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8. Specific suppression of long terminal repeat retrotransposon mobilization in plants.

Author

Brestovitsky, Anna, Iwasaki, Mayumi, Jungnam Cho, Adulyanukosol, Natthawut, Paszkowski, Jerzy, and Catoni, Marco

Abstract

The tissue culture passage necessary for the generation of transgenic plants induces genome instability. This instability predominantly involves the uncontrolled mobilization of LTR retrotransposons (LTR-TEs), which are the most abundant class of mobile genetic elements in plant genomes. Here, we demonstrate that in conditions inductive for high LTR-TE mobilization, like abiotic stress in Arabidopsis (Arabidopsis thaliana) and callus culture in rice (Oryza sativa), application of the reverse transcriptase (RT) inhibitor known as Tenofovir substantially affects LTR-TE RT activity without interfering with plant development. We observed that Tenofovir reduces extrachromosomal DNA accumulation and prevents new genomic integrations of the active LTR-TE ONSEN in heat-stressed Arabidopsis seedlings, and transposons of O. sativa 17 and 19 (Tos17 and Tos19) in rice calli. In addition, Tenofovir allows the recovery of plants free from new LTR-TE insertions. We propose the use of Tenofovir as a tool for studies of LTR-TE transposition and for limiting genetic instabilities of plants derived from tissue culture. [ABSTRACT FROM AUTHOR]

Published
2023
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12. Meta-Analyses of Microarrays of Arabidopsis asymmetric leaves1 (as1), as2 and Their Modifying Mutants Reveal a Critical Role for the ETT Pathway in Stabilization of Adaxial–Abaxial Patterning and Cell Division During Leaf Development

Author

Takahashi, Hiro, Iwakawa, Hidekazu, Ishibashi, Nanako, Kojima, Shoko, Matsumura, Yoko, Prananingrum, Pratiwi, Iwasaki, Mayumi, Takahashi, Anna, Ikezaki, Masaya, Luo, Lilan, Kobayashi, Takeshi, Machida, Yasunori, and Machida, Chiyoko

Published
2013
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13. The Mature Endosperm Governs Early Seedling Development: A Focus on Cuticle Formation

Author

De Giorgi, Julien, primary, Fuchs, Christelle, additional, Iwasaki, Mayumi, additional, Kim, Woohyun, additional, Piskurewicz, Urszula, additional, Gully, Kay, additional, Utz-Pugin, Anne, additional, Mene-Saffrane, Laurent, additional, Waridel, Patrice, additional, Nawrath, Christiane, additional, Longoni, Fiamma Paolo, additional, Loubéry, Sylvain, additional, and Lopez-Molina, Luis, additional

Published
2021
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21. ICE1 and ZOU determine the depth of primary seed dormancy in Arabidopsis independently of their role in endosperm development.

Author

MacGregor, Dana R., Zhang, Naichao, Iwasaki, Mayumi, Chen, Min, Dave, Anuja, Lopez‐Molina, Luis, and Penfield, Steven

Subjects
ENDOSPERM, SEED dormancy, SOIL seed banks, ARABIDOPSIS, SEED morphology, TRANSCRIPTION factors
Abstract

Summary: Seed dormancy is a widespread and key adaptive trait that is essential for the establishment of soil seed banks and prevention of pre‐harvest sprouting. Herein we demonstrate that the endosperm‐expressed transcription factors ZHOUPI (ZOU) and INDUCER OF CBF EXPRESSION1 (ICE1) play a role in determining the depth of primary dormancy in Arabidopsis. We show that ice1 or zou increases seed dormancy and the double mutant has an additive phenotype. This increased dormancy is associated with increased ABA levels, and can be separated genetically from any role in endosperm maturation because loss of ABA biosynthesis or DELAY OF GERMINATION 1 reverses the dormancy phenotype without affecting the aberrant seed morphology. Consistent with these results, ice1 endosperms had an increased capacity for preventing embryo greening, a phenotype previously associated with an increase in endospermic ABA levels. Although ice1 changes the expression of many genes, including some in ABA biosynthesis, catabolism and/or signalling, only ABA INSENSITIVE 3 is significantly misregulated in ice1 mutants. We also demonstrate that ICE1 binds to and inhibits expression of ABA INSENSITIVE 3. Our data demonstrate that Arabidopsis ICE1 and ZOU determine the depth of primary dormancy during maturation independently of their effect on endosperm development. Significance Statement: Our data demonstrate that ICE1 and ZOU determine the depth of primary seed dormancy and that this can be separated from their role in initiating endosperm consumption. These genes effect endospermic ABA production and ICE1 binds to and regulates the expression of ABA INSENSITIVE 3, one of the AFL transcription factors well known for their role in inducing both seed dormancy and the seed maturation programme in the embryo and endosperm. [ABSTRACT FROM AUTHOR]

Published
2019
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22. ASYMMETRIC LEAVES2 and Elongator, a Histone Acetyltransferase Complex, Mediate the Establishment of Polarity in Leaves of Arabidopsis thaliana

Author

Kojima, Shoko, Iwasaki, Mayumi, Takahashi, Hiro, Imai, Tomoya, Matsumura, Yoko, Fleury, Delphine, Van Lijsebettens, Mieke, Machida, Yasunori, Machida, Chiyoko, Kojima, Shoko, Iwasaki, Mayumi, Takahashi, Hiro, Imai, Tomoya, Matsumura, Yoko, Fleury, Delphine, Van Lijsebettens, Mieke, Machida, Yasunori, and Machida, Chiyoko

Abstract

Leaf primordia are generated around the shoot apical meristem. Mutation of the ASYMMETRIC LEAVES2 (AS2) gene of Arabidopsis thaliana results in defects in repression of the meristematic and indeterminate state, establishment of adaxial-abaxial polarity and left-right symmetry in leaves. AS2 represses transcription of meristem-specific class 1 KNOX homeobox genes and of the abaxial-determinant genes ETTIN/ARF3, KANADI2 and YABBY5. To clarify the role of AS2 in the establishment of leaf polarity, we isolated mutations that enhanced the polarity defects associated with as2. We describe here the enhancer-of-asymmetric-leaves-two1 (east1) mutation, which caused the formation of filamentous leaves with abaxialized epidermis on the as2-1 background. Levels of transcripts of class 1 KNOX and abaxial-determinant genes were markedly higher in as2-1 east1-1 mutant plants than in the wild-type and corresponding single-mutant plants. EAST1 encodes the histone acetyltransferase ELONGATA3 (ELO3), a component of the Elongator complex. Genetic analysis, using mutations in genes involved in the biogenesis of a trans-acting small interfering RNA (ta-siRNA), revealed that ELO3 mediated establishment of leaf polarity independently of AS2 and the ta-siRNA-related pathway. Treatment with an inhibitor of histone deacetylases (HDACs) caused additive polarity defects in as2-1 east1-1 mutant plants, suggesting the operation of an ELO3 pathway, independent of the HDAC pathway, in the determination of polarity. We propose that multiple pathways play important roles in repression of the expression of class 1 KNOX and abaxial-determinant genes in the development of the adaxial domain of leaves and, thus, in the establishment of leaf polarity

Published
2017

23. Meta-Analyses of Microarrays of Arabidopsis asymmetric leaves1 (as1), as2 and Their Modifying Mutants Reveal a Critical Role for the ETT Pathway in Stabilization of Adaxial-Abaxial Patterning and Cell Division During Leaf Development

Author

Takahashi, Hiro, Iwakawa, Hidekazu, Ishibashi, Nanako, Kojima, Shoko, Matsumura, Yoko, Prananingrum, Pratiwi, Iwasaki, Mayumi, Takahashi, Anna, Ikezaki, Masaya, Luo, Lilan, Kobayashi, Takeshi, Machida, Yasunori, Machida, Chiyoko, Takahashi, Hiro, Iwakawa, Hidekazu, Ishibashi, Nanako, Kojima, Shoko, Matsumura, Yoko, Prananingrum, Pratiwi, Iwasaki, Mayumi, Takahashi, Anna, Ikezaki, Masaya, Luo, Lilan, Kobayashi, Takeshi, Machida, Yasunori, and Machida, Chiyoko

Abstract

It is necessary to use algorithms to analyze gene expression data from DNA microarrays, such as in clustering and machine learning. Previously, we developed the knowledge-based fuzzy adaptive resonance theory (KB-FuzzyART), a clustering algorithm suitable for analyzing gene expression data, to find clues for identifying gene networks. Leaf primordia form around the shoot apical meristem (SAM), which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial-abaxial patterning is crucial for lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many regulatory genes that specify such patterning have been identified. Analysis by the KB-FuzzyART and subsequent molecular and genetic analyses previously showed that ASYMMETRIC LEAVES1 (AS1) and AS2 repress the expression of some abaxial-determinant genes, such as AUXIN RESPONSE FACTOR3 (ARF3)/ETTIN (ETT) and ARF4, which are responsible for defects in leaf adaxial-abaxial polarity in as1 and as2. In the present study, genetic analysis revealed that ARF3/ETT and ARF4 were regulated by modifier genes, BOBBER1 (BOB1) and ELONGATA3 (ELO3), together with AS1-AS2. We analyzed expression arrays with as2 elo3 and as2 bob1, and extracted genes downstream of ARF3/ETT by using KB-FuzzyART and molecular analyses. The results showed that expression of Kip-related protein (KRP) (for inhibitors of cyclin-dependent protein kinases) and Isopentenyltransferase (IPT) (for biosynthesis of cytokinin) genes were controlled by AS1-AS2 through ARF3/ETT and ARF4 functions, which suggests that the AS1-AS2-ETT pathway plays a critical role in controlling the cell division cycle and the biosynthesis of cytokinin around SAM to stabilize leaf development in Arabidopsis thaliana

Published
2017

28. Dual regulation of ETTIN (ARF3) gene expression by AS1-AS2, which maintains the DNA methylation level, is involved in stabilization of leaf adaxial-abaxial partitioning in Arabidopsis

Author

Iwasaki, Mayumi, primary, Takahashi, Hiro, additional, Iwakawa, Hidekazu, additional, Nakagawa, Ayami, additional, Ishikawa, Takaaki, additional, Tanaka, Hirokazu, additional, Matsumura, Yoko, additional, Pekker, Irena, additional, Eshed, Yuval, additional, Vial-Pradel, Simon, additional, Ito, Toshiro, additional, Watanabe, Yuichiro, additional, Ueno, Yoshihisa, additional, Fukazawa, Hiroshi, additional, Kojima, Shoko, additional, Machida, Yasunori, additional, and Machida, Chiyoko, additional

Published
2013
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31. Expression of theASYMMETRIC LEAVES2gene in the adaxial domain of Arabidopsis leaves represses cell proliferation in this domain and is critical for the development of properly expanded leaves

Author

Iwakawa, Hidekazu, primary, Iwasaki, Mayumi, additional, Kojima, Shoko, additional, Ueno, Yoshihisa, additional, Soma, Teppei, additional, Tanaka, Hirokazu, additional, Semiarti, Endang, additional, Machida, Yasunori, additional, and Machida, Chiyoko, additional

Published
2007
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34. A novel microsatellite locus isolated from an AFLP fragment in the mangrove speciesKandelia obovata(Rhizophoraceae).

Author

Harada, Ko, Okaura, Takatomi, Le Huong Giang, Nguyen Van Huan, Iwasaki, Mayumi, and Nitasaka, Eiji

Subjects
MICROSATELLITE repeats, MANGROVE plants, RHIZOPHORACEAE
Abstract

The study of AFLP analysis inKandelia obovata, one of the major mangrove species in Japan, revealed the existence of a unique fragment showing stuttered peaks. We cloned this fragment and found a novel microsatellite locus. We report the method used for isolation and the polymorphic nature of this locus among the populations on Iriomote Island. [ABSTRACT FROM AUTHOR]

Published
2005
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35. ASYMMETRIC LEAVES2 and Elongator, a Histone Acetyltransferase Complex, Mediate the Establishment of Polarity in Leaves of Arabidopsis thaliana

Author

Kojima, Shoko, Iwasaki, Mayumi, Takahashi, Hiro, Imai, Tomoya, Matsumura, Yoko, Fleury, Delphine, Van Lijsebettens, Mieke, Machida, Yasunori, Machida, Chiyoko, Kojima, Shoko, Iwasaki, Mayumi, Takahashi, Hiro, Imai, Tomoya, Matsumura, Yoko, Fleury, Delphine, Van Lijsebettens, Mieke, Machida, Yasunori, and Machida, Chiyoko

Abstract

Leaf primordia are generated around the shoot apical meristem. Mutation of the ASYMMETRIC LEAVES2 (AS2) gene of Arabidopsis thaliana results in defects in repression of the meristematic and indeterminate state, establishment of adaxial-abaxial polarity and left-right symmetry in leaves. AS2 represses transcription of meristem-specific class 1 KNOX homeobox genes and of the abaxial-determinant genes ETTIN/ARF3, KANADI2 and YABBY5. To clarify the role of AS2 in the establishment of leaf polarity, we isolated mutations that enhanced the polarity defects associated with as2. We describe here the enhancer-of-asymmetric-leaves-two1 (east1) mutation, which caused the formation of filamentous leaves with abaxialized epidermis on the as2-1 background. Levels of transcripts of class 1 KNOX and abaxial-determinant genes were markedly higher in as2-1 east1-1 mutant plants than in the wild-type and corresponding single-mutant plants. EAST1 encodes the histone acetyltransferase ELONGATA3 (ELO3), a component of the Elongator complex. Genetic analysis, using mutations in genes involved in the biogenesis of a trans-acting small interfering RNA (ta-siRNA), revealed that ELO3 mediated establishment of leaf polarity independently of AS2 and the ta-siRNA-related pathway. Treatment with an inhibitor of histone deacetylases (HDACs) caused additive polarity defects in as2-1 east1-1 mutant plants, suggesting the operation of an ELO3 pathway, independent of the HDAC pathway, in the determination of polarity. We propose that multiple pathways play important roles in repression of the expression of class 1 KNOX and abaxial-determinant genes in the development of the adaxial domain of leaves and, thus, in the establishment of leaf polarity

36. Meta-Analyses of Microarrays of Arabidopsis asymmetric leaves1 (as1), as2 and Their Modifying Mutants Reveal a Critical Role for the ETT Pathway in Stabilization of Adaxial-Abaxial Patterning and Cell Division During Leaf Development

Author

Takahashi, Hiro, Iwakawa, Hidekazu, Ishibashi, Nanako, Kojima, Shoko, Matsumura, Yoko, Prananingrum, Pratiwi, Iwasaki, Mayumi, Takahashi, Anna, Ikezaki, Masaya, Luo, Lilan, Kobayashi, Takeshi, Machida, Yasunori, Machida, Chiyoko, Takahashi, Hiro, Iwakawa, Hidekazu, Ishibashi, Nanako, Kojima, Shoko, Matsumura, Yoko, Prananingrum, Pratiwi, Iwasaki, Mayumi, Takahashi, Anna, Ikezaki, Masaya, Luo, Lilan, Kobayashi, Takeshi, Machida, Yasunori, and Machida, Chiyoko

Abstract

It is necessary to use algorithms to analyze gene expression data from DNA microarrays, such as in clustering and machine learning. Previously, we developed the knowledge-based fuzzy adaptive resonance theory (KB-FuzzyART), a clustering algorithm suitable for analyzing gene expression data, to find clues for identifying gene networks. Leaf primordia form around the shoot apical meristem (SAM), which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial-abaxial patterning is crucial for lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many regulatory genes that specify such patterning have been identified. Analysis by the KB-FuzzyART and subsequent molecular and genetic analyses previously showed that ASYMMETRIC LEAVES1 (AS1) and AS2 repress the expression of some abaxial-determinant genes, such as AUXIN RESPONSE FACTOR3 (ARF3)/ETTIN (ETT) and ARF4, which are responsible for defects in leaf adaxial-abaxial polarity in as1 and as2. In the present study, genetic analysis revealed that ARF3/ETT and ARF4 were regulated by modifier genes, BOBBER1 (BOB1) and ELONGATA3 (ELO3), together with AS1-AS2. We analyzed expression arrays with as2 elo3 and as2 bob1, and extracted genes downstream of ARF3/ETT by using KB-FuzzyART and molecular analyses. The results showed that expression of Kip-related protein (KRP) (for inhibitors of cyclin-dependent protein kinases) and Isopentenyltransferase (IPT) (for biosynthesis of cytokinin) genes were controlled by AS1-AS2 through ARF3/ETT and ARF4 functions, which suggests that the AS1-AS2-ETT pathway plays a critical role in controlling the cell division cycle and the biosynthesis of cytokinin around SAM to stabilize leaf development in Arabidopsis thaliana

37. βC1, the pathogenicity factor of TYLCCNV, interacts with AS1 to alter leaf development and suppress selective jasmonic acid responses.

Author

Jun-Yi Yang, Iwasaki, Mayumi, Machida, Chiyoko, Machida, Yasunori, Xueping Zhou, and Nam-Hai Chua

Subjects
*JASMONIC acid
Abstract

An abstract of the article "βC1, the pathogenicity factor of TYLCCNV, interacts with AS1 to alter leaf development and suppress selective jasmonic acid responses," by Jun-Yi Yang, Mayumi Iwasaki, Chiyoko Machida, Yasunori Machida, Xueping Zhou, and Nam-Hai Chua is presented.

Published
2008

38. Arabidopsis thaliana Mature Endosperm Dissection and Isolation of Genomic DNA from Mature Seed Tissues.

Author

Iwasaki M and Lopez-Molina L

Subjects
Arabidopsis Proteins genetics, DNA, Plant isolation & purification, Gene Expression Regulation, Plant, Genome, Plant genetics, Genomics methods, Arabidopsis genetics, DNA, Plant genetics, Endosperm genetics, Seeds genetics
Abstract

We describe methods to separate endosperms and embryos from Arabidopsis thaliana mature seeds in large amounts and to isolate high-quality genomic DNA from those tissues. The resulting materials are suitable for analysis of DNA methylation by bisulfite sequencing or histone modifications by chromatin immunoprecipitation (ChIP).

Published
2021
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39. betaC1, the pathogenicity factor of TYLCCNV, interacts with AS1 to alter leaf development and suppress selective jasmonic acid responses.

Author

Yang JY, Iwasaki M, Machida C, Machida Y, Zhou X, and Chua NH

Subjects
Arabidopsis metabolism, Arabidopsis Proteins genetics, Mutation, Plants, Genetically Modified, Protein Binding, Reverse Transcriptase Polymerase Chain Reaction, Transcription Factors genetics, Virulence, Arabidopsis growth & development, Arabidopsis virology, Arabidopsis Proteins metabolism, Cyclopentanes metabolism, Geminiviridae pathogenicity, Oxylipins metabolism, Plant Leaves growth & development, Transcription Factors metabolism, Viral Proteins metabolism
Abstract

Viruses induce pathogenic symptoms on plants but the molecular basis is poorly understood. Here, we show that transgenic Arabidopsis expressing the pathogenesis protein betaC1 of Tomato yellow leaf curl China virus (TYLCCNV), a geminivirus, can phenocopy to a large extent disease symptoms of virus-infected tobacco plants in having upward curled leaves, radialized leaves with outgrowth tissues from abaxial surfaces, and sterile flowers. These morphological changes are paralleled by a reduction in miR165/166 levels and an increase in PHB and PHV transcript levels. Two factors, ASYMMETRIC LEAVES 1 (AS1) and ASYMMETRIC LEAVES 2 (AS2), are known to regulate leaf development as AS1/AS2 complex. Strikingly, betaC1 plants phenocopy plants overexpressing AS2 at the morphological and molecular level and betaC1 is able to partially complement as2 mutation. betaC1 binds directly to AS1, elicits morphological and gene expression changes dependent on AS1 but not AS2, and attenuates expression of selective jasmonic acid (JA)-responsive gene. Our results show that betaC1 forms a complex with AS1 to execute its pathogenic functions and to suppress a subset of JA responses.

Published
2008
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