Integrated Analysis of the Transcriptome and Metabolome Revealed the Molecular Mechanisms Underlying the Enhanced Salt Tolerance of Rice Due to the Application of Exogenous Melatonin

High salinity is one of the major abiotic stresses limiting rice production. Melatonin has been implicated in the salt tolerance of rice. However, the molecular basis of melatonin-mediated salt tolerance in rice remains unclear. In the present study, we performed an integrated transcriptome and metabolome profiling of rice seedlings treated with salt, melatonin, or salt + melatonin. The application of exogenous melatonin increased the salt tolerance of rice plants by decreasing the sodium content to maintain Na+/K+ homeostasis, alleviating membrane lipid oxidation, and enhancing chlorophyll contention. A comparative transcriptome analysis revealed that complex molecular pathways contribute to melatonin-mediated salt tolerance. More specifically, the AP2/EREBP–HB–WRKY transcriptional cascade and phytohormone (e.g., auxin and abscisic acid) signaling pathways were activated by an exogenous melatonin treatment. On the basis of metabolome profiles, 64 metabolites, such as amino acids, organic acids, nucleotides, and secondary metabolites, were identified with increased abundances only in plants treated with salt + melatonin. Several of these metabolites including endogenous melatonin and its intermediates (5-hydroxy-L-tryptophan, N1-acetyl-N2-formyl-5-methoxykynuramine), gallic acid, diosmetin, and cyanidin 3-O-galactoside had antioxidant functions, suggesting melatonin activates multiple antioxidant pathways to alleviate the detrimental effects of salt stress. Combined transcriptome and metabolome analyses revealed a few gene–metabolite networks related to various pathways, including linoleic acid metabolism and amino acid metabolism that are important for melatonin-mediated salt tolerance. The data presented herein may be useful for further elucidating the multiple regulatory roles of melatonin in plant responses to abiotic stresses.

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Exogenous melatonin improves salt stress adaptation of cotton seedlings by regulating active oxygen metabolism

PeerJ ◽

10.7717/peerj.10486 ◽

2020 ◽

Vol 8 ◽

pp. e10486

Author(s):

Dan Jiang ◽

Bin Lu ◽

Liantao Liu ◽

Wenjing Duan ◽

Li Chen ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Seedling Growth ◽

Lipid Membrane ◽

Soluble Sugars ◽

Oxygen Metabolism ◽

Membrane Lipid ◽

Biotic And Abiotic Stress ◽

Exogenous Melatonin ◽

Cotton Seedling

Melatonin is a small-molecule indole hormone that plays an important role in participating in biotic and abiotic stress resistance. Melatonin has been confirmed to promote the normal development of plants under adversity stress by mediating physiological regulation mechanisms. However, the mechanisms by which exogenous melatonin mediates salt tolerance via regulation of antioxidant activity and osmosis in cotton seedlings remain largely unknown. In this study, the regulatory effects of melatonin on reactive oxygen species (ROS), the antioxidant system, and osmotic modulators of cotton seedlings were determined under 0–500 µM melatonin treatments with salt stress induced by 150 mM NaCl treatment. Cotton seedlings under salt stress exhibited an inhibition of growth, excessive hydrogen peroxide (H2O2), superoxide anion (O2−), and malondialdehyde (MDA) accumulations in leaves, increased activity levels of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), and elevated ascorbic acid (AsA) and glutathione (GSH) content in leaves. However, the content of osmotic regulators (i.e., soluble sugars and proteins) in leaves was reduced under salt stress. This indicates high levels of ROS were produced, and the cell membrane was damaged. Additionally, osmotic regulatory substance content was reduced, resulting in osmotic stress, which seriously affected cotton seedling growth under salt stress. However, exogenous melatonin at different concentrations reduced the contents of H2O2, O2−, and MDA in cotton leaves, increased the activity of antioxidant enzymes and the content of reductive substances (i.e., AsA and GSH), and promoted the accumulation of osmotic regulatory substances in leaves under salt stress. These results suggest that melatonin can inhibit ROS production in cotton seedlings, improve the activity of the antioxidant enzyme system, raise the content of osmotic regulation substances, reduce the level of membrane lipid peroxidation, and protect the integrity of the lipid membrane under salt stress, which reduces damage caused by salt stress to seedlings and effectively enhances inhibition of salt stress on cotton seedling growth. These results indicate that 200 µM melatonin treatment has the best effect on the growth and salt tolerance of cotton seedlings.

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The Alleviation of Photosynthetic Damage in Tomato under Drought and Cold Stress by High CO2 and Melatonin

International Journal of Molecular Sciences ◽

10.3390/ijms21155587 ◽

2020 ◽

Vol 21 (15) ◽

pp. 5587

Author(s):

Rong Zhou ◽

Hongjian Wan ◽

Fangling Jiang ◽

Xiangnan Li ◽

Xiaqing Yu ◽

...

Keyword(s):

Cold Stress ◽

Abiotic Stresses ◽

Starch Content ◽

Biomass Accumulation ◽

Co2 Concentration ◽

Plant Responses ◽

Severe Drought ◽

Exogenous Melatonin ◽

Moderate Drought ◽

Chlorophyll A Content

The atmospheric CO2 concentration (a[CO2]) is increasing at an unprecedented pace. Exogenous melatonin plays positive roles in the response of plants to abiotic stresses, including drought and cold. The effect of elevated CO2 concentration (e[CO2]) accompanied by exogenous melatonin on plants under drought and cold stresses remains unknown. Here, tomato plants were grown under a[CO2] and e[CO2], with half of the plants pre-treated with melatonin. The plants were subsequently treated with drought stress followed by cold stress. The results showed that a decreased net photosynthetic rate (PN) was aggravated by a prolonged water deficit. The PN was partially restored after recovery from drought but stayed low under a successive cold stress. Starch content was downregulated by drought but upregulated by cold. The e[CO2] enhanced PN of the plants under non-stressed conditions, and moderate drought and recovery but not severe drought. Stomatal conductance (gs) and the transpiration rate (E) was less inhibited by drought under e[CO2] than under a[CO2]. Tomato grown under e[CO2] had better leaf cooling than under a[CO2] when subjected to drought. Moreover, melatonin enhanced PN during recovery from drought and cold stress, and enhanced biomass accumulation in tomato under e[CO2]. The chlorophyll a content in plants treated with melatonin was higher than in non-treated plants under e[CO2] during cold stress. Our findings will improve the knowledge on plant responses to abiotic stresses in a future [CO2]-rich environment accompanied by exogenous melatonin.

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Comparative transcriptome and metabolome profiling reveal molecular mechanisms underlying OsDRAP1-mediated salt tolerance in rice

Scientific Reports ◽

10.1038/s41598-021-84638-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yinxiao Wang ◽

Liyu Huang ◽

Fengping Du ◽

Juan Wang ◽

Xiuqin Zhao ◽

...

Keyword(s):

Amino Acids ◽

Salt Stress ◽

Salt Tolerance ◽

Molecular Mechanisms ◽

Redox Homeostasis ◽

Glyceric Acid ◽

Metabolome Analysis ◽

Phenotypic Analysis ◽

Metabolomics Data ◽

Metabolome Profiling

AbstractIntegration of transcriptomics and metabolomics data can provide detailed information for better understanding the molecular mechanisms underlying salt tolerance in rice. In the present study, we report a comprehensive analysis of the transcriptome and metabolome of rice overexpressing the OsDRAP1 gene, which encodes an ERF transcription factor and was previously identified to be conferring drought tolerance. Phenotypic analysis showed that OsDRAP1 overexpression (OE) improved salt tolerance by increasing the survival rate under salt stress. OsDRAP1 affected the physiological indices such as superoxide dismutase (SOD), catalase (CAT) and malondialdehyde (MDA) to enhance redox homeostasis and membrane stability in response to salt stress. Higher basal expression of OsDRAP1 resulted in differential expression of genes that potentially function in intrinsic salt tolerance. A core set of genes with distinct functions in transcriptional regulation, organelle gene expression and ion transport were substantially up-regulated in the OE line in response to salt stress, implying their important role in OsDRAP1-mediated salt tolerance. Correspondingly, metabolome profiling detected a number of differentially metabolites in the OE line relative to the wild type under salt stress. These metabolites, including amino acids (proline, valine), organic acids (glyceric acid, phosphoenolpyruvic acid and ascorbic acid) and many secondary metabolites, accumulated to higher levels in the OE line, demonstrating their role in salt tolerance. Integration of transcriptome and metabolome analysis highlights the crucial role of amino acids and carbohydrate metabolism pathways in OsDRAP1-mediated salt tolerance.

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Plants’ Epigenetic Mechanisms and Abiotic Stress

Genes ◽

10.3390/genes12081106 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1106

Author(s):

Matin Miryeganeh

Keyword(s):

Stress Responses ◽

Environmental Conditions ◽

Abiotic Stresses ◽

Molecular Mechanisms ◽

Plant Stress ◽

Plant Responses ◽

Epigenetic Mechanisms ◽

Epigenetic Marks ◽

Stress Memory ◽

Mechanistic Basis

Plants are sessile organisms that need to adapt to constantly changing environmental conditions. Unpredictable climate change places plants under a variety of abiotic stresses. Studying the regulation of stress-responsive genes can help to understand plants’ ability to adapt to fluctuating environmental conditions. Changes in epigenetic marks such as histone modifications and DNA methylation are known to regulate gene expression by their dynamic variation in response to stimuli. This can then affect their phenotypic plasticity, which helps with the adaptation of plants to adverse conditions. Epigenetic marks may also provide a mechanistic basis for stress memory, which enables plants to respond more effectively and efficiently to recurring stress and prepare offspring for potential future stresses. Studying epigenetic changes in addition to genetic factors is important to better understand the molecular mechanisms underlying plant stress responses. This review summarizes the epigenetic mechanisms behind plant responses to some main abiotic stresses.

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Characterization of Interactions between the Soybean Salt-Stress Responsive Membrane-Intrinsic Proteins GmPIP1 and GmPIP2

Agronomy ◽

10.3390/agronomy11071312 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1312

Author(s):

Jia Liu ◽

Weicong Qi ◽

Haiying Lu ◽

Hongbo Shao ◽

Dayong Zhang

Keyword(s):

Plasma Membrane ◽

Salt Stress ◽

Salt Tolerance ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Early Gene ◽

Plant Responses ◽

Constitutive Overexpression ◽

Important Trait

Salt tolerance is an important trait in soybean cultivation and breeding. Plant responses to salt stress include physiological and biochemical changes that affect the movement of water across the plasma membrane. Plasma membrane intrinsic proteins (PIPs) localize to the plasma membrane and regulate the water and solutes flow. In this study, quantitative real-time PCR and yeast two-hybridization were engaged to analyze the early gene expression profiles and interactions of a set of soybean PIPs (GmPIPs) in response to salt stress. A total of 20 GmPIPs-encoding genes had varied expression profiles after salt stress. Among them, 13 genes exhibited a downregulated expression pattern, including GmPIP1;6, the constitutive overexpression of which could improve soybean salt tolerance, and its close homologs GmPIP1;7 and 1;5. Three genes showed upregulated patterns, including the GmPIP1;6 close homolog GmPIP1;4, when four genes with earlier increased and then decreased expression patterns. GmPIP1;5 and GmPIP1;6 could both physically interact strongly with GmPIP2;2, GmPIP2;4, GmPIP2;6, GmPIP2;8, GmPIP2;9, GmPIP2;11, and GmPIP2;13. Definite interactions between GmPIP1;6 and GmPIP1;7 were detected and GmPIP2;9 performed homo-interaction. The interactions of GmPIP1;5 with GmPIP2;11 and 2;13, GmPIP1;6 with GmPIP2;9, 2;11 and GmPIP2;13, and GmPIP2;9 with itself were strengthened upon salt stress rather than osmotic stress. Taken together, we inferred that GmPIP1 type and GmPIP2 type could associate with each other to synergistically function in the plant cell; a salt-stress environment could promote part of their interactions. This result provided new clues to further understand the soybean PIP–isoform interactions, which lead to potentially functional homo- and heterotetramers for salt tolerance.

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Cloning and overexpression of PeWRKY31 from Populus × euramericana enhances salt and biological tolerance in transgenic Nicotiana

BMC Plant Biology ◽

10.1186/s12870-021-02856-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xiaoyue Yu ◽

Yu Pan ◽

Yan Dong ◽

Bin Lu ◽

Chao Zhang ◽

...

Keyword(s):

Salt Tolerance ◽

Insect Resistance ◽

Enrichment Analysis ◽

Forest Tree ◽

Mapk Signaling ◽

Soil Salinization ◽

Glutathione Metabolism ◽

Plant Responses ◽

Populus Euramericana ◽

Biological Stress

Abstract Background As important forest tree species, biological stress and soil salinization are important factors that restrict the growth of Populus × euramericana. WRKYs are important transcription factors in plants that can regulate plant responses to biotic and abiotic stresses. In this study, PeWRKY31 was isolated from Populus × euramericana, and its bioinformation, salt resistance and insect resistance were analyzed. This study aims to provide guidance for producing salt-resistant and insect-resistant poplars. Results PeWRKY31 has a predicted open reading frame (ORF) of 1842 bp that encodes 613 amino acids. The predicted protein is the unstable, acidic, and hydrophilic protein with a molecular weight of 66.34 kDa, and it has numerous potential phosphorylation sites, chiefly on serines and threonines. PeWRKY31 is a zinc-finger C2H2 type-II WRKY TF that is closely related to WRKY TFs of Populus tomentosa, and localizes to the nucleus. A PeWRKY31 overexpression vector was constructed and transformed into Nicotiana tabacum L. Overexpression of PeWRKY31 improved the salt tolerance and insect resistance of the transgenic tobacco. Transcriptome sequencing and KEGG enrichment analysis showed the elevated expression of genes related to glutathione metabolism, plant hormone signal transduction, and MAPK signaling pathways, the functions of which were important in plant salt tolerance and insect resistance in the overexpressing tobacco line. Conclusions PeWRKY31 was isolated from Populus × euramericana. Overexpression of PeWRKY31 improved the resistance of transgenic plant to salt stress and pest stress. The study provides references for the generation of stress-resistant lines with potentially great economic benefit.

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Molecular mechanisms of local adaptation for salt‐tolerance in a treefrog

Molecular Ecology ◽

10.1111/mec.15867 ◽

2021 ◽

Author(s):

Molly A. Albecker ◽

Adam M.M. Stuckert ◽

Christopher N. Balakrishnan ◽

Michael W. McCoy

Keyword(s):

Salt Tolerance ◽

Local Adaptation ◽

Molecular Mechanisms

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Genome-Wide Mapping of Histone H3 Lysine 4 Trimethylation (H3K4me3) and Its Involvement in Fatty Acid Biosynthesis in Sunflower Developing Seeds

Plants ◽

10.3390/plants10040706 ◽

2021 ◽

Vol 10 (4) ◽

pp. 706

Author(s):

Antonio J. Moreno-Pérez ◽

Raquel Martins-Noguerol ◽

Cristina DeAndrés-Gil ◽

Mónica Venegas-Calerón ◽

Rosario Sánchez ◽

...

Keyword(s):

Fatty Acid ◽

Chromatin Remodeling ◽

Molecular Mechanisms ◽

Acid Metabolism ◽

Fatty Acid Biosynthesis ◽

Acid Synthesis ◽

Sunflower Seeds ◽

Acid Biosynthesis ◽

Functional Regions ◽

Genome Wide

Histone modifications are of paramount importance during plant development. Investigating chromatin remodeling in developing oilseeds sheds light on the molecular mechanisms controlling fatty acid metabolism and facilitates the identification of new functional regions in oil crop genomes. The present study characterizes the epigenetic modifications H3K4me3 in relationship with the expression of fatty acid-related genes and transcription factors in developing sunflower seeds. Two master transcriptional regulators identified in this analysis, VIV1 (homologous to Arabidopsis ABI3) and FUS3, cooperate in the regulation of WRINKLED 1, a transcriptional factor regulating glycolysis, and fatty acid synthesis in developing oilseeds.

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Comprehensive transcriptome and metabolome profiling reveal metabolic mechanisms of Nitraria sibirica Pall. to salt stress

Scientific Reports ◽

10.1038/s41598-021-92317-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Huanyong Li ◽

Xiaoqian Tang ◽

Xiuyan Yang ◽

Huaxin Zhang

Keyword(s):

Salt Stress ◽

Amino Acid ◽

Salt Tolerance ◽

Metabolic Pathways ◽

Amino Acid Metabolism ◽

Acid Metabolism ◽

Sulfur Metabolism ◽

Enrichment Analysis ◽

Extracellular Region ◽

Nitraria Sibirica

AbstractNitraria sibirica Pall., a typical halophyte that can survive under extreme drought conditions and in saline-alkali environments, exhibits strong salt tolerance and environmental adaptability. Understanding the mechanism of molecular and physiological metabolic response to salt stress of plant will better promote the cultivation and use of halophytes. To explore the mechanism of molecular and physiological metabolic of N. sibirica response to salt stress, two-month-old seedlings were treated with 0, 100, and 400 mM NaCl. The results showed that the differentially expressed genes between 100 and 400 mmol L−1 NaCl and unsalted treatment showed significant enrichment in GO terms such as binding, cell wall, extemal encapsulating structure, extracellular region and nucleotide binding. KEGG enrichment analysis found that NaCl treatment had a significant effect on the metabolic pathways in N. sibirica leaves, which mainly including plant-pathogen interaction, amino acid metabolism of the beta alanine, arginine, proline and glycine metabolism, carbon metabolism of glycolysis, gluconeogenesis, galactose, starch and sucrose metabolism, plant hormone signal transduction and spliceosome. Metabolomics analysis found that the differential metabolites between the unsalted treatment and the NaCl treatment are mainly amino acids (proline, aspartic acid, methionine, etc.), organic acids (oxaloacetic acid, fumaric acid, nicotinic acid, etc.) and polyhydric alcohols (inositol, ribitol, etc.), etc. KEGG annotation and enrichment analysis showed that 100 mmol L−1 NaCl treatment had a greater effect on the sulfur metabolism, cysteine and methionine metabolism in N. sibirica leaves, while various amino acid metabolism, TCA cycle, photosynthetic carbon fixation and sulfur metabolism and other metabolic pathways have been significantly affected by 400 mmol L−1 NaCl treatment. Correlation analysis of differential genes in transcriptome and differential metabolites in metabolome have found that the genes of AMY2, BAM1, GPAT3, ASP1, CML38 and RPL4 and the metabolites of L-cysteine, proline, 4-aminobutyric acid and oxaloacetate played an important role in N. sibirica salt tolerance control. This is a further improvement of the salt tolerance mechanism of N. sibirica, and it will provide a theoretical basis and technical support for treatment of saline-alkali soil and the cultivation of halophytes.

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Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview

Metabolites ◽

10.3390/metabo11070445 ◽

2021 ◽

Vol 11 (7) ◽

pp. 445

Author(s):

Morena M. Tinte ◽

Kekeletso H. Chele ◽

Justin J. J. van der Hooft ◽

Fidele Tugizimana

Keyword(s):

Machine Learning ◽

Abiotic Stress ◽

Stress Responses ◽

Abiotic Stresses ◽

Industrial Revolution ◽

Chemical Space ◽

Big Data Analytics ◽

Plant Responses ◽

Next Generation ◽

Computational Tools

Plants are constantly challenged by changing environmental conditions that include abiotic stresses. These are limiting their development and productivity and are subsequently threatening our food security, especially when considering the pressure of the increasing global population. Thus, there is an urgent need for the next generation of crops with high productivity and resilience to climate change. The dawn of a new era characterized by the emergence of fourth industrial revolution (4IR) technologies has redefined the ideological boundaries of research and applications in plant sciences. Recent technological advances and machine learning (ML)-based computational tools and omics data analysis approaches are allowing scientists to derive comprehensive metabolic descriptions and models for the target plant species under specific conditions. Such accurate metabolic descriptions are imperatively essential for devising a roadmap for the next generation of crops that are resilient to environmental deterioration. By synthesizing the recent literature and collating data on metabolomics studies on plant responses to abiotic stresses, in the context of the 4IR era, we point out the opportunities and challenges offered by omics science, analytical intelligence, computational tools and big data analytics. Specifically, we highlight technological advancements in (plant) metabolomics workflows and the use of machine learning and computational tools to decipher the dynamics in the chemical space that define plant responses to abiotic stress conditions.

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