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Liu D, Cui W, Bo C, Wang R, Zhu Y, Duan Y, Wang D, Xue J, Xue T. PtWRKY2, a WRKY transcription factor from Pinellia ternata confers heat tolerance in Arabidopsis. Sci Rep 2024; 14:13807. [PMID: 38877055 PMCID: PMC11178784 DOI: 10.1038/s41598-024-64560-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024] Open
Abstract
High temperatures are a major stress factor that limit the growth of Pinellia ternata. WRKY proteins widely distribute in plants with the important roles in plant growth and stress responses. However, WRKY genes have not been identified in P. ternata thus far. In this study, five PtWRKYs with four functional subgroups were identified in P. ternata. One group III WRKY transcription factor, PtWRKY2, was strongly induced by high temperatures, whereas the other four PtWRKYs were suppressed. Analysis of transcription factor characteristics revealed that PtWRKY2 localized to the nucleus and specifically bound to W-box elements without transcriptional activation activity. Overexpression of PtWRKY2 increased the heat tolerance of Arabidopsis, as shown by the higher percentage of seed germination and survival rate, and the longer root length of transgenic lines under high temperatures compared to the wild-type. Moreover, PtWRKY2 overexpression significantly decreased reactive oxygen species accumulation by increasing the catalase, superoxide dismutase, and peroxidase activities. Furthermore, the selected heat shock-associated genes, including five transcription factors (HSFA1A, HSFA7A, bZIP28, DREB2A, and DREB2B), two heat shock proteins (HSP70 and HSP17.4), and three antioxidant enzymes (POD34, CAT1, and SOD1), were all upregulated in transgenic Arabidopsis. The study identifies that PtWRKY2 functions as a key transcriptional regulator in the heat tolerance of P. ternata, which might provide new insights into the genetic improvement of P. ternata.
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Affiliation(s)
- Dan Liu
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, Huaibei, China
| | - Wanning Cui
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, Huaibei, China
| | - Chen Bo
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, Huaibei, China
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, Huaibei, China
| | - Ru Wang
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, Huaibei, China
| | - Yanfang Zhu
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, Huaibei, China
| | - Yongbo Duan
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, Huaibei, China
| | - Dexin Wang
- College of Agriculture and Engineering, Heze University, Heze, 274015, China.
| | - Jianping Xue
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, Huaibei, China.
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, Huaibei, China.
| | - Tao Xue
- College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, Huaibei, China.
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, Huaibei, China.
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Tan Q, Zhao M, Gao J, Li K, Zhang M, Li Y, Liu Z, Song Y, Lu X, Zhu Z, Lin R, Yin P, Zhou C, Wang G. AtVQ25 promotes salicylic acid-related leaf senescence by fine-tuning the self-repression of AtWRKY53. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1126-1147. [PMID: 38629459 DOI: 10.1111/jipb.13659] [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: 12/04/2023] [Accepted: 03/14/2024] [Indexed: 06/21/2024]
Abstract
Most mechanistic details of chronologically ordered regulation of leaf senescence are unknown. Regulatory networks centered on AtWRKY53 are crucial for orchestrating and integrating various senescence-related signals. Notably, AtWRKY53 binds to its own promoter and represses transcription of AtWRKY53, but the biological significance and mechanism underlying this self-repression remain unclear. In this study, we identified the VQ motif-containing protein AtVQ25 as a cooperator of AtWRKY53. The expression level of AtVQ25 peaked at mature stage and was specifically repressed after the onset of leaf senescence. AtVQ25-overexpressing plants and atvq25 mutants displayed precocious and delayed leaf senescence, respectively. Importantly, we identified AtWRKY53 as an interacting partner of AtVQ25. We determined that interaction between AtVQ25 and AtWRKY53 prevented AtWRKY53 from binding to W-box elements on the AtWRKY53 promoter and thus counteracted the self-repression of AtWRKY53. In addition, our RNA-sequencing data revealed that the AtVQ25-AtWRKY53 module is related to the salicylic acid (SA) pathway. Precocious leaf senescence and SA-induced leaf senescence in AtVQ25-overexpressing lines were inhibited by an SA pathway mutant, atsid2, and NahG transgenic plants; AtVQ25-overexpressing/atwrky53 plants were also insensitive to SA-induced leaf senescence. Collectively, we demonstrated that AtVQ25 directly attenuates the self-repression of AtWRKY53 during the onset of leaf senescence, which is substantially helpful for understanding the timing of leaf senescence onset modulated by AtWRKY53.
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Affiliation(s)
- Qi Tan
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Mingming Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
- College of Chemical Engineering, Shijiazhuang University, Shijiazhuang, 050035, China
| | - Jingwei Gao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Ke Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Mengwei Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yunjia Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Zeting Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yujia Song
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xiaoyue Lu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Zhengge Zhu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Rongcheng Lin
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Pengcheng Yin
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Chunjiang Zhou
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Geng Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
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Wang Z, Fu W, Zhang X, Liusui Y, Saimi G, Zhao H, Zhang J, Guo Y. Identification of the Gossypium hirsutum SDG Gene Family and Functional Study of GhSDG59 in Response to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1257. [PMID: 38732472 PMCID: PMC11085088 DOI: 10.3390/plants13091257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
SET-domain group histone methyltransferases (SDGs) are known to play crucial roles in plant responses to abiotic stress. However, their specific function in cotton's response to drought stress has not been well understood. This study conducted a comprehensive analysis of the SDG gene family in Gossypium hirsutum, identifying a total of 82 SDG genes. An evolutionary analysis revealed that the SDG gene family can be divided into eight subgroups. The expression analysis shows that some GhSDG genes are preferentially expressed in specific tissues, indicating their involvement in cotton growth and development. The transcription level of some GhSDG genes is induced by PEG, with GhSDG59 showing significant upregulation upon polyethylene glycol (PEG) treatment. Quantitative polymerase chain reaction (qPCR) analysis showed that the accumulation of transcripts of the GhSDG59 gene was significantly upregulated under drought stress. Further functional studies using virus-induced gene silencing (VIGS) revealed that silencing GhSDG59 reduced cotton tolerance to drought stress. Under drought conditions, the proline content, superoxide dismutase (SOD) and peroxidase (POD) enzyme activities in the GhSDG59-silenced plants were significantly lower than in the control plants, while the malondialdehyde (MDA) content was significantly higher. Transcriptome sequencing showed that silencing the GhSDG59 gene led to significant changes in the expression levels of 1156 genes. The KEGG enrichment analysis revealed that these differentially expressed genes (DEGs) were mainly enriched in the carbon metabolism and the starch and sucrose metabolism pathways. The functional annotation analysis identified known drought-responsive genes, such as ERF, CIPK, and WRKY, among these DEGs. This indicates that GhSDG59 is involved in the drought-stress response in cotton by affecting the expression of genes related to the carbon metabolism and the starch and sucrose metabolism pathways, as well as known drought-responsive genes. This analysis provides valuable information for the functional genomic study of SDGs and highlights potential beneficial genes for genetic improvement and breeding in cotton.
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Affiliation(s)
| | | | | | | | | | | | - Jingbo Zhang
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, XinjiangNormal University, Urumqi 830017, China; (Z.W.); (W.F.); (X.Z.); (Y.L.); (G.S.); (H.Z.)
| | - Yanjun Guo
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, XinjiangNormal University, Urumqi 830017, China; (Z.W.); (W.F.); (X.Z.); (Y.L.); (G.S.); (H.Z.)
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Meng L, Yang H, Yang J, Wang Y, Ye T, Xiang L, Chan Z, Wang Y. Tulip transcription factor TgWRKY75 activates salicylic acid and abscisic acid biosynthesis to synergistically promote petal senescence. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2435-2450. [PMID: 38243353 DOI: 10.1093/jxb/erae021] [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: 08/25/2023] [Accepted: 01/17/2024] [Indexed: 01/21/2024]
Abstract
WRKY transcription factors play a central role in controlling plant organ senescence; however, it is unclear whether and how they regulate petal senescence in the widely grown ornamental plant tulip (Tulipa gesneriana). In this study, we report that TgWRKY75 promotes petal senescence by enhancing the synthesis of both abscisic acid (ABA) and salicylic acid (SA) in tulip and in transgenic Arabidopsis. The expression level of TgWRKY75 was up-regulated in senescent petals, and exogenous ABA or SA treatment induced its expression. The endogenous contents of ABA and SA significantly increased during petal senescence and in response to TgWRKY75 overexpression. Two SA synthesis-related genes, TgICS1 and TgPAL1, were identified as direct targets of TgWRKY75, which binds to their promoters. In parallel, TgWRKY75 activated the expression of the ABA biosynthesis-related gene TgNCED3 via directly binding to its promoter region. Site mutation of the W-box core motif located in the promoters of TgICS1, TgPAL1, and TgNCED3 eliminated their interactions with TgWRKY75. In summary, our study demonstrates a dual regulation of ABA and SA biosynthesis by TgWRKY75, revealing a synergistic process of tulip petal senescence through feedback regulation between TgWRKY75 and the accumulation of ABA and SA.
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Affiliation(s)
- Lin Meng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
- Hubei Hongshan Laboratory, Wuhan 30070, PR China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Haipo Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
- Hubei Hongshan Laboratory, Wuhan 30070, PR China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jinli Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yaping Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Tiantian Ye
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Lin Xiang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zhulong Chan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
- Hubei Hongshan Laboratory, Wuhan 30070, PR China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yanping Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, PR China
- National R&D Centre for Citrus Preservation, Huazhong Agricultural University, Wuhan 430070, PR China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, PR China
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Apodiakou A, Alseekh S, Hoefgen R, Whitcomb SJ. Overexpression of SLIM1 transcription factor accelerates vegetative development in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2024; 15:1327152. [PMID: 38571711 PMCID: PMC10988502 DOI: 10.3389/fpls.2024.1327152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
The transcription factor Sulfur Limitation 1 (SLIM1) belongs to the plant-specific Ethylene Insenstive3-Like transcription factor family and is known to coordinate gene expression in response to sulfur deficiency. However, the roles of SLIM1 in nutrient-sufficient conditions have not been characterized. Employing constitutive SLIM1 overexpression (35S::SLIM1) and CRISPR/Cas9 mutant plants (slim1-cr), we identified several distinct phenotypes in nutrient-sufficient conditions in Arabidopsis thaliana. Overexpression of SLIM1 results in plants with approximately twofold greater rosette area throughout vegetative development. 35S::SLIM1 plants also bolt earlier and exhibit earlier downregulation of photosynthesis-associated genes and earlier upregulation of senescence-associated genes than Col-0 and slim1-cr plants. This suggests that overexpression of SLIM1 accelerates development in A. thaliana. Genome-wide differential gene expression analysis relative to Col-0 at three time points with slim1-cr and two 35S::SLIM1 lines allowed us to identify 1,731 genes regulated directly or indirectly by SLIM1 in vivo.
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Affiliation(s)
- Anastasia Apodiakou
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Saleh Alseekh
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Rainer Hoefgen
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Sarah J. Whitcomb
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- Cereal Crops Research Unit, United States Department of Agriculture - Agricultural Research Service, Madison, WI, United States
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Kushwaha A, Mishra V, Tripathi DK, Gupta R, Singh VP. Epigenetics governs senescence. PLANT REPRODUCTION 2024; 37:33-36. [PMID: 37594548 DOI: 10.1007/s00497-023-00479-2] [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: 04/14/2023] [Accepted: 07/28/2023] [Indexed: 08/19/2023]
Abstract
Petal is one of the most esthetic and essential parts of a flower that fascinates the pollinators to enhance pollination. Petal senescence is a highly controlled and organized natural phenomenon assisted by phytohormones and gene regulation. It is an inelastically programmed event preceding to which petals give rise to color and scent that captivate pollinators, representing a flower's maturity for sexual reproduction. Till today, many genes involved in the petal senescence through genetic as well as epigenetic changes in response to hormones have been identified. In most of the species, petal senescence is controlled by ethylene, whereas others are independent of this hormone. It has also been proved that the increase in the carbohydrate contents like mannitol, inositol and trehalose delayed the senescence in tulips and Gladiolus. An increased sugar content prevents the biosynthesis of EIN3-like mRNA and further upregulates several senescence correlated genes. A wide range of different transcription factors as well as regulators are disparately expressed in ethylene insensitive and ethylene sensitive petal senescence. DcHB30, a downregulating factor, which upon linking physically to DcWRKY75 leads to the upregulation of ethylene promoting petal senescence. Here we describe the role of ethylene in petal senescence through epigenetic changes. Studies show that ethylene causes petal senescence through epigenetic changes. Feng et al. (Plant Physiol 192:546-564, 2023) observed that ARABIDOPSIS HOMOLOG OF TRITHORAX1 (DcATX1) promotes trimethylation of histone 3 (H3) at 4th lysine (H3K4me3) in Carnation. H3K4me3 further stimulates the expression of genes of ethylene biosynthesis and senescence, leading to senescence in Carnation.
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Affiliation(s)
- Ajayraj Kushwaha
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Vipul Mishra
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Durgesh Kumar Tripathi
- Crop Nanobiology and Molecular Stress Physiology Lab Amity, Institute of Organic Agriculture, Amity University Uttar Pradesh, Sector-125, Noida, 201313, India
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul, 02707, South Korea.
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India.
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Li S, Zhao Y, Tan S, Li Z. Non-coding RNAs and leaf senescence: Small molecules with important roles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108399. [PMID: 38277833 DOI: 10.1016/j.plaphy.2024.108399] [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: 11/22/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Non-coding RNAs (ncRNAs) are a special class of functional RNA molecules that are not translated into proteins. ncRNAs have emerged as pivotal regulators of diverse developmental processes in plants. Recent investigations have revealed the association of ncRNAs with the regulation of leaf senescence, a complex and tightly regulated developmental process. However, a comprehensive review of the involvement of ncRNAs in the regulation of leaf senescence is still lacking. This manuscript aims to summarize the molecular mechanisms underlying ncRNAs-mediated leaf senescence and the potential applications of ncRNAs to manipulate the onset and progression of leaf senescence. Various classes of ncRNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are discussed in terms of their regulatory mechanisms in leaf senescence. Furthermore, we explore the interactions between ncRNA and the key regulators of senescence, including transcription factors as well as core components in phytohormone signaling pathways. We also discuss the possible challenges and approaches related to ncRNA-mediated leaf senescence. This review contributes to a further understanding of the intricate regulatory network involving ncRNAs in leaf senescence.
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Affiliation(s)
- Shichun Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yaning Zhao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuya Tan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhonghai Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Zhang J, Zhao H, Chen L, Lin J, Wang Z, Pan J, Yang F, Ni X, Wang Y, Wang Y, Li R, Pi E, Wang S. Multifaceted roles of WRKY transcription factors in abiotic stress and flavonoid biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1303667. [PMID: 38169626 PMCID: PMC10758500 DOI: 10.3389/fpls.2023.1303667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Increasing biotic and abiotic stresses are seriously impeding the growth and yield of staple crops and threatening global food security. As one of the largest classes of regulators in vascular plants, WRKY transcription factors play critical roles governing flavonoid biosynthesis during stress responses. By binding major W-box cis-elements (TGACCA/T) in target promoters, WRKYs modulate diverse signaling pathways. In this review, we optimized existing WRKY phylogenetic trees by incorporating additional plant species with WRKY proteins implicated in stress tolerance and flavonoid regulation. Based on the improved frameworks and documented results, we aim to deduce unifying themes of distinct WRKY subfamilies governing specific stress responses and flavonoid metabolism. These analyses will generate experimentally testable hypotheses regarding the putative functions of uncharacterized WRKY homologs in tuning flavonoid accumulation to enhance stress resilience.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Erxu Pi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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Zhang Y, Huang D, Miao Y. Epigenetic control of plant senescence and cell death and its application in crop improvement. FRONTIERS IN PLANT SCIENCE 2023; 14:1258487. [PMID: 37965008 PMCID: PMC10642554 DOI: 10.3389/fpls.2023.1258487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
Plant senescence is the last stage of plant development and a type of programmed cell death, occurring at a predictable time and cell. It involves the functional conversion from nutrient assimilation to nutrient remobilization, which substantially impacts plant architecture and plant biomass, crop quality, and horticultural ornamental traits. In past two decades, DNA damage was believed to be a main reason for cell senescence. Increasing evidence suggests that the alteration of epigenetic information is a contributing factor to cell senescence in organisms. In this review, we summarize the current research progresses of epigenetic and epitranscriptional mechanism involved in cell senescence of plant, at the regulatory level of DNA methylation, histone methylation and acetylation, chromatin remodeling, non-coding RNAs and RNA methylation. Furthermore, we discuss their molecular genetic manipulation and potential application in agriculture for crop improvement. Finally we point out the prospects of future research topics.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongmei Huang
- Department of Biochemistry and Molecular Biology, Xiamen Medical College, Xiamen, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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Seni S, Singh RK, Prasad M. Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194966. [PMID: 37532097 DOI: 10.1016/j.bbagrm.2023.194966] [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: 05/30/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
Plants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.
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Affiliation(s)
- Sushmita Seni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India.
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Cao J, Liu H, Tan S, Li Z. Transcription Factors-Regulated Leaf Senescence: Current Knowledge, Challenges and Approaches. Int J Mol Sci 2023; 24:ijms24119245. [PMID: 37298196 DOI: 10.3390/ijms24119245] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/12/2023] [Accepted: 05/14/2023] [Indexed: 06/12/2023] Open
Abstract
Leaf senescence is a complex biological process regulated at multiple levels, including chromatin remodeling, transcription, post-transcription, translation, and post-translational modifications. Transcription factors (TFs) are crucial regulators of leaf senescence, with NAC and WRKY families being the most studied. This review summarizes the progress made in understanding the regulatory roles of these families in leaf senescence in Arabidopsis and various crops such as wheat, maize, sorghum, and rice. Additionally, we review the regulatory functions of other families, such as ERF, bHLH, bZIP, and MYB. Unraveling the mechanisms of leaf senescence regulated by TFs has the potential to improve crop yield and quality through molecular breeding. While significant progress has been made in leaf senescence research in recent years, our understanding of the molecular regulatory mechanisms underlying this process is still incomplete. This review also discusses the challenges and opportunities in leaf senescence research, with suggestions for possible strategies to address them.
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Affiliation(s)
- Jie Cao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hairong Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuya Tan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhonghai Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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12
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Feng S, Jiang X, Wang R, Tan H, Zhong L, Cheng Y, Bao M, Qiao H, Zhang F. Histone H3K4 methyltransferase DcATX1 promotes ethylene induced petal senescence in carnation. PLANT PHYSIOLOGY 2023; 192:546-564. [PMID: 36623846 PMCID: PMC10152666 DOI: 10.1093/plphys/kiad008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 05/03/2023]
Abstract
Petal senescence is controlled by a complex regulatory network. Epigenetic regulation like histone modification influences chromatin state and gene expression. However, the involvement of histone methylation in regulating petal senescence remains poorly understood. Here, we found that the trimethylation of histone H3 at Lysine 4 (H3K4me3) is increased during ethylene-induced petal senescence in carnation (Dianthus caryophyllus L.). H3K4me3 levels were positively associated with the expression of transcription factor DcWRKY75, ethylene biosynthetic genes 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (DcACS1), and ACC oxidase (DcACO1), and senescence associated genes (SAGs) DcSAG12 and DcSAG29. Further, we identified that carnation ARABIDOPSIS HOMOLOG OF TRITHORAX1 (DcATX1) encodes a histone lysine methyltransferase which can methylate H3K4. Knockdown of DcATX1 delayed ethylene-induced petal senescence in carnation, which was associated with the down-regulated expression of DcWRKY75, DcACO1, and DcSAG12, whereas overexpression of DcATX1 exhibited the opposite effects. DcATX1 promoted the transcription of DcWRKY75, DcACO1, and DcSAG12 by elevating the H3K4me3 levels within their promoters. Overall, our results demonstrate that DcATX1 is a H3K4 methyltransferase that promotes the expression of DcWRKY75, DcACO1, DcSAG12 and potentially other downstream target genes by regulating H3K4me3 levels, thereby accelerating ethylene-induced petal senescence in carnation. This study further indicates that epigenetic regulation is important for plant senescence processes.
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Affiliation(s)
- Shan Feng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyu Jiang
- State key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruiming Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hualiang Tan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Linlin Zhong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunjiang Cheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Fan Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Institute of Flowers Research, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
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An B, Cai H, Li B, Zhang S, He Y, Wang R, Jiao C, Guo Y, Xu L, Xu Y. Molecular Evolution of Histone Methylation Modification Families in the Plant Kingdom and Their Genome-Wide Analysis in Barley. Int J Mol Sci 2023; 24:ijms24098043. [PMID: 37175750 PMCID: PMC10178440 DOI: 10.3390/ijms24098043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
In this study, based on the OneKP database and through comparative genetic analysis, we found that HMT and HDM may originate from Chromista and are highly conserved in green plants, and that during the evolution from algae to land plants, histone methylation modifications gradually became complex and diverse, which is more conducive to the adaptation of plants to complex and variable environments. We also characterized the number of members, genetic similarity, and phylogeny of HMT and HDM families in barley using the barley pangenome and the Tibetan Lasa Goumang genome. The results showed that HMT and HDM were highly conserved in the domestication of barley, but there were some differences in the Lasa Goumang SDG subfamily. Expression analysis showed that HvHMTs and HvHDMs were highly expressed in specific tissues and had complex expression patterns under multiple stress treatments. In summary, the amplification and variation of HMT and HDM facilitate plant adaptation to complex terrestrial environments, while they are highly conserved in barley and play an important role in barley growth and development with abiotic stresses. In brief, our findings provide a novel perspective on the origin and evolutionary history of plant HvHMTs and HvHDMs, and lay a foundation for further investigation of their functions in barley.
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Affiliation(s)
- Bingzhuang An
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Haiya Cai
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Bo Li
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Shuo Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yonggang He
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Rong Wang
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Chunhai Jiao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Ying Guo
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Le Xu
- College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Key Laboratory of Ministry of Agriculture and Rural Affairs for Crop Molecular Breeding, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Scientific Observation and Experiment Station for Crop Gene Resources and Germplasm Enhancement in Hubei, Ministry of Agriculture and Rural Affairs, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
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14
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Wang H, Cheng X, Yin D, Chen D, Luo C, Liu H, Huang C. Advances in the Research on Plant WRKY Transcription Factors Responsive to External Stresses. Curr Issues Mol Biol 2023; 45:2861-2880. [PMID: 37185711 PMCID: PMC10136515 DOI: 10.3390/cimb45040187] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
The WRKY transcription factors are a class of transcriptional regulators that are ubiquitous in plants, wherein they play key roles in various physiological activities, including responses to stress. Specifically, WRKY transcription factors mediate plant responses to biotic and abiotic stresses through the binding of their conserved domain to the W-box element of the target gene promoter and the subsequent activation or inhibition of transcription (self-regulation or cross-regulation). In this review, the progress in the research on the regulatory effects of WRKY transcription factors on plant responses to external stresses is summarized, with a particular focus on the structural characteristics, classifications, biological functions, effects on plant secondary metabolism, regulatory networks, and other aspects of WRKY transcription factors. Future research and prospects in this field are also proposed.
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Affiliation(s)
- Hongli Wang
- College of Ecology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Xi Cheng
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Dongmei Yin
- College of Ecology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Dongliang Chen
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chang Luo
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Hua Liu
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Conglin Huang
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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15
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Manh MB, Ost C, Peiter E, Hause B, Krupinska K, Humbeck K. WHIRLY1 Acts Upstream of ABA-Related Reprogramming of Drought-Induced Gene Expression in Barley and Affects Stress-Related Histone Modifications. Int J Mol Sci 2023; 24:ijms24076326. [PMID: 37047301 PMCID: PMC10094662 DOI: 10.3390/ijms24076326] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
WHIRLY1, a small plant-specific ssDNA-binding protein, dually located in chloroplasts and the nucleus, is discussed to act as a retrograde signal transmitting a stress signal from the chloroplast to the nucleus and triggering there a stress-related gene expression. In this work, we investigated the function of WHIRLY1 in the drought stress response of barley, employing two overexpression lines (oeW1-2 and oeW1-15). The overexpression of WHIRLY1 delayed the drought-stress-related onset of senescence in primary leaves. Two abscisic acid (ABA)-dependent marker genes of drought stress, HvNCED1 and HvS40, whose expression in the wild type was induced during drought treatment, were not induced in overexpression lines. In addition, a drought-related increase in ABA concentration in the leaves was suppressed in WHIRLY1 overexpression lines. To analyze the impact of the gain-of-function of WHIRLY1 on the drought-related reprogramming of nuclear gene expression, RNAseq was performed comparing the wild type and an overexpression line. Cluster analyses revealed a set of genes highly up-regulated in response to drought in the wild type but not in the WHIRLY1 overexpression lines. Among these genes were many stress- and abscisic acid (ABA)-related ones. Another cluster comprised genes up-regulated in the oeW1 lines compared to the wild type. These were related to primary metabolism, chloroplast function and growth. Our results indicate that WHIRLY1 acts as a hub, balancing trade-off between stress-related and developmental pathways. To test whether the gain-of-function of WHIRLY1 affects the epigenetic control of stress-related gene expression, we analyzed drought-related histone modifications in different regions of the promoter and at the transcriptional start sites of HvNCED1 and HvS40. Interestingly, the level of euchromatic marks (H3K4me3 and H3K9ac) was clearly decreased in both genes in a WHIRLY1 overexpression line. Our results indicate that WHIRLY1, which is discussed to act as a retrograde signal, affects the ABA-related reprogramming of nuclear gene expression during drought via differential histone modifications.
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Affiliation(s)
- Minh Bui Manh
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Charlotte Ost
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Edgar Peiter
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Karin Krupinska
- Institute of Botany, Christian-Albrechts-University (CAU), 24098 Kiel, Germany
| | - Klaus Humbeck
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
- Correspondence:
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16
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Wang M, He L, Chen B, Wang Y, Wang L, Zhou W, Zhang T, Cao L, Zhang P, Xie L, Zhang Q. Transgenerationally Transmitted DNA Demethylation of a Spontaneous Epialleles Using CRISPR/dCas9-TET1cd Targeted Epigenetic Editing in Arabidopsis. Int J Mol Sci 2022; 23:ijms231810492. [PMID: 36142407 PMCID: PMC9504898 DOI: 10.3390/ijms231810492] [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: 08/02/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR/dCas9 is an important DNA modification tool in which a disarmed Cas9 protein with no nuclease activity is fused with a specific DNA modifying enzyme. A previous study reported that overexpression of the TET1 catalytic domain (TET1cd) reduces genome-wide methylation in Arabidopsis. A spontaneous naturally occurring methylation region (NMR19-4) was identified in the promoter region of the PPH (Pheophytin Pheophorbide Hydrolase) gene, which encodes an enzyme that can degrade chlorophyll and accelerate leaf senescence. The methylation status of NMR19-4 is associated with PPH expression and leaf senescence in Arabidopsis natural accessions. In this study, we show that the CRISPR/dCas9-TET1cd system can be used to target the methylation of hypermethylated NMR19-4 region to reduce the level of methylation, thereby increasing the expression of PPH and accelerating leaf senescence. Furthermore, hybridization between transgenic demethylated plants and hypermethylated ecotypes showed that the demethylation status of edited NMR19-4, along with the enhanced PPH expression and accelerated leaf senescence, showed Mendelian inheritance in F1 and F2 progeny, indicating that spontaneous epialleles are stably transmitted trans-generationally after demethylation editing. Our results provide a rational approach for future editing of spontaneously mutated epialleles and provide insights into the epigenetic mechanisms that control plant leaf senescence.
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Affiliation(s)
- Min Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Li He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Bowei Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Lishan Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Wei Zhou
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Lesheng Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Peng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Linan Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Correspondence:
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17
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Zhang Y, Li Y, Zhang Y, Zhang Z, Zhang D, Wang X, Lai B, Huang D, Gu L, Xie Y, Miao Y. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4696-4715. [PMID: 35429161 DOI: 10.1093/jxb/erac155] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyun Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deyu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaonan Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binfan Lai
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dandan Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yakun Xie
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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18
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Vatov E, Zentgraf U, Ludewig U. Moderate DNA methylation changes associated with nitrogen remobilization and leaf senescence in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4733-4752. [PMID: 35552412 PMCID: PMC9366325 DOI: 10.1093/jxb/erac167] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The lifespan of plants is restricted by environmental and genetic components. Following the transition to reproductive growth, leaf senescence ends cellular life in monocarpic plants to remobilize nutrients to storage organs. In Arabidopsis, we initially observed altered leaf to seed ratios, faster senescence progression, altered leaf nitrogen recovery after transient nitrogen removal, and ultimately enhanced nitrogen remobilization from the leaves in two methylation mutants (ros1 and the triple dmr1/2 cmt3 knockout). Analysis of the DNA methylome in wild type Col-0 leaves identified an initial moderate decline of cytosine methylation with progressing leaf senescence, predominantly in the CG context. Late senescence was associated with moderate de novo methylation of cytosines, primarily in the CHH context. Relatively few differentially methylated regions, including one in the ROS1 promoter linked to down-regulation of ROS1, were present, but these were unrelated to known senescence-associated genes. Differential methylation patterns were identified in transcription factor binding sites, such as the W-boxes that are targeted by WRKYs. Methylation in artificial binding sites impaired transcription factor binding in vitro. However, it remains unclear how moderate methylome changes during leaf senescence are linked with up-regulated genes during senescence.
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Affiliation(s)
- Emil Vatov
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, D-70593, Germany
- Center for Molecular Biology of Plants (ZMBP), University of Tübingen, Tübingen, D-72076, Germany
| | - Ulrike Zentgraf
- Center for Molecular Biology of Plants (ZMBP), University of Tübingen, Tübingen, D-72076, Germany
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Sasi JM, Gupta S, Singh A, Kujur A, Agarwal M, Katiyar-Agarwal S. Know when and how to die: gaining insights into the molecular regulation of leaf senescence. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1515-1534. [PMID: 36389097 PMCID: PMC9530073 DOI: 10.1007/s12298-022-01224-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 06/16/2023]
Abstract
Senescence is the ultimate phase in the life cycle of leaves which is crucial for recycling of nutrients to maintain plant fitness and reproductive success. The earliest visible manifestation of leaf senescence is their yellowing, which usually commences with the breakdown of chlorophyll. The degradation process involves a gradual and highly coordinated disassembly of macromolecules resulting in the accumulation of nutrients, which are subsequently mobilized from the senescing leaves to the developing organs. Leaf senescence progresses under overly tight genetic and molecular control involving a well-orchestrated and intricate network of regulators that coordinate spatio-temporally with the influence of both internal and external cues. Owing to the advancements in omics technologies, the availability of mutant resources, scalability of molecular analyses methodologies and the advanced capacity to integrate multidimensional data, our understanding of the genetic and molecular basis of leaf ageing has greatly expanded. The review provides a compilation of the multitier regulation of senescence process and the interrelation between the environment and the terminal phase of leaf development. The knowledge gained would benefit in devising the strategies for manipulation of leaf senescence process to improve crop quality and productivity.
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Affiliation(s)
- Jyothish Madambikattil Sasi
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Apurva Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Alice Kujur
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
- USDA-ARS Plant Genetics Research Unit, The Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
- Centre of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324 India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007 India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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20
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Huang D, Lan W, Ma W, Huang R, Lin W, Li M, Chen CY, Wu K, Miao Y. WHIRLY1 recruits the histone deacetylase HDA15 repressing leaf senescence and flowering in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1411-1429. [PMID: 35510566 DOI: 10.1111/jipb.13272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Leaf senescence is controlled by a complex regulatory network in which robustness is ensured by the activity of transcription factors and epigenetic regulators. However, how these coordinate the process of leaf senescence remains poorly understood. We found that WHIRLY1 interacts with Histone Deacetylase (HDA)15, a Reduced Potassium Dependence3 (RPD3)/HDA1-type HDA, by using green fluorescent protein-nanotrap-mass spectrum assays. The development-dependent interaction between WHIRLY1 and HDA15 was further confirmed by bimolecular fluorescence complementation assays and co-immunoprecipitation assays in Arabidopsis. Multi-omics genome-wide transcriptome and H3K9 acetylome enrichment analysis showed that HDA15 delays leaf senescence and flowering by repressing the expression of the positive regulators of leaf senescence and flowering, such as LOX2 and LARP1C, and reducing H3K9ac levels at these loci; WHIRLY1 and HDA15 co-target to the region near the transcription start site of a subset of nutrient recycling-related genes (e.g., Glutathione S-transferases 10, non-coding RNA, and photosystem II protein D1 synthesizer attenuator PDIL1-2), as well as WRKY53 and ELF4, and co-repress their expression by removing H3K9 acetylation. Our study revealed a key transcription regulatory node of nutrient recycling and senescence-associated genes involved in leaf senescence and flowering via the recruitment of HDA15 by the single-stranded DNA/RNA-binding protein WHIRLY1.
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Affiliation(s)
- Dongmei Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Lan
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Weibo Ma
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rulin Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenfang Lin
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengsi Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chia-Yang Chen
- Institute of Botany, College of Life Sciences, Taiwan University, Taibei, 106, China
| | - Keqiang Wu
- Institute of Botany, College of Life Sciences, Taiwan University, Taibei, 106, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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21
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Zheng B, Liu J, Gao A, Chen X, Gao L, Liao L, Luo B, Ogutu CO, Han Y. Epigenetic reprogramming of H3K27me3 and DNA methylation during leaf-to-callus transition in peach. HORTICULTURE RESEARCH 2022; 9:uhac132. [PMID: 35937864 PMCID: PMC9350832 DOI: 10.1093/hr/uhac132] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/29/2022] [Indexed: 05/30/2023]
Abstract
Plant tissues are capable of developing unorganized cell masses termed calluses in response to the appropriate combination of auxin and cytokinin. Revealing the potential epigenetic mechanisms involved in callus development can improve our understanding of the regeneration process of plant cells, which will be beneficial for overcoming regeneration recalcitrance in peach. In this study, we report on single-base resolution mapping of DNA methylation and reprogramming of the pattern of trimethylation of histone H3 at lysine 27 (H3K27me3) at the genome-wide level during the leaf-to-callus transition in peach. Overall, mCG and mCHH were predominant at the genome-wide level and mCG was predominant in genic regions. H3K27me3 deposition was mainly detected in the gene body and at the TSS site, and GAGA repetitive sequences were prone to recruit H3K27me3 modification. H3K27me3 methylation was negatively correlated with gene expression. In vitro culture of leaf explants was accompanied by DNA hypomethylation and H3K27me3 demethylation, which could activate auxin- and cytokinin-related regulators to induce callus development. The DNA methylation inhibitor 5-azacytidine could significantly increase callus development, while the H3K27me3 demethylase inhibitor GSK-J4 dramatically reduced callus development. These results demonstrate the roles of DNA methylation and H3K27me3 modification in mediating chromatin status during callus development. Our study provides new insights into the epigenetic mechanisms through which differentiated cells acquire proliferative competence to induce callus development in plants.
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Affiliation(s)
- Beibei Zheng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingjing Liu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Anqi Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Xiaomei Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Lingling Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Binwen Luo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Collins Otieno Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yuepeng Han
- Corresponding author. E-mail:
Equal contribution
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22
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Esmaelpour S, Iranbakhsh A, Dilmaghani K, Marandi SJ, Oraghi Ardebili Z. The potential contribution of the WRKY53 transcription factor, gamma-aminobutyric acid (GABA) transaminase, and histone deacetylase in regulating growth, organogenesis, photosynthesis, and transcriptional responses of tomato to different light-emitting diodes (LEDs). JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 229:112413. [PMID: 35220016 DOI: 10.1016/j.jphotobiol.2022.112413] [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: 10/04/2021] [Revised: 02/09/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Impressive progress in developing light-emitting diodes (LEDs) offers a new dimension for meeting agricultural and biological expectations. The present study addresses how tomato (Solanum lycopersicum) seedlings respond to the different spectral qualities of LEDs (white, red, blue, and blue + red). The light treatments in a wavelength-dependent manner contributed to the variations in biomass accumulation, morphology, and organogenesis pattern. Light quality epigenetically contributed to the transcriptional regulation of the histone deacetylase (HDA3) gene. The expression of WRKY53 transcription factor and gamma-aminobutyric acid transaminase (GABA-TP1) genes displayed a similar upward trend in response to the blue wavelength. On the contrary, the sole red light downregulated the WRKY53 and GABA-TP1 genes. The blue irradiation was associated with the upregulation in the glycolate oxidase (GLO2) and ribulose-1,5-bisphosphate carboxylase‑oxygenase large subunit (rbcL) genes, while the red wavelength down-regulated the GLO2 and rbcL genes. Moreover, rbcL statistically correlated with GLO2, referring to the balanced regulation of photorespiration and the Calvin cycle. The blue wavelengths were more capable of improving the concentrations of photosynthetic pigments and proline. The seedlings grown under the white LEDs displayed the maximum activity of the catalase enzyme. The cultivation of tomato seedlings under the blue lights enhanced the activities of the superoxide dismutase and ascorbate peroxidase enzymes. The light treatments were associated with the variation in the nutritional status of K+ and Ca2+ in both leaves and roots. The presented findings and inferences support the potential contribution of WRKY53, HDA3, and GABA signaling in modulating plant responses to light quality.
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Affiliation(s)
- Soghra Esmaelpour
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Alireza Iranbakhsh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | | | - Sayeh Jafari Marandi
- Department of Biology, Tehran North Branch, Islamic Azad University, Tehran, Iran
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23
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Wen YX, Wang JY, Zhu HH, Han GH, Huang RN, Huang L, Hong YG, Zheng SJ, Yang JL, Chen WW. Potential Role of Domains Rearranged Methyltransferase7 in Starch and Chlorophyll Metabolism to Regulate Leaf Senescence in Tomato. FRONTIERS IN PLANT SCIENCE 2022; 13:836015. [PMID: 35211145 PMCID: PMC8860812 DOI: 10.3389/fpls.2022.836015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Deoxyribonucleic acid (DNA) methylation is an important epigenetic mark involved in diverse biological processes. Here, we report the critical function of tomato (Solanum lycopersicum) Domains Rearranged Methyltransferase7 (SlDRM7) in plant growth and development, especially in leaf interveinal chlorosis and senescence. Using a hairpin RNA-mediated RNA interference (RNAi), we generated SlDRM7-RNAi lines and observed pleiotropic developmental defects including small and interveinal chlorosis leaves. Combined analyses of whole genome bisulfite sequence (WGBS) and RNA-seq revealed that silencing of SlDRM7 caused alterations in both methylation levels and transcript levels of 289 genes, which are involved in chlorophyll synthesis, photosynthesis, and starch degradation. Furthermore, the photosynthetic capacity decreased in SlDRM7-RNAi lines, consistent with the reduced chlorophyll content and repression of genes involved in chlorophyll biosynthesis, photosystem, and photosynthesis. In contrast, starch granules were highly accumulated in chloroplasts of SlDRM7-RNAi lines and associated with lowered expression of genes in the starch degradation pathway. In addition, SlDRM7 was activated by aging- and dark-induced senescence. Collectively, these results demonstrate that SlDRM7 acts as an epi-regulator to modulate the expression of genes related to starch and chlorophyll metabolism, thereby affecting leaf chlorosis and senescence in tomatoes.
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Affiliation(s)
- Yu Xin Wen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jia Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hui Hui Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Guang Hao Han
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ru Nan Huang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Yi Guo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wei Wei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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24
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Ding X, Zhang D, Gu D, Li Z, Liang H, Zhu H, Jiang Y, Duan X. Histone H3K27 demethylase SlJMJ4 promotes dark- and ABA- induced leaf senescence in tomato. HORTICULTURE RESEARCH 2022; 9:uhab077. [PMID: 35043207 PMCID: PMC8973004 DOI: 10.1093/hr/uhab077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 06/12/2023]
Abstract
Leaf senescence is a highly-programmed developmental process during the plant life cycle. ABA plays an important role in leaf senescence. However, the mechanism underlying ABA-mediated leaf senescence, particularly the upstream epigenetic regulatory network, remains largely unclear. Here, we identified that SlJMJ4, a Jumonji C (jmjC) domain-containing protein in tomato, specifically demethylates di- and tri-methylations of lysine 27 of histone H3 (H3K27) in vitro and in vivo. Overexpression of SlJMJ4 results in premature senescence phenotype and promotes dark- and ABA-induced leaf senescence in tomato. Under dark condition, SlJMJ4-promoted leaf senescence is associated with upregulated expression of transcription factors (SlORE1 and SlNAP2) and senescence-associated genes (SlSAG113, SlSAG12) via removal of H3K27me3. In responses to ABA, overexpression of SlJMJ4 increases its binding at the loci of SlORE1, SlNAP2, SlSAG113, SlSAG12, SlABI5 and SlNCED3 and decreases their H3K27me3 levels, and therefore activates their expression and mediates ABA-induced leaf senescence in tomato. Taken together, these results demonstrate that SlJMJ4 plays a positive role in leaf senescence in tomato and is implicated in ABA-induced leaf senescence by binding to many key genes related to ABA synthesis and signaling, transcription regulation and senescence and hence promoting their H3K27me3 demethylation.
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Affiliation(s)
- Xiaochun Ding
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Dandan Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Dachuan Gu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhiwei Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanzhi Liang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Zhu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuewu Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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25
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Miryeganeh M. Epigenetic Mechanisms of Senescence in Plants. Cells 2022; 11:251. [PMID: 35053367 PMCID: PMC8773728 DOI: 10.3390/cells11020251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/30/2022] Open
Abstract
Senescence is a major developmental transition in plants that requires a massive reprogramming of gene expression and includes various layers of regulations. Senescence is either an age-dependent or a stress-induced process, and is under the control of complex regulatory networks that interact with each other. It has been shown that besides genetic reprogramming, which is an important aspect of plant senescence, transcription factors and higher-level mechanisms, such as epigenetic and small RNA-mediated regulators, are also key factors of senescence-related genes. Epigenetic mechanisms are an important layer of this multilevel regulatory system that change the activity of transcription factors (TFs) and play an important role in modulating the expression of senescence-related gene. They include chromatin remodeling, DNA methylation, histone modification, and the RNA-mediated control of transcription factors and genes. This review provides an overview of the known epigenetic regulation of plant senescence, which has mostly been studied in the form of leaf senescence, and it also covers what has been reported about whole-plant senescence.
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Affiliation(s)
- Matin Miryeganeh
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
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26
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Yu Y, Qi Y, Xu J, Dai X, Chen J, Dong CH, Xiang F. Arabidopsis WRKY71 regulates ethylene-mediated leaf senescence by directly activating EIN2, ORE1 and ACS2 genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1819-1836. [PMID: 34296474 DOI: 10.1111/tpj.15433] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 05/13/2023]
Abstract
Leaf senescence is a pivotal step in the last stage of the plant life cycle and is influenced by various external and endogenous cues. A series of reports have indicated the involvement of the WRKY transcription factors in regulating leaf senescence, but the molecular mechanisms and signaling pathways remain largely unclear. Here we provide evidence demonstrating that WRKY71 acts as a positive regulator of leaf senescence in Arabidopsis. WRKY71-1D, an overexpressor of WRKY71, exhibited early leaf senescence, while wrky71-1, the WRKY71 loss-of-function mutant, displayed delayed leaf senescence. Accordingly, a set of senescence-associated genes (SAGs) were substantially elevated in WRKY71-1D but markedly decreased in wrky71-1. Chromatin immunoprecipitation assays indicated that WRKY71 can bind directly to the promoters of SAG13 and SAG201. Transcriptome analysis suggested that WRKY71 might mediate multiple cues to accelerate leaf senescence, such as abiotic stresses, dark and ethylene. WRKY71 was ethylene inducible, and treatment with the ethylene precursor 1-amino-cyclopropane-1-carboxylic acid enhanced leaf senescence in WRKY71-1D but caused only a marginal delay in leaf senescence in wrky71-1. In vitro and in vivo assays demonstrated that WRKY71 can directly regulate ETHYLENE INSENSITIVE2 (EIN2) and ORESARA1 (ORE1), genes of the ethylene signaling pathway. Consistently, leaf senescence of WRKY71-1D was obviously retarded in the ein2-5 and nac2-1 mutants. Moreover, WRKY71 was also proved to interact with ACS2 in vitro and in vivo. Treatment with AgNO3 and aminoethoxyvinylglycine and acs2-1 could greatly arrest the leaf senescence of WRKY71-1D. In conclusion, our data revealed that WRKY71 mediates ethylene signaling and synthesis to hasten leaf senescence in Arabidopsis.
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Affiliation(s)
- Yanchong Yu
- Shandong Key Laboratory of Plant Biotechnology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanan Qi
- Shandong Key Laboratory of Plant Biotechnology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jinpeng Xu
- Shandong Key Laboratory of Plant Biotechnology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xuehuan Dai
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Jiacai Chen
- Shandong Key Laboratory of Plant Biotechnology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chun-Hai Dong
- Shandong Key Laboratory of Plant Biotechnology, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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27
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Guo Y, Ren G, Zhang K, Li Z, Miao Y, Guo H. Leaf senescence: progression, regulation, and application. MOLECULAR HORTICULTURE 2021; 1:5. [PMID: 37789484 PMCID: PMC10509828 DOI: 10.1186/s43897-021-00006-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 05/24/2023]
Abstract
Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants' fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGs) via reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.
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Affiliation(s)
- Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 Shandong China
| | - Guodong Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Kewei Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 Zhejiang China
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, 518055 Guangdong China
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28
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Hu G, Huang B, Wang K, Frasse P, Maza E, Djari A, Benhamed M, Gallusci P, Li Z, Zouine M, Bouzayen M. Histone posttranslational modifications rather than DNA methylation underlie gene reprogramming in pollination-dependent and pollination-independent fruit set in tomato. THE NEW PHYTOLOGIST 2021; 229:902-919. [PMID: 32875585 PMCID: PMC7821339 DOI: 10.1111/nph.16902] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 05/10/2023]
Abstract
Fruit formation comprises a series of developmental transitions among which the fruit set process is essential in determining crop yield. Yet, our understanding of the epigenetic landscape remodelling associated with the flower-to-fruit transition remains poor. We investigated the epigenetic and transcriptomic reprogramming underlying pollination-dependent and auxin-induced flower-to-fruit transitions in the tomato (Solanum lycopersicum) using combined genomewide transcriptomic profiling, global ChIP-sequencing and whole genomic DNA bisulfite sequencing (WGBS). Variation in the expression of the overwhelming majority of genes was associated with change in histone mark distribution, whereas changes in DNA methylation concerned a minor fraction of differentially expressed genes. Reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone posttranslational modifications rather than DNA methylation are associated with the remodelling of the epigenetic landscape underpinning the flower-to-fruit transition. Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations.
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Affiliation(s)
- Guojian Hu
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Baowen Huang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Keke Wang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Pierre Frasse
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Elie Maza
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Anis Djari
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris‐SaclayCNRSINRAUniversity Paris‐SudUniversity of EvryUniversity Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayBatiment 630Orsay91405France
| | - Philippe Gallusci
- UMR EGFVBordeaux Sciences AgroINRAUniversité de Bordeaux210 Chemin de Leysotte, CS 50008Villenave d’Ornon33882France
| | - Zhengguo Li
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
| | - Mohamed Zouine
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Mondher Bouzayen
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
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Single-stranded DNA-binding proteins in plant telomeres. Int J Biol Macromol 2020; 165:1463-1467. [PMID: 32998016 DOI: 10.1016/j.ijbiomac.2020.09.211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/13/2020] [Accepted: 09/23/2020] [Indexed: 11/21/2022]
Abstract
Telomere single-stranded DNA-binding proteins bind to the terminal single-stranded DNA of telomeres, maintaining and protecting the chromosomal end in eukaryotes. This paper focuses on the protective mechanism of single-stranded DNA-binding proteins in plant telomeres. This review summarizes the roles of plant single-stranded DNA-binding proteins and their influence on telomere length and telomerase. This review provides insights into the mechanism and development of single-stranded DNA-binding proteins in plants.
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Nakamura M, Batista RA, Köhler C, Hennig L. Polycomb Repressive Complex 2-mediated histone modification H3K27me3 is associated with embryogenic potential in Norway spruce. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6366-6378. [PMID: 32894759 PMCID: PMC7586741 DOI: 10.1093/jxb/eraa365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/29/2020] [Indexed: 05/28/2023]
Abstract
Epigenetic reprogramming during germ cell formation is essential to gain pluripotency and thus embryogenic potential. The histone modification H3K27me3, which is catalysed by the Polycomb repressive complex 2 (PRC2), regulates important developmental processes in both plants and animals, and defects in PRC2 components cause pleiotropic developmental abnormalities. Nevertheless, the role of H3K27me3 in determining embryogenic potential in gymnosperms is still elusive. To address this, we generated H3K27me3 profiles of Norway spruce (Picea abies) embryonic callus and non-embryogenic callus using CUT&RUN, which is a powerful method for chromatin profiling. Here, we show that H3K27me3 mainly accumulated in genic regions in the Norway spruce genome, similarly to what is observed in other plant species. Interestingly, H3K27me3 levels in embryonic callus were much lower than those in the other examined tissues, but markedly increased upon embryo induction. These results show that H3K27me3 levels are associated with the embryogenic potential of a given tissue, and that the early phase of somatic embryogenesis is accompanied by changes in H3K27me3 levels. Thus, our study provides novel insights into the role of this epigenetic mark in spruce embryogenesis and reinforces the importance of PRC2 as a key regulator of cell fate determination across different plant species.
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Affiliation(s)
- Miyuki Nakamura
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Sweden
| | - Rita A Batista
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Sweden
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Zhao MM, Zhang XW, Liu YW, Li K, Tan Q, Zhou S, Wang G, Zhou CJ. A WRKY transcription factor, TaWRKY42-B, facilitates initiation of leaf senescence by promoting jasmonic acid biosynthesis. BMC PLANT BIOLOGY 2020; 20:444. [PMID: 32993508 PMCID: PMC7526184 DOI: 10.1186/s12870-020-02650-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 09/15/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Leaf senescence comprises numerous cooperative events, integrates environmental signals with age-dependent developmental cues, and coordinates the multifaceted deterioration and source-to-sink allocation of nutrients. In crops, leaf senescence has long been regarded as an essential developmental stage for productivity and quality, whereas functional characterization of candidate genes involved in the regulation of leaf senescence has, thus far, been limited in wheat. RESULTS In this study, we analyzed the expression profiles of 97 WRKY transcription factors (TFs) throughout the progression of leaf senescence in wheat and subsequently isolated a potential regulator of leaf senescence, TaWRKY42-B, for further functional investigation. By phenotypic and physiological analyses in TaWRKY42-B-overexpressing Arabidopsis plants and TaWRKY42-B-silenced wheat plants, we confirmed the positive role of TaWRKY42-B in the initiation of developmental and dark-induced leaf senescence. Furthermore, our results revealed that TaWRKY42-B promotes leaf senescence mainly by interacting with a JA biosynthesis gene, AtLOX3, and its ortholog, TaLOX3, which consequently contributes to the accumulation of JA content. In the present study, we also demonstrated that TaWRKY42-B was functionally conserved with AtWRKY53 in the initiation of age-dependent leaf senescence. CONCLUSION Our results revealed a novel positive regulator of leaf senescence, TaWRKY42-B, which mediates JA-related leaf senescence via activation of JA biosynthesis and has the potential to be a target gene for molecular breeding in wheat.
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Affiliation(s)
- Ming-Ming Zhao
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Xiao-Wen Zhang
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Yong-Wei Liu
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences /Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, 050051, Hebei, China
| | - Ke Li
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Qi Tan
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Shuo Zhou
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences /Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, 050051, Hebei, China
| | - Geng Wang
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, China.
| | - Chun-Jiang Zhou
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, China.
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Liu H, Wang J, Sun H, Han X, Peng Y, Liu J, Liu K, Ding Y, Wang C, Du B. Transcriptome Profiles Reveal the Growth-Promoting Mechanisms of Paenibacillus polymyxa YC0136 on Tobacco ( Nicotiana tabacum L.). Front Microbiol 2020; 11:584174. [PMID: 33101258 PMCID: PMC7546199 DOI: 10.3389/fmicb.2020.584174] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/07/2020] [Indexed: 11/13/2022] Open
Abstract
Paenibacillus polymyxa is an important member of the plant growth-promoting rhizobacteria. P. polymyxa YC0136 inoculation had beneficial effect on growth promotion and biological control of tobacco (Nicotiana tabacum L.) under field conditions. This study aimed to reveal the growth-promoting mechanisms of strain YC0136. In growth-promotion assays, tobacco plant height was increased by 8.42% and 8.25% at 60 and 90 days, respectively, after inoculation with strain YC0136. Strain YC0136 also promoted the accumulation of tobacco biomass in varying degrees. Following inoculation with strain YC0136, 3,525 and 4,368 tobacco genes were up-regulated and down-regulated, respectively. Strain YC0136 induced the expression of plant hormone-related genes in tobacco, including auxin, cytokinin, and gibberellin, as well as transcription factors related to stress resistance such as WRKY and MYB. In addition, strain YC0136 induced the up-regulation of genes in the phenylpropanoid biosynthesis pathway by 1.51-4.59 times. Interaction with tobacco also induced gene expression changes in strain YC0136, with 286 and 223 genes up-regulated and down-regulated, respectively. Tobacco interaction induced up-regulation of the ilvB gene related to auxin biosynthesis in strain YC0136 by 1.72 times and induced expression of some nutrient transport genes. This study contributes to our understanding of the growth-promoting mechanisms of strain YC0136 on tobacco and provides a theoretical basis for the application of P. polymyxa YC0136 as a biological fertilizer.
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Affiliation(s)
- Hu Liu
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Jun Wang
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Huimin Sun
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Xiaobin Han
- Zunyi Tobacco Monopoly Administration of Guizhou, Zunyi, China
| | - Yulong Peng
- Zunyi Tobacco Monopoly Administration of Guizhou, Zunyi, China
| | - Jing Liu
- Zunyi Tobacco Monopoly Administration of Guizhou, Zunyi, China
| | - Kai Liu
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Yanqin Ding
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Chengqiang Wang
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
| | - Binghai Du
- College of Life Sciences, Shandong Engineering Research Center of Plant-Microbial Restoration for Saline-Alkali Land, Shandong Key Laboratory of Agricultural Microbiology, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shandong Agricultural University, Tai'an, China
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Wang X, Ajab Z, Liu C, Hu S, Liu J, Guan Q. Overexpression of transcription factor SlWRKY28 improved the tolerance of Populus davidiana × P. bolleana to alkaline salt stress. BMC Genet 2020; 21:103. [PMID: 32928116 PMCID: PMC7488863 DOI: 10.1186/s12863-020-00904-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/20/2020] [Indexed: 11/24/2022] Open
Abstract
Background WRKY transcription factors (TFs) have been suggested to play crucial roles in the response to biotic and abiotic stresses. This study is the first to report the alkaline salt regulation of the WRKY gene. Results In this study, we cloned a WRKY gene (SlWRKY28) from the Salix linearistipularis and then transferred to the Populus davidiana × P. bolleana for expression. Sequence analysis on the transcriptome of Salix linearistipular showed the significant up-regulation of WRKY gene expression in response to salt-alkali stress in seedlings. Our data showed that SlWRKY28 localized to the nucleus. Furthermore, the expression of the SlWRKY28 from female plants increased with saline-alkali stress according to the northern blot analysis results. The results of 3,3′-Diaminobenzidine (DAB) staining showed that hydrogen peroxide (H2O2) concentration was lower under stress, but ascorbate peroxidase (APX) enzyme activity was significantly higher in the overexpressed plants than that in non-transgenic (NT) plants. Conclusions We found out the SlWRKY28 induced regulation of the enzyme gene in the reactive oxygen species (ROS) scavenging pathway is a potential mechanism for transgenic lines to improve their resistance to alkaline salt. This study shows theoretical and practical significance in determining SlWRKY28 transcription factors involved in the regulation of alkaline salt tolerance.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China
| | - Zainab Ajab
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China
| | - Chenxi Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China
| | - Songmiao Hu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China
| | - Jiali Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China
| | - Qingjie Guan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, 150040, China.
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Baillo EH, Hanif MS, Guo Y, Zhang Z, Xu P, Algam SA. Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench). PLoS One 2020; 15:e0236651. [PMID: 32804948 PMCID: PMC7430707 DOI: 10.1371/journal.pone.0236651] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 07/10/2020] [Indexed: 12/26/2022] Open
Abstract
WRKY transcription factors regulate diverse biological processes in plants, including abiotic and biotic stress responses, and constitute one of the largest transcription factor families in higher plants. Although the past decade has seen significant progress towards identifying and functionally characterizing WRKY genes in diverse species, little is known about the WRKY family in sorghum (Sorghum bicolor (L.) moench). Here we report the comprehensive identification of 94 putative WRKY transcription factors (SbWRKYs). The SbWRKYs were divided into three groups (I, II, and III), with those in group II further classified into five subgroups (IIa–IIe), based on their conserved domains and zinc finger motif types. WRKYs from the model plant Arabidopsis (Arabidopsis thaliana) were used for the phylogenetic analysis of all SbWRKY genes. Motif analysis showed that all SbWRKYs contained either one or two WRKY domains and that SbWRKYs within the same group had similar motif compositions. SbWRKY genes were located on all 10 sorghum chromosomes, and some gene clusters and two tandem duplications were detected. SbWRKY gene structure analysis showed that they contained 0–7 introns, with most SbWRKY genes consisting of two introns and three exons. Gene ontology (GO) annotation functionally categorized SbWRKYs under cellular components, molecular functions and biological processes. A cis-element analysis showed that all SbWRKYs contain at least one stress response-related cis-element. We exploited publicly available microarray datasets to analyze the expression profiles of 78 SbWRKY genes at different growth stages and in different tissues. The induction of SbWRKYs by different abiotic stresses hinted at their potential involvement in stress responses. qRT-PCR analysis revealed different expression patterns for SbWRKYs during drought stress. Functionally characterized WRKY genes in Arabidopsis and other species will provide clues for the functional characterization of putative orthologs in sorghum. Thus, the present study delivers a solid foundation for future functional studies of SbWRKY genes and their roles in the response to critical stresses such as drought.
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Affiliation(s)
- Elamin Hafiz Baillo
- Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- Agricultural Research Corporation (ARC), Ministry of Agriculture, Wad Madani, Gezira, Sudan
- * E-mail: ,
| | - Muhammad Sajid Hanif
- Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yinghui Guo
- Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhengbin Zhang
- Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- * E-mail: ,
| | - Ping Xu
- Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Soad Ali Algam
- Faculty of Agriculture, University of Khartoum, Khartoum, Sudan
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Yuan L, Wang D, Cao L, Yu N, Liu K, Guo Y, Gan S, Chen L. Regulation of Leaf Longevity by DML3-Mediated DNA Demethylation. MOLECULAR PLANT 2020; 13:1149-1161. [PMID: 32561358 DOI: 10.1016/j.molp.2020.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/25/2019] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Leaf senescence is driven by the expression of senescence-associated genes (SAGs). Development-specific genes often undergo DNA demethylation in their promoter and other regions, which regulates gene expression. Whether and how DNA demethylation regulates the expression of SAGs and thus leaf senescence remain elusive. Whole-genome bisulfite sequencing (WGBS) analyses of wild-type (WT) and demeter-like 3 (dml3) Arabidopsis leaves at three developmental stages revealed hypermethylation during leaf senescence in dml3 compared with WT, and 20 556 differentially methylated regions (DMRs) were identified by comparing the methylomes of dml3 and WT in the CG, CHG, and CHH contexts. Furthermore, we identified that 335 DMR-associated genes (DMGs), such as NAC016 and SEN1, are upregulated during leaf senescence, and found an inverse correlation between the DNA methylation levels (especially in the promoter regions) and the transcript abundances of the related SAGs in WT. In contrast, in dml3 the promoters of SAGs were hypermethylated and their transcript levels were remarkably reduced, and leaf senescence was significantly delayed. Collectively, our study unraveled a novel epigenetic regulatory mechanism underlying leaf senescence in which DML3 is expressed at the onset of and during senescence to demethylate promoter, gene body or 3' UTR regions to activate a set of SAGs.
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Affiliation(s)
- Lu Yuan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Dan Wang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Liwen Cao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ningning Yu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ke Liu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Susheng Gan
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Liping Chen
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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Ostrowska-Mazurek A, Kasprzak P, Kubala S, Zaborowska M, Sobieszczuk-Nowicka E. Epigenetic Landmarks of Leaf Senescence and Crop Improvement. Int J Mol Sci 2020; 21:ijms21145125. [PMID: 32698545 PMCID: PMC7404090 DOI: 10.3390/ijms21145125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 01/04/2023] Open
Abstract
This review synthesizes knowledge on epigenetic regulation of leaf senescence and discusses the possibility of using this knowledge to improve crop quality. This control level is implemented by different but interacting epigenetic mechanisms, including DNA methylation, covalent histone modifications, and non-covalent chromatin remodeling. The genetic and epigenetic changes may act alone or together and regulate the gene expression, which may result in heritable (stress memory) changes and may lead to crop survival. In the review, the question also arises whether the mitotically stable epigenetic information can be used for crop improvement. The barley crop model for early and late events of dark-induced leaf senescence (DILS), where the point of no return was defined, revealed differences in DNA and RNA modifications active in DILS compared to developmental leaf senescence. This suggests the possibility of a yet-to-be-discovered epigenetic-based switch between cell survival and cell death. Conclusions from the analyzed research contributed to the hypothesis that chromatin-remodeling mechanisms play a role in the control of induced leaf senescence. Understanding this mechanism in crops might provide a tool for further exploitation toward sustainable agriculture: so-called epibreeding.
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Affiliation(s)
- Agnieszka Ostrowska-Mazurek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
| | - Piotr Kasprzak
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
| | - Szymon Kubala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5A, 02-106 Warsaw, Poland; (S.K.); (M.Z.)
| | - Magdalena Zaborowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5A, 02-106 Warsaw, Poland; (S.K.); (M.Z.)
| | - Ewa Sobieszczuk-Nowicka
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (A.O.-M.); (P.K.)
- Correspondence: ; Tel.: +48-61-829-5892
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Li Z, Kim JH, Kim J, Lyu JI, Zhang Y, Guo H, Nam HG, Woo HR. ATM suppresses leaf senescence triggered by DNA double-strand break through epigenetic control of senescence-associated genes in Arabidopsis. THE NEW PHYTOLOGIST 2020; 227:473-484. [PMID: 32163596 DOI: 10.1111/nph.16535] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
All living organisms are unavoidably exposed to various endogenous and environmental stresses that trigger potentially fatal DNA damage, including double-strand breaks (DSBs). Although a growing body of evidence indicates that DNA damage is one of the prime drivers of aging in animals, little is known regarding the importance of DNA damage and its repair on lifespan control in plants. We found that the level of DSBs increases but DNA repair efficiency decreases as Arabidopsis leaves age. Generation of DSBs by inducible expression of I-PpoI leads to premature senescence phenotypes. We examined the senescence phenotypes in the loss-of-function mutants for 13 key components of the DNA repair pathway and found that deficiency in ATAXIA TELANGIECTASIA MUTATED (ATM), the chief transducer of the DSB signal, results in premature senescence in Arabidopsis. ATM represses DSB-induced expression of senescence-associated genes, including the genes encoding the WRKY and NAC transcription factors, central components of the leaf senescence process, via modulation of histone lysine methylation. Our work highlights the significance of ATM in the control of leaf senescence and has significant implications for the conservation of aging mechanisms in animals and plants.
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Affiliation(s)
- Zhonghai Li
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Jin Hee Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
| | - Jeongsik Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
- Faculty of Science Education, Jeju National University, Jeju, 63243, Korea
| | - Jae Il Lyu
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
| | - Yi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Hongwei Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- Department of Biology, Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
| | - Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
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Li Z, Zhang Y, Zou D, Zhao Y, Wang HL, Zhang Y, Xia X, Luo J, Guo H, Zhang Z. LSD 3.0: a comprehensive resource for the leaf senescence research community. Nucleic Acids Res 2020; 48:D1069-D1075. [PMID: 31599330 PMCID: PMC6943054 DOI: 10.1093/nar/gkz898] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/28/2019] [Accepted: 10/04/2019] [Indexed: 12/02/2022] Open
Abstract
The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reliable services for the plant research community, LSD 3.0 (https://bigd.big.ac.cn/lsd/) has been moved to and maintained by the National Genomics Data Center at Beijing Institute of Genomics, Chinese Academy of Sciences. In the current release, we added some new features: (i) Transcriptome data of leaf senescence in poplar were integrated; (ii) Leaf senescence-associated transcriptome data information in Arabidopsis, rice and soybean were included; (iii) Senescence-differentially expressed small RNAs (Sen-smRNA) in Arabidopsis were identified; (iv) Interaction pairs between Sen-smRNAs and senescence-associated transcription factors (Sen-TF) were established; (v) Senescence phenotypes of 90 natural accessions (ecotypes) and 42 images of ecotypes in Arabidopsis were incorporated; (vi) Mutant seed information of SAGs in rice obtained from Kitbase was integrated; (vii) New options of search engines for ecotypes and transcriptome data were implemented. Together, the updated database bears great utility to continue to provide users with useful resources for studies of leaf senescence.
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Affiliation(s)
- Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yang Zhang
- National Genomics Data Center, Beijing 100101, China.,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center, Beijing 100101, China.,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Zhao
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Hou-Ling Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Xinli Xia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.,College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
| | - Jingchu Luo
- College of Life Sciences, Peking University, Beijing 100871, China.,Center for Bioinformatics, Peking University, Beijing 100871, China
| | - Hongwei Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.,Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Zhang Zhang
- National Genomics Data Center, Beijing 100101, China.,Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Yang Y, Liu J, Zhou X, Liu S, Zhuang Y. Identification of WRKY gene family and characterization of cold stress-responsive WRKY genes in eggplant. PeerJ 2020; 8:e8777. [PMID: 32211240 PMCID: PMC7083166 DOI: 10.7717/peerj.8777] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/21/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND WRKY proteins play a vital role in the plants response to different stresses, growth and development. Studies of WRKY proteins have been mainly focused on model plant Arabidopsis and a few other vegetable plants. However, the systematical study of eggplant WRKY transcription factor superfamily is scarce. METHODS Bioinformatics has been used to identify and characterize the eggplant WRKY gene family. For the exploration of the differentially expressed WRKY genes, two cultivars with different cold-tolerance were used. Finally, we performed a virus-induced gene silencing (VIGS) experiment to verify the functions of SmWRKY26 and SmWRKY32. RESULTS Fifty eight (58) genes encoding eggplant WRKY proteins were identified through searching the eggplant genome. Eggplant WRKY proteins could be classified into three groups or seven subgroups in accordance with other plants. WRKY variants were identified from the eggplant. Gene structure analysis showed that the number of intron in eggplant WRKY family was from 0 to 11, with an average of 4.4. Conserved motif analysis suggested that WRKY DNA-binding domain was conserved in eggplant WRKY proteins. Furthermore, RNA-seq data showed that WRKY genes were differentially expressed in eggplant response to cold stress. By using VIGS, the two differentially expressed genes-SmWRKY26 and SmWRKY32 were verified in response to cold stress. DISCUSSIONS This study provides a foundation for further exploring the functions of WRKY proteins in eggplant response to stresses and eggplant genetic improvement in stresses.
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Affiliation(s)
- Yan Yang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jun Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaohui Zhou
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Songyu Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yong Zhuang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Han R, He X, Pan X, Shi Q, Wu Z. Enhancing xanthine dehydrogenase activity is an effective way to delay leaf senescence and increase rice yield. RICE (NEW YORK, N.Y.) 2020; 13:16. [PMID: 32162142 PMCID: PMC7065298 DOI: 10.1186/s12284-020-00375-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 02/20/2020] [Indexed: 05/17/2023]
Abstract
Xanthine dehydrogenase (XDH) is an important enzyme in purine metabolism. It is involved in regulation of the normal growth and non-biological stress-induced ageing processes in plants. The present study investigated XDH's role in regulating rice leaf senescence. We measured physical characteristics, chlorophyll content and fluorescence parameters, active oxygen metabolism, and purine metabolism in wild-type Kitaake rice (Oryza sativa L.), an OsXDH over-expression transgenic line (OE9), and an OsXDH RNA interference line (Ri3) during different growth stages. The expression patterns of the OsXDH gene confirmed that XDH was involved in the regulation of normal and abiotic stress-induced ageing processes in rice. There was no significant difference between the phenotypes of transgenic lines and wild type at the seedling stage, but differences were observed at the full heading and maturation stages. The OE9 plants were taller, with higher chlorophyll content, and their photosystems had stronger light energy absorption, transmission, dissipation, and distribution capacity, which ultimately improved the seed setting rate and 1000-seed weight. The opposite effect was found in the Ri3 plants. The OE9 line had a strong ability to remove reactive oxygen species, with increased accumulation of allantoin and alantoate. Experimental spraying of allantoin on leaves showed that it could alleviate chlorophyll degradation and decrease the content of H2O2 and malonaldehyde (MDA) in rice leaves after the full heading stage. The urate oxidase gene (UO) expression levels in the interference line were significantly lower than those in the over-expression line and wild-type lines. The allantoinase (ALN) and allantoate amidinohydrolase (AAH) genes had significantly higher expression in the Ri3 plants than the in OE9 or wild-type plants, with OE9 plants showing the lowest levels. The senescence-related genes ACD1, WRKY23, WRKY53, SGR, XERO1, and GH27 in Ri3 plants had the highest expression levels, followed by those in the wild-type plants, with OE9 plants showing the lowest levels. These results suggest that enhanced activity of XDH can regulate the synthesis of urea-related substances, improve plant antioxidant capacity, effectively delay the ageing process in rice leaves, and increase rice yield.
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Affiliation(s)
- Ruicai Han
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
- Rice Research Institute, Jiangxi Academyof Agricultural Sciences/Jiangxi Provincial Key Laboratory for Physiology and Genetics of Rice, Nanchang, China
| | - Xunfeng He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Xiaohua Pan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Qinghua Shi
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, China
| | - Ziming Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, China.
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41
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Hu J, Fang H, Wang J, Yue X, Su M, Mao Z, Zou Q, Jiang H, Guo Z, Yu L, Feng T, Lu L, Peng Z, Zhang Z, Wang N, Chen X. Ultraviolet B-induced MdWRKY72 expression promotes anthocyanin synthesis in apple. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110377. [PMID: 32005382 DOI: 10.1016/j.plantsci.2019.110377] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/07/2019] [Accepted: 12/10/2019] [Indexed: 05/27/2023]
Abstract
Ultraviolet-B (UV-B) radiation promotes anthocyanin synthesis in many plants. Although several transcription factors promote anthocyanin synthesis in response to UV-B radiation, the underlying mechanism remains unclear. In this study, the MdWRKY72 transcription factor gene was isolated from the 'Taishanzaoxia' apple genome. Quantitative real-time PCR analyses revealed that the genes encoding enzymes and transcription factors involved in the anthocyanin synthesis pathway (MdANS, MdDFR, MdUFGT, and MdMYB1) were more highly expressed in MdWRKY72-overexpressing transgenic calli than in the wild-type 'Orin' apple calli. The results indicated that MdWRKY72 increases anthocyanin synthesis in transgenic calli exposed to UV-B radiation. The results of a gel shift assay and chromatin immunoprecipitation proved that MdWRKY72 promotes MdMYB1 expression indirectly by binding to a W-box element in the MdHY5 promoter and directly by binding to a W-box element in the MdMYB1 promoter. Thus, MdWRKY72 increases anthocyanin synthesis via direct and indirect mechanisms. These findings may be useful for elucidating the molecular mechanism underlying UV-B-induced anthocyanin synthesis mediated by MdWRKY72.
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Affiliation(s)
- Jiafei Hu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Tai'an, Shandong, China; State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, Tai'an, Shandong, China
| | - Jie Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xuanxuan Yue
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Mengyu Su
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Zuolin Mao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Qi Zou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Huiyan Jiang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Zhangwen Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Lei Yu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Tian Feng
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Le Lu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Zhenge Peng
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Zongying Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Nan Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China.
| | - Xuesen Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China.
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Cheng K, Xu Y, Yang C, Ouellette L, Niu L, Zhou X, Chu L, Zhuang F, Liu J, Wu H, Charron JB, Luo M. Histone tales: lysine methylation, a protagonist in Arabidopsis development. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:793-807. [PMID: 31560751 DOI: 10.1093/jxb/erz435] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 09/17/2019] [Indexed: 05/20/2023]
Abstract
Histone methylation plays a fundamental role in the epigenetic regulation of gene expression driven by developmental and environmental cues in plants, including Arabidopsis. Histone methyltransferases and demethylases act as 'writers' and 'erasers' of methylation at lysine and/or arginine residues of core histones, respectively. A third group of proteins, the 'readers', recognize and interpret the methylation marks. Emerging evidence confirms the crucial roles of histone methylation in multiple biological processes throughout the plant life cycle. In this review, we summarize the regulatory mechanisms of lysine methylation, especially at histone H3 tails, and focus on the recent advances regarding the roles of lysine methylation in Arabidopsis development, from seed performance to reproductive development, and in callus formation.
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Affiliation(s)
- Kai Cheng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Luc Ouellette
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Longjian Niu
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xiaochen Zhou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liutian Chu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhuang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin Liu
- Institute for Food and Bioresource Engineering, Department of Energy and Resources Engineering and BIC-ESAT, College of Engineering, Peking University, Beijing, China
| | - Hualing Wu
- Tea Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Tea Plant Resources Innovation & Utilization, Guangzhou, Guangdong, China
| | - Jean-Benoit Charron
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Ming Luo
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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Zentgraf U, Doll J. Arabidopsis WRKY53, a Node of Multi-Layer Regulation in the Network of Senescence. PLANTS (BASEL, SWITZERLAND) 2019; 8:E578. [PMID: 31817659 PMCID: PMC6963213 DOI: 10.3390/plants8120578] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 12/24/2022]
Abstract
Leaf senescence is an integral part of plant development aiming at the remobilization of nutrients and minerals out of the senescing tissue into developing parts of the plant. Sequential as well as monocarpic senescence maximize the usage of nitrogen, mineral, and carbon resources for plant growth and the sake of the next generation. However, stress-induced premature senescence functions as an exit strategy to guarantee offspring under long-lasting unfavorable conditions. In order to coordinate this complex developmental program with all kinds of environmental input signals, complex regulatory cues have to be in place. Major changes in the transcriptome imply important roles for transcription factors. Among all transcription factor families in plants, the NAC and WRKY factors appear to play central roles in senescence regulation. In this review, we summarize the current knowledge on the role of WRKY factors with a special focus on WRKY53. In contrast to a holistic multi-omics view we want to exemplify the complexity of the network structure by summarizing the multilayer regulation of WRKY53 of Arabidopsis.
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Affiliation(s)
- Ulrike Zentgraf
- Center for Plant Molecular Biology (ZMBP), University of Tuebingen, Auf der Morgenstelle 32, 72076 Tuebingen, Germany;
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Lin W, Huang D, Shi X, Deng B, Ren Y, Lin W, Miao Y. H 2O 2 as a Feedback Signal on Dual-Located WHIRLY1 Associates with Leaf Senescence in Arabidopsis. Cells 2019; 8:cells8121585. [PMID: 31817716 PMCID: PMC6952816 DOI: 10.3390/cells8121585] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/21/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022] Open
Abstract
Leaf senescence, either as a natural stage of development or as an induced process under stress conditions, incorporates multiple intricate signaling pathways. At the cellular level, retrograde signals have been considered as important players during the initiation and progression of senescence in both animals and plants. The plant-specific single-strand DNA-binding protein WHIRLY1 (WHY1), a repressor of leaf natural senescence, is dually located in both nucleus and plastids. Despite many years of studies, the myth about its dual location and the underlying functional implications remain elusive. Here, we provide further evidence in Arabidopsis showing that alteration in WHY1 allocation between the nucleus and chloroplast causes perturbation in H2O2 homeostasis, resulting in adverse plant senescence phenotypes. The knockout of WHY1 increased H2O2 content at 37 days post-germination, coincident with an early leaf senescence phenotype, which can be rescued by ectopic expression of the nuclear isoform (nWHY1), but not by the plastid isoform (pWHY1). Instead, accumulated pWHY1 greatly provoked H2O2 in cells. On the other hand, exogenous H2O2 treatment induced a substantial plastid accumulation of WHY1 proteins and at the same time reduced the nuclear isoforms. This H2O2-induced loss of nucleus WHY1 isoform was accompanied by enhanced enrichments of histone H3 lysine 9 acetylation (H3K9ac) and recruitment of RNA polymerase II (RNAP II) globally, and specifically at the promoter of the senescence-related transcription factor WRKY53, which in turn activated WRKY53 transcription and led to a senescence phenotype. Thus, the distribution of WHY1 organelle isoforms and the feedback of H2O2 intervene in a circularly integrated regulatory network during plant senescence in Arabidopsis.
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Affiliation(s)
| | | | | | | | | | | | - Ying Miao
- Correspondence: ; Tel.: +86-0591-86392987
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45
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Abstract
Leaf senescence is an important developmental process involving orderly disassembly of macromolecules for relocating nutrients from leaves to other organs and is critical for plants' fitness. Leaf senescence is the response of an intricate integration of various environmental signals and leaf age information and involves a complex and highly regulated process with the coordinated actions of multiple pathways. Impressive progress has been made in understanding how senescence signals are perceived and processed, how the orderly degeneration process is regulated, how the senescence program interacts with environmental signals, and how senescence regulatory genes contribute to plant productivity and fitness. Employment of systems approaches using omics-based technologies and characterization of key regulators have been fruitful in providing newly emerging regulatory mechanisms. This review mainly discusses recent advances in systems understanding of leaf senescence from a molecular network dynamics perspective. Genetic strategies for improving the productivity and quality of crops are also described.
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Affiliation(s)
- Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; ,
| | - Hyo Jung Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu 42988, Republic of Korea
| | - Pyung Ok Lim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; ,
| | - Hong Gil Nam
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; ,
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu 42988, Republic of Korea
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The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis. PLoS Genet 2019; 15:e1008068. [PMID: 30969965 PMCID: PMC6457497 DOI: 10.1371/journal.pgen.1008068] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/06/2019] [Indexed: 11/19/2022] Open
Abstract
The roles of histone demethylation in the regulation of plant flowering, disease resistance, rhythmical response, and seed germination have been elucidated recently; however, how histone demethylation affects leaf senescence remains largely unclear. In this study, we exploited yeast one-hybrid (Y1H) to screen for the upstream regulators of NONYELLOWING1 (NYE1), and identified RELATIVE OF EARLY FLOWERING6 (REF6), a histone H3 lysine 27 tri-methylation (H3K27me3) demethylase, as a putative binding protein of NYE1 promoter. By in vivo and in vitro analyses, we demonstrated that REF6 directly binds to the motif CTCGYTY in NYE1/2 promoters through its zinc finger domain and positively regulates their expression. Loss-of-function of REF6 delayed chlorophyll (Chl) degradation, whereas overexpression of REF6 accelerated Chl degradation. Subsequently, we revealed that REF6 positively regulates the general senescence process by directly up-regulating ETHYLENE INSENSITIVE 2 (EIN2), ORESARA1 (ORE1), NAC-LIKE, ACTIVATED BY AP3/PI (NAP), PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK), PHYTOALEXIN DEFICIENT 4 (PAD4), LIPOXYGENASE 1 (LOX1), NAC DOMAIN CONTAINING PROTEIN 3 (AtNAC3), and NAC TRANSCRIPTION FACTOR-LIKE 9 (NTL9), the key regulatory and functional genes predominantly involved in the regulation of developmental leaf senescence. Importantly, loss-of-function of REF6 increased H3K27me3 levels at all the target Senescence associated genes (SAGs). We therefore conclusively demonstrate that H3K27me3 methylation represents an epigenetic mechanism prohibiting the premature transcriptional activation of key developmentally up-regulated senescence regulatory as well as functional genes in Arabidopsis. Leaves of higher plants start yellowing and subsequently die (senescence) at particular developmental stages as a result of both internal and external regulations. Leaf senescence is evolved to facilitate nutrient remobilization to young/important organs to meet their rapid development, and a large number of genes (Senescence associated genes, SAGs) are activated to regulate/facilitate the process. It has been intriguing how these genes are kept transcriptionally inactive to ensure an effective photosynthesis before the initiation of leaf senescence. Here, we reveal an epigenetic mechanism responsible for the prohibition of their premature transcription. We found that an H3K27me3 demethylase, RELATIVE OF EARLY FLOWERING 6 (REF6), directly promotes the expression of its ten target senescence regulatory and functional genes (EIN2, ORE1, NAP, AtNAC3, NTL9, NYE1/2, LOX1, PAD4, and PPDK), which are involved in major phytohormones’ signaling, biosynthesis, and chlorophyll degradation. Crucially, REF6 is substantially involved in promoting the H3K27me3 demethylation of both their promoter and/or coding regions during the aging process of leaves. We therefore provide conclusive evidence that H3K27me3 methylation is an epigenetic mechanism hindering the premature transcriptional activation of key SAGs, which helps to explain the “aging effect” of senescence initiation.
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Huang YY, Zhang LL, Ma XF, Zhao ZX, Zhao JH, Zhao JQ, Fan J, Li Y, He P, Xiao S, Wang WM. Multiple intramolecular trafficking signals in RESISTANCE TO POWDERY MILDEW 8.2 are engaged in activation of cell death and defense. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:55-70. [PMID: 30552775 DOI: 10.1111/tpj.14199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/03/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
The extrahaustorial membrane (EHM) is a host-derived interfacial membrane encasing the haustorium of powdery mildew fungi. Arabidopsis thaliana RESISTANCE TO POWDERY MILDEW 8.2 (RPW8.2) is specifically targeted to the EHM via two EHM-targeting signals. Here, we demonstrate that proper coordination between the trafficking forces engaged via the EHM-targeting signals and the nuclear localization signals (NLSs), as well as the nuclear export signals (NESs), in RPW8.2 is critical for the activation of cell death and defense. We show that in the absence of pathogens, RPW8.2 is partitioned between the cytoplasm and the nucleus, and turned over via both the 26S proteasome- and the vacuole-dependent pathways. Enhanced cytoplasmic localization of RPW8.2 by tagging it with a NES led to lethal cell death. By contrast, enhanced nuclear localization of RPW8.2 by adding an NLS to it resulted in resistance to powdery mildew. Whereas expression of the NES-containing C-terminal domain of RPW8.2 in the cytoplasm is sufficient to trigger cell death, no such cell death-inducing activity is found with RPW8.2 variants that contain the two EHM-targeting signals along with the NES-containing C-terminal domain. In addition, we present evidence for the involvement of a leaf senescence pathway in RPW8.2-mediated cell death and defense. Taken together, our data suggest that RPW8.2 is subject to adjustment by distinct and perhaps coordinated mechanisms for its localization and function via interaction with the multiple intramolecular trafficking signals, which should provide further insights into RPW8.2-activated, EHM-focused resistance against powdery mildew.
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Affiliation(s)
- Yan-Yan Huang
- Center for Crop Disease and Insect Pests, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ling-Li Zhang
- Center for Crop Disease and Insect Pests, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xian-Feng Ma
- Center for Crop Disease and Insect Pests, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Institute of Biosciences and Biotechnology Research, Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20850, USA
| | - Zhi-Xue Zhao
- Center for Crop Disease and Insect Pests, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing-Hao Zhao
- Center for Crop Disease and Insect Pests, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ji-Qun Zhao
- Center for Crop Disease and Insect Pests, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Fan
- Center for Crop Disease and Insect Pests, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yan Li
- Center for Crop Disease and Insect Pests, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ping He
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Shunyuan Xiao
- Institute of Biosciences and Biotechnology Research, Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20850, USA
| | - Wen-Ming Wang
- Center for Crop Disease and Insect Pests, Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
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Varga S, Soulsbury CD. Arbuscular mycorrhizal fungi change host plant DNA methylation systemically. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:278-283. [PMID: 30253017 DOI: 10.1111/plb.12917] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
DNA methylation is an important epigenetic mechanism regulating gene expression in plants. DNA methylation has been shown to vary among species and also among plant tissues. However, no study has evaluated whether arbuscular mycorrhizal (AM) fungi affect DNA methylation levels in a tissue-specific manner. We investigated whether symbiosis with AM fungi affects DNA methylation in the host, focusing on different plant tissues (roots versus leaves) and across time. We carried out a 6-month pot experiment using Geranium robertianum in symbiosis with the AM fungus Funneliformis mosseae. Our results show that the pattern of total DNA methylation differed between leaves and roots and was related to when plants were harvested, confirming that DNA methylation is a process that occurs dynamically throughout an organism's lifetime. More importantly, the presence of AM fungus in roots of our experimental plants had a positive effect on total DNA methylation in both tissues. This study shows that colonisation by AM fungi can affect DNA methylation levels in their hosts and that plant DNA methylation varies in an age- and tissue-specific manner.
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Affiliation(s)
- S Varga
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, Lincoln, UK
| | - C D Soulsbury
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, Lincoln, UK
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Riester L, Köster-Hofmann S, Doll J, Berendzen KW, Zentgraf U. Impact of Alternatively Polyadenylated Isoforms of ETHYLENE RESPONSE FACTOR4 with Activator and Repressor Function on Senescence in Arabidopsis thaliana L. Genes (Basel) 2019; 10:genes10020091. [PMID: 30696119 PMCID: PMC6409740 DOI: 10.3390/genes10020091] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 02/07/2023] Open
Abstract
Leaf senescence is highly regulated by transcriptional reprogramming, implying an important role for transcriptional regulators. ETHYLENE RESPONSE FACTOR4 (ERF4) was shown to be involved in senescence regulation and to exist in two different isoforms due to alternative polyadenylation of its pre-mRNA. One of these isoforms, ERF4-R, contains an ERF-associated amphiphilic repression (EAR) motif and acts as repressor, whereas the other form, ERF4-A, is lacking this motif and acts as activator. Here, we analyzed the impact of these isoforms on senescence. Both isoforms were able to complement the delayed senescence phenotype of the erf4 mutant with a tendency of ERF4-A for a slightly better complementation. However, overexpression led to accelerated senescence of 35S:ERF4-R plants but not of 35S:ERF4-A plants. We identified CATALASE3 (CAT3) as direct target gene of ERF4 in a yeast-one-hybrid screen. Both isoforms directly bind to the CAT3 promoter but have antagonistic effects on gene expression. The ratio of ERF4-A to ERF4-R mRNA changed during development, leading to a complex age-dependent regulation of CAT3 activity. The RNA-binding protein FPA shifted the R/A-ratio and fpa mutants are pointing towards a role of alternative polyadenylation regulators in senescence.
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Affiliation(s)
- Lena Riester
- Center for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany.
| | - Siliya Köster-Hofmann
- Center for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany.
| | - Jasmin Doll
- Center for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany.
| | - Kenneth W Berendzen
- Center for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany.
| | - Ulrike Zentgraf
- Center for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany.
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50
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He X, Li JJ, Chen Y, Yang JQ, Chen XY. Genome-wide Analysis of the WRKY Gene Family and its Response to Abiotic Stress in Buckwheat ( Fagopyrum Tataricum). Open Life Sci 2019; 14:80-96. [PMID: 33817140 PMCID: PMC7874777 DOI: 10.1515/biol-2019-0010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/15/2019] [Indexed: 12/30/2022] Open
Abstract
The WRKY gene family is an ancient plant transcription factor (TF) family with a vital role in plant growth and development, especially in response to biotic and abiotic stresses. Although many researchers have studied WRKY TFs in numerous plant species, little is known of them in Tartary buckwheat (Fagopyrum tataricum). Based on the recently reported genome sequence of Tartary buckwheat, we identified 78 FtWRKY proteins that could be classified into three major groups. All 77 WRKY genes were distributed unevenly across all eight chromosomes. Exon-intron analysis and motif composition prediction revealed the complexity and diversity of FtWRKYs, indicating that WRKY TFs may be of significance in plant growth regulation and stress response. Two separate pairs of tandem duplication genes were found, but no segmental duplications were identified. Overall, most orthologous gene-pairs between Tartary and common buckwheat evolved under strong purifying selection. qRT-PCR was used to analyze differences in expression among four FtWRKYs (FtWRKY6, 74, 31, and 7) under salt, drought, cold, and heat treatments. The results revealed that all four proteins are related to abiotic stress responses, although they exhibited various expression patterns. In particular, the relative expression levels of FtWRKY6, 74, and 31 were significantly upregulated under salt stress, while the highest expression of FtWRKY7 was observed from heat treatment. This study provides comprehensive insights into the WRKY gene family in Tartary buckwheat, and can support the screening of additional candidate genes for further functional characterization of WRKYs under various stresses.
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Affiliation(s)
- Xia He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou510642, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou510642, China
| | - Jing-jian Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou510642, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou510642, China
| | - Yuan Chen
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou510642, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou510642, China
| | - Jia-qi Yang
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou510642, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou510642, China
| | - Xiao-yang Chen
- ushan road NO.483 Guangzhou city, GuangdongGuangzhou, P.R.China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou510642, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou510642, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou510642, China
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