBeijingChina
| | - Shuang Yuan
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingBeijing Academy of Agriculture & Forestry SciencesBeijingChina
| | - Xinxin Lv
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingBeijing Academy of Agriculture & Forestry SciencesBeijingChina
| | - Lu Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingBeijing Academy of Agriculture & Forestry SciencesBeijingChina
| | - Ya Liu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingBeijing Academy of Agriculture & Forestry SciencesBeijingChina
| | - Jinxiao Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular BreedingBeijing Academy of Agriculture & Forestry SciencesBeijingChina
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22
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Wu Y, Xu W, Wang F, Zhao S, Feng F, Song J, Zhang C, Yang J. Increasing Cytosine Base Editing Scope and Efficiency With Engineered Cas9-PmCDA1 Fusions and the Modified sgRNA in Rice. Front Genet 2019; 10:379. [PMID: 31134125 PMCID: PMC6512751 DOI: 10.3389/fgene.2019.00379] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/09/2019] [Indexed: 12/04/2022] Open
Abstract
Base editors that do not require double-stranded DNA cleavage or homology-directed repair enable higher efficiency and cleaner substitution of targeted single nucleotides in genomic DNA than conventional approaches. However, their broad applications are limited within the editing window of several base pairs from the canonical NGG protospacer adjacent motif (PAM) sequence. In this study, we fused the D10A nickase of several Streptococcus pyogenes Cas9 (SpCas9) variants with Petromyzon marinus cytidine deaminase 1 (PmCDA1) and uracil DNA glycosylase inhibitor (UGI) and developed two new effective PmCDA1-based cytosine base editors (pBEs), SpCas9 nickase (SpCas9n)-pBE and VQR nickase (VQRn)-pBE, which expanded the scope of genome targeting for cytosine-to-thymine (C-to-T) substitutions in rice. Four of six and 12 of 18 target sites selected randomly in SpCas9n-pBE and VQRn-pBE, respectively were base edited with frequencies of 4–90% in T0 plants. The effective deaminase window typically spanned positions 1–7 within the protospacer and the single target C showed the maximum C-to-T frequency at or near position 3, counting the end distal to PAM as position 1. In addition, the modified single guide RNA (sgRNA) improved the base editing efficiencies of VQRn-pBE with 1.3- to 7.6-fold increases compared with the native sgRNA, and targets that could not be mutated using the native sgRNA were edited successfully using the modified sgRNA. These newly developed base editors can be used to realize C-to-T substitutions and may become powerful tools for both basic scientific research and crop breeding in rice.
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Affiliation(s)
- Ying Wu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wen Xu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Feipeng Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Si Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Feng Feng
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinling Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chengwei Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinxiao Yang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Abstract
Genome editing with CRISPR/Cas has rapidly gained popularity. Base editing, a new CRISPR/Cas-based approach, can precisely convert one nucleotide to another in DNA or RNA without inducing a double-strand DNA break (DSB). A combination of catalytically impaired nuclease variants with different deaminases has yielded diverse base-editing platforms that aim to address the key limitations such as specificity, protospacer adjacent motif (PAM) compatibility, editing window length, bystander editing, and sequence context preference. Because new base editors significantly reduce unintended editing in the genome, they hold great promise for treating genetic diseases and for developing superior agricultural crops. We review here the development of various base editors, assess their technical advantages and limitations, and discuss their broad applications in basic research, medicine, and agriculture.
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Affiliation(s)
- Kutubuddin A Molla
- Department of Plant Pathology and Environmental Microbiology, and Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA; ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology, and Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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24
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Li Z, Xiong X, Wang F, Liang J, Li JF. Gene disruption through base editing-induced messenger RNA missplicing in plants. New Phytol 2019; 222:1139-1148. [PMID: 30565255 DOI: 10.1111/nph.15647] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/09/2018] [Indexed: 05/27/2023]
Abstract
Gene knockout tools are highly desirable for basic and applied plant research. Here, we leverage the Cas9-derived cytosine base editor to introduce precise C-to-T mutations to disrupt the highly conserved intron donor site GT or acceptor site AG, thereby inducing messenger RNA (mRNA) missplicing and gene disruption. As proof of concept, we successfully obtained Arabidopsis null mutant of MTA gene in the T2 generation and rice double null mutant of GL1-1 and NAL1 genes in the T0 generation by this strategy. Elimination of the original intron donor site or acceptor site could trigger aberrant splicing at a new specific exonic site, but not at the closest GT or AG site, suggesting cryptic rules governing splice site recognition. The strategy presented expands the applications of base editing technologies in plants by providing a new means for gene inactivation without generating DNA double-strand breaks, and it can potentially serve as a useful tool for studying the biology of mRNA splicing.
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Affiliation(s)
- Zhenxiang Li
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiangyu Xiong
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fengzhu Wang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jieping Liang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jian-Feng Li
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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25
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Hua K, Tao X, Zhu J. Expanding the base editing scope in rice by using Cas9 variants. Plant Biotechnol J 2019; 17:499-504. [PMID: 30051586 PMCID: PMC6335069 DOI: 10.1111/pbi.12993] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/19/2018] [Accepted: 07/23/2018] [Indexed: 05/17/2023]
Abstract
Base editing is a novel genome editing strategy that enables irreversible base conversion at target loci without the need for double stranded break induction or homology-directed repair. Here, we developed new adenine and cytosine base editors with engineered SpCas9 and SaCas9 variants that substantially expand the targetable sites in the rice genome. These new base editors can edit endogenous genes in the rice genome with various efficiencies. Moreover, we show that adenine and cytosine base editing can be simultaneously executed in rice. The new base editors described here will be useful in rice functional genomics research and will advance precision molecular breeding in crops.
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Affiliation(s)
- Kai Hua
- Shanghai Center for Plant Stress BiologyCAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoping Tao
- Shanghai Center for Plant Stress BiologyCAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Jian‐Kang Zhu
- Shanghai Center for Plant Stress BiologyCAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- Department of Horticulture and Landscape ArchitecturePurdue UniversityWest LafayetteINUSA
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