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Article ; Online: Rice Gene Targeting by Homologous Recombination with Positive-Negative Selection Strategy.

Terada, Rie / Shimatani, Zenpei

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2238, Page(s) 241–257

Abstract: Gene targeting (GT) is a technique that alter the structure of the specific genes at their original loci in the genome by homologous recombination (HR). It plays an important role in functional genomics because it enables precise modification of the ... ...

Abstract	Gene targeting (GT) is a technique that alter the structure of the specific genes at their original loci in the genome by homologous recombination (HR). It plays an important role in functional genomics because it enables precise modification of the endogenous genes into desired forms such as knockout, knock-in, introduction of point mutations, as well as generation of fusion genes. Also, site-directed mutagenesis by GT can also be applied as an excellent technique for molecular breeding and gene therapy, because it can directly reflect the knowledge acquired from functional genomics. In this section, we introduce well-established GT procedure in rice in combination with positive-negative-selection (PNS) strategy.
MeSH term(s)	Agrobacterium/genetics ; Gene Targeting/methods ; Genetic Vectors/genetics ; Homologous Recombination ; Oryza/genetics ; Oryza/growth & development ; Oryza/metabolism ; Plant Proteins/genetics ; Plants, Genetically Modified/genetics ; Plants, Genetically Modified/growth & development ; Plants, Genetically Modified/metabolism ; Selection, Genetic ; Transformation, Genetic
Chemical Substances	Plant Proteins
Language	English
Publishing date	2021-01-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1068-8_16
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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: Herbicide tolerance-assisted multiplex targeted nucleotide substitution in rice

Shimatani, Zenpei / Fujikura, Ushio / Ishii, Hisaki / Terada, Rie / Nishida, Keiji / Kondoh, Akihiko

Data in Brief. 2018 Oct., v. 20 p.1325-1331

2018

Abstract: Acetolactate synthase (ALS) catalyzes the initial step in the biosynthesis of branched-chain amino acids, and is highly conserved from bacteria to higher plants. ALS is encoded by a single copy gene in rice genome and is a target enzyme of several ... ...

Abstract	Acetolactate synthase (ALS) catalyzes the initial step in the biosynthesis of branched-chain amino acids, and is highly conserved from bacteria to higher plants. ALS is encoded by a single copy gene in rice genome and is a target enzyme of several classes of herbicides. Although ALS mutations conferring herbicide-resistance property to plants are well documented, effect of Imazamox (IMZ) on rice and the mutations in ALS correlated with IMZ tolerance were unclear. In this article, the effect of IMZ on rice calli and seedlings in tissue culture conditions were evaluated. Also, the ALSA96V mutation was confirmed to improve IMZ tolerance of rice calli. Based on these results, ALS-assisted multiplex targeted base editing in rice was demonstrated in combination with Target-AID, a CRISPR/Cas9-cytidine deaminase fusion system [1], [2].
Keywords	acetolactate synthase ; biosynthesis ; callus ; genes ; herbicide resistance ; imazamox ; mutation ; rice ; tissue culture
Language	English
Dates of publication	2018-10
Size	p. 1325-1331.
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2018.08.124
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Multifunctional chemical inhibitors of the florigen activation complex discovered by structure-based high-throughput screening.

Taoka, Ken-Ichiro / Kawahara, Ikumi / Shinya, Shoko / Harada, Ken-Ichi / Yamashita, Eiki / Shimatani, Zenpei / Furuita, Kyoko / Muranaka, Tomoaki / Oyama, Tokitaka / Terada, Rie / Nakagawa, Atsushi / Fujiwara, Toshimichi / Tsuji, Hiroyuki / Kojima, Chojiro

The Plant journal : for cell and molecular biology

2022 Volume 112, Issue 6, Page(s) 1337–1349

Abstract: Structure-based high-throughput screening of chemical compounds that target protein-protein interactions (PPIs) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At ...

Abstract	Structure-based high-throughput screening of chemical compounds that target protein-protein interactions (PPIs) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At present, there are no examples of using high-throughput screening to identify chemicals that target plant transcriptional complexes, some of which are responsible for regulating multiple physiological functions. Florigen, a protein encoded by FLOWERING LOCUS T (FT), was initially identified as a molecule that promotes flowering and has since been shown to regulate flowering and other developmental phenomena such as tuber formation in potato (Solanum tuberosum). FT functions as a component of the florigen activation complex (FAC) with a 14-3-3 scaffold protein and FD, a bZIP transcription factor that activates downstream gene expression. Although 14-3-3 is an important component of FAC, little is known about the function of the 14-3-3 protein itself. Here, we report the results of a high-throughput in vitro fluorescence resonance energy transfer (FRET) screening of chemical libraries that enabled us to identify small molecules capable of inhibiting FAC formation. These molecules abrogate the in vitro interaction between the 14-3-3 protein and the OsFD1 peptide, a rice (Oryza sativa) FD, by directly binding to the 14-3-3 protein. Treatment with S4, a specific hit molecule, strongly inhibited FAC activity and flowering in duckweed, tuber formation in potato, and branching in rice in a dose-dependent manner. Our results demonstrate that the high-throughput screening approach based on the three-dimensional structure of PPIs is suitable in plants. In this study, we have proposed good candidate compounds for future modification to obtain inhibitors of florigen-dependent processes through inhibition of FAC formation.
MeSH term(s)	Florigen/metabolism ; Plant Proteins/metabolism ; 14-3-3 Proteins/genetics ; 14-3-3 Proteins/metabolism ; High-Throughput Screening Assays ; Oryza/metabolism ; Gene Expression Regulation, Plant ; Flowers/genetics
Chemical Substances	Florigen ; Plant Proteins ; 14-3-3 Proteins
Language	English
Publishing date	2022-11-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.16008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Multifunctional chemical inhibitors of the florigen activation complex discovered by structure‐based high‐throughput screening

Taoka, Ken‐ichiro / Kawahara, Ikumi / Shinya, Shoko / Harada, Ken‐ichi / Yamashita, Eiki / Shimatani, Zenpei / Furuita, Kyoko / Muranaka, Tomoaki / Oyama, Tokitaka / Terada, Rie / Nakagawa, Atsushi / Fujiwara, Toshimichi / Tsuji, Hiroyuki / Kojima, Chojiro

The Plant Journal. 2022 Dec., v. 112, no. 6 p.1337-1349

2022

Abstract: Structure‐based high‐throughput screening of chemical compounds that target protein–protein interactions (PPIs) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At ...

Abstract	Structure‐based high‐throughput screening of chemical compounds that target protein–protein interactions (PPIs) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At present, there are no examples of using high‐throughput screening to identify chemicals that target plant transcriptional complexes, some of which are responsible for regulating multiple physiological functions. Florigen, a protein encoded by FLOWERING LOCUS T (FT), was initially identified as a molecule that promotes flowering and has since been shown to regulate flowering and other developmental phenomena such as tuber formation in potato (Solanum tuberosum). FT functions as a component of the florigen activation complex (FAC) with a 14‐3‐3 scaffold protein and FD, a bZIP transcription factor that activates downstream gene expression. Although 14‐3‐3 is an important component of FAC, little is known about the function of the 14‐3‐3 protein itself. Here, we report the results of a high‐throughput in vitro fluorescence resonance energy transfer (FRET) screening of chemical libraries that enabled us to identify small molecules capable of inhibiting FAC formation. These molecules abrogate the in vitro interaction between the 14‐3‐3 protein and the OsFD1 peptide, a rice (Oryza sativa) FD, by directly binding to the 14‐3‐3 protein. Treatment with S4, a specific hit molecule, strongly inhibited FAC activity and flowering in duckweed, tuber formation in potato, and branching in rice in a dose‐dependent manner. Our results demonstrate that the high‐throughput screening approach based on the three‐dimensional structure of PPIs is suitable in plants. In this study, we have proposed good candidate compounds for future modification to obtain inhibitors of florigen‐dependent processes through inhibition of FAC formation.
Keywords	Araceae ; Oryza sativa ; Solanum tuberosum ; dose response ; energy transfer ; florigen ; fluorescence ; gene expression ; loci ; peptides ; plant development ; potatoes ; rice ; scaffolding proteins ; transcription (genetics) ; transcription factors
Language	English
Dates of publication	2022-12
Size	p. 1337-1349.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.16008
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Bonn / Germany

Z 6071: Show issues

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Article: Herbicide tolerance-assisted multiplex targeted nucleotide substitution in rice.

Shimatani, Zenpei / Fujikura, Ushio / Ishii, Hisaki / Terada, Rie / Nishida, Keiji / Kondo, Akihiko

Data in brief

2018 Volume 20, Page(s) 1325–1331

Abstract	Acetolactate synthase (ALS) catalyzes the initial step in the biosynthesis of branched-chain amino acids, and is highly conserved from bacteria to higher plants. ALS is encoded by a single copy gene in rice genome and is a target enzyme of several classes of herbicides. Although
Language	English
Publishing date	2018-08-30
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2018.08.124
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Targeted Base Editing with CRISPR-Deaminase in Tomato.

Shimatani, Zenpei / Ariizumi, Tohru / Fujikura, Ushio / Kondo, Akihiko / Ezura, Hiroshi / Nishida, Keiji

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1917, Page(s) 297–307

Abstract: The Target-AID system, consisting of a complex of cytidine deaminase and deficient CRISPR/Cas9, enables highly specific genomic nucleotide substitutions without the need for template DNA. The Cas9-fused cytidine deaminase is guided by sgRNAs and ... ...

Abstract	The Target-AID system, consisting of a complex of cytidine deaminase and deficient CRISPR/Cas9, enables highly specific genomic nucleotide substitutions without the need for template DNA. The Cas9-fused cytidine deaminase is guided by sgRNAs and catalyzes the conversion of cytosine to uracil. The resulting U-G DNA mismatches trigger nucleotide substitutions (C to T or G to A) through DNA replication and repair pathways. Target-AID also retains the benefits of conventional CRISPR/Cas9 including robustness in various organisms, high targeting efficiency, and multiplex simultaneous gene editing. Our research group recently developed plant-optimized Target-AID system and demonstrated targeted base editing in tomato and rice. In this chapter, we introduce methods for Target-AID application in tomato.
MeSH term(s)	CRISPR-Cas Systems/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Cytidine Deaminase/genetics ; Gene Editing/methods ; Solanum lycopersicum/genetics
Chemical Substances	Cytidine Deaminase (EC 3.5.4.5)
Language	English
Publishing date	2018-11-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8991-1_22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Novel assays to monitor gene expression and protein-protein interactions in rice using the bioluminescent protein, NanoLuc.

Taoka, Ken-Ichiro / Shimatani, Zenpei / Yamaguchi, Koji / Ogawa, Mana / Saitoh, Hiromi / Ikeda, Yoichi / Akashi, Hiroko / Terada, Rie / Kawasaki, Tsutomu / Tsuji, Hiroyuki

Plant biotechnology (Tokyo, Japan)

2021 Volume 38, Issue 1, Page(s) 89–99

Abstract: Luciferases have been widely utilized as sensitive reporters to monitor gene expression and protein-protein interactions. Compared to firefly luciferase (Fluc), a recently developed luciferase, Nanoluciferase (NanoLuc or Nluc), has several superior ... ...

Abstract	Luciferases have been widely utilized as sensitive reporters to monitor gene expression and protein-protein interactions. Compared to firefly luciferase (Fluc), a recently developed luciferase, Nanoluciferase (NanoLuc or Nluc), has several superior properties such as a smaller size and stronger luminescence activity. We compared the reporter properties of Nluc and Fluc in rice (
Language	English
Publishing date	2021-06-18
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2210142-1
ISSN	1347-6114 ; 1342-4580
ISSN (online)	1347-6114
ISSN	1342-4580
DOI	10.5511/plantbiotechnology.20.1209a
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Article ; Online: Inheritance of co-edited genes by CRISPR-based targeted nucleotide substitutions in rice

Shimatani, Zenpei / Fujikura, Ushio / Ishii, Hisaki / Matsui, Yusuke / Suzuki, Minoru / Ueke, Yuki / Taoka, Ken-ichiro / Terada, Rie / Nishida, Keiji / Kondoh, Akihiko

Plant physiology and biochemistry. 2018 Oct., v. 131 p.78-83

2018

Abstract: The CRISPR/Cas9 system is a revolutionary genome-editing tool for directed gene editing in various organisms. Cas9 variants can be applied as molecular homing devices when combined with various functional effectors such as transcriptional activators or ... ...

Abstract	The CRISPR/Cas9 system is a revolutionary genome-editing tool for directed gene editing in various organisms. Cas9 variants can be applied as molecular homing devices when combined with various functional effectors such as transcriptional activators or DNA modification enzymes. Target-AID is a synthetic complex of nuclease deficient Cas9 fused to an activation-induced cytidine deaminase (AID) that enables targeted nucleotide substitution (C to T or G to A). We previously demonstrated that the introduction of desired point mutations into target genes by Target-AID confers herbicide tolerance to rice callus. Inheritance of the introduced mutations, as well as the removal of transgenes, are key issues that must be addressed in order to fully develop Target-AID as a plant breeding technique. Here we report the transmission of such mutations from the callus to regenerants and their progenies, leading to a generation of selectable marker-free (SMF) herbicide tolerant rice plants with simultaneous multiplex nucleotide substitutions. These findings demonstrate that Target-AID can be developed into novel plant breeding technology which enables improvement of multiplex traits at one time in combination with sophisticated targeted base editing with the simplicity and versatility of CRISPR/Cas9 system.
Keywords	DNA ; callus ; cytidine deaminase ; gene editing ; herbicide resistance ; inheritance (genetics) ; plant breeding ; point mutation ; rice ; transactivators ; transgenes ; Acetolactate synthase (ALS) ; Activation-induced cytidine deaminase (AID) ; Herbicide tolerance ; Rice ; Selectable marker-free (SMF) ; Target-AID ; Targeted nucleotide editing ; CRISPR/Cas9 ; PAM ; sgRNA ; AID ; HPT ; ALS ; IMZ ; NHEJ ; HR ; SMF
Language	English
Dates of publication	2018-10
Size	p. 78-83.
Publishing place	Elsevier Masson SAS
Document type	Article ; Online
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2018.04.028
Database	NAL-Catalogue (AGRICOLA)

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Z 2696: Show issues
Z 2005/727: Show issues

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Article: Positive-negative-selection-mediated gene targeting in rice.

Shimatani, Zenpei / Nishizawa-Yokoi, Ayako / Endo, Masaki / Toki, Seiichi / Terada, Rie

Frontiers in plant science

2015 Volume 5, Page(s) 748

Abstract: Gene targeting (GT) refers to the designed modification of genomic sequence(s) through homologous recombination (HR). GT is a powerful tool both for the study of gene function and for molecular breeding. However, in transformation of higher plants, non- ... ...

Abstract	Gene targeting (GT) refers to the designed modification of genomic sequence(s) through homologous recombination (HR). GT is a powerful tool both for the study of gene function and for molecular breeding. However, in transformation of higher plants, non-homologous end joining (NHEJ) occurs overwhelmingly in somatic cells, masking HR-mediated GT. Positive-negative selection (PNS) is an approach for finding HR-mediated GT events because it can eliminate NHEJ effectively by expression of a negative-selection marker gene. In rice-a major crop worldwide-reproducible PNS-mediated GT of endogenous genes has now been successfully achieved. The procedure is based on strong PNS using diphtheria toxin A-fragment as a negative marker, and has succeeded in the directed modification of several endogenous rice genes in various ways. In addition to gene knock-outs and knock-ins, a nucleotide substitution in a target gene was also achieved recently. This review presents a summary of the development of the rice PNS system, highlighting its advantages. Different types of gene modification and gene editing aimed at developing new plant breeding technology based on PNS are discussed.
Language	English
Publishing date	2015-01-05
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2711035-7
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2014.00748
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