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Lee SW, Nugroho ABD, Park M, Moon H, Kim J, Kim DH. Identification of vernalization-related genes and cold memory element (CME) required for vernalization response in radish (Raphanus sativus L.). PLANT MOLECULAR BIOLOGY 2024; 114:5. [PMID: 38227117 DOI: 10.1007/s11103-023-01412-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024]
Abstract
Floral transition is accelerated by exposure to long-term cold like winter in plants, which is called as vernalization. Acceleration of floral transition by vernalization is observed in a diversity of biennial and perennial plants including Brassicaceae family plants. Scientific efforts to understand molecular mechanism underlying vernalization-mediated floral transition have been intensively focused in model plant Arabidopsis thaliana. To get a better understanding on floral transition by vernalization in radish (Raphanus sativus L.), we investigated transcriptomic changes taking place during vernalization in radish. Thousands of genes were differentially regulated along time course of vernalization compared to non-vernalization (NV) sample. Twelve major clusters of DEGs were identified based on distinctive expression profiles during vernalization. Radish FLC homologs were shown to exert an inhibition of floral transition when transformed into Arabidopsis plants. In addition, DNA region containing RY motifs located within a Raphanus sativus FLC homolog, RsFLC1 was found to be required for repression of RsFLC1 by vernalization. Transgenic plants harboring disrupted RY motifs were impaired in the enrichment of H3K27me3 on RsFLC1 chromatin, thus resulting in the delayed flowering in Arabidopsis. Taken together, we report transcriptomic profiles of radish during vernalization and demonstrate the requirement of RY motif for vernalization-mediated repression of RsFLC homologs in radish (Raphanus sativus L.).
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Affiliation(s)
- Sang Woo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | | | | | - Heewon Moon
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Jun Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea.
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2
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Kinmonth-Schultz H, Sønstebø JH, Croneberger AJ, Johnsen SS, Leder E, Lewandowska-Sabat A, Imaizumi T, Rognli OA, Vinje H, Ward JK, Fjellheim S. Responsiveness to long days for flowering is reduced in Arabidopsis by yearly variation in growing season temperatures. PLANT, CELL & ENVIRONMENT 2023; 46:3337-3352. [PMID: 37249162 DOI: 10.1111/pce.14632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 05/31/2023]
Abstract
Conservative flowering behaviours, such as flowering during long days in summer or late flowering at a high leaf number, are often proposed to protect against variable winter and spring temperatures which lead to frost damage if premature flowering occurs. Yet, due the many factors in natural environments relative to the number of individuals compared, assessing which climate characteristics drive these flowering traits has been difficult. We applied a multidisciplinary approach to 10 winter-annual Arabidopsis thaliana populations from a wide climactic gradient in Norway. We used a variable reduction strategy to assess which of 100 climate descriptors from their home sites correlated most to their flowering behaviours when tested for responsiveness to photoperiod after saturation of vernalization; then, assessed sequence variation of 19 known environmental-response flowering genes. Photoperiod responsiveness inversely correlated with interannual variation in timing of growing season onset. Time to flowering appeared driven by growing season length, curtailed by cold fall temperatures. The distribution of FLM, TFL2 and HOS1 haplotypes, genes involved in ambient temperature response, correlated with growing-season climate. We show that long-day responsiveness and late flowering may be driven not by risk of spring frosts, but by growing season temperature and length, perhaps to opportunistically maximize growth.
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Affiliation(s)
- Hannah Kinmonth-Schultz
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Department of Biology, Tennessee Technological University, Cookeville, Tennessee, USA
| | - Jørn H Sønstebø
- Faculty of Technology, Natural Sciences and Maritime Sciences, University of South-Eastern Norway, Notodden, Norway
| | | | - Sylvia S Johnsen
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Erica Leder
- Department of Marine Science, University of Gothenburg, Gothenburg, Sweden
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Odd Arne Rognli
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Hilde Vinje
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Joy K Ward
- College of Arts and Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - Siri Fjellheim
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
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3
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Field S, Jang GJ, Dean C, Strader LC, Rhee SY. Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development. THE PLANT CELL 2023; 35:3173-3186. [PMID: 36879427 PMCID: PMC10473230 DOI: 10.1093/plcell/koad062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
This review highlights recent literature on biomolecular condensates in plant development and discusses challenges for fully dissecting their functional roles. Plant developmental biology has been inundated with descriptive examples of biomolecular condensate formation, but it is only recently that mechanistic understanding has been forthcoming. Here, we discuss recent examples of potential roles biomolecular condensates play at different stages of the plant life cycle. We group these examples based on putative molecular functions, including sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. We explore how these mechanisms could modulate plant development in response to environmental inputs and discuss challenges and opportunities for further research into deciphering molecular mechanisms to better understand the diverse roles that biomolecular condensates exert on life.
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Affiliation(s)
- Sterling Field
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Geng-Jen Jang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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4
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Shi T, Bai Y, Wu X, Wang Y, Iqbal S, Tan W, Ni Z, Gao Z. PmAGAMOUS recruits polycomb protein PmLHP1 to regulate single-pistil morphogenesis in Japanese apricot. PLANT PHYSIOLOGY 2023; 193:466-482. [PMID: 37204822 DOI: 10.1093/plphys/kiad292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/31/2023] [Accepted: 04/12/2023] [Indexed: 05/20/2023]
Abstract
Japanese apricot (Prunus mume Sieb. et Zucc.) is a traditional fruit tree with a long history. Multiple pistils (MP) lead to the formation of multiple fruits, decreasing fruit quality and yield. In this study, the morphology of flowers was observed at 4 stages of pistil development: undifferentiated stage (S1), predifferentiation stage (S2), differentiation stage (S3), and late differentiation stage (S4). In S2 and S3, the expression of PmWUSCHEL (PmWUS) in the MP cultivar was significantly higher than that in the single-pistil (SP) cultivar, and the gene expression of its inhibitor, PmAGAMOUS (PmAG), also showed the same trend, indicating that other regulators participate in the regulation of PmWUS during this period. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) showed that PmAG could bind to the promoter and the locus of PmWUS, and H3K27me3 repressive marks were also detected at these sites. The SP cultivar exhibited an elevated level of DNA methylation in the promoter region of PmWUS, which partially overlapped with the region of histone methylation. This suggests that the regulation of PmWUS involves both transcription factors and epigenetic modifications. Also, the gene expression of Japanese apricot LIKE HETEROCHROMATIN PROTEIN (PmLHP1), an epigenetic regulator, in MP was significantly lower than that in SP in S2 to 3, contrary to the trend in expression of PmWUS. Our results showed that PmAG recruited sufficient PmLHP1 to maintain the level of H3K27me3 on PmWUS during the S2 of pistil development. This recruitment of PmLHP1 by PmAG inhibits the expression of PmWUS at the precise time, leading to the formation of 1 normal pistil primordium.
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Affiliation(s)
- Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinxin Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- College of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Yike Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shahid Iqbal
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL 32351, USA
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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5
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Nishio H, Kudoh H. Distinct responses to autumn and spring temperatures by the key flowering-time regulator FLOWERING LOCUS C. Curr Opin Genet Dev 2023; 78:102016. [PMID: 36549195 DOI: 10.1016/j.gde.2022.102016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/10/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022]
Abstract
Despite the similarity in temperature regimes between late autumn and early spring, plants exhibit distinct developmental responses that result in distinct morphologies, that is, overwintering and reproductive forms. In Arabidopsis, the control of autumn-spring distinction involves the transcriptional regulation of the floral repressor FLOWERING LOCUS C (FLC). The memory of winter cold is registered as epigenetic silencing of FLC. Recent studies on A. thaliana FLC revealed detailed and additional mechanisms of silencing in response to autumn and winter cold. Studies on perennial Arabidopsis FLC revealed that its expression responds to spring warmth and is robustly upregulated, ignoring cold. These new studies provide mechanistic insights into the distinct regulation of FLC under autumn and spring temperature regimes.
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Affiliation(s)
- Haruki Nishio
- Center for Ecological Research, Kyoto University, Shiga 520-2113, Japan; Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga 522-8522, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Shiga 520-2113, Japan.
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Jeon M, Jeong G, Yang Y, Luo X, Jeong D, Kyung J, Hyun Y, He Y, Lee I. Vernalization-triggered expression of the antisense transcript COOLAIR is mediated by CBF genes. eLife 2023; 12:84594. [PMID: 36722843 PMCID: PMC10036118 DOI: 10.7554/elife.84594] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/31/2023] [Indexed: 02/02/2023] Open
Abstract
To synchronize flowering time with spring, many plants undergo vernalization, a floral-promotion process triggered by exposure to long-term winter cold. In Arabidopsis thaliana, this is achieved through cold-mediated epigenetic silencing of the floral repressor, FLOWERING LOCUS C (FLC). COOLAIR, a cold-induced antisense RNA transcribed from the FLC locus, has been proposed to facilitate FLC silencing. Here, we show that C-repeat (CRT)/dehydration-responsive elements (DREs) at the 3'-end of FLC and CRT/DRE-binding factors (CBFs) are required for cold-mediated expression of COOLAIR. CBFs bind to CRT/DREs at the 3'-end of FLC, both in vitro and in vivo, and CBF levels increase gradually during vernalization. Cold-induced COOLAIR expression is severely impaired in cbfs mutants in which all CBF genes are knocked-out. Conversely, CBF-overexpressing plants show increased COOLAIR levels even at warm temperatures. We show that COOLAIR is induced by CBFs during early stages of vernalization but COOLAIR levels decrease in later phases as FLC chromatin transitions to an inactive state to which CBFs can no longer bind. We also demonstrate that cbfs and FLCΔCOOLAIR mutants exhibit a normal vernalization response despite their inability to activate COOLAIR expression during cold, revealing that COOLAIR is not required for the vernalization process.
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Affiliation(s)
- Myeongjune Jeon
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
| | - Goowon Jeong
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
| | - Yupeng Yang
- Shanghai Center for Plant Stress Biology & National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Daesong Jeong
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
| | - Jinseul Kyung
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
| | - Youbong Hyun
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
| | - Yuehui He
- Shanghai Center for Plant Stress Biology & National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Ilha Lee
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, Republic of Korea
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7
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Mitsui Y, Yokoyama H, Nakaegawa W, Tanaka K, Komatsu K, Koizuka N, Okuzaki A, Matsumoto T, Takahara M, Tabei Y. Epistatic interactions among multiple copies of FLC genes with naturally occurring insertions correlate with flowering time variation in radish. AOB PLANTS 2023; 15:plac066. [PMID: 36751367 PMCID: PMC9893874 DOI: 10.1093/aobpla/plac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Brassicaceae crops, which underwent whole-genome triplication during their evolution, have multiple copies of flowering-related genes. Interactions among multiple gene copies may be involved in flowering time regulation; however, this mechanism is poorly understood. In this study, we performed comprehensive, high-throughput RNA sequencing analysis to identify candidate genes involved in the extremely late-bolting (LB) trait in radish. Then, we examined the regulatory roles and interactions of radish FLOWERING LOCUS C (RsFLC) paralogs, the main flowering repressor candidates. Seven flowering integrator genes, five vernalization genes, nine photoperiodic/circadian clock genes and eight genes from other flowering pathways were differentially expressed in the early-bolting (EB) cultivar 'Aokubinagafuto' and LB radish cultivar 'Tokinashi' under different vernalization conditions. In the LB cultivar, RsFLC1 and RsFLC2 expression levels were maintained after 40 days of cold exposure. Bolting time was significantly correlated with the expression rates of RsFLC1 and RsFLC2. Using the EB × LB F2 population, we performed association analyses of genotypes with or without 1910- and 1627-bp insertions in the first introns of RsFLC1 and RsFLC2, respectively. The insertion alleles prevented the repression of their respective FLC genes under cold conditions. Interestingly, genotypes homozygous for RsFLC2 insertion alleles maintained high RsFLC1 and RsFLC3 expression levels under cold conditions, and two-way analysis of variance revealed that RsFLC1 and RsFLC3 expression was influenced by the RsFLC2 genotype. Our results indicate that insertions in the first introns of RsFLC1 and RsFLC2 contribute to the late-flowering trait in radish via different mechanisms. The RsFLC2 insertion allele conferred a strong delay in bolting by inhibiting the repression of all three RsFLC genes, suggesting that radish flowering time is determined by epistatic interactions among multiple FLC gene copies.
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Affiliation(s)
| | - Hinano Yokoyama
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Atsugi, Kanagawa 243-0034, Japan
| | - Wataru Nakaegawa
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Atsugi, Kanagawa 243-0034, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kenji Komatsu
- Faculty of Agriculture, Tokyo University of Agriculture, 1737 Atsugi, Kanagawa 243-0034, Japan
| | - Nobuya Koizuka
- College of Agriculture, Tamagawa University, 6-1-1 Tamagawa Gakuen, Machida, Tokyo 194-8610, Japan
| | - Ayako Okuzaki
- College of Agriculture, Tamagawa University, 6-1-1 Tamagawa Gakuen, Machida, Tokyo 194-8610, Japan
| | - Takashi Matsumoto
- Faculty of Applied Biology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Manabu Takahara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8634, Japan
| | - Yutaka Tabei
- Faculty of Food and Nutritional Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma 374-0193, Japan
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8
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Soorni A, Karimi M, Al Sharif B, Habibi K. Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa. BMC PLANT BIOLOGY 2023; 23:3. [PMID: 36588159 PMCID: PMC9806901 DOI: 10.1186/s12870-022-04031-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase. RESULTS For identifying unannotated transcripts in these datasets, a 7-step pipeline was employed to filter out these transcripts and terminate with 293 novel lncRNAs predicted by PLncPRO and CREMA. These transcripts were then utilized to predict cis and trans flowering-associated targets and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Computational predictions of target gene function showed the involvement of putative flowering-related genes and enrichment of the floral regulators FLC, CO, FT, and SOC1 in both datasets. Finally, 17 and 18 lncRNAs were proposed as competing endogenous target mimics (eTMs) for novel and known lncRNA miRNAs, respectively. CONCLUSION Overall, this study provides new insights into lncRNAs that control the flowering time of plants known for bolting, such as lettuce, and opens new windows for further study.
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Affiliation(s)
- Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
| | | | - Batoul Al Sharif
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Khashayar Habibi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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9
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Jeong G, Jeon M, Shin J, Lee I. HEAT SHOCK TRANSCRIPTION FACTOR B2b acts as a transcriptional repressor of VIN3, a gene induced by long-term cold for flowering. Sci Rep 2022; 12:10963. [PMID: 35768490 PMCID: PMC9243095 DOI: 10.1038/s41598-022-15052-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/16/2022] [Indexed: 11/21/2022] Open
Abstract
Vernalization, an acceleration of flowering after long-term winter cold, is an intensively studied flowering mechanism in winter annual plants. In Arabidopsis, Polycomb Repressive Complex 2 (PRC2)-mediated suppression of the strong floral repressor, FLOWERING LOCUS C (FLC), is critical for vernalization and a PHD finger domain protein, VERNALIZATION INSENSITIVE 3 (VIN3), recruits PRC2 on FLC chromatin. The level of VIN3 was found to gradually increase in proportion to the length of cold period during vernalization. However, how plants finely regulate VIN3 expression according to the cold environment has not been completely elucidated. As a result, we performed EMS mutagenesis using a transgenic line with a minimal promoter of VIN3 fused to the GUS reporter gene, and isolated a mutant, hyperactivation of VIN3 1 (hov1), which showed increased GUS signal and endogenous VIN3 transcript levels. Using positional cloning combined with whole-genome resequencing, we found that hov1 carries a nonsense mutation, leading to a premature stop codon on the HEAT SHOCK TRANSCRIPTION FACTOR B2b (HsfB2b), which encodes a repressive heat shock transcription factor. HsfB2b directly binds to the VIN3 promoter, and HsfB2b overexpression leads to reduced acceleration of flowering after vernalization. Collectively, our findings reveal a novel fine-tuning mechanism to regulate VIN3 for proper vernalization response.
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Affiliation(s)
- Goowon Jeong
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.,Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Korea
| | - Myeongjune Jeon
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.,Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Korea
| | - Jinwoo Shin
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea.,Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, 02114, USA
| | - Ilha Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea. .,Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Korea.
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10
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Xu G, Tao Z, He Y. Embryonic reactivation of FLOWERING LOCUS C by ABSCISIC ACID-INSENSITIVE 3 establishes the vernalization requirement in each Arabidopsis generation. THE PLANT CELL 2022; 34:2205-2221. [PMID: 35234936 PMCID: PMC9134069 DOI: 10.1093/plcell/koac077] [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: 10/07/2021] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Many over-wintering plants grown in temperate climate acquire competence to flower upon prolonged cold exposure in winter, through vernalization. In Arabidopsis thaliana, prolonged cold exposure induces the silencing of the potent floral repressor FLOWERING LOCUS C (FLC) through repressive chromatin modifications by Polycomb proteins. This repression is maintained to enable flowering after return to warmth, but is reset during seed development. Here, we show that embryonic FLC reactivation occurs in two phases: resetting of cold-induced FLC silencing during embryogenesis and further FLC activation during embryo maturation. We found that the B3 transcription factor (TF) ABSCISIC ACID-INSENSITIVE 3 (ABI3) mediates both FLC resetting in embryogenesis and further activation of FLC expression in embryo maturation. ABI3 binds to the cis-acting cold memory element at FLC and recruits a scaffold protein with active chromatin modifiers to reset FLC chromatin into an active state in late embryogenesis. Moreover, in response to abscisic acid (ABA) accumulation during embryo maturation, ABI3, together with the basic leucine zipper TF ABI5, binds to an ABA-responsive cis-element to further activate FLC expression to high level. Therefore, we have uncovered the molecular circuitries underlying embryonic FLC reactivation following parental vernalization, which ensures that each generation must experience winter cold prior to flowering.
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11
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Ramakrishnan M, Papolu PK, Satish L, Vinod KK, Wei Q, Sharma A, Emamverdian A, Zou LH, Zhou M. Redox status of the plant cell determines epigenetic modifications under abiotic stress conditions and during developmental processes. J Adv Res 2022; 42:99-116. [PMID: 35690579 PMCID: PMC9788946 DOI: 10.1016/j.jare.2022.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/30/2022] [Accepted: 04/12/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The oxidation-reduction (redox) status of the cell influences or regulates transcription factors and enzymes involved in epigenetic changes, such as DNA methylation, histone protein modifications, and chromatin structure and remodeling. These changes are crucial regulators of chromatin architecture, leading to differential gene expression in eukaryotes. But the cell's redox homeostasis is difficult to sustain since the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS) is not equal in plants at different developmental stages and under abiotic stress conditions. Exceeding optimum ROS and RNS levels leads to oxidative stress and thus alters the redox status of the cell. Consequently, this alteration modulates intracellular epigenetic modifications that either mitigate or mediate the plant growth and stress response. AIM OF REVIEW Recent studies suggest that the altered redox status of the cell reform the cellular functions and epigenetic changes. Recent high-throughput techniques have also greatly advanced redox-mediated gene expression discovery, but the integrated view of the redox status, and its associations with epigenetic changes and subsequent gene expression in plants are still scarce. In this review, we accordingly focus on how the redox status of the cell affects epigenetic modifications in plants under abiotic stress conditions and during developmental processes. This is a first comprehensive review on the redox status of the cell covering the redox components and signaling, redox status alters the post-translational modification of proteins, intracellular epigenetic modifications, redox interplay during DNA methylation, redox regulation of histone acetylation and methylation, redox regulation of miRNA biogenesis, redox regulation of chromatin structure and remodeling and conclusion, future perspectives and biotechnological opportunities for the future development of the plants. KEY SCIENTIFIC CONCEPTS OF REVIEW The interaction of redox mediators such as ROS, RNS and antioxidants regulates redox homeostasis and redox-mediated epigenetic changes. We discuss how redox mediators modulate epigenetic changes and show the opportunities for smart use of the redox status of the cell in plant development and abiotic stress adaptation. However, how a redox mediator triggers epigenetic modification without activating other redox mediators remains yet unknown.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China.
| | - Pradeep K Papolu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Lakkakula Satish
- Department of Biotechnology Engineering, & The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva - 84105, Israel; Applied Phycology and Biotechnology Division, Marine Algal Research Station, CSIR - Central Salt and Marine Chemicals Research Institute, Mandapam 623519, Tamil Nadu, India
| | | | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Abolghassem Emamverdian
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Long-Hai Zou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
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12
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Genome-Wide Characterization Analysis of CCT Genes in Raphanus sativus and Their Potential Role in Flowering and Abiotic Stress Response. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
CCT genes play vital roles in flowering, plant growth, development, and response to abiotic stresses. Although they have been reported in many plants, the characterization and expression pattern of CCT genes is still limited in R. sativus. In this study, a total of 58 CCT genes were identified in R. sativus. Phylogenetic tree, gene structure, and conserved domains revealed that all CCT genes were classified into three groups: COL, CMF, and PRR. Genome-wide identification and evolutionary analysis showed that segmental duplication expanded the CCT gene families considerably, with the LF subgenome retaining more CCT genes. We observed strong purifying selection pressure for CCT genes. RsCCT genes showed tissue specificity, and some genes (such as RsCCT22, RsCCT36, RsCCT42 and RsCCT51) were highly expressed in flowers. Promoter cis-elements and RNA-seq data analysis showed that RsCCT genes could play roles in controlling flowering through the photoperiodic pathway and vernalization pathway. The expression profiles of RsCCT genes under Cd, Cr, Pb, and heat and salt stresses revealed that many RsCCT genes could respond to one or more abiotic stresses. Our findings could provide essential information for further studies on the function of RsCCT genes.
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13
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Fulgione A, Neto C, Elfarargi AF, Tergemina E, Ansari S, Göktay M, Dinis H, Döring N, Flood PJ, Rodriguez-Pacheco S, Walden N, Koch MA, Roux F, Hermisson J, Hancock AM. Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages. Nat Commun 2022; 13:1461. [PMID: 35304466 PMCID: PMC8933414 DOI: 10.1038/s41467-022-28800-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 02/07/2022] [Indexed: 12/11/2022] Open
Abstract
Understanding how populations adapt to abrupt environmental change is necessary to predict responses to future challenges, but identifying specific adaptive variants, quantifying their responses to selection and reconstructing their detailed histories is challenging in natural populations. Here, we use Arabidopsis from the Cape Verde Islands as a model to investigate the mechanisms of adaptation after a sudden shift to a more arid climate. We find genome-wide evidence of adaptation after a multivariate change in selection pressures. In particular, time to flowering is reduced in parallel across islands, substantially increasing fitness. This change is mediated by convergent de novo loss of function of two core flowering time genes: FRI on one island and FLC on the other. Evolutionary reconstructions reveal a case where expansion of the new populations coincided with the emergence and proliferation of these variants, consistent with models of rapid adaptation and evolutionary rescue. Detailing how populations adapted to environmental change is needed to predict future responses, but identifying adaptive variants and detailing their fitness effects is rare. Here, the authors show that parallel loss of FRI and FLC function reduces time to flowering and drives adaptation in a drought prone environment.
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Affiliation(s)
- Andrea Fulgione
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Mathematics and Bioscience, Department of Mathematics and Max F. Perutz Labs, University of Vienna, Vienna, Austria.,Vienna Graduate School for Population Genetics, Vienna, Austria
| | - Célia Neto
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | | | - Shifa Ansari
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mehmet Göktay
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Herculano Dinis
- Parque Natural do Fogo, Direção Nacional do Ambiente, Praia, Santiago, Cabo Verde.,Associação Projecto Vitó, São Filipe, Fogo, Cabo Verde
| | - Nina Döring
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Pádraic J Flood
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Nora Walden
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany.,Biosystematics, Wageningen University, Wageningen, The Netherlands
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | - Fabrice Roux
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Joachim Hermisson
- Mathematics and Bioscience, Department of Mathematics and Max F. Perutz Labs, University of Vienna, Vienna, Austria
| | - Angela M Hancock
- Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Mathematics and Bioscience, Department of Mathematics and Max F. Perutz Labs, University of Vienna, Vienna, Austria.
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14
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Liu Y, Yang X, Zhou M, Yang Y, Li F, Yan X, Zhang M, Wei Z, Qin S, Min J. Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain. J Biol Chem 2022; 298:101623. [PMID: 35074427 PMCID: PMC8861120 DOI: 10.1016/j.jbc.2022.101623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Arabidopsis LHP1 (LIKE HETEROCHROMATIN PROTEIN 1), a unique homolog of HP1 in Drosophila, plays important roles in plant development, growth, and architecture. In contrast to specific binding of the HP1 chromodomain to methylated H3K9 histone tails, the chromodomain of LHP1 has been shown to bind to both methylated H3K9 and H3K27 histone tails, and LHP1 carries out its function mainly via its interaction with these two epigenetic marks. However, the molecular mechanism for the recognition of methylated histone H3K9/27 by the LHP1 chromodomain is still unknown. In this study, we characterized the binding ability of LHP1 to histone H3K9 and H3K27 peptides and found that the chromodomain of LHP1 binds to histone H3K9me2/3 and H3K27me2/3 peptides with comparable affinities, although it exhibited no binding or weak binding to unmodified or monomethylated H3K9/K27 peptides. Our crystal structures of the LHP1 chromodomain in peptide-free and peptide-bound forms coupled with mutagenesis studies reveal that the chromodomain of LHP1 bears a slightly different chromodomain architecture and recognizes methylated H3K9 and H3K27 peptides via a hydrophobic clasp, similar to the chromodomains of human Polycomb proteins, which could not be explained only based on primary structure analysis. Our binding and structural studies of the LHP1 chromodomain illuminate a conserved ligand interaction mode between chromodomains of both animals and plants, and shed light on further functional study of the LHP1 protein.
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Affiliation(s)
- Yanli Liu
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China.
| | - Xiajie Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Mengqi Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Yinxue Yang
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | - Fangzhou Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China
| | - Xuemei Yan
- College of Pharmaceutical Sciences, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | | | - Zhengguo Wei
- School of Biology and Basic Medical Science, Soochow University, Su Zhou, Jiangsu 215021, PR China
| | - Su Qin
- Life Science Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, PR China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, PR China.
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15
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Zhu F, Wen W, Cheng Y, Fernie AR. The metabolic changes that effect fruit quality during tomato fruit ripening. MOLECULAR HORTICULTURE 2022; 2:2. [PMID: 37789428 PMCID: PMC10515270 DOI: 10.1186/s43897-022-00024-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/12/2022] [Indexed: 10/05/2023]
Abstract
As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.
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Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany
| | - Weiwei Wen
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam, Golm, Germany.
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16
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Lei Z, Wang L, Kim EY, Cho J. Phase separation of chromatin and small RNA pathways in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1256-1265. [PMID: 34585805 DOI: 10.1111/tpj.15517] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/18/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
Gene expression can be modulated by epigenetic mechanisms, including chromatin modifications and small regulatory RNAs. These pathways are unevenly distributed within a cell and usually take place in specific intracellular regions. Unfortunately, the fundamental driving force and biological relevance of such spatial differentiation is largely unknown. Liquid-liquid phase separation (LLPS) is a natural propensity of demixing liquid phases and has been recently suggested to mediate the formation of biomolecular condensates that are relevant to diverse cellular processes. LLPS provides a mechanistic explanation for the self-assembly of subcellular structures by which the efficiency and specificity of certain cellular reactions are achieved. In plants, LLPS has been observed for several key factors in the chromatin and small RNA pathways. For example, the formation of facultative and obligate heterochromatin involves the LLPS of multiple relevant factors. In addition, phase separation is observed in a set of proteins acting in microRNA biogenesis and the small interfering RNA pathway. In this Focused Review, we highlight and discuss the recent findings regarding phase separation in the epigenetic mechanisms of plants.
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Affiliation(s)
- Zhen Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Eun Yu Kim
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Chinese Academy of Sciences, Shanghai, 200032, China
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17
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Xie W, Tang Q, Yan F, Tao Z. Transcriptional memory and response to adverse temperatures in plants. J Zhejiang Univ Sci B 2021; 22:791-804. [PMID: 34636184 DOI: 10.1631/jzus.b2100287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Temperature is one of the major environmental signals controlling plant development, geographical distribution, and seasonal behavior. Plants perceive adverse temperatures, such as high, low, and freezing temperatures, as stressful signals that can cause physiological defects and even death. As sessile organisms, plants have evolved sophisticated mechanisms to adapt to recurring stressful environments through changing gene expression or transcriptional reprogramming. Transcriptional memory refers to the ability of primed plants to remember previously experienced stress and acquire enhanced tolerance to similar or different stresses. Epigenetic modifications mediate transcriptional memory and play a key role in adapting to adverse temperatures. Understanding the mechanisms of the formation, maintenance, and resetting of stress-induced transcriptional memory will not only enable us to understand why there is a trade-off between plant defense and growth, but also provide a theoretical basis for generating stress-tolerant crops optimized for future climate change. In this review, we summarize recent advances in dissecting the mechanisms of plant transcriptional memory in response to adverse temperatures, based mainly on studies of the model plant Arabidopsis thaliana. We also discuss remaining questions that are important for further understanding the mechanisms of transcriptional memory during the adverse temperature response.
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Affiliation(s)
- Wei Xie
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China.,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianqian Tang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China.,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fei Yan
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China.,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zeng Tao
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China. .,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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18
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Adamski NM, Simmonds J, Brinton JF, Backhaus AE, Chen Y, Smedley M, Hayta S, Florio T, Crane P, Scott P, Pieri A, Hall O, Barclay JE, Clayton M, Doonan JH, Nibau C, Uauy C. Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner. THE PLANT CELL 2021; 33:2296-2319. [PMID: 34009390 PMCID: PMC8364232 DOI: 10.1093/plcell/koab119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/17/2021] [Indexed: 05/20/2023]
Abstract
Flower development is an important determinant of grain yield in crops. In wheat (Triticum spp.), natural variation for the size of spikelet and floral organs is particularly evident in Triticum turgidum ssp. polonicum (also termed Triticum polonicum), a tetraploid subspecies of wheat with long glumes, lemmas, and grains. Using map-based cloning, we identified VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT2), which encodes a MADS-box transcription factor belonging to the SHORT VEGETATIVE PHASE family, as the gene underlying the T. polonicum long-glume (P1) locus. The causal P1 mutation is a sequence rearrangement in intron-1 that results in ectopic expression of the T. polonicum VRT-A2 allele. Based on allelic variation studies, we propose that the intron-1 mutation in VRT-A2 is the unique T. polonicum subspecies-defining polymorphism, which was later introduced into hexaploid wheat via natural hybridizations. Near-isogenic lines differing for the P1 locus revealed a gradient effect of P1 across spikelets and within florets. Transgenic lines of hexaploid wheat carrying the T. polonicum VRT-A2 allele show that expression levels of VRT-A2 are highly correlated with spike, glume, grain, and floral organ length. These results highlight how changes in expression profiles, through variation in cis-regulation, can affect agronomic traits in a dosage-dependent manner in polyploid crops.
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Affiliation(s)
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Yi Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark Smedley
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sadiye Hayta
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Tobin Florio
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Pamela Crane
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Peter Scott
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alice Pieri
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Olyvia Hall
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Myles Clayton
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EE, UK
| | - John H. Doonan
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Candida Nibau
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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19
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Du D, Zhang D, Yuan J, Feng M, Li Z, Wang Z, Zhang Z, Li X, Ke W, Li R, Chen Z, Chai L, Hu Z, Guo W, Xing J, Su Z, Peng H, Xin M, Yao Y, Sun Q, Liu J, Ni Z. FRIZZY PANICLE defines a regulatory hub for simultaneously controlling spikelet formation and awn elongation in bread wheat. THE NEW PHYTOLOGIST 2021; 231:814-833. [PMID: 33837555 DOI: 10.1111/nph.17388] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/01/2021] [Indexed: 05/25/2023]
Abstract
Grain yield in bread wheat (Triticum aestivum L.) is largely determined by inflorescence architecture. Zang734 is an endemic Tibetan wheat variety that exhibits a rare triple spikelet (TRS) phenotype with significantly increased spikelet/floret number per spike. However, the molecular basis underlying this specific spike morphology is completely unknown. Through map-based cloning, the causal genes for TRS trait in Zang734 were isolated. Furthermore, using CRISPR/Cas9-based gene mutation, transcriptome sequencing and protein-protein interaction, the downstream signalling networks related to spikelet formation and awn elongation were defined. Results showed that the null mutation in WFZP-A together with deletion of WFZP-D led to the TRS trait in Zang734. More interestingly, WFZP plays a dual role in simultaneously repressing spikelet formation gene TaBA1 and activating awn development genes, basically through the recruitments of chromatin remodelling elements and the Mediator complex. Our findings provide insights into the molecular bases by which WFZP suppresses spikelet formation but promotes awn elongation and, more importantly, define WFZP-D as a favourable gene for high-yield crop breeding.
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Affiliation(s)
- Dejie Du
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Dongxue Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jun Yuan
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Man Feng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaoju Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zihao Wang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaoheng Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiongtao Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Renhan Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhenqi Su
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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20
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Current understanding of plant Polycomb group proteins and the repressive histone H3 Lysine 27 trimethylation. Biochem Soc Trans 2021; 48:1697-1706. [PMID: 32725200 DOI: 10.1042/bst20200192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022]
Abstract
Polycomb group (PcG) proteins are highly conserved chromatin-modifying complexes that implement gene silencing in higher eukaryotes. Thousands of genes and multiple developmental processes are regulated by PcG proteins. As the first chromatin modifier been identified in model plant Arabidopsis thaliana, the methyltransferase CURLY LEAF (CLF) and its catalyzed histone H3 Lysine 27 trimethylation (H3K27me3) have already become well-established paradigm in plant epigenetic study. Like in animals, PcG proteins mediate plant development and repress homeotic gene expression by antagonizing with trithorax group proteins. Recent researches have advanced our understanding on plant PcG proteins, including the plant-specific components of these well-conserved protein complexes, the close association with transcription factors and noncoding RNA for the spatial and temporal specificity, the dynamic regulation of the repressive mark H3K27me3 and the PcG-mediated chromatin conformation alterations in gene expression. In this review, we will summarize the molecular mechanisms of PcG-implemented gene repression and the relationship between H3K27me3 and another repressive mark histone H2A Lysine 121 mono-ubiquitination (H2A121ub) will also be discussed.
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21
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Beyond the Genetic Pathways, Flowering Regulation Complexity in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22115716. [PMID: 34071961 PMCID: PMC8198774 DOI: 10.3390/ijms22115716] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Flowering is one of the most critical developmental transitions in plants’ life. The irreversible change from the vegetative to the reproductive stage is strictly controlled to ensure the progeny’s success. In Arabidopsis thaliana, seven flowering genetic pathways have been described under specific growth conditions. However, the evidence condensed here suggest that these pathways are tightly interconnected in a complex multilevel regulatory network. In this review, we pursue an integrative approach emphasizing the molecular interactions among the flowering regulatory network components. We also consider that the same regulatory network prevents or induces flowering phase change in response to internal cues modulated by environmental signals. In this sense, we describe how during the vegetative phase of development it is essential to prevent the expression of flowering promoting genes until they are required. Then, we mention flowering regulation under suboptimal growing temperatures, such as those in autumn and winter. We next expose the requirement of endogenous signals in flowering, and finally, the acceleration of this transition by long-day photoperiod and temperature rise signals allowing A. thaliana to bloom in spring and summer seasons. With this approach, we aim to provide an initial systemic view to help the reader integrate this complex developmental process.
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22
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Li Z, Luo X, Ou Y, Jiao H, Peng L, Fu X, Macho AP, Liu R, He Y. JASMONATE-ZIM DOMAIN proteins engage Polycomb chromatin modifiers to modulate Jasmonate signaling in Arabidopsis. MOLECULAR PLANT 2021; 14:732-747. [PMID: 33676023 DOI: 10.1016/j.molp.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/30/2020] [Accepted: 02/27/2021] [Indexed: 05/24/2023]
Abstract
Jasmonate (JA) regulates various aspects of plant growth and development and stress responses, with prominent roles in male reproductive development and defenses against herbivores and necrotrophic pathogens. JASMONATE-ZIM DOMAIN (JAZ) proteins are key regulators in the JA signaling pathway and function to repress the expression of JA-responsive genes. Here, we show that JAZ proteins directly interact with several chromatin-associated Polycomb proteins to mediate repressive chromatin modifications at JA-responsive genes and, thus, their transcriptional repression in Arabidopsis. Genetic analyses revealed that the developmental defects, including anther and pollen abnormalities, resulting from loss or block of JA signaling were partially rescued by loss of Polycomb protein-mediated chromatin silencing (Polycomb repression). We further found that JAZ-mediated transcriptional repression during anther and pollen development requires Polycomb proteins at four key regulatory loci. Analysis of genome-wide occupancy of a Polycomb factor and transcriptome reprogramming in response to JA revealed that Polycomb repression is involved in the repression of various JA-responsive genes. Taken together, our study reveals an important chromatin-based mechanism for JAZ-mediated transcriptional repression and JA signaling in plants.
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Affiliation(s)
- Zicong Li
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China; Ministry of Education Key Laboratory of Plant Development and Environmental Adaption Biology, School of Life Sciences, Shandong University, Qingdao 266237, China; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Xiao Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
| | - Yang Ou
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China
| | - Huijun Jiao
- Ministry of Education Key Laboratory of Plant Development and Environmental Adaption Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China
| | - Alberto P Macho
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China; Center for Agroforestry Mega Data Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuehui He
- Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China; State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China.
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23
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Perspectives for epigenetic editing in crops. Transgenic Res 2021; 30:381-400. [PMID: 33891288 DOI: 10.1007/s11248-021-00252-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/29/2021] [Indexed: 01/10/2023]
Abstract
Site-specific nucleases (SSNs) have drawn much attention in plant biotechnology due to their ability to drive precision mutagenesis, gene targeting or allele replacement. However, when devoid of its nuclease activity, the underlying DNA-binding activity of SSNs can be used to bring other protein functional domains close to specific genomic sites, thus expanding further the range of applications of the technology. In particular, the addition of functional domains encoding epigenetic effectors and chromatin modifiers to the CRISPR/Cas ribonucleoprotein complex opens the possibility to introduce targeted epigenomic modifications in plants in an easily programmable manner. Here we examine some of the most important agronomic traits known to be controlled epigenetically and review the best studied epigenetic catalytic effectors in plants, such as DNA methylases/demethylases or histone acetylases/deacetylases and their associated marks. We also review the most efficient strategies developed to date to functionalize Cas proteins with both catalytic and non-catalytic epigenetic effectors, and the ability of these domains to influence the expression of endogenous genes in a regulatable manner. Based on these new technical developments, we discuss the possibilities offered by epigenetic editing tools in plant biotechnology and their implications in crop breeding.
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24
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Zhang C, Cheng Q, Wang H, Gao H, Fang X, Chen X, Zhao M, Wei W, Song B, Liu S, Wu J, Zhang S, Xu P. GmBTB/POZ promotes the ubiquitination and degradation of LHP1 to regulate the response of soybean to Phytophthora sojae. Commun Biol 2021; 4:372. [PMID: 33742112 PMCID: PMC7979691 DOI: 10.1038/s42003-021-01907-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/24/2021] [Indexed: 01/07/2023] Open
Abstract
Phytophthora sojae is a pathogen that causes stem and root rot in soybean (Glycine max [L.] Merr.). We previously demonstrated that GmBTB/POZ, a BTB/POZ domain-containing nuclear protein, enhances resistance to P. sojae in soybean, via a process that depends on salicylic acid (SA). Here, we demonstrate that GmBTB/POZ associates directly with soybean LIKE HETEROCHROMATIN PROTEIN1 (GmLHP1) in vitro and in vivo and promotes its ubiquitination and degradation. Both overexpression and RNA interference analysis of transgenic lines demonstrate that GmLHP1 negatively regulates the response of soybean to P. sojae by reducing SA levels and repressing GmPR1 expression. The WRKY transcription factor gene, GmWRKY40, a SA-induced gene in the SA signaling pathway, is targeted by GmLHP1, which represses its expression via at least two mechanisms (directly binding to its promoter and impairing SA accumulation). Furthermore, the nuclear localization of GmLHP1 is required for the GmLHP1-mediated negative regulation of immunity, SA levels and the suppression of GmWRKY40 expression. Finally, GmBTB/POZ releases GmLHP1-regulated GmWRKY40 suppression and increases resistance to P. sojae in GmLHP1-OE hairy roots. These findings uncover a regulatory mechanism by which GmBTB/POZ-GmLHP1 modulates resistance to P. sojae in soybean, likely by regulating the expression of downstream target gene GmWRKY40.
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Affiliation(s)
- Chuanzhong Zhang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qun Cheng
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Huiyu Wang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Hong Gao
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Xin Fang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Xi Chen
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Ming Zhao
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Wanling Wei
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Bo Song
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Shanshan Liu
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China
| | - Junjiang Wu
- Soybean Research Institute of Heilongjiang Academy of Agricultural Sciences, Key Laboratory of Soybean Cultivation of Ministry of Agriculture, Harbin, China
| | - Shuzhen Zhang
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China.
| | - Pengfei Xu
- Soybean Research Institute, Northeast Agricultural University, Key Laboratory of Soybean Biology of Chinese Education Ministry, Harbin, China.
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25
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Ma X, Zhang L, Pei Z, Zhang L, Liu Z, Liu D, Hao X, Jin Z, Pei Y. Hydrogen sulfide promotes flowering in heading Chinese cabbage by S-sulfhydration of BraFLCs. HORTICULTURE RESEARCH 2021; 8:19. [PMID: 33518701 PMCID: PMC7848000 DOI: 10.1038/s41438-020-00453-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/03/2020] [Accepted: 11/20/2020] [Indexed: 05/07/2023]
Abstract
Heading Chinese cabbage (Brassica rapa L. syn. B. campestris L. ssp. chinensis Makino var. pekinensis (Rupr.) J. Cao et Sh. Cao) is a cruciferous Brassica vegetable that has a triplicate genome, owing to an ancient genome duplication event. It is unclear whether the duplicated homologs have conserved or diversified functions. Hydrogen sulfide (H2S) is a plant gasotransmitter that plays important physiological roles in growth, development, and responses to environmental stresses. The modification of cysteines through S-sulfhydration is an important mechanism of H2S, which regulates protein functions. H2S promotes flowering in Arabidopsis and heading Chinese cabbage. Here we investigated the molecular mechanisms of H2S used to promote flowering in the latter. Four, five, and four BraFLC, BraSOC I, and BraFT homologs were identified in heading Chinese cabbage. Different BraFLC proteins were bound to different CArG boxes in the promoter regions of the BraSOC I and BraFT homologs, producing different binding patterns. Thus, there may be functionally diverse BraFLC homologs in heading Chinese cabbage. Exogenous H2S at 100 μmol L-1 significantly promoted flowering by compensating for insufficient vernalization. BraFLC 1 and BraFLC 3 underwent S-sulfhydration by H2S, after which their abilities to bind most BraSOC I or BraFT promoter probes weakened or even disappeared. These changes in binding ability were consistent with the expression pattern of the BraFT and BraSOC I homologs in seedlings treated with H2S. These results indicated that H2S signaling regulates flowering time. In summary, H2S signaling promoted plant flowering by weakening or eliminating the binding abilities of BraFLCs to downstream promoters through S-sulfhydration.
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Affiliation(s)
- Xiaoli Ma
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
- Department of Biological Science and Technology, Jinzhong University, Jinzhong, Shanxi Province, 030619, China
| | - Liping Zhang
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
| | - Zhuoya Pei
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
| | - Linlin Zhang
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
| | - Zhiqiang Liu
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
| | - Danmei Liu
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
| | - Xuefeng Hao
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China
- Department of Biology, Taiyuan Normal University, Jinzhong, Shanxi Province, 030619, China
| | - Zhuping Jin
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China.
| | - Yanxi Pei
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, Taiyuan, Shanxi Province, 030006, China.
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26
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Zhang YZ, Yuan J, Zhang L, Chen C, Wang Y, Zhang G, Peng L, Xie SS, Jiang J, Zhu JK, Du J, Duan CG. Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis. Nat Commun 2020; 11:6212. [PMID: 33277495 PMCID: PMC7718874 DOI: 10.1038/s41467-020-20089-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/12/2020] [Indexed: 01/07/2023] Open
Abstract
Histone 3 Lys 27 trimethylation (H3K27me3)-mediated epigenetic silencing plays a critical role in multiple biological processes. However, the H3K27me3 recognition and transcriptional repression mechanisms are only partially understood. Here, we report a mechanism for H3K27me3 recognition and transcriptional repression. Our structural and biochemical data showed that the BAH domain protein AIPP3 and the PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respectively, in Arabidopsis. The BAH-PHD bivalent histone reader complex silences a substantial subset of H3K27me3-enriched loci, including a number of development and stress response-related genes such as the RNA silencing effector gene ARGONAUTE 5 (AGO5). We found that the BAH-PHD module associates with CPL2, a plant-specific Pol II carboxyl terminal domain (CTD) phosphatase, to form the BAH-PHD-CPL2 complex (BPC) for transcriptional repression. The BPC complex represses transcription through CPL2-mediated CTD dephosphorylation, thereby causing inhibition of Pol II release from the transcriptional start site. Our work reveals a mechanism coupling H3K27me3 recognition with transcriptional repression through the alteration of Pol II phosphorylation states, thereby contributing to our understanding of the mechanism of H3K27me3-dependent silencing.
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Affiliation(s)
- Yi-Zhe Zhang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jianlong Yuan
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Lingrui Zhang
- grid.169077.e0000 0004 1937 2197Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Chunxiang Chen
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Yuhua Wang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Guiping Zhang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Li Peng
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Si-Si Xie
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jing Jiang
- grid.256922.80000 0000 9139 560XState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Jian-Kang Zhu
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.169077.e0000 0004 1937 2197Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Jiamu Du
- grid.263817.9Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Cheng-Guo Duan
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.256922.80000 0000 9139 560XState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
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27
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Sharma N, Geuten K, Giri BS, Varma A. The molecular mechanism of vernalization in Arabidopsis and cereals: role of Flowering Locus C and its homologs. PHYSIOLOGIA PLANTARUM 2020; 170:373-383. [PMID: 32623749 DOI: 10.1111/ppl.13163] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/25/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Winter varieties of plants can flower only after exposure to prolonged cold. This phenomenon is known as vernalization and has been widely studied in the model plant Arabidopsis thaliana as well as in monocots. Through the repression of floral activator genes, vernalization prevents flowering in winter. In Arabidopsis, FLOWERING LOCUS C or FLC is the key repressor during vernalization, while in monocots vernalization is regulated through VRN1, VRN2 and VRN3 (or FLOWERING LOCUS T). Interestingly, VRN genes are not homologous to FLC but FLC homologs are found to have a significant role in vernalization response in cereals. The presence of FLC homologs in monocots opens new dimensions to understand, compare and retrace the evolution of vernalization pathways between monocots and dicots. In this review, we discuss the molecular mechanism of vernalization-induced flowering along with epigenetic regulations in Arabidopsis and temperate cereals. A better understanding of cold-induced flowering will be helpful in crop breeding strategies to modify the vernalization requirement of economically important temperate cereals.
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Affiliation(s)
- Neha Sharma
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Koen Geuten
- Department of Biology, KU Leuven, Leuven, B-3001, Belgium
| | - Balendu Shekhar Giri
- Department of Chemical Engineering and Technology, Indian Institute of Technology (IIT-BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
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28
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Luo X, Ou Y, Li R, He Y. Maternal transmission of the epigenetic 'memory of winter cold' in Arabidopsis. NATURE PLANTS 2020; 6:1211-1218. [PMID: 32958896 DOI: 10.1038/s41477-020-00774-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/24/2020] [Indexed: 05/11/2023]
Abstract
Some plants can 'remember' past environmental experience to become adapted to a given environment. For instance, after experiencing prolonged low-temperature exposure in winter (winter cold), vernalization-responsive plants remember past cold experience when temperature rises in spring, to acquire competence to flower at a later season favourable for seed production1,2. In Arabidopsis thaliana, prolonged cold induces silencing of the potent floral repressor FLOWERING LOCUS C (FLC) by Polycomb group (PcG) chromatin modifiers. This Polycomb-repressed chromatin state is epigenetically maintained and thus 'memorized' in subsequent growth and development upon return to warmth1,3. 'Memory of winter cold' has been viewed as being mitotically stable but meiotically unstable3-5, and thus not to be transmitted intergenerationally. In general, whether and how chromatin-mediated environmental memories are transmitted across generations are unknown in plants. Here, we show that the cold-induced Polycomb-repressed chromatin state at FLC or memory of winter cold is maintained in the egg cell, that is meiotically stable in the process of female gamete formation, and provide evidence that this Polycomb-mediated memory is not maintained in the sperm cell. Moreover, we show that this cold memory is inherited maternally but not paternally to the zygote and early embryos. Our study demonstrates and further provides mechanistic insights into intergenerational transmission of chromatin state-mediated environmental memories in plants.
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Affiliation(s)
- Xiao Luo
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, China
| | - Yang Ou
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Renjie Li
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, China
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yuehui He
- Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai, China.
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29
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Hepworth J, Antoniou-Kourounioti RL, Berggren K, Selga C, Tudor EH, Yates B, Cox D, Collier Harris BR, Irwin JA, Howard M, Säll T, Holm S, Dean C. Natural variation in autumn expression is the major adaptive determinant distinguishing Arabidopsis FLC haplotypes. eLife 2020; 9:57671. [PMID: 32902380 PMCID: PMC7518893 DOI: 10.7554/elife.57671] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/08/2020] [Indexed: 12/27/2022] Open
Abstract
In Arabidopsis thaliana, winter is registered during vernalization through the temperature-dependent repression and epigenetic silencing of floral repressor FLOWERING LOCUS C (FLC). Natural Arabidopsis accessions show considerable variation in vernalization. However, which aspect of the FLC repression mechanism is most important for adaptation to different environments is unclear. By analysing FLC dynamics in natural variants and mutants throughout winter in three field sites, we find that autumnal FLC expression, rather than epigenetic silencing, is the major variable conferred by the distinct Arabidopsis FLChaplotypes. This variation influences flowering responses of Arabidopsis accessions resulting in an interplay between promotion and delay of flowering in different climates to balance survival and, through a post-vernalization effect, reproductive output. These data reveal how expression variation through non-coding cis variation at FLC has enabled Arabidopsis accessions to adapt to different climatic conditions and year-on-year fluctuations.
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Affiliation(s)
- Jo Hepworth
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | | | - Kristina Berggren
- Department of Natural Sciences, Mid Sweden University, Sundsvall, Sweden
| | - Catja Selga
- Department of Biology, Lund University, Lund, Sweden
| | - Eleri H Tudor
- Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Bryony Yates
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Deborah Cox
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | | | - Judith A Irwin
- Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Martin Howard
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Torbjörn Säll
- Department of Biology, Lund University, Lund, Sweden
| | - Svante Holm
- Department of Natural Sciences, Mid Sweden University, Sundsvall, Sweden
| | - Caroline Dean
- Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
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Yan B, Lv Y, Zhao C, Wang X. Knowing When to Silence: Roles of Polycomb-Group Proteins in SAM Maintenance, Root Development, and Developmental Phase Transition. Int J Mol Sci 2020; 21:ijms21165871. [PMID: 32824274 PMCID: PMC7461556 DOI: 10.3390/ijms21165871] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 01/01/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) and PRC2 are the major complexes composed of polycomb-group (PcG) proteins in plants. PRC2 catalyzes trimethylation of lysine 27 on histone 3 to silence target genes. Like Heterochromatin Protein 1/Terminal Flower 2 (LHP1/TFL2) recognizes and binds to H3K27me3 generated by PRC2 activities and enrolls PRC1 complex to further silence the chromatin through depositing monoubiquitylation of lysine 119 on H2A. Mutations in PcG genes display diverse developmental defects during shoot apical meristem (SAM) maintenance and differentiation, seed development and germination, floral transition, and so on so forth. PcG proteins play essential roles in regulating plant development through repressing gene expression. In this review, we are focusing on recent discovery about the regulatory roles of PcG proteins in SAM maintenance, root development, embryo development to seedling phase transition, and vegetative to reproductive phase transition.
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31
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Xi Y, Park SR, Kim DH, Kim ED, Sung S. Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1490-1502. [PMID: 32412129 PMCID: PMC7434698 DOI: 10.1111/tpj.14817] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/24/2020] [Accepted: 05/05/2020] [Indexed: 05/05/2023]
Abstract
Vernalization accelerates flowering after prolonged winter cold. Transcriptional and epigenetic changes are known to be involved in the regulation of the vernalization response. Despite intensive applications of next-generation sequencing in diverse aspects of plant research, genome-wide transcriptome and epigenome profiling during the vernalization response has not been conducted. In this work, to our knowledge, we present the first comprehensive analyses of transcriptomic and epigenomic dynamics during the vernalization process in Arabidopsis thaliana. Six major clusters of genes exhibiting distinctive features were identified. Temporary changes in histone H3K4me3 levels were observed that likely coordinate photosynthesis and prevent oxidative damage during cold exposure. In addition, vernalization induced a stable accumulation of H3K27me3 over genes encoding many development-related transcription factors, which resulted in either inhibition of transcription or a bivalent status of the genes. Lastly, FLC-like and VIN3-like genes were identified that appear to be novel components of the vernalization pathway.
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Chen C, Kim D, Yun HR, Lee YM, Yogendra B, Bo Z, Kim HE, Min JH, Lee YS, Rim YG, Kim HU, Sung S, Heo JB. Nuclear import of LIKE HETEROCHROMATIN PROTEIN1 is redundantly mediated by importins α-1, α-2 and α-3. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1205-1214. [PMID: 32365248 PMCID: PMC7810169 DOI: 10.1111/tpj.14796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 04/09/2020] [Accepted: 04/24/2020] [Indexed: 05/19/2023]
Abstract
LIKE HETEROCHROMATIN PROTEIN1 (LHP1) encodes the only plant homologue of the metazoan HETEROCHROMATIN PROTEIN1 (HP1) protein family. The LHP1 protein is necessary for proper epigenetic regulation of a range of developmental processes in plants. LHP1 is a transcriptional repressor of flowering-related genes, such as FLOWERING LOCUS T (FT), FLOWERING LOCUS C (FLC), AGAMOUS (AG) and APETALA 3 (AP3). We found that LHP1 interacts with importin α-1 (IMPα-1), importin α-2 (IMPα-2) and importin α-3 (IMPα-3) both in vitro and in vivo. A genetic approach revealed that triple mutation of impα-1, impα-2 and impα-3 resulted in Arabidopsis plants with a rapid flowering phenotype similar to that of plants with mutations in lhp1 due to the upregulation of FT expression. Nuclear targeting of LHP1 was severely impaired in the impα triple mutant, resulting in the de-repression of LHP1 target genes AG, AP3 and SHATTERPROOF 1 as well as FT. Therefore, the importin proteins IMPα-1, -2 and -3 are necessary for the nuclear import of LHP1.
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Affiliation(s)
- Chong Chen
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Daewon Kim
- Department of Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Hee Rang Yun
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Yun Mi Lee
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Bordiya Yogendra
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - Zhao Bo
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - Hae Eun Kim
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Jun Hong Min
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Yong-Suk Lee
- Department of Biotechnology, Dong-A University, Busan 604-714, Korea
| | - Yeong Gil Rim
- Systems & Synthetic Agrobiotech Center, Gyeongsang National University, Jinju 660-701 Korea
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Sejong University, Seoul, 05006 Korea
| | - Sibum Sung
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
- International Scholar, Kyung-Hee University, Suwon, Korea
- Corresponding author: Tel: +82 51 200 7520; Fax: +82 51 200 7505. ;
| | - Jae Bok Heo
- Department of Molecular Genetic Biotechnology, Dong-A University, Busan 604-714, Korea
- Corresponding author: Tel: +82 51 200 7520; Fax: +82 51 200 7505. ;
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Liang Q, Deng H, Li Y, Liu Z, Shu P, Fu R, Zhang Y, Pirrello J, Zhang Y, Grierson D, Bouzayen M, Liu Y, Liu M. Like Heterochromatin Protein 1b represses fruit ripening via regulating the H3K27me3 levels in ripening-related genes in tomato. THE NEW PHYTOLOGIST 2020; 227:485-497. [PMID: 32181875 DOI: 10.1111/nph.16550] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/07/2020] [Indexed: 06/10/2023]
Abstract
Polycomb group (PcG) proteins play vital roles in plant development via epigenetically repressing the transcription of target genes. However, to date, their function in fruit ripening is largely unknown. Combining reverse genetic approaches, physiological methods, yeast two-hybrid, co-immunoprecipitation, and chromatin immunoprecipitation assays, we show that Like Heterochromatin Protein 1b (SlLHP1b), a tomato Polycomb Repressive Complex 1 (PRC1)-like protein with a ripening-related expression pattern, represses fruit ripening via colocalization with epigenetic mark H3K27me3. RNA interference (RNAi)-mediated downregulation of SlLHP1b advanced ripening initiation, climacteric ethylene production, and fruit softening, whereas SlLHP1b overexpression delayed these events. Ripening-related genes were significantly upregulated in SlLHP1b RNAi fruits and downregulated in overexpressing fruits compared with wild-type. Furthermore, SlLHP1b protein interacts with ripening regulator MSI1, a subunit of the PRC2 complex. Moreover, SlLHP1b also binds the epigenetic histone mark H3K27me3 in vivo and chromatin immunoprecipitation-quantitative PCR results showed binding occurs preferentially to regions of ripening-associated chromatin marked by histone H3K27me3. Furthermore, the H3K27me3 levels in chromatin of ripening-related genes is negatively correlated with accumulation of their transcripts in SlLHP1b down or upregulated fruits during ripening. Our findings reveal a novel regulatory function of SlLHP1b in fruit and provide new insights into the PcG-mediated epigenetic regulation of climacteric fruit ripening.
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Affiliation(s)
- Qi Liang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Heng Deng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yuxiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Ziyu Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Peng Shu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Rao Fu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Yaoxin Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Julien Pirrello
- GBF Laboratory, Université de Toulouse, INRA, Castanet-Tolosan, 31320, France
| | - Yang Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Don Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Mondher Bouzayen
- GBF Laboratory, Université de Toulouse, INRA, Castanet-Tolosan, 31320, France
| | - Yongsheng Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Mingchun Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
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Ding Y, Shi Y, Yang S. Molecular Regulation of Plant Responses to Environmental Temperatures. MOLECULAR PLANT 2020; 13:544-564. [PMID: 32068158 DOI: 10.1016/j.molp.2020.02.004] [Citation(s) in RCA: 255] [Impact Index Per Article: 63.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 05/19/2023]
Abstract
Temperature is a key factor governing the growth and development, distribution, and seasonal behavior of plants. The entire plant life cycle is affected by environmental temperatures. Plants grow rapidly and exhibit specific changes in morphology under mild average temperature conditions, a response termed thermomorphogenesis. When exposed to chilling or moist chilling low temperatures, flowering or seed germination is accelerated in some plant species; these processes are known as vernalization and cold stratification, respectively. Interestingly, once many temperate plants are exposed to chilling temperatures for some time, they can acquire the ability to resist freezing stress, a process termed cold acclimation. In the face of global climate change, heat stress has emerged as a frequent challenge, which adversely affects plant growth and development. In this review, we summarize and discuss recent progress in dissecting the molecular mechanisms regulating plant thermomorphogenesis, vernalization, and responses to extreme temperatures. We also discuss the remaining issues that are crucial for understanding the interactions between plants and temperature.
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Affiliation(s)
- Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Qüesta JI, Antoniou-Kourounioti RL, Rosa S, Li P, Duncan S, Whittaker C, Howard M, Dean C. Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC. Genes Dev 2020; 34:446-461. [PMID: 32001513 PMCID: PMC7050481 DOI: 10.1101/gad.333245.119] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/06/2020] [Indexed: 12/21/2022]
Abstract
In Arabidopsis thaliana, the cold-induced epigenetic regulation of FLOWERING LOCUS C (FLC) involves distinct phases of Polycomb repressive complex 2 (PRC2) silencing. During cold, a PHD-PRC2 complex metastably and digitally nucleates H3K27me3 within FLC On return to warm, PHD-PRC2 spreads across the locus delivering H3K27me3 to maintain long-term silencing. Here, we studied natural variation in this process in Arabidopsis accessions, exploring Lov-1, which shows FLC reactivation on return to warm, a feature characteristic of FLC in perennial Brassicaceae This analysis identifies an additional phase in this Polycomb silencing mechanism downstream from H3K27me3 spreading. In this long-term silencing (perpetuated) phase, the PHD proteins are lost from the nucleation region and silencing is likely maintained by the read-write feedbacks associated with H3K27me3. A combination of noncoding SNPs in the nucleation region mediates instability in this long-term silencing phase with the result that Lov-1 FLC frequently digitally reactivates in individual cells, with a probability that diminishes with increasing cold duration. We propose that this decrease in reactivation probability is due to reduced DNA replication after flowering. Overall, this work defines an additional phase in the Polycomb mechanism instrumental in natural variation of silencing, and provides avenues to dissect broader evolutionary changes at FLC.
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Affiliation(s)
- Julia I Qüesta
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | | | - Stefanie Rosa
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Peijin Li
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Susan Duncan
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Charles Whittaker
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Martin Howard
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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Larqué-García H, Torres-Tapia LW, Vera-Ku M, Gamboa-León R, Novelo-Castilla S, Coral-Martínez TI, Peraza-Sánchez SR. Quantitative seasonal variation of the falcarinol-type polyacetylene (3S)-16,17-didehydrofalcarinol and its spatial tissue distribution in Tridax procumbens. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:183-190. [PMID: 31343078 DOI: 10.1002/pca.2878] [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: 03/27/2019] [Accepted: 06/25/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION (3S)-16,17-Didehydrofalcarinol (1) has been isolated from Tridax procumbens and has proved to have notorious bioactivity against Leishmania mexicana. In this study, hexane fractions obtained from the methanol extract of each plant part (roots, stems, leaves, flowers, and fruits) of T. procumbens collected monthly during a year were analysed in order to determine the quantity of 1 associated with biotic variables. OBJECTIVE The aim of this study was to find the season of the year in which the bioactive metabolite 1 is at the highest concentration and to correlate it with temperature, length of day light, and rainfall. METHODS Hexane fractions were obtained by liquid-liquid extraction and an accurate quantitation of 1 was performed using gas chromatography with a flame ionisation detector (GC-FID) employing pelargonic acid vanillyl amide (2) as internal standard. Partial validation was based on linearity and precision. RESULTS Our results indicated that the total content of 1 has significant variation (P ≤ 0.05) during the different collecting months. The total content of the metabolite reached its highest level in the roots of the plant during June in the rainfall season (0.0358 ± 0.001 mg/g), and its lowest values in February and March during the drought season (0.0015 ± 0.000 and 0.0008 ± 0.000 mg/g, respectively). CONCLUSION Our study provided evidence that the content of 1 in roots is strongly influenced by the variables of the harvesting season, also indicating that the biosynthesis of the active metabolite is enhanced during the warm and rainy months.
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Affiliation(s)
- Horacio Larqué-García
- Centro de Investigación Científica de Yucatán (CICY), Unidad de Biotecnología, Calle 43 #130, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Luis W Torres-Tapia
- Centro de Investigación Científica de Yucatán (CICY), Unidad de Biotecnología, Calle 43 #130, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Marina Vera-Ku
- Centro de Investigación Científica de Yucatán (CICY), Unidad de Recursos Naturales, Calle 43 #130, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Rubí Gamboa-León
- Universidad Autónoma de San Luis Potosí (UASLP), Coordinación Huasteca Sur, Km. 5 Carretera Tamazunchale-San Martin, C.P. 79960, Tamazunchale, San Luis Potosí, Mexico
| | - Salett Novelo-Castilla
- Facultad de Química, Universidad Autónoma de Yucatán (UADY), Calle 43 #613, Col. Inalámbrica, C.P. 97069, Mérida, Yucatán, Mexico
| | - Tania I Coral-Martínez
- Facultad de Química, Universidad Autónoma de Yucatán (UADY), Calle 43 #613, Col. Inalámbrica, C.P. 97069, Mérida, Yucatán, Mexico
| | - Sergio R Peraza-Sánchez
- Centro de Investigación Científica de Yucatán (CICY), Unidad de Biotecnología, Calle 43 #130, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
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Liu ZW, Zhao N, Su YN, Chen SS, He XJ. Exogenously overexpressed intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis. Sci Rep 2020; 10:3094. [PMID: 32080227 PMCID: PMC7033118 DOI: 10.1038/s41598-020-59697-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/17/2020] [Indexed: 11/09/2022] Open
Abstract
Involvement of long non-coding RNAs (lncRNAs) in the regulation of gene expression in cis has been well studied in eukaryotes but relatively little is known whether and how lncRNAs affect gene expression in tans. In Arabidopsis thaliana, COLDAIR, a previously reported lncRNA, is produced from the first intron of FLOWERING LOCUS C (FLC), which encodes a repressor of flowering time. Our results indicated that the exogenously overexpressed COLDAIR enhances the expression of FLC in trans, resulting in a late-flowering phenotype. In 35S-COLDAIR lines, the enhanced expression of FLC is correlated with the down-regulation of the repressive histone mark H3K27me3 and with the up-regulation of the active histone mark H3K4me3 at the FLC chromatin. Furthermore, we demonstrated that overexpression of intronic lncRNAs from several other H3K27me3-enriched MADS-box genes also activates the expression of their host genes. This study suggests that the involvement of overexpressed intronic lncRNAs in gene activation may be conserved in H3K27me3-enriched genes in eukaryotes.
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Affiliation(s)
- Zhang-Wei Liu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Nan Zhao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Shan-Shan Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 10084, Beijing, China.
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He Y, Chen T, Zeng X. Genetic and Epigenetic Understanding of the Seasonal Timing of Flowering. PLANT COMMUNICATIONS 2020; 1:100008. [PMID: 33404547 PMCID: PMC7747966 DOI: 10.1016/j.xplc.2019.100008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The developmental transition to flowering in many plants is timed by changing seasons, which enables plants to flower at a season that is favorable for seed production. Many plants grown at high latitudes perceive the seasonal cues of changing day length and/or winter cold (prolonged cold exposure), to regulate the expression of flowering-regulatory genes through the photoperiod pathway and/or vernalization pathway, and thus align flowering with a particular season. Recent studies in the model flowering plant Arabidopsis thaliana have revealed that diverse transcription factors engage various chromatin modifiers to regulate several key flowering-regulatory genes including FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT) in response to seasonal signals. Here, we summarize the current understanding of molecular and chromatin-regulatory or epigenetic mechanisms underlying the vernalization response and photoperiodic control of flowering in Arabidopsis. Moreover, the conservation and divergence of regulatory mechanisms for seasonal flowering in crops and other plants are briefly discussed.
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Luo X, He Y. Experiencing winter for spring flowering: A molecular epigenetic perspective on vernalization. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:104-117. [PMID: 31829495 DOI: 10.1111/jipb.12896] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/10/2019] [Indexed: 05/17/2023]
Abstract
Many over-wintering plants, through vernalization, overcome a block to flowering and thus acquire competence to flower in the following spring after experiencing prolonged cold exposure or winter cold. The vernalization pathways in different angiosperm lineages appear to have convergently evolved to adapt to temperate climates. Molecular and epigenetic mechanisms for vernalization regulation have been well studied in the crucifer model plant Arabidopsis thaliana. Here, we review recent progresses on the vernalization pathway in Arabidopsis. In addition, we summarize current molecular and genetic understandings of vernalization regulation in temperate grasses including wheat and Brachypodium, two monocots from Pooideae, followed by a brief discussion on divergence of the vernalization pathways between Brassicaceae and Pooideae.
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Affiliation(s)
- Xiao Luo
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yuehui He
- National Key Laboratory of Plant Molecular Genetics & Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, The Chinese Academy of Sciences, Shanghai, 201602, China
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Zhao T, Zhan Z, Jiang D. Histone modifications and their regulatory roles in plant development and environmental memory. J Genet Genomics 2019; 46:467-476. [PMID: 31813758 DOI: 10.1016/j.jgg.2019.09.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/29/2019] [Indexed: 11/24/2022]
Abstract
Plants grow in dynamic environments where they receive diverse environmental signals. Swift and precise control of gene expression is essential for plants to align their development and metabolism with fluctuating surroundings. Modifications on histones serve as "histone code" to specify chromatin and gene activities. Different modifications execute distinct functions on the chromatin, promoting either active transcription or gene silencing. Histone writers, erasers, and readers mediate the regulation of histone modifications by catalyzing, removing, and recognizing modifications, respectively. Growing evidence indicates the important function of histone modifications in plant development and environmental responses. Histone modifications also serve as environmental memory for plants to adapt to environmental changes. Here we review recent progress on the regulation of histone modifications in plants, the impact of histone modifications on environment-controlled developmental transitions including germination and flowering, and the role of histone modifications in environmental memory.
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Affiliation(s)
- Ting Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenping Zhan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100101, China.
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Ito T, Nishio H, Tarutani Y, Emura N, Honjo MN, Toyoda A, Fujiyama A, Kakutani T, Kudoh H. Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment. Genes (Basel) 2019; 10:genes10070544. [PMID: 31319612 PMCID: PMC6679105 DOI: 10.3390/genes10070544] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/14/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022] Open
Abstract
DNA methylation has been considered a stable epigenetic mark but may respond to fluctuating environments. However, it is unclear how they behave in natural environments. Here, we analyzed seasonal patterns of genome-wide DNA methylation in a single clone from a natural population of the perennial Arabidopsis halleri. The genome-wide pattern of DNA methylation was primarily stable, and most of the repetitive regions were methylated across the year. Although the proportion was small, we detected seasonally methylated cytosines (SeMCs) in the genome. SeMCs in the CHH context were detected predominantly at repetitive sequences in intergenic regions. In contrast, gene-body CG methylation (gbM) itself was generally stable across seasons, but the levels of gbM were positively associated with seasonal stability of RNA expression of the genes. These results suggest the existence of two distinct aspects of DNA methylation in natural environments: sources of epigenetic variation and epigenetic marks for stable gene expression.
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Affiliation(s)
- Tasuku Ito
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Haruki Nishio
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Yoshiaki Tarutani
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Naoko Emura
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
- Department of Environmental Sciences and Technology, Faculty of Agriculture, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Tetsuji Kakutani
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan.
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Storing memories: the distinct phases of Polycomb-mediated silencing of Arabidopsis FLC. Biochem Soc Trans 2019; 47:1187-1196. [DOI: 10.1042/bst20190255] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/06/2019] [Accepted: 06/14/2019] [Indexed: 12/19/2022]
Abstract
Abstract
Polycomb-mediated epigenetic silencing is central to correct growth and development in higher eukaryotes. The evolutionarily conserved Polycomb repressive complex 2 (PRC2) transcriptionally silences target genes through a mechanism requiring the histone modification H3K27me3. However, we still do not fully understand what defines Polycomb targets, how their expression state is switched from epigenetically ON to OFF and how silencing is subsequently maintained through many cell divisions. An excellent system in which to dissect the sequence of events underlying an epigenetic switch is the Arabidopsis FLC locus. Exposure to cold temperatures progressively induces a PRC2-dependent switch in an increasing proportion of cells, through a mechanism that is driven by the local chromatin environment. Temporally distinct phases of this silencing mechanism have been identified. First, the locus is transcriptionally silenced in a process involving cold-induced antisense transcripts; second, nucleation at the first exon/intron boundary of a Polycomb complex containing cold-induced accessory proteins induces a metastable epigenetically silenced state; third, a Polycomb complex with a distinct composition spreads across the locus in a process requiring DNA replication to deliver long-term epigenetic silencing. Detailed understanding from this system is likely to provide mechanistic insights important for epigenetic silencing in eukaryotes generally.
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43
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Friedman J. Variation in gene regulation underlying annual and perennial flowering in Arabideae species. Mol Ecol 2019. [PMID: 28632342 DOI: 10.1111/mec.14171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The diversity of life history strategies within the angiosperms illustrates the evolutionary flexibility of reproductive characteristics. The number of times an individual reproduces is a key life history trait, and transitions from iteroparous perennials to semelparous annuals have occurred frequently in the flowering plants. Despite the frequency of this evolutionary transition, and the importance of annuality versus perenniality to both agriculture and ecology, understanding the molecular and genetic mechanisms involved in perennial flowering is in their infancy. In this issue of Molecular Ecology, Kiefer et al. () make significant progress towards understanding divergence in seasonal flowering between annual and perennial species in the Arabideae tribe of Brassicaceae. By combining a comparative approach with gene expression and sequence comparisons, they show that transcriptional differences in FLC orthologs, a floral inhibitor in Arabidopsis thaliana, have occurred repeatedly and underlie differences in flowering between annuals and perennials.
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Abuyusuf M, Nath UK, Kim HT, Islam MR, Park JI, Nou IS. Molecular markers based on sequence variation in BoFLC1.C9 for characterizing early- and late-flowering cabbage genotypes. BMC Genet 2019; 20:42. [PMID: 31029104 PMCID: PMC6487051 DOI: 10.1186/s12863-019-0740-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cabbage (Brassica oleracea var. capitata) is popular worldwide for consumption as a leafy vegetable. Premature flowering is triggered by low temperature, and deteriorates quality of cabbage as vegetable. In general, growers prefer late-flowering varieties to assure good quality compact head. Here, we report BoFLC1.C9 as a gene with clear sequence variation between cabbage lines with different flowering times, and proposed as molecular marker to characterize early- and late-flowering cabbage lines. RESULTS We identified sequence variation of 67 bp insertions in intron 2, which were contributed in flowering time variation between two inbred lines through rapid down-regulation of the BoFLC1.C9 gene in early-flowering line compared to late-flowering one upon vernalization. One set of primer 'F7R7' proposed as marker, of which was explained with 83 and 80% of flowering time variation in 141 F2 individuals and 20 commercial lines, respectively. CONCLUSIONS This F7R7 marker could be used as genetic tools to characterize flowering time variation and to select as well to develop early- and late-flowering cabbage cultivars.
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Affiliation(s)
- Md Abuyusuf
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,Department of Agronomy, Patuakhali Science and Technology University, Patuakhali, 8602, Bangladesh
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Hoy-Taek Kim
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.,University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Md Rafiqul Islam
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea.
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Shibuta MK, Matsunaga S. Seasonal and Diurnal Regulation of Flowering <i>via</i> an Epigenetic Mechanism in <i>Arabidopsis thaliana</i>. CYTOLOGIA 2019. [DOI: 10.1508/cytologia.84.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Mio K. Shibuta
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
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Xu S, Chong K. Remembering winter through vernalisation. NATURE PLANTS 2018; 4:997-1009. [PMID: 30478363 DOI: 10.1038/s41477-018-0301-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 10/12/2018] [Indexed: 05/10/2023]
Abstract
Vernalisation is the programmed physiological process in which prolonged cold-exposure provides competency to flower in plants; widely found in winter and biennial species, such as Arabidopsis, fruit trees, vegetables and wheat. This phenomenon is regulated by diverse genetic networks, and memory of vernalisation in a life cycle mainly depends on epigenetic mechanisms. However, less is known about how to count winter-dosage for flowering in plants. Here, we compare the vernalisation genetic framework between the dicots Arabidopsis, temperate grasses, wheat, barley and Brachypodium. We discuss vernalisation mechanisms involving crosstalk between phosphorylation and O-GlcNAcylation modification of key proteins, and epigenetic modifications of the key gene VRN1 in wheat. We also highlight the potential evolutionary origins of vernalisation in various species. Current progress toward understanding the regulation of vernalisation requirements provides insight that will inform the design of molecular breeding strategies for winter crops.
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Affiliation(s)
- Shujuan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Dorn KM, Johnson EB, Daniels EC, Wyse DL, Marks MD. Spring flowering habit in field pennycress ( Thlaspi arvense) has arisen multiple independent times. PLANT DIRECT 2018; 2:e00097. [PMID: 31245698 PMCID: PMC6508777 DOI: 10.1002/pld3.97] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/18/2018] [Accepted: 10/25/2018] [Indexed: 05/11/2023]
Abstract
Field pennycress (Thlaspi arvense L.) is currently being developed as a new cold-tolerant oilseed crop. In natural populations, pennycress, like many Brassicaceae relatives, can exhibit either a winter or spring annual phenotype. Pennycress is a diploid relative of Arabidopsis thaliana, a model species that has been used to study many adaptive phenotypes, including flowering time and developmental timing. In Arabidopsis and other Brassicaceae species, mutations in negative regulators of flowering, including FLOWERING LOCUS C and FRIGIDA can cause the transition to a spring annual habit. The genetics underlying the difference between spring and winter annual pennycress lines are currently unknown. Here, we report the identification of four natural alleles of FLC in pennycress that confer a spring annual growth habit identified through whole genome sequencing, cosegregation analyses, and comparative genomics. The global distribution of these spring annual alleles of FLC suggests that the spring annual growth habit has arisen on several independent occasions. The two spring annual FLC alleles present in European accessions were only identified in North American accessions collected in southern Montana, which indicates accessions harboring these two alleles were introduced to North America, likely after pennycress became a widespread species on the continent. These findings provide new information on the natural history of the introduction and spread of spring annual pennycress accessions from Europe into North America. At the molecular level, these findings are important for the ongoing development of pennycress as a winter annual crop. An enhanced understanding of the regulation of flowering in this species should allow for the fine-tuning of flowering in commercial varieties.
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Affiliation(s)
- Kevin M. Dorn
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota
| | - Evan B. Johnson
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota
| | - Erin C. Daniels
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota
| | - Donald L. Wyse
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMinnesota
| | - Michael D. Marks
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota
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Epigenetic Environmental Memories in Plants: Establishment, Maintenance, and Reprogramming. Trends Genet 2018; 34:856-866. [PMID: 30144941 DOI: 10.1016/j.tig.2018.07.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/15/2018] [Accepted: 07/19/2018] [Indexed: 12/21/2022]
Abstract
Plants are immobile and must respond to or endure fluctuating surroundings and diverse environmental challenges. Environmental inputs often induce chromatin modifications at various responsive genes and consequent changes in their expression. Environment-induced chromatin marks at certain loci are transmittable through cell divisions after relief from the original external signals, leading to acquired 'memorization' of environmental experiences in plants, namely epigenetic environmental memories, which enable plants to adapt to environmental changes or to perform better when events recur. Here, we review recent progress in epigenetic or chromatin-mediated environmental memories in plants, including defense priming, stress memories, and 'epigenetic memory of winter cold' or vernalization. Various advances in epigenetic mechanisms underlying plant-environment interactions highlight that plant environmental epigenetics is emerging as an important area in plant biology.
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Li Z, Fu X, Wang Y, Liu R, He Y. Polycomb-mediated gene silencing by the BAH–EMF1 complex in plants. Nat Genet 2018; 50:1254-1261. [DOI: 10.1038/s41588-018-0190-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/16/2018] [Indexed: 12/14/2022]
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