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Liu L, Yahaya BS, Li J, Wu F. Enigmatic role of auxin response factors in plant growth and stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1398818. [PMID: 38903418 PMCID: PMC11188990 DOI: 10.3389/fpls.2024.1398818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
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Ando S, Nomoto M, Iwakawa H, Vial-Pradel S, Luo L, Sasabe M, Ohbayashi I, Yamamoto KT, Tada Y, Sugiyama M, Machida Y, Kojima S, Machida C. Arabidopsis ASYMMETRIC LEAVES2 and Nucleolar Factors Are Coordinately Involved in the Perinucleolar Patterning of AS2 Bodies and Leaf Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:3621. [PMID: 37896084 PMCID: PMC10610122 DOI: 10.3390/plants12203621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023]
Abstract
Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a key role in the formation of flat symmetric leaves. AS2 represses the expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). AS2 interacts in vitro with the CGCCGC sequence in ETT/ARF3 exon 1. In cells of leaf primordia, AS2 localizes at peripheral regions of the nucleolus as two AS2 bodies, which are partially overlapped with chromocenters that contain condensed 45S ribosomal DNA repeats. AS2 contains the AS2/LOB domain, which consists of three sequences conserved in the AS2/LOB family: the zinc finger (ZF) motif, the ICG sequence including the conserved glycine residue, and the LZL motif. AS2 and the genes NUCLEOLIN1 (NUC1), RNA HELICASE10 (RH10), and ROOT INITIATION DEFECTIVE2 (RID2) that encode nucleolar proteins coordinately act as repressors against the expression of ETT/ARF3. Here, we examined the formation and patterning of AS2 bodies made from as2 mutants with amino acid substitutions in the ZF motif and the ICG sequence in cells of cotyledons and leaf primordia. Our results showed that the amino acid residues next to the cysteine residues in the ZF motif were essential for both the formation of AS2 bodies and the interaction with ETT/ARF3 DNA. The conserved glycine residue in the ICG sequence was required for the formation of AS2 bodies, but not for the DNA interaction. We also examined the effects of nuc1, rh10, and rid2 mutations, which alter the metabolism of rRNA intermediates and the morphology of the nucleolus, and showed that more than two AS2 bodies were observed in the nucleolus and at its periphery. These results suggested that the patterning of AS2 bodies is tightly linked to the morphology and functions of the nucleolus and the development of flat symmetric leaves in plants.
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Affiliation(s)
- Sayuri Ando
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Simon Vial-Pradel
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Lilan Luo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
| | - Michiko Sasabe
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho, Hirosaki 036-8561, Japan;
| | - Iwai Ohbayashi
- Department of Life Sciences, National Cheng Kung University, Tainan City 701, Taiwan;
| | - Kotaro T. Yamamoto
- Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yasuomi Tada
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Munetaka Sugiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Yasunori Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan; (M.N.); (L.L.); (Y.T.)
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan; (S.A.); (H.I.); (S.V.-P.); (Y.M.)
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Fu Y, Zhang H, Ma Y, Li C, Zhang K, Liu X. A model worker: Multifaceted modulation of AUXIN RESPONSE FACTOR3 orchestrates plant reproductive phases. FRONTIERS IN PLANT SCIENCE 2023; 14:1123059. [PMID: 36923132 PMCID: PMC10009171 DOI: 10.3389/fpls.2023.1123059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The key phytohormone auxin is involved in practically every aspect of plant growth and development. Auxin regulates these processes by controlling gene expression through functionally distinct AUXIN RESPONSE FACTORs (ARFs). As a noncanonical ARF, ARF3/ETTIN (ETT) mediates auxin responses to orchestrate multiple developmental processes during the reproductive phase. The arf3 mutation has pleiotropic effects on reproductive development, causing abnormalities in meristem homeostasis, floral determinacy, phyllotaxy, floral organ patterning, gynoecium morphogenesis, ovule development, and self-incompatibility. The importance of ARF3 is also reflected in its precise regulation at the transcriptional, posttranscriptional, translational, and epigenetic levels. Recent studies have shown that ARF3 controls dynamic shoot apical meristem (SAM) maintenance in a non-cell autonomous manner. Here, we summarize the hierarchical regulatory mechanisms by which ARF3 is regulated and the diverse roles of ARF3 regulating developmental processes during the reproductive phase.
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Affiliation(s)
- Yunze Fu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Hao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Yuru Ma
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Cundong Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
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Machida Y, Suzuki T, Sasabe M, Iwakawa H, Kojima S, Machida C. Arabidopsis ASYMMETRIC LEAVES2 (AS2): roles in plant morphogenesis, cell division, and pathogenesis. JOURNAL OF PLANT RESEARCH 2022; 135:3-14. [PMID: 34668105 PMCID: PMC8755679 DOI: 10.1007/s10265-021-01349-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/21/2021] [Indexed: 05/26/2023]
Abstract
The ASYMMETRIC LEAVES2 (AS2) gene in Arabidopsis thaliana is responsible for the development of flat, symmetric, and extended leaf laminae and their vein systems. AS2 protein is a member of the plant-specific AS2/LOB protein family, which includes 42 members comprising the conserved amino-terminal domain referred to as the AS2/LOB domain, and the variable carboxyl-terminal region. Among the members, AS2 has been most intensively investigated on both genetic and molecular levels. AS2 forms a complex with the myb protein AS1, and is involved in epigenetic repression of the abaxial genes ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3), ARF4, and class 1 KNOX homeobox genes. The repressed expression of these genes by AS2 is markedly enhanced by the cooperative action of various modifier genes, some of which encode nucleolar proteins. Further downstream, progression of the cell division cycle in the developing organs is stimulated; meristematic states are suppressed in determinate leaf primordia; and the extension of leaf primordia is induced. AS2 binds the specific sequence in exon 1 of ETT/ARF3 and maintains methylated CpGs in several exons of ETT/ARF3. AS2 forms bodies (designated as AS2 bodies) at nucleolar peripheries. AS2 bodies partially overlap chromocenters, including inactive 45S ribosomal DNA repeats, suggesting the presence of molecular and functional links among AS2, the 45S rDNAs, and the nucleolus to exert the repressive regulation of ETT/ARF3. The AS2/LOB domain is characterized by three subdomains, the zinc finger (ZF) motif, the internally conserved-glycine containing (ICG) region, and the leucine-zipper-like (LZL) region. Each of these subdomains is essential for the formation of AS2 bodies. ICG to LZL are required for nuclear localization, but ZF is not. LZL intrinsically has the potential to be exported to the cytoplasm. In addition to its nuclear function, it has been reported that AS2 plays a positive role in geminivirus infection: its protein BV1 stimulates the expression of AS2 and recruits AS2 to the cytoplasm, which enhances virus infectivity by suppression of cytoplasmic post transcriptional gene silencing.
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Affiliation(s)
- Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan.
| | - Takanori Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan
- Central Research Institute, Ishihara Sangyo Kaisha, Ltd., 2-3-1 Nishi-Shibukawa, Kusatsu, Shiga, 525-0025, Japan
| | - Michiko Sasabe
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, 036-8561, Japan
| | - Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan
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Iwakawa H, Takahashi H, Machida Y, Machida C. Roles of ASYMMETRIC LEAVES2 (AS2) and Nucleolar Proteins in the Adaxial-Abaxial Polarity Specification at the Perinucleolar Region in Arabidopsis. Int J Mol Sci 2020; 21:E7314. [PMID: 33022996 PMCID: PMC7582388 DOI: 10.3390/ijms21197314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
Leaves of Arabidopsis develop from a shoot apical meristem grow along three (proximal-distal, adaxial-abaxial, and medial-lateral) axes and form a flat symmetric architecture. ASYMMETRIC LEAVES2 (AS2), a key regulator for leaf adaxial-abaxial partitioning, encodes a plant-specific nuclear protein and directly represses the abaxial-determining gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). How AS2 could act as a critical regulator, however, has yet to be demonstrated, although it might play an epigenetic role. Here, we summarize the current understandings of the genetic, molecular, and cellular functions of AS2. A characteristic genetic feature of AS2 is the presence of a number of (about 60) modifier genes, mutations of which enhance the leaf abnormalities of as2. Although genes for proteins that are involved in diverse cellular processes are known as modifiers, it has recently become clear that many modifier proteins, such as NUCLEOLIN1 (NUC1) and RNA HELICASE10 (RH10), are localized in the nucleolus. Some modifiers including ribosomal proteins are also members of the small subunit processome (SSUP). In addition, AS2 forms perinucleolar bodies partially colocalizing with chromocenters that include the condensed inactive 45S ribosomal RNA genes. AS2 participates in maintaining CpG methylation in specific exons of ETT/ARF3. NUC1 and RH10 genes are also involved in maintaining the CpG methylation levels and repressing ETT/ARF3 transcript levels. AS2 and nucleolus-localizing modifiers might cooperatively repress ETT/ARF3 to develop symmetric flat leaves. These results raise the possibility of a nucleolus-related epigenetic repression system operating for developmental genes unique to plants and predict that AS2 could be a molecule with novel functions that cannot be explained by the conventional concept of transcription factors.
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Affiliation(s)
- Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200, Matsumoto-cho, Kasugai, Aichi 487-8501, Japan;
| | - Hiro Takahashi
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan;
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200, Matsumoto-cho, Kasugai, Aichi 487-8501, Japan;
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Luo L, Ando S, Sakamoto Y, Suzuki T, Takahashi H, Ishibashi N, Kojima S, Kurihara D, Higashiyama T, Yamamoto KT, Matsunaga S, Machida C, Sasabe M, Machida Y. The formation of perinucleolar bodies is important for normal leaf development and requires the zinc-finger DNA-binding motif in Arabidopsis ASYMMETRIC LEAVES2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1118-1134. [PMID: 31639235 PMCID: PMC7155070 DOI: 10.1111/tpj.14579] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 05/27/2023]
Abstract
In Arabidopsis, the ASYMMETRIC LEAVES2 (AS2) protein plays a key role in the formation of flat symmetric leaves via direct repression of the abaxial gene ETT/ARF3. AS2 encodes a plant-specific nuclear protein that contains the AS2/LOB domain, which includes a zinc-finger (ZF) motif that is conserved in the AS2/LOB family. We have shown that AS2 binds to the coding DNA of ETT/ARF3, which requires the ZF motif. AS2 is co-localized with AS1 in perinucleolar bodies (AS2 bodies). To identify the amino acid signals in AS2 required for formation of AS2 bodies and function(s) in leaf formation, we constructed recombinant DNAs that encoded mutant AS2 proteins fused to yellow fluorescent protein. We examined the subcellular localization of these proteins in cells of cotyledons and leaf primordia of transgenic plants and cultured cells. The amino acid signals essential for formation of AS2 bodies were located within and adjacent to the ZF motif. Mutant AS2 that failed to form AS2 bodies also failed to rescue the as2-1 mutation. Our results suggest the importance of the formation of AS2 bodies and the nature of interactions of AS2 with its target DNA and nucleolar factors including NUCLEOLIN1. The partial overlap of AS2 bodies with perinucleolar chromocenters with condensed ribosomal RNA genes implies a correlation between AS2 bodies and the chromatin state. Patterns of AS2 bodies in cells during interphase and mitosis in leaf primordia were distinct from those in cultured cells, suggesting that the formation and distribution of AS2 bodies are developmentally modulated in plants.
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Affiliation(s)
- Lilan Luo
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
- Present address:
Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Sayuri Ando
- Graduate School of Bioscience and BiotechnologyChubu UniversityKasugaiAichi487‐8501Japan
| | - Yuki Sakamoto
- Department of Applied Biological ScienceFaculty of Science and TechnologyTokyo University of ScienceNodaChiba278‐8510Japan
- Department of Biological SciencesGraduate School of ScienceOsaka University1‐1 Machikaneyama‐choToyonakaOsaka560‐0043Japan
| | - Takanori Suzuki
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
- Central Research InstituteIshihara Sangyo Kaisha, Ltd.2‐3‐1 Nishi‐ShibukawaKusatsuShiga525‐0025Japan
| | - Hiro Takahashi
- Graduate School of Medical SciencesKanazawa UniversityKakuma‐machiKanazawaIshikawa920‐1192Japan
| | - Nanako Ishibashi
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
| | - Shoko Kojima
- Graduate School of Bioscience and BiotechnologyChubu UniversityKasugaiAichi487‐8501Japan
| | - Daisuke Kurihara
- JST, PRESTOFuro‐cho, Chikusa‐kuNagoyaAichi464‐8601Japan
- Institute of Transformative Bio‐Molecules (ITbM)Nagoya UniversityFuro‐cho, Chiku00sa‐kuNagoyaAichi464‐8601Japan
| | - Tetsuya Higashiyama
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
- Institute of Transformative Bio‐Molecules (ITbM)Nagoya UniversityFuro‐cho, Chiku00sa‐kuNagoyaAichi464‐8601Japan
- Department of Biological SciencesGraduate School of ScienceUniversity of Tokyo7‐3‐1 Hongo, Bukyo‐kuTokyo113‐0033Japan
| | - Kotaro T. Yamamoto
- Division of Biological SciencesFaculty of ScienceHokkaido UniversitySapporo060‐0810Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological ScienceFaculty of Science and TechnologyTokyo University of ScienceNodaChiba278‐8510Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and BiotechnologyChubu UniversityKasugaiAichi487‐8501Japan
| | - Michiko Sasabe
- Department of BiologyFaculty of Agriculture and Life ScienceHirosaki University3 Bunkyo‐choHirosaki036‐8561Japan
| | - Yasunori Machida
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
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Luong TQ, Keta S, Asai T, Kojima S, Nakagawa A, Micol JL, Xia S, Machida Y, Machida C. A genetic link between epigenetic repressor AS1-AS2 and DNA replication factors in establishment of adaxial-abaxial leaf polarity of Arabidopsis. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:39-49. [PMID: 31275036 PMCID: PMC6543732 DOI: 10.5511/plantbiotechnology.18.0129b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/29/2018] [Indexed: 05/27/2023]
Abstract
Balanced development of adaxial and abaxial domains in leaf primordia is critical for the formation of flat symmetric leaf lamina. Arabidopsis ASYMMETRIC LEAVES1 (AS1) and AS2 proteins form a complex (AS1-AS2), which acts as key regulators for the adaxial development by the direct repression of expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). Many modifier mutations have been identified, which enhance the defect of as1 and as2 mutations to generate abaxialized filamentous leaves without adaxial traits, suggesting that the development of the adaxial domain is achieved by cooperative repression by AS1-AS2 and the wild-type proteins corresponding to the modifiers. Mutations of several genes for DNA replication-related chromatin remodeling factors such as Chromatin Assembly Factor-1 (CAF-1) have been also identified as modifiers. It is still unknown, however, whether mutations in genes involved in DNA replication themselves might act as modifiers. Here we report that as1 and as2 mutants grown in the presence of hydroxyurea, a known inhibitor of DNA replication, form abaxialized filamentous leaves in a concentration-dependent manner. We further show that a mutation of the INCURVATA2 (ICU2) gene, which encodes the putative catalytic subunit of DNA polymerase α, and a mutation of the Replication Factor C Subunit3 (RFC3) gene, which encodes a protein used in replication as a clamp loader, act as modifiers. In addition, as2-1 icu2-1 double mutants showed increased mRNA levels of the genes for leaf abaxialization. These results suggest a tight link between DNA replication and the function of AS1-AS2 in the development of flat leaves.
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Affiliation(s)
- Toan Quy Luong
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Sumie Keta
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Toshiharu Asai
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth and Development, Hunan Agricultural University, Changsha 410128, China
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
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Spatial specificity of auxin responses coordinates wood formation. Nat Commun 2018; 9:875. [PMID: 29491423 PMCID: PMC5830446 DOI: 10.1038/s41467-018-03256-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 01/31/2018] [Indexed: 12/21/2022] Open
Abstract
Spatial organization of signalling events of the phytohormone auxin is fundamental for maintaining a dynamic transition from plant stem cells to differentiated descendants. The cambium, the stem cell niche mediating wood formation, fundamentally depends on auxin signalling but its exact role and spatial organization is obscure. Here we show that, while auxin signalling levels increase in differentiating cambium descendants, a moderate level of signalling in cambial stem cells is essential for cambium activity. We identify the auxin-dependent transcription factor ARF5/MONOPTEROS to cell-autonomously restrict the number of stem cells by directly attenuating the activity of the stem cell-promoting WOX4 gene. In contrast, ARF3 and ARF4 function as cambium activators in a redundant fashion from outside of WOX4-expressing cells. Our results reveal an influence of auxin signalling on distinct cambium features by specific signalling components and allow the conceptual integration of plant stem cell systems with distinct anatomies. Auxin activity controls plant stem cell function. Here the authors show that in the cambium, moderate auxin activity restricts cambial stem cell number via ARF5-dependent repression of the stem‐cell‐promoting factor WOX4, while ARF3 and ARF4 promote cambial activity outside of the WOX4‐expression domain.
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Tsukaya H. A Consideration of Leaf Shape Evolution in the Context of the Primary Function of the Leaf as a Photosynthetic Organ. THE LEAF: A PLATFORM FOR PERFORMING PHOTOSYNTHESIS 2018. [DOI: 10.1007/978-3-319-93594-2_1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Matsumura Y, Ohbayashi I, Takahashi H, Kojima S, Ishibashi N, Keta S, Nakagawa A, Hayashi R, Saéz-Vásquez J, Echeverria M, Sugiyama M, Nakamura K, Machida C, Machida Y. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open 2016; 5:942-54. [PMID: 27334696 PMCID: PMC4958277 DOI: 10.1242/bio.019109] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Although the DEAD-box RNA helicase family is ubiquitous in eukaryotes, its developmental role remains unelucidated. Here, we report that cooperative action between the Arabidopsis nucleolar protein RH10, an ortholog of human DEAD-box RNA helicase DDX47, and the epigenetic repressor complex of ASYMMETRIC-LEAVES1 (AS1) and AS2 (AS1-AS2) is critical to repress abaxial (ventral) genes ETT/ARF3 and ARF4, which leads to adaxial (dorsal) development in leaf primordia at shoot apices. Double mutations of rh10-1 and as2 (or as1) synergistically up-regulated the abaxial genes, which generated abaxialized filamentous leaves with loss of the adaxial domain. DDX47 is part of the small subunit processome (SSUP) that mediates rRNA biogenesis. In rh10-1 we found various defects in SSUP-related events, such as: accumulation of 35S/33S rRNA precursors; reduction in the 18S/25S ratio; and nucleolar hypertrophy. Double mutants of as2 with mutations of genes that encode other candidate SSUP-related components such as nucleolin and putative rRNA methyltransferase exhibited similar synergistic defects caused by up-regulation of ETT/ARF3 and ARF4. These results suggest a tight link between putative SSUP and AS1-AS2 in repression of the abaxial-determining genes for cell fate decisions for adaxial development. Summary: This paper reports the importance of cooperative action between the nucleus-localized epigenetic repressor and the nucleolus-localized proteins involved in ribosomal RNA processing for polarity establishment of Arabidopsis leaves.
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Affiliation(s)
- Yoko Matsumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Iwai Ohbayashi
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Hakusan 3-7-1, Bunkyo-ku, Tokyo 112-0001, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-shi, Chiba 271-8510, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Nanako Ishibashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Sumie Keta
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Rika Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Julio Saéz-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan 66860, France Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan F-66860, France
| | - Manuel Echeverria
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan 66860, France Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan F-66860, France
| | - Munetaka Sugiyama
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Hakusan 3-7-1, Bunkyo-ku, Tokyo 112-0001, Japan
| | - Kenzo Nakamura
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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11
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Ichihashi Y, Tsukaya H. Behavior of Leaf Meristems and Their Modification. FRONTIERS IN PLANT SCIENCE 2015; 6:1060. [PMID: 26648955 PMCID: PMC4664833 DOI: 10.3389/fpls.2015.01060] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/13/2015] [Indexed: 05/06/2023]
Abstract
A major source of diversity in flowering plant form is the extensive variability of leaf shape and size. Leaf formation is initiated by recruitment of a handful of cells flanking the shoot apical meristem (SAM) to develop into a complex three-dimensional structure. Leaf organogenesis depends on activities of several distinct meristems that are established and spatiotemporally differentiated after the initiation of leaf primordia. Here, we review recent findings in the gene regulatory networks that orchestrate leaf meristem activities in a model plant Arabidopsis thaliana. We then discuss recent key studies investigating the natural variation in leaf morphology to understand how the gene regulatory networks modulate leaf meristems to yield a substantial diversity of leaf forms during the course of evolution.
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Affiliation(s)
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of TokyoTokyo, Japan
- Bio-Next Project, Okazaki Institute for Integrative Bioscience, National Institutes of Natural SciencesOkazaki, Japan
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12
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Takahashi H, Kaniwa N, Saito Y, Sai K, Hamaguchi T, Shirao K, Shimada Y, Matsumura Y, Ohtsu A, Yoshino T, Doi T, Takahashi A, Odaka Y, Okuyama M, Sawada JI, Sakamoto H, Yoshida T. Construction of possible integrated predictive index based on EGFR and ANXA3 polymorphisms for chemotherapy response in fluoropyrimidine-treated Japanese gastric cancer patients using a bioinformatic method. BMC Cancer 2015; 15:718. [PMID: 26475168 PMCID: PMC4609065 DOI: 10.1186/s12885-015-1721-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 10/08/2015] [Indexed: 12/23/2022] Open
Abstract
Background Variability in drug response between individual patients is a serious concern in medicine. To identify single-nucleotide polymorphisms (SNPs) related to drug response variability, many genome-wide association studies have been conducted. Methods We previously applied a knowledge-based bioinformatic approach to a pharmacogenomics study in which 119 fluoropyrimidine-treated gastric cancer patients were genotyped at 109,365 SNPs using the Illumina Human-1 BeadChip. We identified the SNP rs2293347 in the human epidermal growth factor receptor (EGFR) gene as a novel genetic factor related to chemotherapeutic response. In the present study, we reanalyzed these hypothesis-free genomic data using extended knowledge. Results We identified rs2867461 in annexin A3 (ANXA3) gene as another candidate. Using logistic regression, we confirmed that the performance of the rs2867461 + rs2293347 model was superior to those of the single factor models. Furthermore, we propose a novel integrated predictive index (iEA) based on these two polymorphisms in EGFR and ANXA3. The p value for iEA was 1.47 × 10−8 by Fisher’s exact test. Recent studies showed that the mutations in EGFR is associated with high expression of dihydropyrimidine dehydrogenase, which is an inactivating and rate-limiting enzyme for fluoropyrimidine, and suggested that the combination of chemotherapy with fluoropyrimidine and EGFR-targeting agents is effective against EGFR-overexpressing gastric tumors, while ANXA3 overexpression confers resistance to tyrosine kinase inhibitors targeting the EGFR pathway. Conclusions These results suggest that the iEA index or a combination of polymorphisms in EGFR and ANXA3 may serve as predictive factors of drug response, and therefore could be useful for optimal selection of chemotherapy regimens. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1721-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan. .,Plant Biology Research Center, Chubu University, Matsumoto-cho 1200, Kasugai, Aichi, 487-8501, Japan. .,Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Nahoko Kaniwa
- Division of Medicinal Safety Science, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan.
| | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan.
| | - Kimie Sai
- Division of Medicinal Safety Science, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan.
| | - Tetsuya Hamaguchi
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Kuniaki Shirao
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Yasuhiro Shimada
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Yasuhiro Matsumura
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
| | - Atsushi Ohtsu
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
| | - Takayuki Yoshino
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
| | - Toshihiko Doi
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, Matsumoto-cho 1200, Kasugai, Aichi, 487-8501, Japan.
| | - Yoko Odaka
- Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Misuzu Okuyama
- Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Jun-Ichi Sawada
- Division of Functional Biochemistry and Genomics, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan. .,Present address: Pharmaceutical and Medical Devices Agency, Shinkasumigaseki-building, 3-3-2 Kasumigaseki, Chiyoda-ku, Tokyo, 100-0013, Japan.
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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13
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Machida C, Nakagawa A, Kojima S, Takahashi H, Machida Y. The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 4:655-71. [PMID: 26108442 PMCID: PMC4744985 DOI: 10.1002/wdev.196] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/23/2015] [Accepted: 05/12/2015] [Indexed: 01/17/2023]
Abstract
Leaf primordia are born around meristem‐containing stem cells at shoot apices, grow along three axes (proximal–distal, adaxial–abaxial, medial–lateral), and develop into flat symmetric leaves with adaxial–abaxial polarity. Axis development and polarity specification of Arabidopsis leaves require a network of genes for transcription factor‐like proteins and small RNAs. Here, we summarize present understandings of adaxial‐specific genes, ASYMMETRIC LEAVES1 (AS1) and AS2. Their complex (AS1–AS2) functions in the regulation of the proximal–distal leaf length by directly repressing class 1 KNOX homeobox genes (BP, KNAT2) that are expressed in the meristem periphery below leaf primordia. Adaxial–abaxial polarity specification involves antagonistic interaction of adaxial and abaxial genes including AS1 and AS2 for the development of two respective domains. AS1–AS2 directly represses the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3) and indirectly represses ETT/ARF3 and ARF4 through tasiR‐ARF. Modifier mutations have been identified that abolish adaxialization and enhance the defect in the proximal–distal patterning in as1 and as2. AS1–AS2 and its modifiers synergistically repress both ARFs and class 1 KNOXs. Repression of ARFs is critical for establishing adaxial–abaxial polarity. On the other hand, abaxial factors KANADI1 (KAN1) and KAN2 directly repress AS2 expression. These data delineate a molecular framework for antagonistic gene interactions among adaxial factors, AS1, AS2, and their modifiers, and the abaxial factors ARFs as key regulators in the establishment of adaxial–abaxial polarity. Possible AS1–AS2 epigenetic repression and activities downstream of ARFs are discussed. WIREs Dev Biol 2015, 4:655–671. doi: 10.1002/wdev.196 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Chiba, Japan
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14
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Costanzo E, Trehin C, Vandenbussche M. The role of WOX genes in flower development. ANNALS OF BOTANY 2014; 114:1545-53. [PMID: 24973416 PMCID: PMC4204783 DOI: 10.1093/aob/mcu123] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/29/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND WOX (Wuschel-like homeobOX) genes form a family of plant-specific HOMEODOMAIN transcription factors, the members of which play important developmental roles in a diverse range of processes. WOX genes were first identified as determining cell fate during embryo development, as well as playing important roles in maintaining stem cell niches in the plant. In recent years, new roles have been identified in plant architecture and organ development, particularly at the flower level. SCOPE In this review, the role of WOX genes in flower development and flower architecture is highlighted, as evidenced from data obtained in the last few years. The roles played by WOX genes in different species and different flower organs are compared, and differential functional recruitment of WOX genes during flower evolution is considered. CONCLUSIONS This review compares available data concerning the role of WOX genes in flower and organ architecture among different species of angiosperms, including representatives of monocots and eudicots (rosids and asterids). These comparative data highlight the usefulness of the WOX gene family for evo-devo studies of floral development.
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Affiliation(s)
- Enrico Costanzo
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Christophe Trehin
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France
| | - Michiel Vandenbussche
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France
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15
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Analysis of gene expression profiles of soft tissue sarcoma using a combination of knowledge-based filtering with integration of multiple statistics. PLoS One 2014; 9:e106801. [PMID: 25188299 PMCID: PMC4154757 DOI: 10.1371/journal.pone.0106801] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 08/01/2014] [Indexed: 12/21/2022] Open
Abstract
The diagnosis and treatment of soft tissue sarcomas (STS) have been difficult. Of the diverse histological subtypes, undifferentiated pleomorphic sarcoma (UPS) is particularly difficult to diagnose accurately, and its classification per se is still controversial. Recent advances in genomic technologies provide an excellent way to address such problems. However, it is often difficult, if not impossible, to identify definitive disease-associated genes using genome-wide analysis alone, primarily because of multiple testing problems. In the present study, we analyzed microarray data from 88 STS patients using a combination method that used knowledge-based filtering and a simulation based on the integration of multiple statistics to reduce multiple testing problems. We identified 25 genes, including hypoxia-related genes (e.g., MIF, SCD1, P4HA1, ENO1, and STAT1) and cell cycle- and DNA repair-related genes (e.g., TACC3, PRDX1, PRKDC, and H2AFY). These genes showed significant differential expression among histological subtypes, including UPS, and showed associations with overall survival. STAT1 showed a strong association with overall survival in UPS patients (logrank p = 1.84 × 10(-6) and adjusted p value 2.99 × 10(-3) after the permutation test). According to the literature, the 25 genes selected are useful not only as markers of differential diagnosis but also as prognostic/predictive markers and/or therapeutic targets for STS. Our combination method can identify genes that are potential prognostic/predictive factors and/or therapeutic targets in STS and possibly in other cancers. These disease-associated genes deserve further preclinical and clinical validation.
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16
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Takahashi H, Sai K, Saito Y, Kaniwa N, Matsumura Y, Hamaguchi T, Shimada Y, Ohtsu A, Yoshino T, Doi T, Okuda H, Ichinohe R, Takahashi A, Doi A, Odaka Y, Okuyama M, Saijo N, Sawada JI, Sakamoto H, Yoshida T. Application of a combination of a knowledge-based algorithm and 2-stage screening to hypothesis-free genomic data on irinotecan-treated patients for identification of a candidate single nucleotide polymorphism related to an adverse effect. PLoS One 2014; 9:e105160. [PMID: 25127363 PMCID: PMC4134257 DOI: 10.1371/journal.pone.0105160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 07/17/2014] [Indexed: 01/27/2023] Open
Abstract
Interindividual variation in a drug response among patients is known to cause serious problems in medicine. Genomic information has been proposed as the basis for “personalized” health care. The genome-wide association study (GWAS) is a powerful technique for examining single nucleotide polymorphisms (SNPs) and their relationship with drug response variation; however, when using only GWAS, it often happens that no useful SNPs are identified due to multiple testing problems. Therefore, in a previous study, we proposed a combined method consisting of a knowledge-based algorithm, 2 stages of screening, and a permutation test for identifying SNPs. In the present study, we applied this method to a pharmacogenomics study where 109,365 SNPs were genotyped using Illumina Human-1 BeadChip in 168 cancer patients treated with irinotecan chemotherapy. We identified the SNP rs9351963 in potassium voltage-gated channel subfamily KQT member 5 (KCNQ5) as a candidate factor related to incidence of irinotecan-induced diarrhea. The p value for rs9351963 was 3.31×10−5 in Fisher's exact test and 0.0289 in the permutation test (when multiple testing problems were corrected). Additionally, rs9351963 was clearly superior to the clinical parameters and the model involving rs9351963 showed sensitivity of 77.8% and specificity of 57.6% in the evaluation by means of logistic regression. Recent studies showed that KCNQ4 and KCNQ5 genes encode members of the M channel expressed in gastrointestinal smooth muscle and suggested that these genes are associated with irritable bowel syndrome and similar peristalsis diseases. These results suggest that rs9351963 in KCNQ5 is a possible predictive factor of incidence of diarrhea in cancer patients treated with irinotecan chemotherapy and for selecting chemotherapy regimens, such as irinotecan alone or a combination of irinotecan with a KCNQ5 opener. Nonetheless, clinical importance of rs9351963 should be further elucidated.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
| | - Kimie Sai
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Nahoko Kaniwa
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Yasuhiro Matsumura
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Tetsuya Hamaguchi
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuhiro Shimada
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, Japan
| | - Atsushi Ohtsu
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Takayuki Yoshino
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Toshihiko Doi
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Haruhiro Okuda
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Risa Ichinohe
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Faculty of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Ayano Doi
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Faculty of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Yoko Odaka
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Misuzu Okuyama
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Nagahiro Saijo
- National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Jun-ichi Sawada
- Division of Functional Biochemistry and Genomics, National Institute of Health Sciences, Tokyo, Japan
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
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17
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Takahashi H, Nakayama R, Hayashi S, Nemoto T, Murase Y, Nomura K, Takahashi T, Kubo K, Marui S, Yasuhara K, Nakamura T, Sueo T, Takahashi A, Tsutsumiuchi K, Ohta T, Kawai A, Sugita S, Yamamoto S, Kobayashi T, Honda H, Yoshida T, Hasegawa T. Macrophage migration inhibitory factor and stearoyl-CoA desaturase 1: potential prognostic markers for soft tissue sarcomas based on bioinformatics analyses. PLoS One 2013; 8:e78250. [PMID: 24167613 PMCID: PMC3805525 DOI: 10.1371/journal.pone.0078250] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 09/10/2013] [Indexed: 11/18/2022] Open
Abstract
The diagnosis and treatment of soft tissue sarcomas (STSs) has been particularly difficult, because STSs are a group of highly heterogeneous tumors in terms of histopathology, histological grade, and primary site. Recent advances in genome technologies have provided an excellent opportunity to determine the complete biological characteristics of neoplastic tissues, resulting in improved diagnosis, treatment selection, and investigation of therapeutic targets. We had previously developed a novel bioinformatics method for marker gene selection and applied this method to gene expression data from STS patients. This previous analysis revealed that the extracted gene combination of macrophage migration inhibitory factor (MIF) and stearoyl-CoA desaturase 1 (SCD1) is an effective diagnostic marker to discriminate between subtypes of STSs with highly different outcomes. In the present study, we hypothesize that the combination of MIF and SCD1 is also a prognostic marker for the overall outcome of STSs. To prove this hypothesis, we first analyzed microarray data from 88 STS patients and their outcomes. Our results show that the survival rates for MIF- and SCD1-positive groups were lower than those for negative groups, and the p values of the log-rank test are 0.0146 and 0.00606, respectively. In addition, survival rates are more significantly different (p = 0.000116) between groups that are double-positive and double-negative for MIF and SCD1. Furthermore, in vitro cell growth inhibition experiments by MIF and SCD1 inhibitors support the hypothesis. These results suggest that the gene set is useful as a prognostic marker associated with tumor progression.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
| | - Robert Nakayama
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Transcriptome Project, National Cancer Center Research Institute, Tokyo, Japan
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Shuhei Hayashi
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, Kumamoto, Japan
| | - Takeshi Nemoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Dermatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuyuki Murase
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Koji Nomura
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Teruyoshi Takahashi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Kenji Kubo
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Shigetaka Marui
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Koji Yasuhara
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Tetsuro Nakamura
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Takuya Sueo
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Kaname Tsutsumiuchi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Tsutomu Ohta
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Kawai
- Orthopedics Division, National Cancer Center Hospital, Tokyo, Japan
| | - Shintaro Sugita
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Shinjiro Yamamoto
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, Kumamoto, Japan
| | - Takeshi Kobayashi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Hiroyuki Honda
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tadashi Hasegawa
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
- Pathology Division, National Cancer Center Hospital, Tokyo, Japan,
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Takahashi H, Kaniwa N, Saito Y, Sai K, Hamaguchi T, Shirao K, Shimada Y, Matsumura Y, Ohtsu A, Yoshino T, Takahashi A, Odaka Y, Okuyama M, Sawada JI, Sakamoto H, Yoshida T. Identification of a candidate single-nucleotide polymorphism related to chemotherapeutic response through a combination of knowledge-based algorithm and hypothesis-free genomic data. J Biosci Bioeng 2013; 116:768-73. [PMID: 23816762 DOI: 10.1016/j.jbiosc.2013.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/02/2013] [Accepted: 05/13/2013] [Indexed: 01/06/2023]
Abstract
Inter-individual variations in drug responses among patients are known to cause serious problems in medicine. Genome-wide association study (GWAS) is powerful for examining single-nucleotide polymorphisms (SNPs) and their relationships with drug response variations. However, no significant SNP has been identified using GWAS due to multiple testing problems. Therefore, we propose a combination method consisting of knowledge-based algorithm, two stages of screening, and permutation test for identifying SNPs in the present study. We applied this method to a genome-wide pharmacogenomics study for which 109,365 SNPs had been genotyped using Illumina Human-1 BeadChip for 119 gastric cancer patients treated with fluoropyrimidine. We identified rs2293347 in epidermal growth factor receptor (EGFR) is as a candidate SNP related to chemotherapeutic response. The p value for the rs2293347 was 2.19 × 10(-5) for Fisher's exact test, and the p value was 0.00360 for the permutation test (multiple testing problems are corrected). Additionally, rs2293347 was clearly superior to clinical parameters and showed a sensitivity value of 55.0% and specificity value of 94.4% in the evaluation by using multiple regression models. Recent studies have shown that combination chemotherapy of fluoropyrimidine and EGFR-targeting agents is effective for gastric cancer patients highly expressing EGFR. These results suggest that rs2293347 is a potential predictive factor for selecting chemotherapies, such as fluoropyrimidine alone or combination chemotherapies.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan; Plant Biology Research Center, Chubu University, Matsumoto-cho 1200, Kasugai, Aichi 487-8501, Japan; Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
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Iwasaki M, Takahashi H, Iwakawa H, Nakagawa A, Ishikawa T, Tanaka H, Matsumura Y, Pekker I, Eshed Y, Vial-Pradel S, Ito T, Watanabe Y, Ueno Y, Fukazawa H, Kojima S, Machida Y, Machida C. 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. Development 2013; 140:1958-69. [PMID: 23571218 DOI: 10.1242/dev.085365] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Leaf primordia are generated at the periphery of the shoot apex, developing into flat symmetric organs with adaxial-abaxial polarity, in which the indeterminate state is repressed. Despite the crucial role of the ASYMMETRIC LEAVES1 (AS1)-AS2 nuclear-protein complex in leaf adaxial-abaxial polarity specification, information on mechanisms controlling their downstream genes has remained elusive. We systematically analyzed transcripts by microarray and chromatin immunoprecipitation assays and performed genetic rescue of as1 and as2 phenotypic abnormalities, which identified a new target gene, ETTIN (ETT)/AUXIN RESPONSE FACTOR3 (ARF3), which encodes an abaxial factor acting downstream of the AS1-AS2 complex. While the AS1-AS2 complex represses ETT by direct binding of AS1 to the ETT promoter, it also indirectly activates miR390- and RDR6-dependent post-transcriptional gene silencing to negatively regulate both ETT and ARF4 activities. Furthermore, AS1-AS2 maintains the status of DNA methylation in the ETT coding region. In agreement, filamentous leaves formed in as1 and as2 plants treated with a DNA methylation inhibitor were rescued by loss of ETT and ARF4 activities. We suggest that negative transcriptional, post-transcriptional and epigenetic regulation of the ARFs by AS1-AS2 is important for stabilizing early leaf partitioning into abaxial and adaxial domains.
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Affiliation(s)
- Mayumi Iwasaki
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, Japan
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Machida Y, Fukaki H, Araki T. Plant meristems and organogenesis: the new era of plant developmental research. PLANT & CELL PHYSIOLOGY 2013; 54:295-301. [PMID: 23468554 DOI: 10.1093/pcp/pct034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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