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Article ; Online: Transversion Expansion of Base Editing.

Nishida, Keiji / Kondo, Akihiko

2021 Volume 4, Issue 4, Page(s) 462–463

MeSH term(s)	CRISPR-Cas Systems ; Cytosine ; Gene Editing/methods ; Guanidine ; Humans ; Mutagenesis ; Point Mutation
Chemical Substances	Cytosine (8J337D1HZY) ; Guanidine (JU58VJ6Y3B)
Language	English
Publishing date	2021-08-18
Publishing country	United States
Document type	Letter
ZDB-ID	3017891-5
ISSN	2573-1602 ; 2573-1599
ISSN (online)	2573-1602
ISSN	2573-1599
DOI	10.1089/crispr.2021.29134.kni
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Article ; Online: LsMybW-encoding R2R3-MYB transcription factor is responsible for a shift from black to white in lettuce seed.

Seki, Kousuke / Komatsu, Kenji / Yamaguchi, Kanami / Murai, Yoshinori / Nishida, Keiji / Koyama, Ryohei / Uno, Yuichi

Plant cell reports

2024 Volume 43, Issue 2, Page(s) 35

Abstract: Key message: We identified LsMybW as the allele responsible for the shift in color from black to white seeds in wild ancestors of lettuce to modern cultivars. Successfully selected white seeds are a key agronomic trait for lettuce cultivation and ... ...

Abstract	Key message: We identified LsMybW as the allele responsible for the shift in color from black to white seeds in wild ancestors of lettuce to modern cultivars. Successfully selected white seeds are a key agronomic trait for lettuce cultivation and breeding; however, the mechanism underlying the shift from black-in its wild ancestor-to white seeds remains uncertain. We aimed to identify the gene/s responsible for white seed trait in lettuce. White seeds accumulated less proanthocyanidins than black seeds, similar to the phenotype observed in Arabidopsis TT2 mutants. Genetic mapping of a candidate gene was performed with double-digest RAD sequencing using an F
MeSH term(s)	Transcription Factors/genetics ; Lactuca/genetics ; Arabidopsis/genetics ; Plant Breeding ; Seeds/genetics
Chemical Substances	Transcription Factors
Language	English
Publishing date	2024-01-11
Publishing country	Germany
Document type	Journal Article
ZDB-ID	8397-5
ISSN	1432-203X ; 0721-085X ; 0721-7714
ISSN (online)	1432-203X
ISSN	0721-085X ; 0721-7714
DOI	10.1007/s00299-023-03124-4
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Article ; Online: CRISPR-derived genome editing technologies for metabolic engineering

Nishida, Keiji / Kondoh, Akihiko

Metabolic engineering. 2021 Jan., v. 63 p.141-147

2021

Abstract: In metabolic engineering, genome editing tools make it much easier to discover and evaluate relevant genes and pathways and construct strains. Clustered regularly interspaced palindromic repeats (CRISPR)-associated (Cas) systems now have become the first ...

Abstract	In metabolic engineering, genome editing tools make it much easier to discover and evaluate relevant genes and pathways and construct strains. Clustered regularly interspaced palindromic repeats (CRISPR)-associated (Cas) systems now have become the first choice for genome engineering in many organisms includingindustrially relevant ones. Targeted DNA cleavage by CRISPR-Cas provides variousgenome engineering modes such as indels, replacements, large deletions, knock-in and chromosomal rearrangements, while host-dependent differences in repair pathways need to be considered. The versatility of the CRISPR system has given rise to derivative technologies that complement nuclease-based editing, which causes cytotoxicity especially in microorganisms. Deaminase-mediated base editing installs targeted point mutations with much less toxicity. CRISPRi and CRISPRa can temporarily control gene expression without changing the genomic sequence. Multiplex, combinatorial and large scale editing are made possible by streamlined design and construction of gRNA libraries to further accelerates comprehensive discovery, evaluation and building of metabolic pathways. This review summarizes the technical basis and recent advances in CRISPR-related genome editing tools applied for metabolic engineering purposes, with representative examples of industrially relevant eukaryotic and prokaryotic organisms.
Keywords	CRISPR-Cas systems ; DNA damage ; cytotoxicity ; gene expression ; nucleotide sequences ; Genome editing ; Metabolic engineering ; CRISPR ; Recombineering ; Base editing
Language	English
Dates of publication	2021-01
Size	p. 141-147.
Publishing place	Elsevier Inc.
Document type	Article ; Online
Note	NAL-AP-2-clean
ZDB-ID	1470383-x
ISSN	1096-7184 ; 1096-7176
ISSN (online)	1096-7184
ISSN	1096-7176
DOI	10.1016/j.ymben.2020.12.002
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Article ; Online: CRISPR-derived genome editing technologies for metabolic engineering.

Nishida, Keiji / Kondo, Akihiko

Metabolic engineering

2020 Volume 63, Page(s) 141–147

Abstract	In metabolic engineering, genome editing tools make it much easier to discover and evaluate relevant genes and pathways and construct strains. Clustered regularly interspaced palindromic repeats (CRISPR)-associated (Cas) systems now have become the first choice for genome engineering in many organisms includingindustrially relevant ones. Targeted DNA cleavage by CRISPR-Cas provides variousgenome engineering modes such as indels, replacements, large deletions, knock-in and chromosomal rearrangements, while host-dependent differences in repair pathways need to be considered. The versatility of the CRISPR system has given rise to derivative technologies that complement nuclease-based editing, which causes cytotoxicity especially in microorganisms. Deaminase-mediated base editing installs targeted point mutations with much less toxicity. CRISPRi and CRISPRa can temporarily control gene expression without changing the genomic sequence. Multiplex, combinatorial and large scale editing are made possible by streamlined design and construction of gRNA libraries to further accelerates comprehensive discovery, evaluation and building of metabolic pathways. This review summarizes the technical basis and recent advances in CRISPR-related genome editing tools applied for metabolic engineering purposes, with representative examples of industrially relevant eukaryotic and prokaryotic organisms.
MeSH term(s)	CRISPR-Cas Systems/genetics ; Gene Editing ; Genome ; Metabolic Engineering ; Metabolic Networks and Pathways
Language	English
Publishing date	2020-12-08
Publishing country	Belgium
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1470383-x
ISSN	1096-7184 ; 1096-7176
ISSN (online)	1096-7184
ISSN	1096-7176
DOI	10.1016/j.ymben.2020.12.002
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Article: Phenotypic Characterization of High Carotenoid Tomato Mutants Generated by the Target-AID Base-Editing Technology.

Hunziker, Johan / Nishida, Keiji / Kondo, Akihiko / Ariizumi, Tohru / Ezura, Hiroshi

Frontiers in plant science

2022 Volume 13, Page(s) 848560

Abstract: Our previous study demonstrated that Target-AID which is the modified CRISPR/Cas9 system enabling base-editing is an efficient tool for targeting multiple genes. Three genes, ...

Abstract	Our previous study demonstrated that Target-AID which is the modified CRISPR/Cas9 system enabling base-editing is an efficient tool for targeting multiple genes. Three genes,
Language	English
Publishing date	2022-07-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2022.848560
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Article: Production of Herbicide-Sensitive Strain to Prevent Volunteer Rice Infestation Using a CRISPR-Cas9 Cytidine Deaminase Fusion.

Komatsu, Akira / Ohtake, Miki / Shimatani, Zenpei / Nishida, Keiji

Frontiers in plant science

2020 Volume 11, Page(s) 925

Abstract: When cultivated rice seed fall into fields, they may overwinter and spontaneously germinate the next spring. Such germinated plants are termed "volunteer rice." Volunteer grains originating from feed rice varieties may differ in certain traits, such as ... ...

Abstract	When cultivated rice seed fall into fields, they may overwinter and spontaneously germinate the next spring. Such germinated plants are termed "volunteer rice." Volunteer grains originating from feed rice varieties may differ in certain traits, such as quality and taste, as compared with those of rice cultivated for human consumption, which may reduce the overall quality of the final harvested grain. Many rice varieties show resistance to benzobicyclon (BBC), a beta-triketone herbicide (bTH) that inhibits 4-hydroxyphenylpyruvate dioxygenase (HPPD). Recently, the rice gene
Language	English
Publishing date	2020-08-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711035-7
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2020.00925
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Article ; Online: Cytosine base editing systems with minimized off-target effect and molecular size.

Li, Ang / Mitsunobu, Hitoshi / Yoshioka, Shin / Suzuki, Takahisa / Kondo, Akihiko / Nishida, Keiji

Nature communications

2022 Volume 13, Issue 1, Page(s) 4531

Abstract: Cytosine base editing enables the installation of specific point mutations without double-strand breaks in DNA and is advantageous for various applications such as gene therapy, but further reduction of off-target risk and development of efficient ... ...

Abstract	Cytosine base editing enables the installation of specific point mutations without double-strand breaks in DNA and is advantageous for various applications such as gene therapy, but further reduction of off-target risk and development of efficient delivery methods are desired. Here we show structure-based rational engineering of the cytosine base editing system Target-AID to minimize its off-target effect and molecular size. By intensive and careful truncation, DNA-binding domain of its deaminase PmCDA1 is eliminated and additional mutations are introduced to restore enzyme function. The resulting tCDA1EQ is effective in N-terminal fusion (AID-2S) or inlaid architecture (AID-3S) with Cas9, showing minimized RNA-mediated editing and gRNA-dependent/independent DNA off-targets, as assessed in human cells. Combining with the smaller Cas9 ortholog system (SaCas9), a cytosine base editing system is created that is within the size limit of AAV vector.
MeSH term(s)	CRISPR-Associated Protein 9/genetics ; CRISPR-Associated Protein 9/metabolism ; CRISPR-Cas Systems/genetics ; Cytosine ; DNA/genetics ; Gene Editing/methods ; Humans ; RNA, Guide, CRISPR-Cas Systems
Chemical Substances	Cytosine (8J337D1HZY) ; DNA (9007-49-2) ; CRISPR-Associated Protein 9 (EC 3.1.-)
Language	English
Publishing date	2022-08-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-32157-8
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Article ; Online: Mammalian synthetic biology by CRISPRs engineering and applications.

Katayama, Kenta / Mitsunobu, Hitoshi / Nishida, Keiji

Current opinion in chemical biology

2019 Volume 52, Page(s) 79–84

Abstract: Technologies harnessing CRISPR systems have been rapidly evolving and expanding the capacity of researchers for understanding of mammalian cell behavior and its underlying mechanisms through genome and epigenome manipulations. In this review, we ... ...

Abstract	Technologies harnessing CRISPR systems have been rapidly evolving and expanding the capacity of researchers for understanding of mammalian cell behavior and its underlying mechanisms through genome and epigenome manipulations. In this review, we summarized the recent developments of CRISPR-based technologies for genetic and epigenetic modifications that include engineering of Cas9 for PAM simplification, non-cleaving base editing tools and alteration of gene expression. Applications such as genome-wide screening methods or CRISPR-based DNA barcoding for cellular lineage tracking are highlighted. Anticipated and upcoming development for mammalian synthetic biology that includes organelle engineering is also discussed.
MeSH term(s)	Animals ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Barcoding, Taxonomic ; DNA Breaks, Double-Stranded ; Epigenesis, Genetic ; Genetic Engineering ; Mammals ; RNA Editing ; Synthetic Biology
Language	English
Publishing date	2019-06-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1439176-4
ISSN	1879-0402 ; 1367-5931
ISSN (online)	1879-0402
ISSN	1367-5931
DOI	10.1016/j.cbpa.2019.05.020
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Article ; Online: Targeted Nucleotide Editing Technologies for Microbial Metabolic Engineering.

Arazoe, Takayuki / Kondo, Akihiko / Nishida, Keiji

Biotechnology journal

2018 Volume 13, Issue 9, Page(s) e1700596

Abstract: Since the emergence of programmable RNA-guided nucleases based on clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems, genome editing technologies have become a simplified and versatile tool for ... ...

Abstract	Since the emergence of programmable RNA-guided nucleases based on clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems, genome editing technologies have become a simplified and versatile tool for genome editing in various organisms and cell types. Although genome editing enables efficient genome manipulations, such as gene disruptions, gene knockins, and chromosomal translocations via DNA double-strand break (DSB) repair in eukaryotes, DSBs induced by the CRISPR/Cas system are lethal or severely toxic to many microorganisms. Therefore, in many prokaryotes, including industrially useful microbes, the CRISPR/Cas system is often used as a negative selection component in combination with recombineering or other related strategies. Novel and revolutionary technologies have been recently developed to re-write targeted nucleotides (C:G to T:A and A:T to G:C) without DSBs and donor DNA templates. These technologies rely on the recruitment of deaminases at specific target loci using the nuclease-deficient CRISPR/Cas system. Here, the authors review and compare CRISPR-based genome editing, current base editing platforms and their spectra. The authors discuss how these technologies can be applied in various aspects of microbial metabolic engineering to overcome barriers to cellular regulation in prokaryotes.
MeSH term(s)	Bacteria/genetics ; CRISPR-Cas Systems ; DNA Breaks, Double-Stranded ; Fungi/genetics ; Gene Editing/methods ; Metabolic Engineering ; RNA, Guide, CRISPR-Cas Systems/genetics
Chemical Substances	RNA, Guide, CRISPR-Cas Systems
Language	English
Publishing date	2018-06-19
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2221885-3
ISSN	1860-7314 ; 1860-6768
ISSN (online)	1860-7314
ISSN	1860-6768
DOI	10.1002/biot.201700596
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Article ; Online: Efficient base editing in tomato using a highly expressed transient system

Yuan, Shaoze / Kawasaki, Shunsuke / Abdellatif, Islam M. Y. / Nishida, Keiji / Kondoh, Akihiko / Ariizumi, Tohru / Ezura, Hiroshi / Miura, Kenji

Plant cell reports. 2021 Apr., v. 40, no. 4 p.667-676

2021

Abstract: KEY MESSAGE: Base editing in tomatoes was achieved by transient expression. The Solanaceae plants, particularly the tomato (Solanum lycopersicum), is of huge economic value worldwide. The tomato is a unique model plant for studying the functions of genes ...

Abstract	KEY MESSAGE: Base editing in tomatoes was achieved by transient expression. The Solanaceae plants, particularly the tomato (Solanum lycopersicum), is of huge economic value worldwide. The tomato is a unique model plant for studying the functions of genes related to fruit ripening. Deeper understanding of tomatoes is of great importance for both plant research and the economy. Genome editing technology, such as CRISPR/Cas9, has been used for functional genetic research. However, some challenges, such as low transformation efficiency, remain with this technology. Moreover, the foreign Cas9 and gRNA expression cassettes must be removed to obtain null-segregants In this study, we used a high-level transient expression system to improve the base editing technology. A high-level transient expression system has been established previously using geminiviral replication and a double terminator. The pBYR2HS vector was used for this transient expression system. nCas9-CDA and sgRNA-SlHWS were introduced into this vector, and the protein and RNA were then transiently expressed in tomato tissues by agroinfiltration. The homozygous mutant produced by base editing was obtained in the next generation with an efficiency of about 18%. nCas9-free next-generation plants were 71%. All the homozygous base-edited plants in next generation are nCas9-free. These findings show that the high-level transient expression system is useful for base editing in tomatoes.
Keywords	CRISPR-Cas systems ; RNA ; Solanum lycopersicum ; agroinfiltration ; economic valuation ; homozygosity ; mutants ; tomatoes
Language	English
Dates of publication	2021-04
Size	p. 667-676.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
Note	NAL-AP-2-clean
ZDB-ID	8397-5
ISSN	1432-203X ; 0721-085X ; 0721-7714
ISSN (online)	1432-203X
ISSN	0721-085X ; 0721-7714
DOI	10.1007/s00299-021-02662-z
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