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Li C, Qi L, Zhang S, Dong X, Jing Y, Cheng J, Feng Z, Peng J, Li H, Zhou Y, Wang X, Han R, Duan J, Terzaghi W, Lin R, Li J. Mutual upregulation of HY5 and TZP in mediating phytochrome A signaling. THE PLANT CELL 2022; 34:633-654. [PMID: 34741605 PMCID: PMC8774092 DOI: 10.1093/plcell/koab254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/08/2021] [Indexed: 05/25/2023]
Abstract
Phytochrome A (phyA) is the far-red (FR) light photoreceptor in plants that is essential for seedling de-etiolation under FR-rich environments, such as canopy shade. TANDEM ZINC-FINGER/PLUS3 (TZP) was recently identified as a key component of phyA signal transduction in Arabidopsis thaliana; however, how TZP is integrated into the phyA signaling networks remains largely obscure. Here, we demonstrate that ELONGATED HYPOCOTYL5 (HY5), a well-characterized transcription factor promoting photomorphogenesis, mediates FR light induction of TZP expression by directly binding to a G-box motif in the TZP promoter. Furthermore, TZP physically interacts with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), an E3 ubiquitin ligase targeting HY5 for 26S proteasome-mediated degradation, and this interaction inhibits COP1 interaction with HY5. Consistent with those results, TZP post-translationally promotes HY5 protein stability in FR light, and in turn, TZP protein itself is destabilized by COP1 in both dark and FR light conditions. Moreover, tzp hy5 double mutants display an additive phenotype relative to their respective single mutants under high FR light intensities, indicating that TZP and HY5 also function in largely independent pathways. Together, our data demonstrate that HY5 and TZP mutually upregulate each other in transmitting the FR light signal, thus providing insights into the complicated but delicate control of phyA signaling networks.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lijuan Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaoman Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaojing Dong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ziyi Feng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jing Peng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yangyang Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoji Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Run Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jie Duan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania 18766, USA
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Mao Z, Wei X, Li L, Xu P, Zhang J, Wang W, Guo T, Kou S, Wang W, Miao L, Cao X, Zhao J, Yang G, Zhang S, Lian H, Yang HQ. Arabidopsis cryptochrome 1 controls photomorphogenesis through regulation of H2A.Z deposition. THE PLANT CELL 2021; 33:1961-1979. [PMID: 33768238 PMCID: PMC8290288 DOI: 10.1093/plcell/koab091] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/23/2021] [Indexed: 05/20/2023]
Abstract
Light is a key environmental cue that fundamentally regulates plant growth and development, which is mediated by the multiple photoreceptors including the blue light (BL) photoreceptor cryptochrome 1 (CRY1). The signaling mechanism of Arabidopsis thaliana CRY1 involves direct interactions with CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1)/SUPPRESSOR OF PHYA-105 1 and stabilization of COP1 substrate ELONGATED HYPOCOTYL 5 (HY5). H2A.Z is an evolutionarily conserved histone variant, which plays a critical role in transcriptional regulation through its deposition in chromatin catalyzed by SWR1 complex. Here we show that CRY1 physically interacts with SWC6 and ARP6, the SWR1 complex core subunits that are essential for mediating H2A.Z deposition, in a BL-dependent manner, and that BL-activated CRY1 enhances the interaction of SWC6 with ARP6. Moreover, HY5 physically interacts with SWC6 and ARP6 to direct the recruitment of SWR1 complex to HY5 target loci. Based on previous studies and our findings, we propose that CRY1 promotes H2A.Z deposition to regulate HY5 target gene expression and photomorphogenesis in BL through the enhancement of both SWR1 complex activity and HY5 recruitment of SWR1 complex to HY5 target loci, which is likely mediated by interactions of CRY1 with SWC6 and ARP6, and CRY1 stabilization of HY5, respectively.
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Affiliation(s)
- Zhilei Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xuxu Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ling Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Xu
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jingyi Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenxiu Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Tongtong Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Shuang Kou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wanting Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Langxi Miao
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoli Cao
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiachen Zhao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Guangqiong Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Shilong Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Hongli Lian
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong-Quan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
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3
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Cañibano E, Bourbousse C, García-León M, Garnelo Gómez B, Wolff L, García-Baudino C, Lozano-Durán R, Barneche F, Rubio V, Fonseca S. DET1-mediated COP1 regulation avoids HY5 activity over second-site gene targets to tune plant photomorphogenesis. MOLECULAR PLANT 2021; 14:963-982. [PMID: 33711490 DOI: 10.1101/2020.09.30.318253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/11/2021] [Accepted: 03/05/2021] [Indexed: 05/23/2023]
Abstract
DE-ETIOLATED 1 (DET1) and CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1) are two essential repressors of Arabidopsis photomorphogenesis. These proteins can associate with CULLIN4 to form independent CRL4-based E3 ubiquitin ligases that mediate the degradation of several photomorphogenic transcription factors, including ELONGATED HYPOCOTYL 5 (HY5), thereby controlling multiple gene-regulatory networks. Despite extensive biochemical and genetic analyses of their multi-subunit complexes, the functional links between DET1 and COP1 have long remained elusive. Here, we report that DET1 associates with COP1 in vivo, enhances COP1-HY5 interaction, and promotes COP1 destabilization in a process that dampens HY5 protein abundance. By regulating its accumulation, DET1 avoids HY5 association with hundreds of second-site genomic loci, which are also frequently targeted by the skotomorphogenic transcription factor PHYTOCHROME-INTERACTING FACTOR 3. Accordingly, ectopic HY5 chromatin enrichment favors local gene repression and can trigger fusca-like phenotypes. This study therefore shows that DET1-mediated regulation of COP1 stability tunes down the HY5 cistrome, avoiding hyper-photomorphogenic responses that might compromise plant viability.
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Affiliation(s)
- Esther Cañibano
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid 28049, Spain
| | - Clara Bourbousse
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | | | - Borja Garnelo Gómez
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Léa Wolff
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | | | - Rosa Lozano-Durán
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China; Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, 72076 Tübingen, Germany
| | - Fredy Barneche
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Vicente Rubio
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid 28049, Spain.
| | - Sandra Fonseca
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid 28049, Spain.
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4
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Cañibano E, Bourbousse C, García-León M, Garnelo Gómez B, Wolff L, García-Baudino C, Lozano-Durán R, Barneche F, Rubio V, Fonseca S. DET1-mediated COP1 regulation avoids HY5 activity over second-site gene targets to tune plant photomorphogenesis. MOLECULAR PLANT 2021; 14:963-982. [PMID: 33711490 DOI: 10.1016/j.molp.2021.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/11/2021] [Accepted: 03/05/2021] [Indexed: 05/14/2023]
Abstract
DE-ETIOLATED 1 (DET1) and CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1) are two essential repressors of Arabidopsis photomorphogenesis. These proteins can associate with CULLIN4 to form independent CRL4-based E3 ubiquitin ligases that mediate the degradation of several photomorphogenic transcription factors, including ELONGATED HYPOCOTYL 5 (HY5), thereby controlling multiple gene-regulatory networks. Despite extensive biochemical and genetic analyses of their multi-subunit complexes, the functional links between DET1 and COP1 have long remained elusive. Here, we report that DET1 associates with COP1 in vivo, enhances COP1-HY5 interaction, and promotes COP1 destabilization in a process that dampens HY5 protein abundance. By regulating its accumulation, DET1 avoids HY5 association with hundreds of second-site genomic loci, which are also frequently targeted by the skotomorphogenic transcription factor PHYTOCHROME-INTERACTING FACTOR 3. Accordingly, ectopic HY5 chromatin enrichment favors local gene repression and can trigger fusca-like phenotypes. This study therefore shows that DET1-mediated regulation of COP1 stability tunes down the HY5 cistrome, avoiding hyper-photomorphogenic responses that might compromise plant viability.
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Affiliation(s)
- Esther Cañibano
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid 28049, Spain
| | - Clara Bourbousse
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | | | - Borja Garnelo Gómez
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Léa Wolff
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | | | - Rosa Lozano-Durán
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China; Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, 72076 Tübingen, Germany
| | - Fredy Barneche
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Vicente Rubio
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid 28049, Spain.
| | - Sandra Fonseca
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid 28049, Spain.
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5
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Isolation of Lineage Specific Nuclei Based on Distinct Endoreduplication Levels and Tissue-Specific Markers to Study Chromatin Accessibility Landscapes. PLANTS 2020; 9:plants9111478. [PMID: 33153046 PMCID: PMC7692515 DOI: 10.3390/plants9111478] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/31/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
The capacity for achieving immense specificity and resolution in science increases day to day. Fluorescence-activated nuclear sorting (FANS) offers this great precision, enabling one to count and separate distinct types of nuclei from specific cells of heterogeneous mixtures. We developed a workflow to collect nuclei from Arabidopsis thaliana by FANS according to cell lineage and endopolyploidy level with high efficiency. We sorted GFP-labeled nuclei with different ploidy levels from the epidermal tissue layer of three-day, dark-grown hypocotyls followed by a shift to light for one day and compared them to plants left in the dark. We then accessed early chromatin accessibility patterns associated with skotomorphogenesis and photomorphogenesis by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) within primarily stomatal 2C and fully endoreduplicated 16C nuclei. Our quantitative analysis shows that dark- and light-treated samples in 2C nuclei do not exhibit any different chromatin accessibility landscapes, whereas changes in 16C can be linked to transcriptional changes involved in light response.
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Hamasaki H, Ayano M, Nakamura A, Fujioka S, Asami T, Takatsuto S, Yoshida S, Oka Y, Matsui M, Shimada Y. Light Activates Brassinosteroid Biosynthesis to Promote Hook Opening and Petiole Development in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2020; 61:1239-1251. [PMID: 32333772 DOI: 10.1093/pcp/pcaa053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Although brassinosteroids (BRs) have been proposed to be negative regulators of photomorphogenesis, their physiological role therein has remained elusive. We studied light-induced photomorphogenic development in the presence of the BR biosynthesis inhibitor, brassinazole (Brz). Hook opening was inhibited in the presence of Brz; this inhibition was reversed in the presence of brassinolide (BL). Hook opening was accompanied by cell expansion on the inner (concave) side of the hook. This cell expansion was inhibited in the presence of Brz but was restored upon the addition of BL. We then evaluated light-induced organ-specific expression of three BR biosynthesis genes, DWF4, BR6ox1 and BR6ox2, and a BR-responsive gene, SAUR-AC1, during the photomorphogenesis of Arabidopsis. Expression of these genes was induced, particularly in the hook region, in response to illumination. The induction peaked after 3 h of light exposure and preceded hook opening. Phytochrome-deficient mutants, hy1, hy2 and phyAphyB, and a light-signaling mutant, hy5, were defective in light-induced expression of BR6ox1, BR6ox2 and SAUR-AC1. Light induced both expression of BR6ox genes and petiole development. Petiole development was inhibited in the presence of Brz. Our results largely contradict the early view that BRs are negative regulators of photomorphogenesis. Our data collectively suggest that light activates the expression of BR biosynthesis genes in the hook region via a phytochrome-signaling pathway and HY5 and that BR biosynthesis is essential for hook opening and petiole development during photomorphogenesis.
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Affiliation(s)
- Hidefumi Hamasaki
- Kihara Institute for Biological Research, Yokohama City University Kihara Institute for Biological Research, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813 Japan
| | - Madoka Ayano
- RIKEN Plant Science Center, Suehirocho 1-7-22, Tsurumi, Yokohama, 230-0045 Japan
| | - Ayako Nakamura
- Kihara Institute for Biological Research, Yokohama City University Kihara Institute for Biological Research, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813 Japan
| | - Shozo Fujioka
- RIKEN Plant Science Center, Suehirocho 1-7-22, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Advanced Science Institute, Wako, Saitama, 351-0198 Japan
| | - Tadao Asami
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, 113-8657 Japan
| | - Suguru Takatsuto
- Department of Chemistry, Joetsu University of Education, Joetsu, Niigata, 943-8512 Japan
| | - Shigeo Yoshida
- RIKEN Plant Science Center, Suehirocho 1-7-22, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Advanced Science Institute, Wako, Saitama, 351-0198 Japan
| | - Yoshito Oka
- RIKEN Plant Science Center, Suehirocho 1-7-22, Tsurumi, Yokohama, 230-0045 Japan
| | - Minami Matsui
- RIKEN Plant Science Center, Suehirocho 1-7-22, Tsurumi, Yokohama, 230-0045 Japan
- RIKEN Center for Sustainable Resource Science, Suehirocho 1-7-22, Tsurumi, Yokohama, 230-0045 Japan
| | - Yukihisa Shimada
- Kihara Institute for Biological Research, Yokohama City University Kihara Institute for Biological Research, Maiokacho 641-12, Totsuka, Yokohama, Kanagawa, 244-0813 Japan
- RIKEN Plant Science Center, Suehirocho 1-7-22, Tsurumi, Yokohama, 230-0045 Japan
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7
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Marzi D, Brunetti P, Mele G, Napoli N, Calò L, Spaziani E, Matsui M, De Panfilis S, Costantino P, Serino G, Cardarelli M. Light controls stamen elongation via cryptochromes, phytochromes and COP1 through HY5 and HYH. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:379-394. [PMID: 32142184 DOI: 10.1111/tpj.14736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/18/2020] [Accepted: 02/27/2020] [Indexed: 05/25/2023]
Abstract
In Arabidopsis, stamen elongation, which ensures male fertility, is controlled by the auxin response factor ARF8, which regulates the expression of the auxin repressor IAA19. Here, we uncover a role for light in controlling stamen elongation. By an extensive genetic and molecular analysis we show that the repressor of light signaling COP1, through its targets HY5 and HYH, controls stamen elongation, and that HY5 - oppositely to ARF8 - directly represses the expression of IAA19 in stamens. In addition, we show that in closed flower buds, when light is shielded by sepals and petals, the blue light receptors CRY1/CRY2 repress stamen elongation. Coherently, at flower disclosure and in subsequent stages, stamen elongation is repressed by the red and far-red light receptors PHYA/PHYB. In conclusion, different light qualities - sequentially perceived by specific photoreceptors - and the downstream COP1-HY5/HYH module finely tune auxin-induced stamen elongation and thus male fertility.
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Affiliation(s)
- Davide Marzi
- IBPM-CNR c/o Sapienza Università di Roma, Roma, Italy
- Dipartimento di Biologia e Biotecnologie Sapienza, Università di Roma, Roma, Italy
| | | | | | - Nadia Napoli
- Dipartimento di Biologia e Biotecnologie Sapienza, Università di Roma, Roma, Italy
| | - Lorenzo Calò
- Dipartimento di Biologia e Biotecnologie Sapienza, Università di Roma, Roma, Italy
| | - Erica Spaziani
- Dipartimento di Biologia e Biotecnologie Sapienza, Università di Roma, Roma, Italy
| | - Minami Matsui
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Simone De Panfilis
- Centre for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, Roma, I-00161, Italy
| | - Paolo Costantino
- IBPM-CNR c/o Sapienza Università di Roma, Roma, Italy
- Dipartimento di Biologia e Biotecnologie Sapienza, Università di Roma, Roma, Italy
| | - Giovanna Serino
- Dipartimento di Biologia e Biotecnologie Sapienza, Università di Roma, Roma, Italy
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8
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Regulatory Potential of bHLH-Type Transcription Factors on the Road to Rubber Biosynthesis in Hevea brasiliensis. PLANTS 2020; 9:plants9060674. [PMID: 32466493 PMCID: PMC7355734 DOI: 10.3390/plants9060674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/23/2020] [Indexed: 11/17/2022]
Abstract
Natural rubber is the main component of latex obtained from laticifer cells of Hevea brasiliensis. For improving rubber yield, it is essential to understand the genetic molecular mechanisms responsible for laticifer differentiation and rubber biosynthesis. Jasmonate enhances both secondary laticifer differentiation and rubber biosynthesis. Here, we carried out time-course RNA-seq analysis in suspension-cultured cells treated with methyljasmonic acid (MeJA) to characterize the gene expression profile. Gene Ontology (GO) analysis showed that the term "cell differentiation" was enriched in upregulated genes at 24 hours after treatment, but inversely, the term was enriched in downregulated genes at 5 days, indicating that MeJA could induce cell differentiation at an early stage of the response. Jasmonate signaling is activated by MYC2, a basic helix-loop-helix (bHLH)-type transcription factor (TF). The aim of this work was to find any links between transcriptomic changes after MeJA application and regulation by TFs. Using an in vitro binding assay, we traced candidate genes throughout the whole genome that were targeted by four bHLH TFs: Hb_MYC2-1, Hb_MYC2-2, Hb_bHLH1, and Hb_bHLH2. The latter two are highly expressed in laticifer cells. Their physical binding sites were found in the promoter regions of a variety of other TF genes, which are differentially expressed upon MeJA exposure, and rubber biogenesis-related genes including SRPP1 and REF3. These studies suggest the possibilities that Hb_MYC2-1 and Hb_MYC2-2 regulate cell differentiation and that Hb_bHLH1 and Hb_bHLH2 promote rubber biosynthesis. We expect that our findings will help to increase natural rubber yield through genetic control in the future.
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Burko Y, Seluzicki A, Zander M, Pedmale UV, Ecker JR, Chory J. Chimeric Activators and Repressors Define HY5 Activity and Reveal a Light-Regulated Feedback Mechanism. THE PLANT CELL 2020; 32:967-983. [PMID: 32086365 PMCID: PMC7145465 DOI: 10.1105/tpc.19.00772] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/17/2020] [Accepted: 02/19/2020] [Indexed: 05/20/2023]
Abstract
The first exposure to light marks a crucial transition in plant development. This transition relies on the transcription factor HY5 controlling a complex downstream growth program. Despite its importance, its function in transcription remains unclear. Previous studies have generated lists of thousands of potential target genes and competing models of HY5 transcription regulation. In this work, we carry out detailed phenotypic and molecular analysis of constitutive activator and repressor HY5 fusion proteins. Using this strategy, we were able to filter out large numbers of genes that are unlikely to be direct targets, allowing us to eliminate several proposed models of HY5's mechanism of action. We demonstrate that the primary activity of HY5 is promoting transcription and that this function relies on other, likely light-regulated, factors. In addition, this approach reveals a molecular feedback loop via the COP1/SPA E3 ubiquitin ligase complex, suggesting a mechanism that maintains low HY5 in the dark, primed for rapid accumulation to reprogram growth upon light exposure. Our strategy is broadly adaptable to the study of transcription factor activity. Lastly, we show that modulating this feedback loop can generate significant phenotypic diversity in both Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum).
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Affiliation(s)
- Yogev Burko
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Adam Seluzicki
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Mark Zander
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Ullas V Pedmale
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Joseph R Ecker
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Joanne Chory
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
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Time-Course Transcriptome Study Reveals Mode of bZIP Transcription Factors on Light Exposure in Arabidopsis. Int J Mol Sci 2020; 21:ijms21061993. [PMID: 32183354 PMCID: PMC7139404 DOI: 10.3390/ijms21061993] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
The etiolation process, which occurs after germination, is terminated once light is perceived and then de-etiolation commences. During the de-etiolation period, monochromatic lights (blue, red and far-red) induce differences in gene expression profiles and plant behavior through their respective photoreceptors. ELONGATED HYPOCOTYL 5 (HY5), a bZIP-type transcription factor (TF), regulates gene expression in the de-etiolation process, and other bZIP TFs are also involved in this regulation. However, transcriptomic changes that occur in etiolated seedlings upon monochromatic light irradiation and the relationship with the bZIP TFs still remain to be elucidated. Here, we track changes in the transcriptome after exposure to white, blue, red and far-red light following darkness and reveal both shared and non-shared trends of transcriptomic change between the four kinds of light. Interestingly, after exposure to light, HY5 expression synchronized with those of the related bZIP TF genes, GBF2 and GBF3, rather than HY5 HOMOLOG (HYH). To speculate on the redundancy of target genes between the bZIP TFs, we inspected the genome-wide physical binding sites of homodimers of seven bZIP TFs, HY5, HYH, GBF1, GBF2, GBF3, GBF4 and EEL, using an in vitro binding assay. The results reveal large overlaps of target gene candidates, indicating a complicated regulatory literature among TFs. This work provides novel insight into understanding the regulation of gene expression of the plant response to monochromatic light irradiation.
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Ohtani M, Demura T. The quest for transcriptional hubs of lignin biosynthesis: beyond the NAC-MYB-gene regulatory network model. Curr Opin Biotechnol 2018; 56:82-87. [PMID: 30390602 DOI: 10.1016/j.copbio.2018.10.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 01/15/2023]
Abstract
Lignin is an important secondary metabolite in plants. The biosynthesis of lignin is initiated by the transcriptional upregulation of genes encoding enzymes involved in monolignol biosynthesis and lignin polymerization. Based on studies of xylem differentiation over the last two decades, the NAC-MYB-based gene regulatory network (NAC-MYB-GRN) model is widely considered to underpin developmental lignin biosynthesis. We are now standing on the threshold of a new direction in transcriptional regulation research; the search for novel molecular hubs connecting developmental/environmental signals in lignin biosynthesis. Emerging genome-wide 'omics' technologies are a promising approach for understanding such hubs. Elucidating these molecular hubs may enable us to control lignification in harmony with plant development and environmental adaptation.
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Affiliation(s)
- Misato Ohtani
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Taku Demura
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
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12
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Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in Arabidopsis. Proc Natl Acad Sci U S A 2018; 115:7831-7836. [PMID: 29915080 PMCID: PMC6064979 DOI: 10.1073/pnas.1804971115] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The upstream ORFs (uORFs) in the 5′UTRs of mRNA often function as repressors of main ORF translation or triggers of nonsense-mediated mRNA decay. In this study, we report on transcription start site (TSS) selection when etiolated Arabidopsis seedlings are exposed to blue light, and reveal that transcription from uORF-avoiding TSSs is induced throughout the genome. It is possible that transcripts arising from TSSs downstream of uORFs evade uORF-mediated inhibition of gene expression. Thus, uORF-avoiding transcription starts are an important mechanism of gene expression regulation during a plant’s response to environmental changes. Plants adapt to alterations in light conditions by controlling their gene expression profiles. Expression of light-inducible genes is transcriptionally induced by transcription factors such as HY5. However, few detailed analyses have been carried out on the control of transcription start sites (TSSs). Of the various wavelengths of light, it is blue light (BL) that regulates physiological responses such as hypocotyl elongation and flowering time. To understand how gene expression is controlled not only by transcript abundance but also by TSS selection, we examined genome-wide TSS profiles in Arabidopsis seedlings after exposure to BL irradiation following initial growth in the dark. Thousands of genes use multiple TSSs, and some transcripts have upstream ORFs (uORFs) that take precedence over the main ORF (mORF) encoding proteins. The uORFs often function as translation inhibitors of the mORF or as triggers of nonsense-mediated mRNA decay (NMD). Transcription from TSSs located downstream of the uORFs in 220 genes is enhanced by BL exposure. This type of regulation is found in HY5 and HYH, major regulators of light-dependent gene expression. Translation efficiencies of the genes showing enhanced usage of these TSSs increased upon BL exposure. We also show that transcripts from TSSs upstream of uORFs in 45 of the 220 genes, including HY5, accumulated in a mutant of NMD. These results suggest that BL controls gene expression not only by enhancing transcriptions but also by choosing the TSS, and transcripts from downstream TSSs evade uORF-mediated inhibition to ensure high expression of light-regulated genes.
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Sinclair SA, Larue C, Bonk L, Khan A, Castillo-Michel H, Stein RJ, Grolimund D, Begerow D, Neumann U, Haydon MJ, Krämer U. Etiolated Seedling Development Requires Repression of Photomorphogenesis by a Small Cell-Wall-Derived Dark Signal. Curr Biol 2017; 27:3403-3418.e7. [PMID: 29103938 DOI: 10.1016/j.cub.2017.09.063] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/05/2017] [Accepted: 09/28/2017] [Indexed: 11/27/2022]
Abstract
Etiolated growth in darkness or the irreversible transition to photomorphogenesis in the light engages alternative developmental programs operating across all organs of a plant seedling. Dark-grown Arabidopsis de-etiolated by zinc (dez) mutants exhibit morphological, cellular, metabolic, and transcriptional characteristics of light-grown seedlings. We identify the causal mutation in TRICHOME BIREFRINGENCE encoding a putative acyl transferase. Pectin acetylation is decreased in dez, as previously found in the reduced wall acetylation2-3 mutant, shown here to phenocopy dez. Moreover, pectin of dez is excessively methylesterified. The addition of very short fragments of homogalacturonan, tri-galacturonate, and tetra-galacturonate, restores skotomorphogenesis in dark-grown dez and similar mutants, suggesting that the mutants are unable to generate these de-methylesterified pectin fragments. In combination with genetic data, we propose a model of spatiotemporally separated photoreceptive and signal-responsive cell types, which contain overlapping subsets of the regulatory network of light-dependent seedling development and communicate via a pectin-derived dark signal.
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Affiliation(s)
- Scott A Sinclair
- Department of Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Universitätsstrasse, 44801 Bochum, Germany
| | - Camille Larue
- Department of Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Universitätsstrasse, 44801 Bochum, Germany
| | - Laura Bonk
- Department of Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Universitätsstrasse, 44801 Bochum, Germany; Geobotany, Ruhr University Bochum, Universitätsstrasse, 44801 Bochum, Germany
| | - Asif Khan
- Department of Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Universitätsstrasse, 44801 Bochum, Germany
| | - Hiram Castillo-Michel
- ID21 Beamline, European Synchrotron Radiation Facility, Avenue des Martyrs, 38043 Grenoble, France
| | - Ricardo J Stein
- Department of Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Universitätsstrasse, 44801 Bochum, Germany
| | - Daniel Grolimund
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Dominik Begerow
- Geobotany, Ruhr University Bochum, Universitätsstrasse, 44801 Bochum, Germany
| | - Ulla Neumann
- Central Microscopy, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, 50829 Cologne, Germany
| | - Michael J Haydon
- Department of Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Universitätsstrasse, 44801 Bochum, Germany
| | - Ute Krämer
- Department of Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Universitätsstrasse, 44801 Bochum, Germany.
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Seluzicki A, Burko Y, Chory J. Dancing in the dark: darkness as a signal in plants. PLANT, CELL & ENVIRONMENT 2017; 40:2487-2501. [PMID: 28044340 PMCID: PMC6110299 DOI: 10.1111/pce.12900] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 05/21/2023]
Abstract
Daily cycles of light and dark provide an organizing principle and temporal constraints under which life on Earth evolved. While light is often the focus of plant studies, it is only half the story. Plants continuously adjust to their surroundings, taking both dawn and dusk as cues to organize their growth, development and metabolism to appropriate times of day. In this review, we examine the effects of darkness on plant physiology and growth. We describe the similarities and differences between seedlings grown in the dark versus those grown in light-dark cycles, and the evolution of etiolated growth. We discuss the integration of the circadian clock into other processes, looking carefully at the points of contact between clock genes and growth-promoting gene-regulatory networks in temporal gating of growth. We also examine daily starch accumulation and degradation, and the possible contribution of dark-specific metabolic controls in regulating energy and growth. Examining these studies together reveals a complex and continuous balancing act, with many signals, dark included, contributing information and guiding the plant through its life cycle. The extraordinary interconnection between light and dark is manifest during cycles of day and night and during seedling emergence above versus below the soil surface.
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Affiliation(s)
- Adam Seluzicki
- Salk Institute for Biological Studies, Plant Biology Laboratory, La Jolla, CA, 92037, USA
| | - Yogev Burko
- Salk Institute for Biological Studies, Plant Biology Laboratory, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Joanne Chory
- Salk Institute for Biological Studies, Plant Biology Laboratory, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
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15
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Ong WD, Okubo-Kurihara E, Kurihara Y, Shimada S, Makita Y, Kawashima M, Honda K, Kondoh Y, Watanabe N, Osada H, Cutler SR, Sudesh K, Matsui M. Chemical-Induced Inhibition of Blue Light-Mediated Seedling Development Caused by Disruption of Upstream Signal Transduction Involving Cryptochromes in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2017; 58:95-105. [PMID: 28011868 DOI: 10.1093/pcp/pcw181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
Plants have a remarkable ability to perceive and respond to various wavelengths of light and initiate regulation of different cascades of light signaling and molecular components. While the perception of red light and the mechanisms of its signaling involving phytochromes are largely known, knowledge of the mechanisms of blue light signaling is still limited. Chemical genetics involves the use of diverse small active or synthetic molecules to evaluate biological processes. By combining chemicals and analyzing the effects they have on plant morphology, we identified a chemical, 3-bromo-7-nitroindazole (3B7N), that promotes hypocotyl elongation of wild-type Arabidopsis only under continuous blue light. Further evaluation with loss-of-function mutants confirmed that 3B7N inhibits photomorphogenesis through cryptochrome-mediated light signaling. Microarray analysis demonstrated that the effect of 3B7N treatment on gene expression in cry1cry2 is considerably smaller than that in the wild type, indicating that 3B7N specifically interrupts cryptochrome function in the control of seedling development in a light-dependent manner. We demonstrated that 3B7N directly binds to CRY1 protein using an in vitro binding assay. These results suggest that 3B7N is a novel chemical that directly inhibits plant cryptochrome function by physical binding. The application of 3B7N can be used on other plants to study further the blue light mechanism and the genetic control of cryptochromes in the growth and development of plant species.
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Affiliation(s)
- Wen-Dee Ong
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Emiko Okubo-Kurihara
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Yukio Kurihara
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Setsuko Shimada
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Yuko Makita
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Mika Kawashima
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Kaori Honda
- Bio-Active Compounds Discovery Research Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Nobumoto Watanabe
- Bio-Active Compounds Discovery Research Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Sean R Cutler
- Department of Botany and Plant Sciences, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Minami Matsui
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
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16
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Okubo-Kurihara E, Ohtani M, Kurihara Y, Kakegawa K, Kobayashi M, Nagata N, Komatsu T, Kikuchi J, Cutler S, Demura T, Matsui M. Modification of plant cell wall structure accompanied by enhancement of saccharification efficiency using a chemical, lasalocid sodium. Sci Rep 2016; 6:34602. [PMID: 27694977 PMCID: PMC5046155 DOI: 10.1038/srep34602] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 09/15/2016] [Indexed: 11/25/2022] Open
Abstract
The cell wall is one major determinant of plant cell morphology, and is an attractive bioresource. Here, we report a novel strategy to modify plant cell wall property by small molecules. Lasalocid sodium (LS) was isolated by chemical screening to identify molecules that affect the cell morphology of tobacco BY-2 cells. LS treatment led to an increase in cell wall thickness, whilst the quantity and sugar composition of the cell wall remained unchanged in BY-2 cells. The chemical also disordered the cellular arrangement of hypocotyls of Arabidopsis plants, resulting in a decrease in hypocotyl length. LS treatment enhanced enzymatic saccharification efficiency in both BY-2 cells and Arabidopsis plants. Microarray analysis on Arabidopsis showed that exposure to LS upregulated type III peroxidase genes, of which some are involved in lignin biogenesis, and jasmonic acid response genes, and phloroglucinol staining supported the activation of lignification by the LS treatment. As jasmonic acid-mediated lignification is a typical reaction to cell wall damage, it is possible that LS induces cell wall loosening, which can trigger cell wall damage response. Thus, LS is a unique chemical for modification of cell wall and morphology through changes in cell wall architecture.
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Affiliation(s)
- Emiko Okubo-Kurihara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Misato Ohtani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yukio Kurihara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Koichi Kakegawa
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305–8687, Japan
| | - Megumi Kobayashi
- Faculty of Science, Japan Woman’s University, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Noriko Nagata
- Faculty of Science, Japan Woman’s University, Bunkyo-ku, Tokyo 112-8681, Japan
| | - Takanori Komatsu
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Sean Cutler
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California Riverside, 5451 Boyce Hall, Riverside, CA 92521, USA
| | - Taku Demura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Minami Matsui
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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17
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Hayami N, Sakai Y, Kimura M, Saito T, Tokizawa M, Iuchi S, Kurihara Y, Matsui M, Nomoto M, Tada Y, Yamamoto YY. The Responses of Arabidopsis Early Light-Induced Protein2 to Ultraviolet B, High Light, and Cold Stress Are Regulated by a Transcriptional Regulatory Unit Composed of Two Elements. PLANT PHYSIOLOGY 2015; 169:840-55. [PMID: 26175515 PMCID: PMC4577391 DOI: 10.1104/pp.15.00398] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 07/13/2015] [Indexed: 05/05/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) Early Light-Induced Protein (ELIP) is thought to act as a photoprotectant, reducing the damaging effects of high light (HL). Expression of ELIP2 is activated by multiple environmental stresses related to photoinhibition. We have identified putative regulatory elements in an ELIP2 promoter using an octamer-based frequency comparison method, analyzed the role of these elements using synthetic promoters, and revealed a key transcriptional regulatory unit for ultraviolet B (UV-B) radiation, HL, and cold stress responses. The unit is composed of two elements, designated as Elements A (TACACACC) and B (GGCCACGCCA), and shows functionality only when paired. Our genome-wide correlation analysis between possession of these elements in the promoter region and expression profiles in response to UV-B, HL, and cold suggests that Element B receives and integrates these multiple stress signals. In vitro protein-DNA binding assays revealed that LONG HYPOCOTYL5 (HY5), a basic domain-Leucine zipper transcription factor, directly binds to Element B. In addition, mutant analysis of HY5 showed partial involvement in the UV-B and HL responses but not in the cold stress response. These results suggest that signals for UV-B, HL, and cold stress join at Element B, which recognizes the signals of multiple transcription factors, including HY5.
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Affiliation(s)
- Natsuki Hayami
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
| | - Yusaku Sakai
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
| | - Mitsuhiro Kimura
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
| | - Tatsunori Saito
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
| | - Mutsutomo Tokizawa
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
| | - Satoshi Iuchi
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
| | - Yukio Kurihara
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
| | - Minami Matsui
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
| | - Mika Nomoto
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
| | - Yasuomi Tada
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
| | - Yoshiharu Y Yamamoto
- Faculty of Applied Biological Sciences (N.H., Y.S., T.S., Y.Y.Y.) and United Graduate School of Agricultural Science (M.T., Y.Y.Y.), Gifu University, Gifu 501-1103, Japan; Department of Frontier Research, Kazusa DNA Research Institute, Kazusa-kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan (M.K.);RIKEN Bioresource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan (S.I.);RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan (Y.K., M.M., Y.Y.Y.); andCenter for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan (M.N., Y.T.)
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