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Dong K, Wu F, Cheng S, Li S, Zhang F, Xing X, Jin X, Luo S, Feng M, Miao R, Chang Y, Zhang S, You X, Wang P, Zhang X, Lei C, Ren Y, Zhu S, Guo X, Wu C, Yang DL, Lin Q, Cheng Z, Wan J. OsPRMT6a-mediated arginine methylation of OsJAZ1 regulates jasmonate signaling and spikelet development in rice. MOLECULAR PLANT 2024; 17:900-919. [PMID: 38704640 DOI: 10.1016/j.molp.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/04/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Although both protein arginine methylation (PRMT) and jasmonate (JA) signaling are crucial for regulating plant development, the relationship between these processes in the control of spikelet development remains unclear. In this study, we used the CRISPR/Cas9 technology to generate two OsPRMT6a loss-of-function mutants that exhibit various abnormal spikelet structures. Interestingly, we found that OsPRMT6a can methylate arginine residues in JA signal repressors OsJAZ1 and OsJAZ7. We showed that arginine methylation of OsJAZ1 enhances the binding affinity of OsJAZ1 with the JA receptors OsCOI1a and OsCOI1b in the presence of JAs, thereby promoting the ubiquitination of OsJAZ1 by the SCFOsCOI1a/OsCOI1b complex and degradation via the 26S proteasome. This process ultimately releases OsMYC2, a core transcriptional regulator in the JA signaling pathway, to activate or repress JA-responsive genes, thereby maintaining normal plant (spikelet) development. However, in the osprmt6a-1 mutant, reduced arginine methylation of OsJAZ1 impaires the interaction between OsJAZ1 and OsCOI1a/OsCOI1b in the presence of JAs. As a result, OsJAZ1 proteins become more stable, repressing JA responses, thus causing the formation of abnormal spikelet structures. Moreover, we discovered that JA signaling reduces the OsPRMT6a mRNA level in an OsMYC2-dependent manner, thereby establishing a negative feedback loop to balance JA signaling. We further found that OsPRMT6a-mediated arginine methylation of OsJAZ1 likely serves as a switch to tune JA signaling to maintain normal spikelet development under harsh environmental conditions such as high temperatures. Collectively, our study establishes a direct molecular link between arginine methylation and JA signaling in rice.
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Affiliation(s)
- Kun Dong
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fuqing Wu
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Siqi Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Li
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Feng Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinxin Xing
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Jin
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sheng Luo
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Miao Feng
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rong Miao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanqi Chang
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuang Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoman You
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiran Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shanshan Zhu
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuanyin Wu
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong-Lei Yang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qibing Lin
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhijun Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Gene Resources and Breeding, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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Qiu C, Wang T, Wang H, Tao Z, Wang C, Ma J, Li S, Zhao Y, Liu J, Li P. SISTER OF FCA physically associates with SKB1 to regulate flowering time in Arabidopsis thaliana. BMC PLANT BIOLOGY 2024; 24:188. [PMID: 38486139 PMCID: PMC10941358 DOI: 10.1186/s12870-024-04887-y] [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: 10/31/2023] [Accepted: 03/07/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Proper flowering time is important for the growth and development of plants, and both too early and too late flowering impose strong negative influences on plant adaptation and seed yield. Thus, it is vitally important to study the mechanism underlying flowering time control in plants. In a previous study by the authors, genome-wide association analysis was used to screen the candidate gene SISTER OF FCA (SSF) that regulates FLOWERING LOCUS C (FLC), a central gene encoding a flowering suppressor in Arabidopsis thaliana. RESULTS SSF physically interacts with Protein arginine methyltransferase 5 (PRMT5, SKB1). Subcellular co-localization analysis showed that SSF and SKB1 interact in the nucleus. Genetically, SSF and SKB1 exist in the same regulatory pathway that controls FLC expression. Furthermore, RNA-sequencing analysis showed that both SSF and SKB1 regulate certain common pathways. CONCLUSIONS This study shows that PRMT5 interacts with SSF, thus controlling FLC expression and facilitating flowering time control.
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Affiliation(s)
- Chunhong Qiu
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Tengyue Wang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hui Wang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhen Tao
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chuanhong Wang
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Jing Ma
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shuai Li
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yibing Zhao
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Jifang Liu
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Peijin Li
- The National Key Engineering Lab of Crop Stress Resistance Breeding, Schoolof Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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Wei Y, Li A, Zhao Y, Li W, Dong Z, Zhang L, Zhu Y, Zhang H, Gao Y, Zhang Q. Time-Course Transcriptomic Analysis Reveals Molecular Insights into the Inflorescence and Flower Development of Cardiocrinum giganteum. PLANTS (BASEL, SWITZERLAND) 2024; 13:649. [PMID: 38475495 DOI: 10.3390/plants13050649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024]
Abstract
Cardiocrinum giganteum is an endemic species of east Asia which is famous for its showy inflorescence and medicinal bulbs. Its inflorescence is a determinate raceme and the flowers bloom synchronously. Morphological observation and time-course transcriptomic analysis were combined to study the process of inflorescence and flower development of C. giganteum. The results show that the autonomic pathway, GA pathway, and the vernalization pathway are involved in the flower formation pathway of C. giganteum. A varied ABCDE flowering model was deduced from the main development process. Moreover, it was found that the flowers in different parts of the raceme in C. giganteum gradually synchronized during development, which is highly important for both evolution and ecology. The results obtained in this work improve our understanding of the process and mechanism of inflorescence and flower development and could be useful for the flowering period regulation and breeding of C. giganteum.
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Affiliation(s)
- Yu Wei
- Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex Situ Conservation, Beijing Botanical Garden, Beijing 100093, China
| | - Aihua Li
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex Situ Conservation, Beijing Botanical Garden, Beijing 100093, China
| | - Yiran Zhao
- Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Wenqi Li
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex Situ Conservation, Beijing Botanical Garden, Beijing 100093, China
| | - Zhiyang Dong
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex Situ Conservation, Beijing Botanical Garden, Beijing 100093, China
| | - Lei Zhang
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex Situ Conservation, Beijing Botanical Garden, Beijing 100093, China
| | - Yuntao Zhu
- Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Hui Zhang
- Key Laboratory of National Forestry and Grassland Administration on Plant Ex Situ Conservation, Beijing Botanical Garden, Beijing 100093, China
| | - Yike Gao
- Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
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Mahmood T, He S, Abdullah M, Sajjad M, Jia Y, Ahmar S, Fu G, Chen B, Du X. Epigenetic insight into floral transition and seed development in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111926. [PMID: 37984609 DOI: 10.1016/j.plantsci.2023.111926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Seasonal changes are crucial in shifting the developmental stages from the vegetative phase to the reproductive phase in plants, enabling them to flower under optimal conditions. Plants grown at different latitudes sense and interpret these seasonal variations, such as changes in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These environmental factors influence the expression of various genes related to flowering. Plants have evolved to stimulate a rapid response to environmental conditions through genetic and epigenetic mechanisms. Multiple epigenetic regulation systems have emerged in plants to interpret environmental signals. During the transition to the flowering phase, changes in gene expression are facilitated by chromatin remodeling and small RNAs interference, particularly in annual and perennial plants. Key flowering regulators, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with various factors and undergo chromatin remodeling in response to seasonal cues. The Polycomb silencing complex (PRC) controls the expression of flowering-related genes in photoperiodic flowering regulation. Under vernalization-dependent flowering, FLC acts as a potent flowering suppressor by downregulating the gene expression of various flower-promoting genes. Eventually, PRCs are critically involved in the regulation of FLC and FT locus interacting with several key genes in photoperiod and vernalization. Subsequently, PRCs also regulate Epigenetical events during gametogenesis and seed development as a driving force. Furthermore, DNA methylation in the context of CHG, CG, and CHH methylation plays a critical role in embryogenesis. DNA glycosylase DME (DEMETER) is responsible for demethylation during seed development. Thus, the review briefly discusses flowering regulation through light signaling, day length variation, temperature variation and seed development in plants.
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Affiliation(s)
- Tahir Mahmood
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Muhammad Abdullah
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Guoyong Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang (CAAS), Anyang 455000, China.
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Shi M, Wang C, Wang P, Yun F, Liu Z, Ye F, Wei L, Liao W. Role of methylation in vernalization and photoperiod pathway: a potential flowering regulator? HORTICULTURE RESEARCH 2023; 10:uhad174. [PMID: 37841501 PMCID: PMC10569243 DOI: 10.1093/hr/uhad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/23/2023] [Indexed: 10/17/2023]
Abstract
Recognized as a pivotal developmental transition, flowering marks the continuation of a plant's life cycle. Vernalization and photoperiod are two major flowering pathways orchestrating numerous florigenic signals. Methylation, including histone, DNA and RNA methylation, is one of the recent foci in plant development. Considerable studies reveal that methylation seems to show an increasing potential regulatory role in plant flowering via altering relevant gene expression without altering the genetic basis. However, little has been reviewed about whether and how methylation acts on vernalization- and photoperiod-induced flowering before and after FLOWERING LOCUS C (FLC) reactivation, what role RNA methylation plays in vernalization- and photoperiod-induced flowering, how methylation participates simultaneously in both vernalization- and photoperiod-induced flowering, the heritability of methylation memory under the vernalization/photoperiod pathway, and whether and how methylation replaces vernalization/photoinduction to regulate flowering. Our review provides insight about the crosstalk among the genetic control of the flowering gene network, methylation (methyltransferases/demethylases) and external signals (cold, light, sRNA and phytohormones) in vernalization and photoperiod pathways. The existing evidence that RNA methylation may play a potential regulatory role in vernalization- and photoperiod-induced flowering has been gathered and represented for the first time. This review speculates about and discusses the possibility of substituting methylation for vernalization and photoinduction to promote flowering. Current evidence is utilized to discuss the possibility of future methylation reagents becoming flowering regulators at the molecular level.
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Affiliation(s)
- Meimei Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Peng Wang
- Vegetable and Flower Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fahong Yun
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhiya Liu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Fujin Ye
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Lijuan Wei
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
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Laanen P, Cuypers A, Saenen E, Horemans N. Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:246-259. [PMID: 36731286 DOI: 10.1016/j.plaphy.2023.01.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.
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Affiliation(s)
- Pol Laanen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Ann Cuypers
- Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
| | - Eline Saenen
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium.
| | - Nele Horemans
- Biosphere Impact Studies, SCK CEN, Boeretang 200, 2400, Mol, Belgium; Centre for Environmental Research, University of Hasselt, Martelarenlaan 42, 3500, Hasselt, Belgium.
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Liu Y, Wang J, Liu B, Xu ZY. Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2252-2274. [PMID: 36149776 DOI: 10.1111/jipb.13368] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Cao H, Liang Y, Zhang L, Liu Z, Liu D, Cao X, Deng X, Jin Z, Pei Y. AtPRMT5-mediated AtLCD methylation improves Cd2+ tolerance via increased H2S production in Arabidopsis. PLANT PHYSIOLOGY 2022; 190:2637-2650. [PMID: 35972421 PMCID: PMC9706440 DOI: 10.1093/plphys/kiac376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) PROTEIN ARGININE METHYLTRANSFERASE5 (PRMT5), a highly conserved arginine (Arg) methyltransferase protein, regulates multiple aspects of the growth, development, and environmental stress responses by methylating Arg in histones and some mRNA splicing-related proteins in plants. Hydrogen sulfide (H2S) is a recently characterized gasotransmitter that also regulates various important physiological processes. l-cysteine desulfhydrase (LCD) is a key enzyme of endogenous H2S production. However, our understanding of the upstream regulatory mechanisms of endogenous H2S production is limited in plant cells. Here, we confirmed that AtPRMT5 increases the enzymatic activity of AtLCD through methylation modifications during stress responses. Both atprmt5 and atlcd mutants were sensitive to cadmium (Cd2+), whereas the overexpression (OE) of AtPRMT5 or AtLCD enhanced the Cd2+ tolerance of plants. AtPRMT5 methylated AtLCD at Arg-83, leading to a significant increase in AtLCD enzymatic activity. The Cd2+ sensitivity of atprmt5-2 atlcd double mutants was consistent with that of atlcd plants. When AtPRMT5 was overexpressed in the atlcd mutant, the Cd2+ tolerance of plants was significantly lower than that of AtPRMT5-OE plants in the wild-type background. These results were confirmed in pharmacological experiments. Thus, AtPRMT5 methylation of AtLCD increases its enzymatic activity, thereby strengthening the endogenous H2S signal and ultimately improving plant tolerance to Cd2+ stress. These findings provide further insights into the substrates of AtPRMT5 and increase our understanding of the regulatory mechanism upstream of H2S signals.
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Affiliation(s)
- Haiyan Cao
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, 030006 Taiyuan, China
| | - Yali Liang
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, 030006 Taiyuan, China
| | - Liping Zhang
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, 030006 Taiyuan, China
| | - Zhiqiang Liu
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, 030006 Taiyuan, China
| | - Danmei Liu
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, 030006 Taiyuan, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Zhuping Jin
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, 030006 Taiyuan, China
| | - Yanxi Pei
- School of Life Science and Shanxi Key Laboratory for Research and Development of Regional Plants, Shanxi University, 030006 Taiyuan, China
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Cheng G, Zhang F, Shu X, Wang N, Wang T, Zhuang W, Wang Z. Identification of Differentially Expressed Genes Related to Floral Bud Differentiation and Flowering Time in Three Populations of Lycoris radiata. Int J Mol Sci 2022; 23:ijms232214036. [PMID: 36430515 PMCID: PMC9699370 DOI: 10.3390/ijms232214036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
The transition from vegetative to reproductive growth is important for controlling the flowering of Lycoris radiata. However, the genetic control of this complex developmental process remains unclear. In this study, 18 shoot apical meristem (SAM) samples were collected from early-, mid- and late-flowering populations during floral bud differentiation. The histological analysis of paraffin sections showed that the floral bud differentiation could be divided into six stages; the differentiation time of the early group was earlier than that of the middle and late groups, and the late group was the latest. In different populations, some important differential genes affecting the flowering time were identified by transcriptome profiles of floral bud differentiation samples. Weighted gene co-expression network analysis (WGCNA) was performed to enrich the gene co-expression modules of diverse flowering time populations (FT) and floral bud differentiation stages (ST). In the MEyellow module, five core hub genes were identified, including CO14, GI, SPL8, SPL9, and SPL15. The correlation network of hub genes showed that they interact with SPLs, AP2, hormone response factors (auxin, gibberellin, ethylene, and abscisic acid), and several transcription factors (MADS-box transcription factor, bHLH, MYB, and NAC3). It suggests the important role of these genes and the complex molecular mechanism of floral bud differentiation and flowering time in L. radiata. These results can preliminarily explain the molecular mechanism of floral bud differentiation and provide new candidate genes for the flowering regulation of Lycoris.
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Affiliation(s)
- Guanghao Cheng
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Xiaochun Shu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Ning Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Tao Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Weibing Zhuang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Zhong Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
- Correspondence:
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10
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Li Y, Wang C, Guo Q, Song C, Wang X, Guo L, Hou X. Characteristics of PoVIN3, a Key Gene of Vernalization Pathway, Affects Flowering Time. Int J Mol Sci 2022; 23:ijms232214003. [PMID: 36430482 PMCID: PMC9697302 DOI: 10.3390/ijms232214003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The tree peony (Paeonia section Moutan DC.) is the candidate flower in China, with abundant germplasm resources and high ornamental value. However, the short and concentrated flowering period severely restricted the improvement of the economic value of tree peonies. Based on the full-length transcriptome database of tree peonies, the PoVIN3 (GenBank ID: OP341879), involved in the flowering regulation of tree peonies were identified and cloned for the first time. The PoVIN3 was also characterized by bioinformatics methods, quantitative real-time PCR (qRT-PCR), and the establishment of a transgenic system. The expression levels of PoVIN3 in seven different petals developmental stages were the highest at the initial flowering stage of the variant cultivar of Paeonia ostii 'Fengdan,' the initial decay stage of the normal flowering Paeonia ostii 'Fengdan,' and the half opening stage of the late flowering Paeonia suffruticosa 'Lianhe.' Tissue-specific expression analysis showed that the relative expression levels of PoVIN3 were the highest in sepals of both normal flowering Paeonia ostii 'Fengdan' and the late flowering Paeonia suffruticosa 'Lianhe,' and the highest expression was in stamens of early flowering mutant Paeonia ostii 'Fengdan.' In addition, the flowering time of pCAMBIA2300-PoVIN3 transgenic plants was significantly earlier than that of the wild-type, indicating that PoVIN3 could promote plant flowering. The results provide a theoretical basis for exploring the role of PoVIN3 in the regulation of flowering in tree peonies.
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Affiliation(s)
- Yuying Li
- College of Agronomy/Tree Peony, Henan University of Science and Technology, Luoyang 471023, China
| | - Can Wang
- College of Agronomy/Tree Peony, Henan University of Science and Technology, Luoyang 471023, China
| | - Qi Guo
- College of Agronomy/Tree Peony, Henan University of Science and Technology, Luoyang 471023, China
| | - Chengwei Song
- College of Agronomy/Tree Peony, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiaohui Wang
- Luoyang Academy of Agriculture and Forestry Sciences, Luoyang 471023, China
| | - Lili Guo
- College of Agronomy/Tree Peony, Henan University of Science and Technology, Luoyang 471023, China
| | - Xiaogai Hou
- College of Agronomy/Tree Peony, Henan University of Science and Technology, Luoyang 471023, China
- Correspondence: ; Tel.: +86-136-5387-3065
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11
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Su J, Yao Z, Wu Y, Lee J, Jeong J. Minireview: Chromatin-based regulation of iron homeostasis in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:959840. [PMID: 36186078 PMCID: PMC9523571 DOI: 10.3389/fpls.2022.959840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/31/2022] [Indexed: 05/26/2023]
Abstract
Plants utilize delicate mechanisms to effectively respond to changes in the availability of nutrients such as iron. The responses to iron status involve controlling gene expression at multiple levels. The regulation of iron deficiency response by a network of transcriptional regulators has been extensively studied and recent research has shed light on post-translational control of iron homeostasis. Although not as considerably investigated, an increasing number of studies suggest that histone modification and DNA methylation play critical roles during iron deficiency and contribute to fine-tuning iron homeostasis in plants. This review will focus on the current understanding of chromatin-based regulation on iron homeostasis in plants highlighting recent studies in Arabidopsis and rice. Understanding iron homeostasis in plants is vital, as it is not only relevant to fundamental biological questions, but also to agriculture, biofortification, and human health. A comprehensive overview of the effect and mechanism of chromatin-based regulation in response to iron status will ultimately provide critical insights in elucidating the complexities of iron homeostasis and contribute to improving iron nutrition in plants.
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Affiliation(s)
- Justin Su
- Department of Biology, Amherst College, Amherst, MA, United States
| | - Zhujun Yao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
| | - Yixuan Wu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
| | - Jeeyon Jeong
- Department of Biology, Amherst College, Amherst, MA, United States
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12
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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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13
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Drozda A, Kurpisz B, Arasimowicz-Jelonek M, Kuźnicki D, Jagodzik P, Guan Y, Floryszak-Wieczorek J. Nitric Oxide Implication in Potato Immunity to Phytophthora infestans via Modifications of Histone H3/H4 Methylation Patterns on Defense Genes. Int J Mol Sci 2022; 23:ijms23074051. [PMID: 35409411 PMCID: PMC8999698 DOI: 10.3390/ijms23074051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 12/18/2022] Open
Abstract
Nitric oxide (NO) is an essential redox-signaling molecule operating in many physiological and pathophysiological processes. However, evidence on putative NO engagement in plant immunity by affecting defense gene expressions, including histone modifications, is poorly recognized. Exploring the effect of biphasic NO generation regulated by S-nitrosoglutathione reductase (GNSOR) activity after avr Phytophthora infestans inoculation, we showed that the phase of NO decline at 6 h post-inoculation (hpi) was correlated with the rise of defense gene expressions enriched in the TrxG-mediated H3K4me3 active mark in their promoter regions. Here, we report that arginine methyltransferase PRMT5 catalyzing histone H4R3 symmetric dimethylation (H4R3sme2) is necessary to ensure potato resistance to avr P. infestans. Both the pathogen and S-nitrosoglutathione (GSNO) altered the methylation status of H4R3sme2 by transient reduction in the repressive mark in the promoter of defense genes, R3a and HSR203J (a resistance marker), thereby elevating their transcription. In turn, the PRMT5-selective inhibitor repressed R3a expression and attenuated the hypersensitive response to the pathogen. In conclusion, we postulate that lowering the NO level (at 6 hpi) might be decisive for facilitating the pathogen-induced upregulation of stress genes via histone lysine methylation and PRMT5 controlling potato immunity to late blight.
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Affiliation(s)
- Andżelika Drozda
- Department of Plant Physiology, Faculty of Agronomy, Horticulture and Bioengineering, Poznan University of Life Sciences, 60-637 Poznan, Poland; (A.D.); (B.K.); (D.K.); (Y.G.)
| | - Barbara Kurpisz
- Department of Plant Physiology, Faculty of Agronomy, Horticulture and Bioengineering, Poznan University of Life Sciences, 60-637 Poznan, Poland; (A.D.); (B.K.); (D.K.); (Y.G.)
| | - Magdalena Arasimowicz-Jelonek
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland; (M.A.-J.); (P.J.)
| | - Daniel Kuźnicki
- Department of Plant Physiology, Faculty of Agronomy, Horticulture and Bioengineering, Poznan University of Life Sciences, 60-637 Poznan, Poland; (A.D.); (B.K.); (D.K.); (Y.G.)
| | - Przemysław Jagodzik
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland; (M.A.-J.); (P.J.)
| | - Yufeng Guan
- Department of Plant Physiology, Faculty of Agronomy, Horticulture and Bioengineering, Poznan University of Life Sciences, 60-637 Poznan, Poland; (A.D.); (B.K.); (D.K.); (Y.G.)
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland; (M.A.-J.); (P.J.)
| | - Jolanta Floryszak-Wieczorek
- Department of Plant Physiology, Faculty of Agronomy, Horticulture and Bioengineering, Poznan University of Life Sciences, 60-637 Poznan, Poland; (A.D.); (B.K.); (D.K.); (Y.G.)
- Correspondence: ; Tel.: +48-61-848-71-81
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14
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Zhang P, Li X, Wang Y, Guo W, Chachar S, Riaz A, Geng Y, Gu X, Yang L. PRMT6 physically associates with nuclear factor Y to regulate photoperiodic flowering in Arabidopsis. ABIOTECH 2021; 2:403-414. [PMID: 36304422 PMCID: PMC9590495 DOI: 10.1007/s42994-021-00065-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/12/2021] [Indexed: 05/14/2023]
Abstract
UNLABELLED The timing of floral transition is critical for reproductive success in flowering plants. In long-day (LD) plant Arabidopsis, the floral regulator gene FLOWERING LOCUS T (FT) is a major component of the mobile florigen. FT expression is rhythmically activated by CONSTANS (CO), and specifically accumulated at dusk of LDs. However, the underlying mechanism of adequate regulation of FT transcription in response to day-length cues to warrant flowering time still remains to be investigated. Here, we identify a homolog of human protein arginine methyltransferases 6 (HsPRMT6) in Arabidopsis, and confirm AtPRMT6 physically interacts with three positive regulators of flowering Nuclear Factors YC3 (NF-YC3), NF-YC9, and NF-YB3. Further investigations find that AtPRMT6 and its encoding protein accumulate at dusk of LDs. PRMT6-mediated H3R2me2a modification enhances the promotion of NF-YCs on FT transcription in response to inductive LD signals. Moreover, AtPRMT6 and its homologues proteins AtPRMT4a and AtPRMT4b coordinately inhibit the expression of FLOWERING LOCUS C, a suppressor of FT. Taken together, our study reveals the role of arginine methylation in photoperiodic pathway and how the PRMT6-mediating H3R2me2a system interacts with NF-CO module to dynamically control FT expression and facilitate flowering time. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s42994-021-00065-y.
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Affiliation(s)
- Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, 100081 China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Xiulan Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, 100081 China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, 100081 China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, 100081 China
| | - Sadaruddin Chachar
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, 100081 China
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, 100081 China
| | - Yuke Geng
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081 China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, 100081 China
| | - Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, 100081 China
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15
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Dikaya V, El Arbi N, Rojas-Murcia N, Nardeli SM, Goretti D, Schmid M. Insights into the role of alternative splicing in plant temperature response. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab234. [PMID: 34105719 DOI: 10.1093/jxb/erab234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 05/21/2023]
Abstract
Alternative splicing occurs in all eukaryotic organisms. Since the first description of multiexon genes and the splicing machinery, the field has expanded rapidly, especially in animals and yeast. However, our knowledge about splicing in plants is still quite fragmented. Though eukaryotes show some similarity in the composition and dynamics of the splicing machinery, observations of unique plant traits are only starting to emerge. For instance, plant alternative splicing is closely linked to their ability to perceive various environmental stimuli. Due to their sessile lifestyle, temperature is a central source of information allowing plants to adjust their development to match current growth conditions. Hence, seasonal temperature fluctuations and day-night cycles can strongly influence plant morphology across developmental stages. Here we discuss the available data about temperature-dependent alternative splicing in plants. Given its fragmented state it is not always possible to fit specific observations into a coherent picture, yet it is sufficient to estimate the complexity of this field and the need of further research. Better understanding of alternative splicing as a part of plant temperature response and adaptation may also prove to be a powerful tool for both, fundamental and applied sciences.
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Affiliation(s)
- Varvara Dikaya
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Nabila El Arbi
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Nelson Rojas-Murcia
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Sarah Muniz Nardeli
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Daniela Goretti
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Markus Schmid
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, People's Republic of China
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16
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Yan J, Kim YJ, Somers DE. Post-Translational Mechanisms of Plant Circadian Regulation. Genes (Basel) 2021; 12:325. [PMID: 33668215 PMCID: PMC7995963 DOI: 10.3390/genes12030325] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
The molecular components of the circadian system possess the interesting feature of acting together to create a self-sustaining oscillator, while at the same time acting individually, and in complexes, to confer phase-specific circadian control over a wide range of physiological and developmental outputs. This means that many circadian oscillator proteins are simultaneously also part of the circadian output pathway. Most studies have focused on transcriptional control of circadian rhythms, but work in plants and metazoans has shown the importance of post-transcriptional and post-translational processes within the circadian system. Here we highlight recent work describing post-translational mechanisms that impact both the function of the oscillator and the clock-controlled outputs.
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Affiliation(s)
| | | | - David E. Somers
- Department of Molecular Genetics, The Ohio State University; Columbus, OH 43210, USA; (J.Y.); (Y.J.K.)
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17
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Genome-wide identification and expression analysis of the MADS-box transcription factor family in Camellia sinensis. J Appl Genet 2021; 62:249-264. [PMID: 33598859 DOI: 10.1007/s13353-021-00621-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/06/2021] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
The MADS-box genes are an important class of transcription factors and play critical roles in flower development. However, the functions of these genes in the economically important drinking plant, Camellia sinensis, are still not reported. Here, an evolutionary analysis of tea MADS-box genes was performed at whole genome level. A total of 83 MADS-box genes were identified in tea, and their gene structures and expression patterns were further analyzed. The tea MADS-box genes were classified into Mα (26), Mβ (12), Mγ (9), MIKC* (7), and MIKCC (29) clade according to their phylogenetic relationship with Arabidopsis thaliana. Several cis-elements were identified in the promoter regions of the CsMADS genes that are important in regulating growth, development, light responses, and the response to several stresses. Most CsMADS genes display clear different expression patterns in different organs and different species of tea plant. The expression of CsMADS genes can be regulated by abiotic stresses and phytohormone treatment. Our results lay the foundation for future research on the function of CsMADS genes and beneficial for improving tea agricultural traits in the future.
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18
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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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19
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Yuan S, Li Z, Yuan N, Hu Q, Zhou M, Zhao J, Li D, Luo H. MiR396 is involved in plant response to vernalization and flower development in Agrostis stolonifera. HORTICULTURE RESEARCH 2020; 7:173. [PMID: 33328434 PMCID: PMC7603517 DOI: 10.1038/s41438-020-00394-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 08/23/2020] [Accepted: 08/30/2020] [Indexed: 05/05/2023]
Abstract
MicroRNA396 (miR396) has been demonstrated to regulate flower development by targeting growth-regulating factors (GRFs) in annual species. However, its role in perennial grasses and its potential involvement in flowering time control remain unexplored. Here we report that overexpression of miR396 in a perennial species, creeping bentgrass (Agrostis stolonifera L.), alters flower development. Most significantly, transgenic (TG) plants bypass the vernalization requirement for flowering. Gene expression analysis reveals that miR396 is induced by long-day (LD) photoperiod and vernalization. Further study identifies VRN1, VRN2, and VRN3 homologs whose expression patterns in wild-type (WT) plants are similar to those observed in wheat and barley during transition from short-day (SD) to LD, and SD to cold conditions. However, compared to WT controls, TG plants overexpressing miR396 exhibit significantly enhanced VRN1 and VRN3 expression, but repressed VRN2 expression under SD to LD conditions without vernalization, which might be associated with modified expression of methyltransferase genes. Collectively, our results unveil a potentially novel mechanism by which miR396 suppresses the vernalization requirement for flowering which might be related to the epigenetic regulation of VRN genes and provide important new insight into critical roles of a miRNA in regulating vernalization-mediated transition from vegetative to reproductive growth in monocots.
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Affiliation(s)
- Shuangrong Yuan
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Zhigang Li
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Ning Yuan
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Qian Hu
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Man Zhou
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Junming Zhao
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
- Department of Grassland Science, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China
| | - Dayong Li
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and forestry Science, 100097, Beijing, China
| | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA.
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20
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Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement. Funct Integr Genomics 2020; 20:739-761. [PMID: 33089419 DOI: 10.1007/s10142-020-00756-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/21/2023]
Abstract
Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits.
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21
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Wang L, Qiao H. Chromatin regulation in plant hormone and plant stress responses. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:164-170. [PMID: 33142261 PMCID: PMC8237520 DOI: 10.1016/j.pbi.2020.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 05/05/2023]
Abstract
The gene expression is tightly regulated temporally and spatially to ensure the plant and animal proper development, function, growth, and survival under different environmental conditions. Chromatin regulation plays a central role in the gene expression by providing transcription factors and the transcription machinery with dynamic access to an otherwise tightly packaged genome. In this review, we will summarize recent progress in understanding the roles of chromatin regulation in the gene expression, and their contribution to the plant hormone and stress responses. We highlight the most recent publications within this topic and underline the roles of chromatin regulation in gene expression.
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Affiliation(s)
- Likai Wang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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22
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Ma X, Su Z, Ma H. Molecular genetic analyses of abiotic stress responses during plant reproductive development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2870-2885. [PMID: 32072177 PMCID: PMC7260722 DOI: 10.1093/jxb/eraa089] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/12/2020] [Indexed: 05/20/2023]
Abstract
Plant responses to abiotic stresses during vegetative growth have been extensively studied for many years. Daily environmental fluctuations can have dramatic effects on plant vegetative growth at multiple levels, resulting in molecular, cellular, physiological, and morphological changes. Plants are even more sensitive to environmental changes during reproductive stages. However, much less is known about how plants respond to abiotic stresses during reproduction. Fortunately, recent advances in this field have begun to provide clues about these important processes, which promise further understanding and a potential contribution to maximize crop yield under adverse environments. Here we summarize information from several plants, focusing on the possible mechanisms that plants use to cope with different types of abiotic stresses during reproductive development, and present a tentative molecular portrait of plant acclimation during reproductive stages. Additionally, we discuss strategies that plants use to balance between survival and productivity, with some comparison among different plants that have adapted to distinct environments.
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Affiliation(s)
- Xinwei Ma
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Zhao Su
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Correspondence:
| | - Hong Ma
- Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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23
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Liang Q, Geng Q, Jiang L, Liang M, Li L, Zhang C, Wang W. Protein methylome analysis in Arabidopsis reveals regulation in RNA-related processes. J Proteomics 2020; 213:103601. [PMID: 31809900 DOI: 10.1016/j.jprot.2019.103601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/23/2019] [Accepted: 11/25/2019] [Indexed: 01/09/2023]
Abstract
Protein methylation has been proposed as an important post-translational modification, which occurs predominantly on lysine and arginine residues. Recent discoveries have revealed that protein methylation is also present on non-histones besides histones, and plays critical roles in regulating protein stability and function. However, proteome-wide identification of methylated proteins in plants remains unexplored. Here, we present the first global survey of monomethyl arginine, symmetric and asymmetric dimethyl arginine, and monomethyl, dimethyl, trimethyl lysine modifications in the proteomes of 10-day-old Arabidopsis seedlings through a combination of immunoaffinity purification and mass spectrometry analysis. In total, we identified 617 methylation sites which mapped to 412 proteins, with 263 proteins harboring 381 lysine methylation sites and 149 proteins harboring 236 arginine methylation sites. Among them, 607 methylation sites on 408 proteins were novel findings. Motif analysis revealed that glycine preferentially flanked methylated arginine residues, whereas aspartate and glutamate enriched around mono- and dimethylated lysine sites. Methylated proteins were involved in a variety of metabolic processes, showing significant enrichment in RNA-related metabolic pathways including spliceosome, RNA transport, and ribosome. Our data provide a global view of methylated non-histone proteins in Arabidopsis, laying foundations for elucidating the biological function of protein methylation in plants. SIGNIFICANCE: Protein methylation has emerged as a common and important modification both in eukaryotes and prokaryotes. The identification of methylated sites/peptides is fundamental for further functional analysis of protein methylation. This study was the first proteome-scale identification of lysine and arginine methylation in plants. We found that methylation occurred widely on non-histone proteins in Arabidopsis and was involved in diverse biological functions. The results provide foundations for the investigation of the protein methylome in Arabidopsis and provide powerful resources for the functional analysis of protein methylation in plants.
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Affiliation(s)
- Qiuju Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qinghe Geng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Meng Liang
- Jingjie PTM BioLab (Hangzhou) Co.Ltd, Hangzhou 310018, China
| | - Linhan Li
- Jingjie PTM BioLab (Hangzhou) Co.Ltd, Hangzhou 310018, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Weixuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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24
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Bai G, Yang DH, Cao P, Yao H, Zhang Y, Chen X, Xiao B, Li F, Wang ZY, Yang J, Xie H. Genome-Wide Identification, Gene Structure and Expression Analysis of the MADS-Box Gene Family Indicate Their Function in the Development of Tobacco ( Nicotiana tabacum L.). Int J Mol Sci 2019; 20:E5043. [PMID: 31614589 PMCID: PMC6829366 DOI: 10.3390/ijms20205043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/06/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
MADS-box genes play a pivotal role in various processes, including floral and seed development, controlling flowering time, regulation of fruits ripening, and respond to abiotic and biotic stressors in planta. Tobacco (Nicotiana tabacum) has been widely used as a model plant for analyzing the gene function, however, there has been less information on the regulation of flowering, and the associated genes. In the present study, a total of 168 NtMADS-box genes were identified from tobacco, and their phylogenetic relationship, chromosome locations, and gene structures were further analyzed. NtMADS-box genes can be clustered into four sub-families of Mα, Mγ, MIKC*, and MIKCC. A total of 111 NtMADS-box genes were distributed on 20 chromosomes, and 57 NtMADS-box genes were located on the unanchored scaffolds due to the complex and incomplete assembly of the tobacco genome. Expression profiles of NtMADS-box genes by microarray from 23 different tissues indicated that members in different NtMADS-box gene subfamilies might play specific roles in the growth and flower development, and the transcript levels of 24 NtMADS-box genes were confirmed by quantitative real-time PCR. Importantly, overexpressed NtSOC1/NtMADS133 could promote early flowering and dwarfism in transgenic tobacco plants. Therefore, our findings provide insights on the characterization of NtMADS-box genes to further study their functions in plant development.
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Affiliation(s)
- Ge Bai
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Da-Hai Yang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Peijian Cao
- China Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
| | - Heng Yao
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Yihan Zhang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Xuejun Chen
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Bingguang Xiao
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
| | - Feng Li
- China Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
| | - Zhen-Yu Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China.
| | - Jun Yang
- China Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
| | - He Xie
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China.
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, 650021, China.
- National Tobacco Genetic Engineering Research Center, Kunming, 650021, China.
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25
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Bi X, van Esse W, Mulki MA, Kirschner G, Zhong J, Simon R, von Korff M. CENTRORADIALIS Interacts with FLOWERING LOCUS T-Like Genes to Control Floret Development and Grain Number. PLANT PHYSIOLOGY 2019; 180:1013-1030. [PMID: 31004004 PMCID: PMC6548242 DOI: 10.1104/pp.18.01454] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/08/2019] [Indexed: 05/20/2023]
Abstract
CENTRORADIALIS (CEN) is a key regulator of flowering time and inflorescence architecture in plants. Natural variation in the barley (Hordeum vulgare) homolog HvCEN is important for agricultural range expansion of barley cultivation, but its effects on shoot and spike architecture and consequently yield have not yet been characterized. Here, we evaluated 23 independent hvcen, also termed mat-c, mutants to determine the pleiotropic effects of HvCEN on developmental timing and shoot and spike morphologies of barley under outdoor and controlled conditions. All hvcen mutants flowered early and showed a reduction in spikelet number per spike, tiller number, and yield in the outdoor experiments. Mutations in hvcen accelerated spikelet initiation and reduced axillary bud number in a photoperiod-independent manner but promoted floret development only under long days (LDs). The analysis of a flowering locus t3 (hvft3) hvcen double mutant showed that HvCEN interacts with HvFT3 to control spikelet initiation. Furthermore, early flowering3 (hvelf3) hvcen double mutants with high HvFT1 expression levels under short days suggested that HvCEN interacts with HvFT1 to repress floral development. Global transcriptome profiling in developing shoot apices and inflorescences of mutant and wild-type plants revealed that HvCEN controlled transcripts involved in chromatin remodeling activities, cytokinin and cell cycle regulation and cellular respiration under LDs and short days, whereas HvCEN affected floral homeotic genes only under LDs. Understanding the stage and organ-specific functions of HvCEN and downstream molecular networks will allow the manipulation of different shoot and spike traits and thereby yield.
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Affiliation(s)
- Xiaojing Bi
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Wilma van Esse
- Laboratory of Molecular Biology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mohamed Aman Mulki
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Gwendolyn Kirschner
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs" 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Jinshun Zhong
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Rüdiger Simon
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs" 40225 Düsseldorf, Germany
- Institute for Developmental Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Maria von Korff
- Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Institute of Plant Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences "SMART Plants for Tomorrow's Needs" 40225 Düsseldorf, Germany
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26
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Lee K, Park OS, Seo PJ. JMJ30-mediated demethylation of H3K9me3 drives tissue identity changes to promote callus formation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:961-975. [PMID: 29923261 DOI: 10.1111/tpj.14002] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 05/20/2023]
Abstract
Plant somatic cells can be reprogrammed by in vitro tissue culture methods, and massive genome-wide chromatin remodeling occurs, particularly during callus formation. Since callus tissue resembles root primordium, conversion of tissue identity is essentially required when leaf explants are used. Consistent with the fact that the differentiation state is defined by chromatin structure, which permits limited gene profiles, epigenetic changes underlie cellular reprogramming for changes to tissue identity. Although a histone methylation process suppressing leaf identity during leaf-to-callus transition has been demonstrated, the epigenetic factor involved in activation of root identity remains elusive. Here, we report that JUMONJI C DOMAIN-CONTAINING PROTEIN 30 (JMJ30) stimulates callus formation by promoting expression of a subset of LATERAL ORGAN BOUNDARIES-DOMAIN (LBD) genes that establish root primordia. The JMJ30 protein binds to promoters of the LBD16 and LBD29 genes along with AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 and activates LBD expression. Consistently, the JMJ30-deficient mutant displays reduced callus formation with low LBD transcript levels. The ARF-JMJ30 complex catalyzes the removal of methyl groups from H3K9me3, especially at the LBD16 and LBD29 loci to activate their expression during leaf-to-callus transition. Moreover, the ARF-JMJ30 complex further recruits ARABIDOPSIS TRITHORAX-RELATED 2 (ATXR2), which promotes deposition of H3K36me3 at the LBD16 and LBD29 promoters, and the tripartite complex ensures stable LBD activation during callus formation. These results indicate that the coordinated epigenetic modifications promote callus formation by establishing root primordium identity.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Ok-Sun Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
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27
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Tang X, Wang Q, Yuan H, Huang X. Chilling-induced DNA Demethylation is associated with the cold tolerance of Hevea brasiliensis. BMC PLANT BIOLOGY 2018; 18:70. [PMID: 29685105 PMCID: PMC5913804 DOI: 10.1186/s12870-018-1276-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/29/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Low temperature influences the development and latex production of rubber trees (Hevea brasiliensis) when extension to suboptimal high-latitude areas. The successful extension of Hevea brasiliensis cultivation to high-latitude areas has long believed to benefit from the breeding of cold-tolerant cultivars. A puzzling incongruity is the variation in cold tolerance among the cultivated clones despite their similar genetic make-up. RESULTS To investigate this, we first transferred cultivar Reyan 7-33-97 to short-term cold treatment, and showed that cold-related genes (such as HbICE1 and HbCBF2), cold-responsive (COR) genes, and DNA-methylation related genes (such as HbMET1) were induced by cold treatment. Furthermore, long-term cold treatment not only elevated the transcriptional activities of the HbICE1, HbCBF2, and HbMET, but also induced DNA demethylation of their promoters. Cold treatment increased the transcriptional activities of demethylation-related genes such as the HbDME, HbROS, and HbDML genes, but did not alter the promoter methylation status. Furthermore, the HbICE1 and HbMET promoters showed hypomethylation status in samples collected at the end of winter from 12 different cultivars grown in four geographical locations, but switched to hypermethylation status at the end of summer. Expression of COR was correlated with the low temperature. Given that little genetic diversity exists in the HbICE1 and HbMET promoters among different cultivars, the DNA demethylation induced by cold was highly correlated with low temperature, but not with the genetic backgrounds of cultivars. CONCLUSION Cold-induced epigenetic modification might play an important role in cold tolerance of H. brasiliensis.
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Affiliation(s)
- Xiao Tang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Renmin Rd. 58, Haikou, 570228 People’s Republic of China
| | - Qichao Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Renmin Rd. 58, Haikou, 570228 People’s Republic of China
| | | | - Xi Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Renmin Rd. 58, Haikou, 570228 People’s Republic of China
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28
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Fu Y, Ma H, Chen S, Gu T, Gong J. Control of proline accumulation under drought via a novel pathway comprising the histone methylase CAU1 and the transcription factor ANAC055. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:579-588. [PMID: 29253181 PMCID: PMC5853435 DOI: 10.1093/jxb/erx419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proline plays a crucial role in the drought stress response in plants. However, there are still gaps in our knowledge about the molecular mechanisms that regulate proline metabolism under drought stress. Here, we report that the histone methylase encoded by CAU1, which is genetically upstream of P5CS1 (encoding the proline biosynthetic enzyme Δ1-pyrroline-5-carboxylate synthetase 1), plays a crucial role in proline-mediated drought tolerance. We determined that the transcript level of CAU1 decreased while that of ANAC055 (encoding a transcription factor) increased in wild-type Arabidopsis under drought stress. Further analyses showed that CAU1 bound to the promoter of ANAC055 and suppressed its expression via H4R3sme2-type histone methylation in the promoter region. Thus, under drought stress, a decreased level of CAU1 led to an increased transcript level of ANAC055, which induced the expression of P5CS1 and increased proline level independently of CAS. Drought tolerance and the level of proline were found to be decreased in the cau1 anac055 double-mutant, while proline supplementation restored drought sensitivity in the anac055 mutant. Our results reveal the details of a novel pathway leading to drought tolerance mediated by CAU1.
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Affiliation(s)
- Yanlei Fu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- Correspondence:
| | - Hailing Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Siying Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Tianyu Gu
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Jiming Gong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
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29
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Fu Y, Ma H, Chen S, Gu T, Gong J. Control of proline accumulation under drought via a novel pathway comprising the histone methylase CAU1 and the transcription factor ANAC055. JOURNAL OF EXPERIMENTAL BOTANY 2018. [PMID: 29253181 DOI: 10.5061/dryad.hc4bj] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Proline plays a crucial role in the drought stress response in plants. However, there are still gaps in our knowledge about the molecular mechanisms that regulate proline metabolism under drought stress. Here, we report that the histone methylase encoded by CAU1, which is genetically upstream of P5CS1 (encoding the proline biosynthetic enzyme Δ1-pyrroline-5-carboxylate synthetase 1), plays a crucial role in proline-mediated drought tolerance. We determined that the transcript level of CAU1 decreased while that of ANAC055 (encoding a transcription factor) increased in wild-type Arabidopsis under drought stress. Further analyses showed that CAU1 bound to the promoter of ANAC055 and suppressed its expression via H4R3sme2-type histone methylation in the promoter region. Thus, under drought stress, a decreased level of CAU1 led to an increased transcript level of ANAC055, which induced the expression of P5CS1 and increased proline level independently of CAS. Drought tolerance and the level of proline were found to be decreased in the cau1 anac055 double-mutant, while proline supplementation restored drought sensitivity in the anac055 mutant. Our results reveal the details of a novel pathway leading to drought tolerance mediated by CAU1.
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Affiliation(s)
- Yanlei Fu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Hailing Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Siying Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Tianyu Gu
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jiming Gong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
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Li Y, Ding X, Wang X, He T, Zhang H, Yang L, Wang T, Chen L, Gai J, Yang S. Genome-wide comparative analysis of DNA methylation between soybean cytoplasmic male-sterile line NJCMS5A and its maintainer NJCMS5B. BMC Genomics 2017; 18:596. [PMID: 28806912 PMCID: PMC5557475 DOI: 10.1186/s12864-017-3962-5] [Citation(s) in RCA: 26] [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: 03/24/2017] [Accepted: 07/25/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND DNA methylation is an important epigenetic modification. It can regulate the expression of many key genes without changing the primary structure of the genomic DNA, and plays a vital role in the growth and development of the organism. The genome-wide DNA methylation profile of the cytoplasmic male sterile (CMS) line in soybean has not been reported so far. RESULTS In this study, genome-wide comparative analysis of DNA methylation between soybean CMS line NJCMS5A and its maintainer NJCMS5B was conducted by whole-genome bisulfite sequencing. The results showed 3527 differentially methylated regions (DMRs) and 485 differentially methylated genes (DMGs), including 353 high-credible methylated genes, 56 methylated genes coding unknown protein and 76 novel methylated genes with no known function were identified. Among them, 25 DMRs were further validated that the genome-wide DNA methylation data were reliable through bisulfite treatment, and 9 DMRs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. Finally, 8 key DMGs possibly associated with soybean CMS were identified. CONCLUSIONS Genome-wide DNA methylation profile of the soybean CMS line NJCMS5A and its maintainer NJCMS5B was obtained for the first time. Several specific DMGs which participated in pollen and flower development were further identified to be probably associated with soybean CMS. This study will contribute to further understanding of the molecular mechanism behind soybean CMS.
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Affiliation(s)
- Yanwei Li
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xianlong Ding
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xuan Wang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tingting He
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Zhang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Longshu Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tanliu Wang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Linfeng Chen
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Junyi Gai
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
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Hu J, Yang H, Mu J, Lu T, Peng J, Deng X, Kong Z, Bao S, Cao X, Zuo J. Nitric Oxide Regulates Protein Methylation during Stress Responses in Plants. Mol Cell 2017; 67:702-710.e4. [PMID: 28757206 DOI: 10.1016/j.molcel.2017.06.031] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/25/2017] [Accepted: 06/26/2017] [Indexed: 01/05/2023]
Abstract
Methylation and nitric oxide (NO)-based S-nitrosylation are highly conserved protein posttranslational modifications that regulate diverse biological processes. In higher eukaryotes, PRMT5 catalyzes Arg symmetric dimethylation, including key components of the spliceosome. The Arabidopsis prmt5 mutant shows severe developmental defects and impaired stress responses. However, little is known about the mechanisms regulating the PRMT5 activity. Here, we report that NO positively regulates the PRMT5 activity through S-nitrosylation at Cys-125 during stress responses. In prmt5-1 plants, a PRMT5C125S transgene, carrying a non-nitrosylatable mutation at Cys-125, fully rescues the developmental defects, but not the stress hypersensitive phenotype and the responsiveness to NO during stress responses. Moreover, the salt-induced Arg symmetric dimethylation is abolished in PRMT5C125S/prmt5-1 plants, correlated to aberrant splicing of pre-mRNA derived from a stress-related gene. These findings define a mechanism by which plants transduce stress-triggered NO signal to protein methylation machinery through S-nitrosylation of PRMT5 in response to environmental alterations.
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Affiliation(s)
- Jiliang Hu
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanjie Yang
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China
| | - Jinye Mu
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China
| | - Tiancong Lu
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juli Peng
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Science, Beijing 100101, China
| | - Shilai Bao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China
| | - Jianru Zuo
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China.
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Liu H, Ma X, Han HN, Hao YJ, Zhang XS. AtPRMT5 Regulates Shoot Regeneration through Mediating Histone H4R3 Dimethylation on KRPs and Pre-mRNA Splicing of RKP in Arabidopsis. MOLECULAR PLANT 2016; 9:1634-1646. [PMID: 27780782 DOI: 10.1016/j.molp.2016.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 05/25/2023]
Abstract
Protein arginine methylation plays important roles in diverse biological processes, but its role in regulating shoot regeneration remains elusive. In this study, we characterized the function of the protein arginine methyltransferase AtPRMT5 during de novo shoot regeneration in Arabidopsis. AtPRMT5 encodes a type II protein arginine methyltransferase that methylates proteins, including histones and RNA splicing factors. The frequency of shoot regeneration and the number of shoots per callus were decreased in the atprmt5 mutant compared with those in the wild type. Chromatin immunoprecipitation analysis revealed that AtPRMT5 targets KIP-RELATED PROTEINs (KRPs), which encode the cyclin-dependent kinase inhibitors that repress the cell cycle. During shoot regeneration, the KRP transcript level increased in the atprmt5 mutant, which resulted from reduced histone H4R3 methylation in the KRP promoter. Overexpression of KRP significantly reduced the frequency of shoot regeneration and shoot number per callus. Furthermore, abnormal pre-mRNA splicing in the gene RELATED TO KPC1 (RKP), which encodes an ubiquitin E3 ligase, was detected in the atprmt5 mutant. RKP functions in regulating KRP protein degradation, and mutation in RKP inhibited shoot regeneration. Thus, AtPRMT5 regulated shoot regeneration through histone modification-mediated KRP transcription and RKP pre-mRNA splicing. Our findings provide new insights into the function of protein arginine methylation in de novo shoot regeneration.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China; College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xu Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Hua Nan Han
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China
| | - Yu Jin Hao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, Shandong, China.
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Amara Korba R, Alayat MS, Bouiba L, Boudrissa A, Bouslama Z, Boukraa S, Francis F, Failloux AB, Boubidi SC. Ecological differentiation of members of the Culex pipiens complex, potential vectors of West Nile virus and Rift Valley fever virus in Algeria. Parasit Vectors 2016; 9:455. [PMID: 27534938 PMCID: PMC4989528 DOI: 10.1186/s13071-016-1725-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 07/25/2016] [Indexed: 12/24/2022] Open
Abstract
Background We investigated the ecological differentiation of two members of the Culex pipiens complex, Cx. p. pipiens form pipiens and Cx. p. pipiens form molestus in three sites, El-Kala, M'Sila and Tinerkouk in Algeria. These two forms are the most widespread mosquito vectors in temperate regions exhibiting important behavioural and physiological differences. Nevertheless, this group of potential vectors has been poorly studied, particularly in North Africa. Methods Ten larval populations of Cx. p. pipiens were sampled from various above- and underground habitats in three zones representing the three bioclimatic regions in Algeria. The reproduction characteristics were also investigated in the laboratory to define the rates of autogeny and stenogamy. Identification of Cx. p. pipiens members present in Algeria was achieved using a molecular analysis with the microsatellite CQ11 locus. Results We detected larvae of Cx. p. pipiens in all areas suggesting that the species is a ubiquitous mosquito well adapted to various environments. To our knowledge, this study provides the first molecular evidence of the presence of the Cx. p. pipiens form molestus and hybrids (molestus/pipiens) in Algeria with a high proportion of molestus form (48.3 %) in comparison with hybrids (36.8 %) and pipiens form (14.9 %). Conclusions Some unexpected correlations between the proportion of forms pipiens, molestus and hybrids, and mosquito biological characteristics were observed suggesting some epigenetic effects controlling Cx. p. pipiens mating and reproduction. Consequences for pathogen transmission are discussed. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1725-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raouf Amara Korba
- Laboratoire Ecologie des Systèmes Terrestres et Aquatiques, Département de Biologie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie. .,Institut Pasteur d'Alger, Unité d'Entomologie Médicale, Service d'Eco-épidémiologie parasitaire et génétique des populations, Alger, Algérie.
| | - Moufida Saoucen Alayat
- Laboratoire de Biologie Animale Appliquée, Faculté des Sciences, Département de Biologie, Université Badji Mokhtar, Annaba, Algérie
| | - Lazhari Bouiba
- Institut Pasteur d'Alger, Unité d'Entomologie Médicale, Service d'Eco-épidémiologie parasitaire et génétique des populations, Alger, Algérie
| | - Abdelkarim Boudrissa
- Institut Pasteur d'Alger, Unité d'Entomologie Médicale, Service d'Eco-épidémiologie parasitaire et génétique des populations, Alger, Algérie
| | - Zihad Bouslama
- Laboratoire Ecologie des Systèmes Terrestres et Aquatiques, Département de Biologie, Faculté des Sciences, Université Badji Mokhtar, Annaba, Algérie
| | - Slimane Boukraa
- Unit of Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Frederic Francis
- Unit of Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Anna-Bella Failloux
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, Paris, France
| | - Saïd Chaouki Boubidi
- Institut Pasteur d'Alger, Unité d'Entomologie Médicale, Service d'Eco-épidémiologie parasitaire et génétique des populations, Alger, Algérie
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Abstract
Prion proteins provide a unique mode of biochemical memory through self-perpetuating changes in protein conformation and function. They have been studied in fungi and mammals, but not yet identified in plants. Using a computational model, we identified candidate prion domains (PrDs) in nearly 500 plant proteins. Plant flowering is of particular interest with respect to biological memory, because its regulation involves remembering and integrating previously experienced environmental conditions. We investigated the prion-forming capacity of three prion candidates involved in flowering using a yeast model, where prion attributes are well defined and readily tested. In yeast, prions heritably change protein functions by templating monomers into higher-order assemblies. For most yeast prions, the capacity to convert into a prion resides in a distinct prion domain. Thus, new prion-forming domains can be identified by functional complementation of a known prion domain. The prion-like domains (PrDs) of all three of the tested proteins formed higher-order oligomers. Uniquely, the Luminidependens PrD (LDPrD) fully replaced the prion-domain functions of a well-characterized yeast prion, Sup35. Our results suggest that prion-like conformational switches are evolutionarily conserved and might function in a wide variety of normal biological processes.
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35
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Kudoh H. Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments. THE NEW PHYTOLOGIST 2016; 210:399-412. [PMID: 26523957 DOI: 10.1111/nph.13733] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/27/2015] [Indexed: 06/05/2023]
Abstract
Phenology refers to the study of seasonal schedules of organisms. Molecular phenology is defined here as the study of the seasonal patterns of organisms captured by molecular biology techniques. The history of molecular phenology is reviewed briefly in relation to advances in the quantification technology of gene expression. High-resolution molecular phenology (HMP) data have enabled us to study phenology with an approach of in natura systems biology. I review recent analyses of FLOWERING LOCUS C (FLC), a temperature-responsive repressor of flowering, along the six steps in the typical flow of in natura systems biology. The extensive studies of the regulation of FLC have made this example a successful case in which a comprehensive understanding of gene functions has been progressing. The FLC-mediated long-term memory of past temperatures creates time lags with other seasonal signals, such as photoperiod and short-term temperature. Major signals that control flowering time have a phase lag between them under natural conditions, and hypothetical phase lag calendars are proposed as mechanisms of season detection in plants. Transcriptomic HMP brings a novel strategy to the study of molecular phenology, because it provides a comprehensive representation of plant functions. I discuss future perspectives of molecular phenology from the standpoints of molecular biology, evolutionary biology and ecology.
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Affiliation(s)
- Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
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Ay N, Janack B, Fischer A, Reuter G, Humbeck K. Alterations of histone modifications at the senescence-associated gene HvS40 in barley during senescence. PLANT MOLECULAR BIOLOGY 2015; 89:127-41. [PMID: 26249045 DOI: 10.1007/s11103-015-0358-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 08/02/2015] [Indexed: 05/09/2023]
Abstract
The barley gene HvS40, encoding a putative regulator of leaf senescence, is strongly induced during leaf senescence. As shown by chromatin immunoprecipitation, euchromatic histone modification H3K9ac is added at promoter close to ATG and coding sequence of HvS40 after onset of senescence. In parallel, level of heterochromatic H3K9me2 decreases at this gene. Bisulfite sequencing revealed no DNA-methylation in this region, but a heavily methylated DNA-island, starting 664 bp upstream from translational start site in both, mature and senescent leaves. A decrease in DNA methylation in senescing leaves could be shown at one specific CpG motif at the end of this methylation island. In addition, global changes in chromatin structure during senescence were analyzed via immunocytology, revealing senescence-associated changes in spatial distribution of heterochromatic H3K9me2 patterns in the nuclei. Our results prove a senescence-specific mechanism, altering histone modification marks at distinct sequences of the senescence-associated gene HvS40 and altering distribution of heterochromatic areas in the nuclei.
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Affiliation(s)
- Nicole Ay
- Department of Plant Physiology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany
| | - Bianka Janack
- Department of Plant Physiology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany
| | - Andreas Fischer
- Department of Genetics, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany
| | - Gunter Reuter
- Department of Genetics, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany
| | - Klaus Humbeck
- Department of Plant Physiology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, 06120, Halle, Germany.
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Epigenetic variation in the Egfr gene generates quantitative variation in a complex trait in ants. Nat Commun 2015; 6:6513. [PMID: 25758336 DOI: 10.1038/ncomms7513] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 02/05/2015] [Indexed: 11/08/2022] Open
Abstract
Complex quantitative traits, like size and behaviour, are a pervasive feature of natural populations. Quantitative trait variation is the product of both genetic and environmental factors, yet little is known about the mechanisms through which their interaction generates this variation. Epigenetic processes, such as DNA methylation, can mediate gene-by-environment interactions during development to generate discrete phenotypic variation. We therefore investigated the developmental role of DNA methylation in generating continuous size variation of workers in an ant colony, a key trait associated with division of labour. Here we show that, in the carpenter ant Camponotus floridanus, global (genome-wide) DNA methylation indirectly regulates quantitative methylation of the conserved cell-signalling gene Epidermal growth factor receptor to generate continuous size variation of workers. DNA methylation can therefore generate quantitative variation in a complex trait by quantitatively regulating the transcription of a gene. This mechanism, alongside genetic variation, may determine the phenotypic possibilities of loci for generating quantitative trait variation in natural populations.
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Xu J, Xu H, Liu Y, Wang X, Xu Q, Deng X. Genome-wide identification of sweet orange (Citrus sinensis) histone modification gene families and their expression analysis during the fruit development and fruit-blue mold infection process. FRONTIERS IN PLANT SCIENCE 2015; 6:607. [PMID: 26300904 PMCID: PMC4525380 DOI: 10.3389/fpls.2015.00607] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/23/2015] [Indexed: 05/20/2023]
Abstract
In eukaryotes, histone acetylation and methylation have been known to be involved in regulating diverse developmental processes and plant defense. These histone modification events are controlled by a series of histone modification gene families. To date, there is no study regarding genome-wide characterization of histone modification related genes in citrus species. Based on the two recent sequenced sweet orange genome databases, a total of 136 CsHMs (Citrus sinensis histone modification genes), including 47 CsHMTs (histone methyltransferase genes), 23 CsHDMs (histone demethylase genes), 50 CsHATs (histone acetyltransferase genes), and 16 CsHDACs (histone deacetylase genes) were identified. These genes were categorized to 11 gene families. A comprehensive analysis of these 11 gene families was performed with chromosome locations, phylogenetic comparison, gene structures, and conserved domain compositions of proteins. In order to gain an insight into the potential roles of these genes in citrus fruit development, 42 CsHMs with high mRNA abundance in fruit tissues were selected to further analyze their expression profiles at six stages of fruit development. Interestingly, a numbers of genes were expressed highly in flesh of ripening fruit and some of them showed the increasing expression levels along with the fruit development. Furthermore, we analyzed the expression patterns of all 136 CsHMs response to the infection of blue mold (Penicillium digitatum), which is the most devastating pathogen in citrus post-harvest process. The results indicated that 20 of them showed the strong alterations of their expression levels during the fruit-pathogen infection. In conclusion, this study presents a comprehensive analysis of the histone modification gene families in sweet orange and further elucidates their behaviors during the fruit development and the blue mold infection responses.
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Affiliation(s)
| | | | | | | | | | - Xiuxin Deng
- *Correspondence: Xiuxin Deng, Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China,
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Matsoukas IG. Interplay between sugar and hormone signaling pathways modulate floral signal transduction. Front Genet 2014; 5:218. [PMID: 25165468 PMCID: PMC4131243 DOI: 10.3389/fgene.2014.00218] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/24/2014] [Indexed: 11/13/2022] Open
Abstract
NOMENCLATURE The following nomenclature will be used in this article: Names of genes are written in italicized upper-case letters, e.g., ABI4.Names of proteins are written in non-italicized upper-case letters, e.g., ABI4.Names of mutants are written in italicized lower-case letters, e.g., abi4. The juvenile-to-adult and vegetative-to-reproductive phase transitions are major determinants of plant reproductive success and adaptation to the local environment. Understanding the intricate molecular genetic and physiological machinery by which environment regulates juvenility and floral signal transduction has significant scientific and economic implications. Sugars are recognized as important regulatory molecules that regulate cellular activity at multiple levels, from transcription and translation to protein stability and activity. Molecular genetic and physiological approaches have demonstrated different aspects of carbohydrate involvement and its interactions with other signal transduction pathways in regulation of the juvenile-to-adult and vegetative-to-reproductive phase transitions. Sugars regulate juvenility and floral signal transduction through their function as energy sources, osmotic regulators and signaling molecules. Interestingly, sugar signaling has been shown to involve extensive connections with phytohormone signaling. This includes interactions with phytohormones that are also important for the orchestration of developmental phase transitions, including gibberellins, abscisic acid, ethylene, and brassinosteroids. This article highlights the potential roles of sugar-hormone interactions in regulation of floral signal transduction, with particular emphasis on Arabidopsis thaliana mutant phenotypes, and suggests possible directions for future research.
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Affiliation(s)
- Ianis G Matsoukas
- Institute for Renewable Energy and Environmental Technologies, University of Bolton Bolton, UK ; Systems and Synthetic Biology, Institute for Materials Research and Innovation, University of Bolton Bolton, UK
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40
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Han SK, Wagner D. Role of chromatin in water stress responses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2785-99. [PMID: 24302754 PMCID: PMC4110454 DOI: 10.1093/jxb/ert403] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
As sessile organisms, plants are exposed to environmental stresses throughout their life. They have developed survival strategies such as developmental and morphological adaptations, as well as physiological responses, to protect themselves from adverse environments. In addition, stress sensing triggers large-scale transcriptional reprogramming directed at minimizing the deleterious effect of water stress on plant cells. Here, we review recent findings that reveal a role of chromatin in water stress responses. In addition, we discuss data in support of the idea that chromatin remodelling and modifying enzymes may be direct targets of stress signalling pathways. Modulation of chromatin regulator activity by these signaling pathways may be critical in minimizing potential trade-offs between growth and stress responses. Alterations in the chromatin organization and/or in the activity of chromatin remodelling and modifying enzymes may furthermore contribute to stress memory. Mechanistic insight into these phenomena derived from studies in model plant systems should allow future engineering of broadly drought-tolerant crop plants that do not incur unnecessary losses in yield or growth.
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Affiliation(s)
- Soon-Ki Han
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Woods DP, Ream TS, Amasino RM. Memory of the vernalized state in plants including the model grass Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2014; 5:99. [PMID: 24723926 PMCID: PMC3971174 DOI: 10.3389/fpls.2014.00099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 02/28/2014] [Indexed: 05/03/2023]
Abstract
Plant species that have a vernalization requirement exhibit variation in the ability to "remember" winter - i.e., variation in the stability of the vernalized state. Studies in Arabidopsis have demonstrated that molecular memory involves changes in the chromatin state and expression of the flowering repressor FLOWERING LOCUS C, and have revealed that single-gene differences can have large effects on the stability of the vernalized state. In the perennial Arabidopsis relative Arabis alpina, the lack of memory of winter is critical for its perennial life history. Our studies of flowering behavior in the model grass Brachypodium distachyon reveal extensive variation in the vernalization requirement, and studies of a particular Brachypodium accession that has a qualitative requirement for both cold exposure and inductive day length to flower reveal that Brachypodium can exhibit a highly stable vernalized state.
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Affiliation(s)
- Daniel P. Woods
- Department of Biochemistry, University of Wisconsin-MadisonMadison, WI, USA
- U.S. Department of Energy–Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, MadisonWI, USA
- Laboratory of Genetics, University of Wisconsin-Madison, MadisonWI, USA
| | - Thomas S. Ream
- Department of Biochemistry, University of Wisconsin-MadisonMadison, WI, USA
- U.S. Department of Energy–Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, MadisonWI, USA
| | - Richard M. Amasino
- Department of Biochemistry, University of Wisconsin-MadisonMadison, WI, USA
- U.S. Department of Energy–Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, MadisonWI, USA
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42
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The B-box family gene STO (BBX24) in Arabidopsis thaliana regulates flowering time in different pathways. PLoS One 2014; 9:e87544. [PMID: 24498334 PMCID: PMC3911981 DOI: 10.1371/journal.pone.0087544] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 12/31/2013] [Indexed: 12/13/2022] Open
Abstract
Flowering at the appropriate time is crucial for reproductive success and is strongly influenced by various pathways such as photoperiod, circadian clock, FRIGIDA and vernalization. Although each separate pathway has been extensively studied, much less is known about the interactions between them. In this study we have investigated the relationship between the photoperiod/circadian clock gene and FRIGIDA/FLC by characterizing the function of the B-box STO gene family. STO has two B-box Zn-finger domains but lacks the CCT domain. Its expression is controlled by circadian rhythm and is affected by environmental factors and phytohormones. Loss and gain of function mutants show diversiform phenotypes from seed germination to flowering. The sto-1 mutant flowers later than the wild type (WT) under short day growth conditions, while over-expression of STO causes early flowering both in long and short days. STO over-expression not only reduces FLC expression level but it also activates FT and SOC1 expression. It also does not rely on the other B-box gene CO or change the circadian clock system to activate FT and SOC1. Furthermore, the STO activation of FT and SOC1 expression is independent of the repression of FLC; rather STO and FLC compete with each other to regulate downstream genes. Our results indicate that photoperiod and the circadian clock pathway gene STO can affect the key flowering time genes FLC and FT/SOC1 separately, and reveals a novel perspective to the mechanism of flowering regulation.
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DNA methylation, epigenetics, and evolution in vertebrates: facts and challenges. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2014; 2014:475981. [PMID: 24551476 PMCID: PMC3914449 DOI: 10.1155/2014/475981] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 11/11/2013] [Accepted: 11/23/2013] [Indexed: 12/22/2022]
Abstract
DNA methylation is a key epigenetic modification in the vertebrate genomes known to be involved in biological processes such as regulation of gene expression, DNA structure and control of transposable elements. Despite increasing knowledge about DNA methylation, we still lack a complete understanding of its specific functions and correlation with environment and gene expression in diverse organisms. To understand how global DNA methylation levels changed under environmental influence during vertebrate evolution, we analyzed its distribution pattern along the whole genome in mammals, reptiles and fishes showing that it is correlated with temperature, independently on phylogenetic inheritance. Other studies in mammals and plants have evidenced that environmental stimuli can promote epigenetic changes that, in turn, might generate localized changes in DNA sequence resulting in phenotypic effects. All these observations suggest that environment can affect the epigenome of vertebrates by generating hugely different methylation patterns that could, possibly, reflect in phenotypic differences. We are at the first steps towards the understanding of mechanisms that underlie the role of environment in molding the entire genome over evolutionary times. The next challenge will be to map similarities and differences of DNA methylation in vertebrates and to associate them with environmental adaptation and evolution.
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Fan H, Zhang Z, Wang N, Cui Y, Sun H, Liu Y, Wu H, Zheng S, Bao S, Ling HQ. SKB1/PRMT5-mediated histone H4R3 dimethylation of Ib subgroup bHLH genes negatively regulates iron homeostasis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:209-21. [PMID: 24298997 DOI: 10.1111/tpj.12380] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/26/2013] [Accepted: 11/04/2013] [Indexed: 05/21/2023]
Abstract
Histone modifications play critical roles in the perception of environmental cues by plants. Here, we report that Shk1 binding protein 1 (SKB1/AtPRMT5), which catalyzes the symmetric dimethylation of histone H4R3 (H4R3sme2), is involved in iron homeostasis in Arabidopsis. The SKB1 lesion mutant exhibited higher iron accumulation in shoots and greater tolerance to iron deficiency than the wild type. The expression of SKB1 was not affected by iron, but the level of H4R3sme2 mediated by SKB1 was related to iron status in plants. We showed by chromatin immunoprecipitation (ChIP) and genome-wide ChIP-seq that SKB1 associated with the chromatin of the Ib subgroup bHLH genes (AtbHLH38, AtbHLH39, AtbHLH100 and AtbHLH101), and symmetrically dimethylated histone H4R3. The quantity of SKB1 that associated with chromatin of the Ib subgroup bHLH genes and the level of H4R3sme2 corresponded to the iron status of plants (higher with increased iron supply and lower when iron was removed). We conclude that SKB1-mediated H4R3sme2 regulates iron homeostasis in Arabidopsis in the context of increasing or decreasing expression of Ib subgroup bHLH genes. Iron deficiency may cause an increase in the disassociation of SKB1 from chromatin of the bHLH genes and a decrease in the level of H4R3sme2, thereby elevating their transcription and enhancing iron uptake. Our findings provide new insight into the molecular mechanisms of iron homeostasis in strategy I plants.
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Affiliation(s)
- Huajie Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
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45
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Fu YL, Zhang GB, Lv XF, Guan Y, Yi HY, Gong JM. Arabidopsis histone methylase CAU1/PRMT5/SKB1 acts as an epigenetic suppressor of the calcium signaling gene CAS to mediate stomatal closure in response to extracellular calcium. THE PLANT CELL 2013; 25:2878-91. [PMID: 23943859 PMCID: PMC3784586 DOI: 10.1105/tpc.113.113886] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Elevations in extracellular calcium ([Ca(2+)]o) are known to stimulate cytosolic calcium ([Ca(2+)]cyt) oscillations to close stomata. However, the underlying mechanisms regulating this process remain largely to be determined. Here, through the functional characterization of the calcium underaccumulation mutant cau1, we report that the epigenetic regulation of CAS, a putative Ca(2+) binding protein proposed to be an external Ca(2+) sensor, is involved in this process. cau1 mutant plants display increased drought tolerance and stomatal closure. A mutation in CAU1 significantly increased the expression level of the calcium signaling gene CAS, and functional disruption of CAS abolished the enhanced drought tolerance and stomatal [Ca(2+)]o signaling in cau1. Map-based cloning revealed that CAU1 encodes the H4R3sme2 (for histone H4 Arg 3 with symmetric dimethylation)-type histone methylase protein arginine methytransferase5/Shk1 binding protein1. Chromatin immunoprecipitation assays showed that CAU1 binds to the CAS promoter and modulates the H4R3sme2-type histone methylation of the CAS chromatin. When exposed to elevated [Ca(2+)]o, the protein levels of CAU1 decreased and less CAU1 bound to the CAS promoter. In addition, the methylation level of H4R3sme2 decreased in the CAS chromatin. Together, these data suggest that in response to increases in [Ca(2+)]o, fewer CAU1 protein molecules bind to the CAS promoter, leading to decreased H4R3sme2 methylation and consequent derepression of the expression of CAS to mediate stomatal closure and drought tolerance.
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46
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Chromatin remodeling and alternative splicing: pre- and post-transcriptional regulation of the Arabidopsis circadian clock. Semin Cell Dev Biol 2013; 24:399-406. [PMID: 23499867 DOI: 10.1016/j.semcdb.2013.02.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/27/2013] [Indexed: 12/22/2022]
Abstract
Circadian clocks are endogenous mechanisms that translate environmental cues into temporal information to generate the 24-h rhythms in metabolism and physiology. The circadian function relies on the precise regulation of rhythmic gene expression at the core of the oscillator, which temporally modulates the genome transcriptional activity in virtually all multicellular organisms examined to date. Emerging evidence in plants suggests a highly sophisticated interplay between the circadian patterns of gene expression and the rhythmic changes in chromatin remodeling and histone modifications. Alternative precursor messenger RNA (pre-mRNA) splicing has also been recently defined as a fundamental pillar within the circadian system, providing the required plasticity and specificity for fine-tuning the circadian clock. This review highlights the relationship between the plant circadian clock with both chromatin remodeling and alternative splicing and compares the similarities and divergences with analogous studies in animal circadian systems.
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47
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Wollenberg AC, Amasino RM. Natural variation in the temperature range permissive for vernalization in accessions of Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2012; 35:2181-91. [PMID: 22639792 DOI: 10.1111/j.1365-3040.2012.02548.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Vernalization is an acceleration of flowering in response to chilling, and is normally studied in the laboratory at near-freezing (2-4 °C) temperatures. Many vernalization-requiring species, such as Arabidopsis thaliana, are found in a range of habitats with varying winter temperatures. Natural variation in the temperature range that elicits a vernalization response in Arabidopsis has not been fully explored. We characterized the effect of intermediate temperatures (7-19 °C) on 15 accessions and the well-studied reference line Col-FRI. Although progressively warmer temperatures are gradually less effective at activating expression of the vernalization-specific gene VERNALIZATION-INSENSITIVE 3 (VIN3) and in accelerating flowering, there is substantial natural variation in the upper threshold (T(max) ) of the flowering-time response. VIN3 is required for the T(max) (13 °C) response of Col-FRI. Surprisingly, even 16 °C treatment caused induction of VIN3 in six tested lines, despite the ineffectiveness of this temperature in accelerating flowering for two of them. Finally, we present evidence that mild acceleration of flowering by 19 °C exposure may counterbalance the flowering time delay caused by non-inductive photoperiods in at least one accession, creating an appearance of photoperiod insensitivity.
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Affiliation(s)
- Amanda C Wollenberg
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
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48
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Song J, Angel A, Howard M, Dean C. Vernalization - a cold-induced epigenetic switch. J Cell Sci 2012; 125:3723-31. [PMID: 22935652 DOI: 10.1242/jcs.084764] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Growth and development are modulated by environmental signals in many organisms. These signals are often perceived at one stage and 'remembered' until later in development. An increasingly well-understood example of this process in plants is provided by vernalization, which refers to the acquisition of the ability to flower after prolonged exposure to cold. In Arabidopsis thaliana, vernalization involves downregulation and epigenetic silencing of the gene encoding the floral repressor FLOWERING LOCUS C (FLC). This epigenetic silencing is quantitative and increases with the duration of exposure to cold. Vernalization involves a Polycomb-based switching mechanism, with localized nucleation of silencing during periods of cold, and spreading of the silencing complex over the whole gene after the exposure to cold. A number of characteristics of vernalization have recently been elaborated on through the use of mathematical modelling. This has revealed the importance of chromatin dynamics for the switching mechanism and has shown that the quantitative nature of the process is due to cell-autonomous switching of an increasing proportion of cells. The principles derived from vernalization are likely to be widely relevant to epigenetic reprogramming in many organisms.
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Affiliation(s)
- Jie Song
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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49
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Russell SD, Gou X, Wong CE, Wang X, Yuan T, Wei X, Bhalla PL, Singh MB. Genomic profiling of rice sperm cell transcripts reveals conserved and distinct elements in the flowering plant male germ lineage. THE NEW PHYTOLOGIST 2012; 195:560-573. [PMID: 22716952 DOI: 10.1111/j.1469-8137.2012.04199.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Genomic assay of sperm cell RNA provides insight into functional control, modes of regulation, and contributions of male gametes to double fertilization. Sperm cells of rice (Oryza sativa) were isolated from field-grown, disease-free plants and RNA was processed for use with the full-genome Affymetrix microarray. Comparison with Gene Expression Omnibus (GEO) reference arrays confirmed expressionally distinct gene profiles. A total of 10,732 distinct gene sequences were detected in sperm cells, of which 1668 were not expressed in pollen or seedlings. Pathways enriched in male germ cells included ubiquitin-mediated pathways, pathways involved in chromatin modeling including histones, histone modification and nonhistone epigenetic modification, and pathways related to RNAi and gene silencing. Genome-wide expression patterns in angiosperm sperm cells indicate common and divergent themes in the male germline that appear to be largely self-regulating through highly up-regulated chromatin modification pathways. A core of highly conserved genes appear common to all sperm cells, but evidence is still emerging that another class of genes have diverged in expression between monocots and dicots since their divergence. Sperm cell transcripts present at fusion may be transmitted through plasmogamy during double fertilization to effect immediate post-fertilization expression of early embryo and (or) endosperm development.
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Affiliation(s)
- Scott D Russell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Xiaoping Gou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Chui E Wong
- Plant Molecular Biology and Biotechnology Laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xinkun Wang
- Higuchi Biosciences Center, University of Kansas, Lawrence, KS 66047, USA
| | - Tong Yuan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Xiaoping Wei
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia
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50
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Niu L, Lu F, Zhao T, Liu C, Cao X. The enzymatic activity of Arabidopsis protein arginine methyltransferase 10 is essential for flowering time regulation. Protein Cell 2012; 3:450-9. [PMID: 22729397 DOI: 10.1007/s13238-012-2935-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 05/21/2012] [Indexed: 01/15/2023] Open
Abstract
Arabidopsis AtPRMT10 is a plant-specific type I protein arginine methyltransferase that can asymmetrically dimethylate arginine 3 of histone H4 with auto-methylation activity. Mutations of AtPRMT10 derepress FLOWERING LOCUS C (FLC) expression resulting in a late-flowering phenotype. Here, to further investigate the biochemical characteristics of AtPRMT10, we analyzed a series of mutated forms of the AtPRMT10 protein. We demonstrate that the conserved "VLD" residues and "double-E loop" are essential for enzymatic activity of AtPRMT10. In addition, we show that Arg54 and Cys259 of AtPRMT10, two residues unreported in animals, are also important for its enzymatic activity. We find that Arg13 of AtPRMT10 is the auto-methylation site. However, substitution of Arg13 to Lys13 does not affect its enzymatic activity. In vivo complementation assays reveal that plants expressing AtPRMT10 with VLD-AAA, E143Q or E152Q mutations retain high levels of FLC expression and fail to rescue the late-flowering phenotype of atprmt10 plants. Taken together, we conclude that the methyltransferase activity of AtPRMT10 is essential for repressing FLC expression and promoting flowering in Arabidopsis.
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Affiliation(s)
- Lifang Niu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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