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Li J, Wang J, Pang Q, Yan X. Analysis of N 6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sugar beet (Beta vulgaris). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111794. [PMID: 37459955 DOI: 10.1016/j.plantsci.2023.111794] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/31/2023]
Abstract
Salinity is an important environmental factor in crop growth and development. N6-methyladenosine (m6A) is an essential epigenetic modification that regulates plant-environment interaction. Sugar beet is a major sugar-yielding crop that has a certain tolerance to salt, but the dynamic response elicited by the m6A modification of transcripts under salt stress remains unknown. In this study, sugar beet was exposed to 300 mM NaCl to investigate its physiological response to high salinity and transcriptome-wide m6A modification profile. After the salt treatment, 7737 significantly modified m6A sites and 4981 differentially expressed genes (DEGs) were identified. Among the 312 m6A-modified DEGs, 113 hypomethylated DEGs were up-regulated and 99 hypermethylated DEGs were down-regulated, indicating a negative correlation between m6A modification and gene expression. Well-known salt tolerance genes (e.g., sodium/hydrogen exchanger 1, choline monooxygenase, and nucleoredoxin 2) and phospholipid signaling pathway genes (phosphoinositol-specific phospholipase C, phospholipase D, diacylglycerol kinase 1, etc.) were also among the m6A-modified genes. Further analysis showed that m6A modification may regulate salt-tolerant related gene expression by controlling mRNA stability. Therefore, changes in m6A modification may negatively regulate the expression of the salt-resistant genes in sugar beet, at least in part by modulating the stability of the mRNA via demethylase BvAlkbh10B. These findings could provide a better understanding of the epigenetic mechanisms of salt tolerance in sugar beets and uncover new candidate genes for improving the production of sugar beets planted in high-salinity soil.
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Affiliation(s)
- Junliang Li
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Institute for Eco-environmental Research of Sanyang Wetland, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China; Post-doctoral Research Stations, Northeast Forestry University, Harbin 150040, China
| | - Jiayuan Wang
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Institute for Eco-environmental Research of Sanyang Wetland, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China
| | - Qiuying Pang
- Post-doctoral Research Stations, Northeast Forestry University, Harbin 150040, China; Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China.
| | - Xiufeng Yan
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Institute for Eco-environmental Research of Sanyang Wetland, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China.
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Li J, Pang Q, Yan X. Unique Features of the m 6A Methylome and Its Response to Salt Stress in the Roots of Sugar Beet ( Beta vulgaris). Int J Mol Sci 2023; 24:11659. [PMID: 37511417 PMCID: PMC10380635 DOI: 10.3390/ijms241411659] [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: 06/23/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Salt is one of the most important environmental factors in crop growth and development. N6-methyladenosine (m6A) is an epigenetic modification that regulates plant-environment interaction at transcriptional and translational levels. Sugar beet is a salt-tolerant sugar-yielding crop, but how m6A modification affects its response to salt stress remains unknown. In this study, m6A-seq was used to explore the role of m6A modification in response to salt stress in sugar beet (Beta vulgaris). Transcriptome-wide m6A methylation profiles and physiological responses to high salinity were investigated in beet roots. After treatment with 300 mM NaCl, the activities of peroxidase and catalase, the root activity, and the contents of Na+, K+, and Ca2+ in the roots were significantly affected by salt stress. Compared with the control plants, 6904 differentially expressed genes (DEGs) and 566 differentially methylated peaks (DMPs) were identified. Association analysis revealed that 243 DEGs contained DMP, and 80% of these DEGs had expression patterns that were negatively correlated with the extent of m6A modification. Further analysis verified that m6A methylation may regulate the expression of some genes by controlling their mRNA stability. Functional analysis revealed that m6A modifications primarily affect the expression of genes involved in energy metabolism, transport, signal transduction, transcription factors, and cell wall organization. This study provides evidence that a post-transcriptional regulatory mechanism mediates gene expression during salt stress by affecting the stability of mRNA in the root.
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Affiliation(s)
- Junliang Li
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Institute for Eco-Environmental Research of Sanyang Wetland, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China
- Post-Doctoral Research Stations, Northeast Forestry University, Harbin 150040, China
| | - Qiuying Pang
- Post-Doctoral Research Stations, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Xiufeng Yan
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Institute for Eco-Environmental Research of Sanyang Wetland, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China
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Sun K, Mehari TG, Fang H, Han J, Huo X, Zhang J, Chen Y, Wang D, Zhuang Z, Ditta A, Khan MK, Zhang J, Wang K, Wang B. Transcriptome, proteome and functional characterization reveals salt stress tolerance mechanisms in upland cotton ( Gossypium hirsutum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1092616. [PMID: 36875590 PMCID: PMC9978342 DOI: 10.3389/fpls.2023.1092616] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/03/2023] [Indexed: 06/05/2023]
Abstract
Uncovering the underlying mechanism of salt tolerance is important to breed cotton varieties with improved salt tolerance. In this study, transcriptome and proteome sequencing were performed on upland cotton (Gossypium hirsutum L.) variety under salt stress, and integrated analysis was carried out to exploit salt-tolerance genes in cotton. Enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed on differentially expressed genes (DEGs) obtained from transcriptome and proteome sequencing. GO enrichment was carried out mainly in the cell membrane, organelle, cellular process, metabolic process, and stress response. The expression of 23,981 genes was changed in physiological and biochemical processes such as cell metabolism. The metabolic pathways obtained by KEGG enrichment included glycerolipid metabolism, sesquiterpene and triterpenoid biosynthesis, flavonoid production, and plant hormone signal transduction. Combined transcriptome and proteome analysis to screen and annotate DEGs yielded 24 candidate genes with significant differential expression. The quantitative real-time polymerase chain reaction (qRT-PCR) validation of the candidate genes showed that two genes (Gh_D11G0978 and Gh_D10G0907) responded significantly to the induction of NaCl, and these two genes were further selected as target genes for gene cloning and functional validation through virus-induced gene silencing (VIGS). The silenced plants exhibited early wilting with a greater degree of salt damage under salt treatment. Moreover, they showed higher levels of reactive oxygen species (ROS) than the control. Therefore, we can infer that these two genes have a pivotal role in the response to salt stress in upland cotton. The findings in this research will facilitate the breeding of salt tolerance cotton varieties that can be grown on saline alkaline lands.
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Affiliation(s)
- Kangtai Sun
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | | | - Hui Fang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Xuehan Huo
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Dongmei Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Zhimin Zhuang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Allah Ditta
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Muhammad K.R. Khan
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs of China, Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
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Jain N, Farhat S, Kumar R, Singh N, Singh S, Sreevathsa R, Kalia S, Singh NK, Teruhiro T, Rai V. Alteration of proteome in germinating seedlings of piegonpea ( Cajanus cajan) after salt stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2833-2848. [PMID: 35035139 PMCID: PMC8720132 DOI: 10.1007/s12298-021-01116-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/07/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Pigeonpea (Cajanus cajan) is an important crop in semi-arid regions and a significant source of dietary proteins in India. The plant is sensitive to salinity stress, which adversely affects its productivity. Based on the dosage-dependent influence of salinity stress on the growth and ion contents in the young seedlings of pigeonpea, a comparative proteome analysis of control and salt stressed (150 mM NaCl) plants was conducted using 7 days-old seedlings. Among various amino acids, serine, aspartate and asparagine were the amino acids that showed increment in the root, whereas serine, aspartate and phenylalanine showed an upward trend in shoots under salt stress. Furthermore, a label-free and gel-free comparative Q-Tof, Liquid Chromatography-Mass spectrometry (LC-MS) revealed total of 118 differentially abundant proteins in roots and shoots with and without salt stress conditions. Proteins related to DNA-binding with one finger (Dof) transcription factor family and glycine betaine (GB) biosynthesis were differentially expressed in the shoot and root of the salinity-stressed seedlings. Exogenous application of choline on GB accumulation under salt stress showed the increase of GB pathway in C. cajan. Gene expression analysis for differentially abundant proteins revealed the higher induction of ethanolamine kinase (CcEthKin), choline-phosphate cytidylyltransferase 1-like (CcChoPh), serine hydroxymethyltransferase (CcSHMT) and Dof protein (CcDof29). The results indicate the importance of, choline precursor, serine biosynthetic pathways and glycine betaine synthesis in salinity stress tolerance. The glycine betaine protects plant from cellular damages and acts as osmoticum under stress condition. Protein interaction network (PIN) analysis demonstrated that 61% of the differentially expressed proteins exhibited positive interactions and 10% of them formed the center of the PIN. Further, The PIN analysis also highlighted the potential roles of the cytochrome c oxidases in sensing and signaling cascades governing salinity stress responses in pigeonpea. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01116-w.
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Affiliation(s)
- Neha Jain
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | - Sufia Farhat
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
- IK Gujral Punjab Technical University, Jalandhar, Punjab India
| | - Ram Kumar
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | - Nisha Singh
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | - Sangeeta Singh
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | | | - Nagendra Kumar Singh
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
| | - Takabe Teruhiro
- Research Institute, Meijo University, Nagoya, 468-8502 Japan
| | - Vandna Rai
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Road, New Delhi, 110012 India
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Yolcu S, Alavilli H, Ganesh P, Panigrahy M, Song K. Salt and Drought Stress Responses in Cultivated Beets ( Beta vulgaris L.) and Wild Beet ( Beta maritima L.). PLANTS (BASEL, SWITZERLAND) 2021; 10:1843. [PMID: 34579375 PMCID: PMC8472689 DOI: 10.3390/plants10091843] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/22/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022]
Abstract
Cultivated beets, including leaf beets, garden beets, fodder beets, and sugar beets, which belong to the species Beta vulgaris L., are economically important edible crops that have been originated from a halophytic wild ancestor, Beta maritima L. (sea beet or wild beet). Salt and drought are major abiotic stresses, which limit crop growth and production and have been most studied in beets compared to other environmental stresses. Characteristically, beets are salt- and drought-tolerant crops; however, prolonged and persistent exposure to salt and drought stress results in a significant drop in beet productivity and yield. Hence, to harness the best benefits of beet cultivation, knowledge of stress-coping strategies, and stress-tolerant beet varieties, are prerequisites. In the current review, we have summarized morpho-physiological, biochemical, and molecular responses of sugar beet, fodder beet, red beet, chard (B. vulgaris L.), and their ancestor, wild beet (B. maritima L.) under salt and drought stresses. We have also described the beet genes and noncoding RNAs previously reported for their roles in salt and drought response/tolerance. The plant biologists and breeders can potentiate the utilization of these resources as prospective targets for developing crops with abiotic stress tolerance.
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Affiliation(s)
- Seher Yolcu
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - Hemasundar Alavilli
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea
| | - Pushpalatha Ganesh
- Department of Plant Biotechnology, M. S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Khurda 761211, Odisha, India;
| | - Madhusmita Panigrahy
- Biofuel & Bioprocessing Research Center, Institute of Technical Education & Research, Siksha ‘O’ Anusandhan Deemed to Be University, Bhubaneswar 751030, Odisha, India;
| | - Kihwan Song
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea
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Song Y, Liu J, Wang J, Liu F. Growth, Stoichiometry, and Palatability of Suaeda salsa From Different Habitats Are Demonstrated by Differentially Expressed Proteins and Their Enriched Pathways. FRONTIERS IN PLANT SCIENCE 2021; 12:733882. [PMID: 34539722 PMCID: PMC8440984 DOI: 10.3389/fpls.2021.733882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Suaeda salsa (L.) Pall., a medicinal and edible plant, has green and red-violet ecotypes that exhibit different phenotypes, tastes, and growth characteristics. However, few studies have focused on these differences from the aspect of differentially expressed proteins under the conditions of different habitats in the field. In this study, two ecotypes of S. salsa from the intertidal (control) and supratidal (treatment) habitats of the Yellow River Delta were selected. A total of 30 individual leaves were mixed into six samples (three biological replicates for each) and subjected to protein extraction by using tandem mass tag-labeled quantitative proteomic technology. A total of 4771 proteins were quantitated. They included 317 differentially expressed proteins (2.0-fold change, p < 0.05), among which 143 were upregulated and the remaining 174 were downregulated. These differentially expressed proteins mainly participated in biological processes, such as response to stimulus, stress, and biotic stimulus; in molecular functions, such as methyltransferase activity, transferase activity, one-C group transfer, and tetrapyrrole binding; and in cell components, such as non-membrane-bound organelles, intracellular non-membrane-bound organelles, chromosomes, and photosystems. The differentially expressed proteins were mainly enriched in eight pathways, among which the ribosome, phenylpropanoid biosynthesis, and photosynthesis pathways had higher protein numbers than the other pathways. The upregulation of differentially expressed proteins related to the ribosome and photosynthesis increased the relative growth rate and reduced the N:P ratio of S. salsa from the supratidal habitat, thereby improving its palatability. By contrast, most of the differentially expressed proteins involved in phenylpropanoid biosynthesis were downregulated in S. salsa from the intertidal habitat. This result indicated that S. salsa from the intertidal habitat might accumulate flavonoids, lignin, and other secondary metabolites in its leaves that confer a bitter taste. However, these secondary metabolites might increase the medicinal value of S. salsa from the intertidal habitat. This work could provide a theoretical basis and data support for the sustainable and high-value utilization of medicinal and edible plants from coastal wetlands.
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Affiliation(s)
- Ye Song
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Jinan Fruit Research Institute, All China Federation of Supply and Marketing Co-Operatives, Jinan, China
| | - Jiayuan Liu
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin, China
| | - Jianzhong Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Fude Liu
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin, China
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Whole-Transcriptome RNA Sequencing Reveals the Global Molecular Responses and CeRNA Regulatory Network of mRNAs, lncRNAs, miRNAs and circRNAs in Response to Salt Stress in Sugar Beet ( Beta vulgaris). Int J Mol Sci 2020; 22:ijms22010289. [PMID: 33396637 PMCID: PMC7795855 DOI: 10.3390/ijms22010289] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/25/2020] [Accepted: 12/27/2020] [Indexed: 12/13/2022] Open
Abstract
Sugar beet is an important sugar-yielding crop with some tolerance to salt, but the mechanistic basis of this tolerance is not known. In the present study, we have used whole-transcriptome RNA-seq and degradome sequencing in response to salt stress to uncover differentially expressed (DE) mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in both leaves and roots. A competitive endogenous RNA (ceRNA) network was constructed with the predicted DE pairs, which revealed regulatory roles under salt stress. A functional analysis suggests that ceRNAs are implicated in copper redistribution, plasma membrane permeability, glycometabolism and energy metabolism, NAC transcription factor and the phosphoinositol signaling system. Overall, we conducted for the first time a full transcriptomic analysis of sugar beet under salt stress that involves a potential ceRNA network, thus providing a basis to study the potential functions of lncRNAs/circRNAs.
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