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Rudolf J, Tomovicova L, Panzarova K, Fajkus J, Hejatko J, Skalak J. Epigenetics and plant hormone dynamics: a functional and methodological perspective. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5267-5294. [PMID: 38373206 PMCID: PMC11389840 DOI: 10.1093/jxb/erae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators of epigenetic processes governing gene expression and phenotypic plasticity. This review addresses the complex interplay between plant hormones and epigenetic mechanisms, highlighting the diverse methodologies that have been harnessed to decipher these intricate relationships. We present a comprehensive overview to understand how phytohormones orchestrate epigenetic modifications, shaping plant adaptation and survival strategies. Conversely, we explore how epigenetic regulators ensure hormonal balance and regulate the signalling pathways of key plant hormones. Furthermore, our investigation includes a search for novel genes that are regulated by plant hormones under the control of epigenetic processes. Our review offers a contemporary overview of the epigenetic-plant hormone crosstalk, emphasizing its significance in plant growth, development, and potential agronomical applications.
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Affiliation(s)
- Jiri Rudolf
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, CZ-61265 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Lucia Tomovicova
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Klara Panzarova
- Photon Systems Instruments, Prumyslova 470, CZ-664 24 Drasov, Czech Republic
| | - Jiri Fajkus
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, CZ-61265 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Jan Hejatko
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Jan Skalak
- Mendel Centre for Plant Genomics and Proteomics, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
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Chen Z, Liu Y, Wang Q, Fei J, Liu X, Zhang C, Yin Y. miRNA Sequencing Analysis in Maize Roots Treated with Neutral and Alkaline Salts. Curr Issues Mol Biol 2024; 46:8874-8889. [PMID: 39194741 DOI: 10.3390/cimb46080524] [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: 07/03/2024] [Revised: 08/04/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024] Open
Abstract
Soil salinization/alkalization is a complex environmental factor that includes not only neutral salt NaCl but also other components like Na2CO3. miRNAs, as small molecules that regulate gene expression post-transcriptionally, are involved in plant responses to abiotic stress. In this study, maize seedling roots were treated for 5 h with 100 mM NaCl, 50 mM Na2CO3, and H2O, respectively. Sequencing analysis of differentially expressed miRNAs under these conditions revealed that the Na2CO3 treatment group had the most differentially expressed miRNAs. Cluster analysis indicated their main involvement in the regulation of ion transport, binding, metabolism, and phenylpropanoid and flavonoid biosynthesis pathways. The unique differentially expressed miRNAs in the NaCl treatment group were related to the sulfur metabolism pathway. This indicates a significant difference in the response patterns of maize to different treatment groups. This study provides theoretical evidence and genetic resources for further analysis of the molecular mechanisms behind maize's salt-alkali tolerance.
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Affiliation(s)
- Ziqi Chen
- Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Yang Liu
- Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Qi Wang
- Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Jianbo Fei
- Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Chuang Zhang
- Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Yuejia Yin
- Institute of Agricultural Biotechnology/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
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Jiao B, Peng Q, Wu B, Liu S, Zhou J, Yuan B, Lin H, Xi D. The miR172/TOE3 module regulates resistance to tobacco mosaic virus in tobacco. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39040005 DOI: 10.1111/tpj.16941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/01/2024] [Accepted: 07/04/2024] [Indexed: 07/24/2024]
Abstract
The outcome of certain plant-virus interaction is symptom recovery, which is accompanied with the emergence of asymptomatic tissues in which the virus accumulation decreased dramatically. This phenomenon shows the potential to reveal critical molecular factors for controlling viral disease. MicroRNAs act as master regulators in plant growth, development, and immunity. However, the mechanism by which miRNA participates in regulating symptom recovery remains largely unknown. Here, we reported that miR172 was scavenged in the recovered tissue of tobacco mosaic virus (TMV)-infected Nicotiana tabacum plants. Overexpression of miR172 promoted TMV infection, whereas silencing of miR172 inhibited TMV infection. Then, TARGET OF EAT3 (TOE3), an APETALA2 transcription factor, was identified as a downstream target of miR172. Overexpression of NtTOE3 significantly improved plant resistance to TMV infection, while knockout of NtTOE3 facilitated virus infection. Furthermore, transcriptome analysis indicated that TOE3 promoted the expression of defense-related genes, such as KL1 and MLP43. Overexpression of these genes conferred resistance of plant against TMV infection. Importantly, results of dual-luciferase assay, chromatin immunoprecipitation-quantitative PCR, and electrophoretic mobility shift assay proved that TOE3 activated the transcription of KL1 and MLP43 by binding their promoters. Moreover, overexpression of rTOE3 (the miR172-resistant form of TOE3) significantly reduced TMV accumulation compared to the overexpression of TOE3 (the normal form of TOE3) in miR172 overexpressing Nicotiana benthamiana plants. Taken together, our study reveals the pivotal role of miR172/TOE3 module in regulating plant immunity and in the establishment of recovery in virus-infected tobacco plants, elucidating a regulatory mechanism integrating plant growth, development, and immune response.
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Affiliation(s)
- Bolei Jiao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Qiding Peng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Baijun Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Sucen Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Jingya Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Bowen Yuan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Dehui Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, China
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Li X, Lin C, Lan C, Tao Z. Genetic and epigenetic basis of phytohormonal control of floral transition in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4180-4194. [PMID: 38457356 DOI: 10.1093/jxb/erae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/06/2024] [Indexed: 03/10/2024]
Abstract
The timing of the developmental transition from the vegetative to the reproductive stage is critical for angiosperms, and is fine-tuned by the integration of endogenous factors and external environmental cues to ensure successful reproduction. Plants have evolved sophisticated mechanisms to response to diverse environmental or stress signals, and these can be mediated by hormones to coordinate flowering time. Phytohormones such as gibberellin, auxin, cytokinin, jasmonate, abscisic acid, ethylene, and brassinosteroids and the cross-talk among them are critical for the precise regulation of flowering time. Recent studies of the model flowering plant Arabidopsis have revealed that diverse transcription factors and epigenetic regulators play key roles in relation to the phytohormones that regulate floral transition. This review aims to summarize our current knowledge of the genetic and epigenetic mechanisms that underlie the phytohormonal control of floral transition in Arabidopsis, offering insights into how these processes are regulated and their implications for plant biology.
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Affiliation(s)
- Xiaoxiao Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chuyu Lin
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenghao Lan
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zeng Tao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Meyer RC, Weigelt-Fischer K, Tschiersch H, Topali G, Altschmied L, Heuermann MC, Knoch D, Kuhlmann M, Zhao Y, Altmann T. Dynamic growth QTL action in diverse light environments: characterization of light regime-specific and stable QTL in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5341-5362. [PMID: 37306093 DOI: 10.1093/jxb/erad222] [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: 10/17/2022] [Accepted: 06/10/2023] [Indexed: 06/13/2023]
Abstract
Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throughput phenotyping and genome-wide association studies. Daily automated non-invasive phenotyping of a collection of 382 Arabidopsis accessions provided growth data during developmental progression under different light regimes at high temporal resolution. Quantitative trait loci (QTL) for projected leaf area, relative growth rate, and PSII operating efficiency detected under the two light regimes were predominantly condition-specific and displayed distinct temporal activity patterns, with active phases ranging from 2 d to 9 d. Eighteen protein-coding genes and one miRNA gene were identified as potential candidate genes at 10 QTL regions consistently found under both light regimes. Expression patterns of three candidate genes affecting projected leaf area were analysed in time-series experiments in accessions with contrasting vegetative leaf growth. These observations highlight the importance of considering both environmental and temporal patterns of QTL/allele actions and emphasize the need for detailed time-resolved analyses under diverse well-defined environmental conditions to effectively unravel the complex and stage-specific contributions of genes affecting plant growth processes.
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Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Georgia Topali
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
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Guo R, Wen X, Zhang W, Huang L, Peng Y, Jin L, Han H, Zhang L, Li W, Guo H. Arabidopsis EIN2 represses ABA responses during germination and early seedling growth by inactivating HLS1 protein independently of the canonical ethylene pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1514-1527. [PMID: 37269223 DOI: 10.1111/tpj.16335] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/30/2023] [Accepted: 05/29/2023] [Indexed: 06/05/2023]
Abstract
The signaling pathways for the phytohormones ethylene and abscisic acid (ABA) have antagonistic effects on seed germination and early seedling establishment. However, the underlying molecular mechanisms remain unclear. In Arabidopsis thaliana, ETHYLENE INSENSITIVE 2 (EIN2) localizes to the endoplasmic reticulum (ER); although its biochemical function is unknown, it connects the ethylene signal with the key transcription factors EIN3 and EIN3-LIKE 1 (EIL1), leading to the transcriptional activation of ethylene-responsive genes. In this study, we uncovered an EIN3/EIL1-independent role for EIN2 in regulating the ABA response. Epistasis analysis demonstrated that this distinct role of EIN2 in the ABA response depends on HOOKLESS 1 (HLS1), the putative histone acetyltransferase acting as a positive regulator of ABA responses. Protein interaction assays supported a direct physical interaction between EIN2 and HLS1 in vitro and in vivo. Loss of EIN2 function resulted in an alteration of HLS1-mediated histone acetylation at the ABA-INSENSITIVE 3 (ABI3) and ABI5 loci, which promotes gene expression and the ABA response during seed germination and early seedling growth, indicating that the EIN2-HLS1 module contributes to ABA responses. Our study thus revealed that EIN2 modulates ABA responses by repressing HLS1 function, independently of the canonical ethylene pathway. These findings shed light on the intricate regulatory mechanisms underling the antagonistic interactions between ethylene and ABA signaling, with significant implications for our understanding of plant growth and development.
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Affiliation(s)
- Renkang Guo
- Harbin Institute of Technology, Harbin, 150001, China
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xing Wen
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wei Zhang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Li Huang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yang Peng
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lian Jin
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Huihui Han
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Linlin Zhang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wenyang Li
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
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7
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Racca S, Gras DE, Canal MV, Ferrero LV, Rojas BE, Figueroa CM, Ariel FD, Welchen E, Gonzalez DH. Cytochrome c and the transcription factor ABI4 establish a molecular link between mitochondria and ABA-dependent seed germination. THE NEW PHYTOLOGIST 2022; 235:1780-1795. [PMID: 35637555 DOI: 10.1111/nph.18287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
During germination, seed reserves are mobilised to sustain the metabolic and energetic demands of plant growth. Mitochondrial respiration is presumably required to drive germination in several species, but only recently its role in this process has begun to be elucidated. Using Arabidopsis thaliana lines with changes in the levels of the respiratory chain component cytochrome c (CYTc), we investigated the role of this protein in germination and its relationship with hormonal pathways. Cytochrome c deficiency causes delayed seed germination, which correlates with decreased cyanide-sensitive respiration and ATP production at the onset of germination. In addition, CYTc affects the sensitivity of germination to abscisic acid (ABA), which negatively regulates the expression of CYTC-2, one of two CYTc-encoding genes in Arabidopsis. CYTC-2 acts downstream of the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), which binds to a region of the CYTC-2 promoter required for repression by ABA and regulates its expression. The results show that CYTc is a main player during seed germination through its role in respiratory metabolism and energy production. In addition, the direct regulation of CYTC-2 by ABI4 and its effect on ABA-responsive germination establishes a link between mitochondrial and hormonal functions during this process.
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Affiliation(s)
- Sofía Racca
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Diana E Gras
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - M Victoria Canal
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Lucía V Ferrero
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Bruno E Rojas
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Carlos M Figueroa
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Daniel H Gonzalez
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
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8
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Zhang M, Liu S, Tong S, Zhang D, Qi Q, Wang Y, Wang X, An Y, Lu X. Effects of Melatonin Priming on Suaeda corniculata Seed Germination, Antioxidant Defense, and Reserve Mobilization: Implications for Salinized Wetland Restoration. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.941032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Melatonin priming has been widely reported to positively affect seed germination under abiotic stresses. However, there is still a gap in knowledge on how melatonin priming impacts the seed germination and physiological change of wetland plant species. We assessed the effects of different melatonin concentrations on germination characteristics, antioxidant defense, and reserve mobilization of Suaeda corniculata seeds. Priming of S. corniculata seeds with 50 μM melatonin significantly improved the germination rate, germination speed, germination index, superoxide dismutase and peroxidase activity, and soluble sugar content as compared with the control, and effectively reduced the malondialdehyde content, promoted starch, soluble protein, and fat mobilization. However, the stress tolerance ability of S. corniculata seeds was reduced by high melatonin concentration. The structural equation model indicated that the melatonin priming directly affects the seed germination, while also indirectly regulating the antioxidant defense system and reserve mobilization. In conclusion, melatonin priming affects the S. corniculata seed germination under salinization stress in a concentration-dependent manner via both direct and indirect regulatory pathways. Insights into these aspects will advance our understanding of how melatonin priming affects S. corniculata seed germination and provide invaluable information and technical support for the restoration of salinized wetlands in the Momoge National Nature Reserve.
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Mehdi SMM, Krishnamoorthy S, Szczesniak MW, Ludwików A. Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis. Int J Mol Sci 2021; 22:7153. [PMID: 34281207 PMCID: PMC8268864 DOI: 10.3390/ijms22137153] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5' RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.
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Affiliation(s)
- Syed Muhammad Muntazir Mehdi
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
| | - Sivakumar Krishnamoorthy
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
| | - Michal Wojciech Szczesniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland;
| | - Agnieszka Ludwików
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
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10
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Lv Y, Pan J, Wang H, Reiter RJ, Li X, Mou Z, Zhang J, Yao Z, Zhao D, Yu D. Melatonin inhibits seed germination by crosstalk with abscisic acid, gibberellin, and auxin in Arabidopsis. J Pineal Res 2021; 70:e12736. [PMID: 33811388 DOI: 10.1111/jpi.12736] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022]
Abstract
Seed germination, an important developmental stage in the life cycle of seed plants, is regulated by complex signals. Melatonin is a signaling molecule associated with seed germination under stressful conditions, although the underlying regulatory mechanisms are largely unknown. In this study, we showed that a low concentration (10 µM or 100 µM) of melatonin had no effect on seed germination, but when the concentration of melatonin increased to 500 µM or 1000 µM, seed germination was significantly inhibited in Arabidopsis. RNA sequencing analysis showed that melatonin regulated seed germination correlated to phytohormones abscisic acid (ABA), gibberellin (GA), and auxin. Further investigation revealed that ABA and melatonin synergistically inhibited seed germination, while GA and auxin antagonized the inhibitory effect of seed germination by melatonin. Disruption of the melatonin biosynthesis enzyme gene serotonin N-acetyltransferase (SNAT) or N-acetylserotonin methyltransferase (ASMT) promoted seed germination, while overexpression of ASMT inhibited seed germination. Taken together, our study sheds new light on the function and mechanism of melatonin in modulating seed germination in Arabidopsis.
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Affiliation(s)
- Yan Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jinjing Pan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Houping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, Long School of Medicine, San Antonio, TX, USA
| | - Xia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zongmin Mou
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jiemei Zhang
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Zhengping Yao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Dake Zhao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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Feyissa BA, Amyot L, Nasrollahi V, Papadopoulos Y, Kohalmi SE, Hannoufa A. Involvement of the miR156/SPL module in flooding response in Medicago sativa. Sci Rep 2021; 11:3243. [PMID: 33547346 PMCID: PMC7864954 DOI: 10.1038/s41598-021-82450-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/20/2021] [Indexed: 01/30/2023] Open
Abstract
The highly conserved plant microRNA, miR156, affects plant development, metabolite composition, and stress response. Our previous research revealed the role of miR156 in abiotic stress response in Medicago sativa exerted by downregulating SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE transcription factors. Here we investigated the involvement and possible mechanism of action of the miR156/SPL module in flooding tolerance in alfalfa. For that, we used miR156 overexpressing, SPL13RNAi, flood-tolerant (AAC-Trueman) and -sensitive (AC-Caribou) alfalfa cultivars exposed to flooding. We also used Arabidopsis ABA insensitive (abi1-2, abi5-8) mutants and transgenic lines with either overexpressed (KIN10-OX1, KIN10-OX2) or silenced (KIN10RNAi-1, KIN10RNAi-2) catalytic subunit of SnRK1 to investigate a possible role of ABA and SnRK1 in regulating miR156 expression under flooding. Physiological analysis, hormone profiling and global transcriptome changes revealed a role for miR156/SPL module in flooding tolerance. We also identified nine novel alfalfa SPLs (SPL1, SPL1a, SPL2a, SPL7, SPL7a, SPL8, SPL13a, SPL14, SPL16) responsive to flooding. Our results also showed a possible ABA-dependent SnRK1 upregulation to enhance miR156 expression, resulting in downregulation of SPL4, SPL7a, SPL8, SPL9, SPL13, and SPL13a. We conclude that these effects induce flooding adaptive responses in alfalfa and modulate stress physiology by affecting the transcriptome, ABA metabolites and secondary metabolism.
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Affiliation(s)
- Biruk A. Feyissa
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada ,grid.39381.300000 0004 1936 8884Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A5B7 Canada
| | - Lisa Amyot
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Vida Nasrollahi
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada ,grid.39381.300000 0004 1936 8884Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A5B7 Canada
| | | | - Susanne E. Kohalmi
- grid.39381.300000 0004 1936 8884Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A5B7 Canada
| | - Abdelali Hannoufa
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada ,grid.39381.300000 0004 1936 8884Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A5B7 Canada
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Gao Y, Yang F, Liu J, Xie W, Zhang L, Chen Z, Peng Z, Ou Y, Yao Y. Genome-Wide Identification of Metal Tolerance Protein Genes in Populus trichocarpa and Their Roles in Response to Various Heavy Metal Stresses. Int J Mol Sci 2020; 21:ijms21051680. [PMID: 32121430 PMCID: PMC7084629 DOI: 10.3390/ijms21051680] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 01/22/2023] Open
Abstract
Metal tolerance proteins (MTPs) are plant divalent cation transporters that play important roles in plant metal tolerance and homeostasis. Poplar is an ideal candidate for the phytoremediation of heavy metals because of its numerous beneficial attributes. However, the definitive phylogeny and heavy metal transport mechanisms of the MTP family in poplar remain unknown. Here, 22 MTP genes in P. trichocarpa were identified and classified into three major clusters and seven groups according to phylogenetic relationships. An evolutionary analysis suggested that PtrMTP genes had undergone gene expansion through tandem or segmental duplication events. Moreover, all PtrMTPs were predicted to localize in the vacuole and/or cell membrane, and contained typical structural features of the MTP family, cation efflux domain. The temporal and spatial expression pattern analysis results indicated the involvement of PtrMTP genes in poplar developmental control. Under heavy metal stress, most of PtrMTP genes were induced by at least two metal ions in roots, stems or leaves. In addition, PtrMTP8.1, PtrMTP9 and PtrMTP10.4 displayed the ability of Mn transport in yeast cells, and PtrMTP6 could transport Co, Fe and Mn. These findings will provide an important foundation to elucidate the biological functions of PtrMTP genes, and especially their role in regulating heavy metal tolerance in poplar.
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Paffendorf BAM, Qassrawi R, Meys AM, Trimborn L, Schrader A. TRANSPARENT TESTA GLABRA 1 participates in flowering time regulation in Arabidopsis thaliana. PeerJ 2020; 8:e8303. [PMID: 31998554 PMCID: PMC6977477 DOI: 10.7717/peerj.8303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022] Open
Abstract
Pleiotropic regulatory factors mediate concerted responses of the plant’s trait network to endogenous and exogenous cues. TRANSPARENT TESTA GLABRA 1 (TTG1) is such a factor that has been predominantly described as a regulator of early developmental traits. Although its closest homologs LIGHT-REGULATED WD1 (LWD1) and LWD2 affect photoperiodic flowering, a role of TTG1 in flowering time regulation has not been reported. Here we reveal that TTG1 is a regulator of flowering time in Arabidopsis thaliana and changes transcript levels of different targets within the flowering time regulatory pathway. TTG1 mutants flower early and TTG1 overexpression lines flower late at long-day conditions. Consistently, TTG1 can suppress the transcript levels of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CO1 and can act as an activator of circadian clock components. Moreover, TTG1 might form feedback loops at the protein level. The TTG1 protein interacts with PSEUDO RESPONSE REGULATOR (PRR)s and basic HELIX-LOOP-HELIX 92 (bHLH92) in yeast. In planta, the respective pairs exhibit interesting patterns of localization including a recruitment of TTG1 by PRR5 to subnuclear foci. This mechanism proposes additional layers of regulation by TTG1 and might aid to specify the function of bHLH92. Within another branch of the pathway, TTG1 can elevate FLOWERING LOCUS C (FLC) transcript levels. FLC mediates signals from the vernalization, ambient temperature and autonomous pathway and the circadian clock is pivotal for the plant to synchronize with diurnal cycles of environmental stimuli like light and temperature. Our results suggest an unexpected positioning of TTG1 upstream of FLC and upstream of the circadian clock. In this light, this points to an adaptive value of the role of TTG1 in respect to flowering time regulation.
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Affiliation(s)
| | - Rawan Qassrawi
- Botanical Institute, Department of Biology, University of Cologne, Cologne, Germany
| | - Andrea M Meys
- Botanical Institute, Department of Biology, University of Cologne, Cologne, Germany
| | - Laura Trimborn
- Botanical Institute, Department of Biology, University of Cologne, Cologne, Germany
| | - Andrea Schrader
- Botanical Institute, Department of Biology, University of Cologne, Cologne, Germany.,RWTH Aachen University, Institute for Biology I, Aachen, Germany
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14
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Su J, Yang X, He J, Zhang Y, Duan X, Wang R, Shen W. Methyl-coenzyme M reductase-dependent endogenous methane enhances plant tolerance against abiotic stress and alters ABA sensitivity in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2019; 101:439-454. [PMID: 31471780 DOI: 10.1007/s11103-019-00914-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/27/2019] [Indexed: 05/05/2023]
Abstract
Our study firstly elaborated the underlying mechanism of endogenous CH4-induced abiotic tolerance, along with an alteration of ABA sensitivity by mimicking the endogenous CH4 production in MtMCR transgenic Arabidopsis. Endogenous methane (CH4) production and/or emission have been ubiquitously observed in stressed plants. However, their physiological roles remain unclear. Here, the methyl-coenzyme M reductase gene from Methanobacterium thermoautotrophicum (MtMCR), encoding the enzyme of methanogenesis, was expressed in Arabidopsis thaliana, to mimic the production of endogenous CH4. In response to salinity and osmotic stress, MtMCR expression was up-regulated in transgenic plants, resulting in significant increase of endogenous CH4 levels. Similar results were observed in abscisic acid (ABA) treatment. The functions of endogenous CH4 were characterized by the changes in plant phenotypes related to stress and ABA sensitivity during the germination and post-germination periods. When challenged with osmotic stress, a reduction in water loss and stomatal closure, were observed. Redox homeostasis was reestablished during osmotic and salinity stress, and ion imbalance was also restored in salinity conditions. The expression of several stress/ABA-responsive genes was up-regulated, and ABA sensitivity, in particularly, was significantly altered in the MtMCR transgenic plants. Together, our genetic study for the first time elaborated the possible mechanism of endogenous CH4-enhanced salinity and osmotic tolerance, along with an alteration of ABA sensitivity. These findings thus provided novel cues for understanding the possible roles of endogenous CH4 in plants.
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Affiliation(s)
- Jiuchang Su
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinghao Yang
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junjie He
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihua Zhang
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingliang Duan
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ren Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Wenbiao Shen
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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15
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Hwang JU, Yim S, Do THT, Kang J, Lee Y. Arabidopsis thaliana Raf22 protein kinase maintains growth capacity during postgerminative growth arrest under stress. PLANT, CELL & ENVIRONMENT 2018; 41:1565-1578. [PMID: 29575093 DOI: 10.1111/pce.13199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 02/14/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
When seeds are exposed to drought and salinity during germination, newly germinated embryos stop growth and enter a quiescent state called postgerminative growth (PGG) arrest. PGG arrest protects embryos from the stress, but it is not known how PGG is restored from the arrest when stress is eased. In this study, we show that under stress- or abscisic acid-induced PGG arrest conditions, Arabidopsis thaliana Raf-type protein kinase 22 (AtRaf22) overexpression accelerated photoautotrophic seedling establishment, whereas atraf22 knockout mutations enhanced the arrest. Furthermore, when the stress intensity was reduced subsequently, AtRaf22 overexpression plants resumed growth and accomplished photoautotrophic transition much faster than the knockout or wild-type plants. These results suggest that AtRaf22 activity is important for maintaining growth capacity during stress-induced PGG arrest, which is most likely critical for competitive growth when the stress subsides and plants resume growth. Such a factor has not been reported before.
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Affiliation(s)
- Jae-Ung Hwang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Sojeong Yim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Thanh Ha Thi Do
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joohyun Kang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Youngsook Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, 37673, Republic of Korea
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16
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Frachon L, Bartoli C, Carrère S, Bouchez O, Chaubet A, Gautier M, Roby D, Roux F. A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale. FRONTIERS IN PLANT SCIENCE 2018; 9:967. [PMID: 30042773 PMCID: PMC6048436 DOI: 10.3389/fpls.2018.00967] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
Understanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a micro-geographic scale, most genomic maps of climate adaptation have been established at broader geographical scales. Here, by using a Pool-Seq approach combined with a Bayesian hierarchical model that control for confounding by population structure, we performed a genome-environment association (GEA) analysis to investigate the genetic basis of adaptation to six climate variables in 168 natural populations of Arabidopsis thaliana distributed in south-west of France. Climate variation among the 168 populations represented up to 24% of climate variation among 521 European locations where A. thaliana inhabits. We identified neat and strong peaks of association, with most of the associated SNPs being significantly enriched in likely functional variants and/or in the extreme tail of genetic differentiation among populations. Furthermore, genes involved in transcriptional mechanisms appear predominant in plant functions associated with local climate adaptation. Globally, our results suggest that climate adaptation is an important driver of genomic variation in A. thaliana at a small spatial scale and mainly involves genome-wide changes in fundamental mechanisms of gene regulation. The identification of climate-adaptive genetic loci at a micro-geographic scale also highlights the importance to include within-species genetic diversity in ecological niche models for projecting potential species distributional shifts over short geographic distances.
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Affiliation(s)
- Léa Frachon
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
- Department of Systematic and Evolutionary Botany, University of Zurich, Zürich, Switzerland
| | - Claudia Bartoli
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Sébastien Carrère
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Olivier Bouchez
- Institut National de la Recherche Agronomique, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Adeline Chaubet
- Institut National de la Recherche Agronomique, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Mathieu Gautier
- Centre de Biologie pour la Gestion des Populations, Institut National de la Recherche Agronomique, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Institut de Recherche pour le Développement, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Dominique Roby
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
- *Correspondence: Fabrice Roux,
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18
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Sahito ZA, Wang L, Sun Z, Yan Q, Zhang X, Jiang Q, Ullah I, Tong Y, Li X. The miR172c-NNC1 module modulates root plastic development in response to salt in soybean. BMC PLANT BIOLOGY 2017; 17:229. [PMID: 29191158 PMCID: PMC5709930 DOI: 10.1186/s12870-017-1161-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 11/08/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant roots are highly plastic to high salinity. However, the molecular mechanism by which root developmental plasticity is regulated remains largely unknown. Previously we reported that miR172c-NNC1 module plays a key role in soybean-rhizobial symbiosis. The fact that the miR172c promoter contains several stress-related cis elements indicates that miR172c may have a role in root response to abiotic stress. RESULTS Here we showed that miR172c is greatly induced by salt stress in soybean. Overexpression of miR172c and knockdown of miR172c activity resulted in substantially increased and reduced root sensitivity to salt stress, respectively. Furthermore, we show that the target gene NNC1 (Nodule Number Control 1) of miR172c was downregulated by salt stress. The transgenic roots overexpressing or knocking down NNC1 expression also exhibited the altered root sensitivity to salt stress. CONCLUSION The study reveals the crucial role of miR172c-NNC1 module in root stress tolerance to salt stress in soybean.
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Affiliation(s)
- Zulfiqar Ali Sahito
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Lixiang Wang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
| | - Zhengxi Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qiqi Yan
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Xingke Zhang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Qiong Jiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Ihteram Ullah
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, Hebei 050021 People’s Republic of China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xia Li
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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Yu L, Shao C, Ye X, Meng Y, Zhou Y, Chen M. miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining. Sci Rep 2016; 6:18901. [PMID: 26732371 PMCID: PMC4702050 DOI: 10.1038/srep18901] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/27/2015] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression. The recent advances in high-throughput sequencing (HTS) technique have greatly facilitated large-scale detection of the miRNAs. However, thoroughly discovery of novel miRNAs from the available HTS data sets remains a major challenge. In this study, we observed that Dicer-mediated cleavage sites for the processing of the miRNA precursors could be mapped by using degradome sequencing data in both animals and plants. In this regard, a novel tool, miRNA Digger, was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. To test its sensitivity and reliability, miRNA Digger was applied to discover miRNAs from four organs of Arabidopsis. The results revealed that a majority of already known mature miRNAs along with their miRNA*s expressed in these four organs were successfully recovered. Notably, a total of 30 novel miRNA-miRNA* pairs that have not been registered in miRBase were discovered by miRNA Digger. After target prediction and degradome sequencing data-based validation, eleven miRNA-target interactions involving six of the novel miRNAs were identified. Taken together, miRNA Digger could be applied for sensitive detection of novel miRNAs and it could be freely downloaded from http://www.bioinfolab.cn/miRNA_Digger/index.html.
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Affiliation(s)
- Lan Yu
- College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China
| | - Chaogang Shao
- College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China
| | - Xinghuo Ye
- College of Life Sciences, Huzhou University, Huzhou 313000, P.R. China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, P.R. China
| | - Yincong Zhou
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China
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Duan H, Lu X, Lian C, An Y, Xia X, Yin W. Genome-Wide Analysis of MicroRNA Responses to the Phytohormone Abscisic Acid in Populus euphratica. FRONTIERS IN PLANT SCIENCE 2016; 7:1184. [PMID: 27582743 PMCID: PMC4988358 DOI: 10.3389/fpls.2016.01184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 07/22/2016] [Indexed: 05/20/2023]
Abstract
MicroRNA (miRNA) is a type of non-coding small RNA with a regulatory function at the posttranscriptional level in plant growth development and in response to abiotic stress. Previous studies have not reported on miRNAs responses to the phytohormone abscisic acid (ABA) at a genome-wide level in Populus euphratica, a model tree for studying abiotic stress responses in woody plants. Here we analyzed the miRNA response to ABA at a genome-wide level in P. euphratica utilizing high-throughput sequencing. To systematically perform a genome-wide analysis of ABA-responsive miRNAs in P. euphratica, nine sRNA libraries derived from three groups (control, treated with ABA for 1 day and treated with ABA for 4 days) were constructed. Each group included three libraries from three individual plantlets as biological replicate. In total, 151 unique mature sequences belonging to 75 conserved miRNA families were identified, and 94 unique sequences were determined to be novel miRNAs, including 56 miRNAs with miRNA(*) sequences. In all, 31 conserved miRNAs and 31 novel miRNAs response to ABA significantly differed among the groups. In addition, 4132 target genes were predicted for the conserved and novel miRNAs. Confirmed by real-time qPCR, expression changes of miRNAs were inversely correlated with the expression profiles of their putative targets. The Populus special or novel miRNA-target interactions were predicted might be involved in some biological process related stress tolerance. Our analysis provides a comprehensive view of how P. euphratica miRNA respond to ABA, and moreover, different temporal dynamics were observed in different ABA-treated libraries.
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Li W, Wang T, Zhang Y, Li Y. Overexpression of soybean miR172c confers tolerance to water deficit and salt stress, but increases ABA sensitivity in transgenic Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:175-94. [PMID: 26466661 DOI: 10.1093/jxb/erv450] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
MiRNAs play crucial roles in many aspects of plant development and the response to the environment. The miR172 family has been shown to participate in the control of flowering time and the response to abiotic stress. This family regulates the expression of APETALA2 (AP2)-like transcription factors in Arabidopsis. In the present study, soybean (Glycine max L. Merr.) miR172c, a member of the miR172 family, and its target gene were investigated for abiotic stress responses in transgenic Arabidopsis. gma-miR172c was induced by abscisic acid (ABA) treatments and abiotic stresses, including salt and water deficit. 5'-RACE (5'-rapid amplification of cDNA ends) assays indicated that miR172c directed Glyma01g39520 mRNA cleavage in soybeans. Overexpression of gma-miR172c in Arabidopsis resulted in reduced leaf water loss and increased survival rate under stress conditions. Meanwhile, the root length, germination rate, and cotyledon greening of transgenic plants were improved during both high salt and water deficit conditions. In addition, transgenic plants exhibited hypersensitivity to ABA during both the seed germination and post-germination seedling growth stages. Stress-related physiological indicators and the expression of stress/ABA-responsive genes were affected by abiotic treatments. The overexpression of gma-miR172c in Arabidopsis promoted earlier flowering compared with the wild type through modulation of the expression of flowering genes, such as FT and LFY during long days, especially under drought conditions. Glyma01g39520 weakened ABA sensitivity and reduced the tolerance to drought stress in the snz mutant of Arabidopsis by reducing the expression of ABI3 and ABI5. Overall, the present results demonstrate that gma-miR172c confers water deficit and salt tolerance but increased ABA sensitivity by regulating Glyma01g39520, which also accelerates flowering under abiotic stresses.
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Affiliation(s)
- Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030, China
| | - Tao Wang
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030, China
| | - Yuhang Zhang
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030, China
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics & Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, 150030, China
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Genome-wide analysis of microRNAs and their target genes related to leaf senescence of rice. PLoS One 2014; 9:e114313. [PMID: 25479006 PMCID: PMC4257594 DOI: 10.1371/journal.pone.0114313] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/05/2014] [Indexed: 01/04/2023] Open
Abstract
Grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human beings. One of the approaches to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. MicroRNAs (miRNAs) are key regulators of aging and cellular senescence in eukaryotes. Here, to help understand their biological role in rice leaf senescence, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). In total 372 known miRNAs, 162 miRNA candidates and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding.
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Vidal EA, Moyano TC, Canales J, Gutiérrez RA. Nitrogen control of developmental phase transitions in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5611-8. [PMID: 25129132 DOI: 10.1093/jxb/eru326] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nitrogen (N) is an essential macronutrient and a key structural component of macromolecules in plants. N nutrients and metabolites can act as signals that impact on many aspects of plant biology. The plant life cycle involves a series of developmental phase transitions that must be tightly coordinated to external and internal cues in order to ensure plant survival and reproduction. N availability is one of the factors controlling phase changes. In this review, we integrate and summarize the known effects of N over different developmental stages in plants. Substantial advances have been made in our understanding of signalling and N-responsive gene regulatory networks. We focus on the molecular mechanisms underlying N regulation of developmental transitions and the role of putative new regulators that might link N availability to pathways controlling Arabidopsis growth and development from seed germination through the plant reproductive transition.
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Affiliation(s)
- Elena A Vidal
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Tomás C Moyano
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javier Canales
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
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