Synchronization and interaction of proline, ascorbate and oxidative stress pathways under abiotic stress combination in tomato plants
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ABSTRACT:
PROVIDER: PRJNA639840 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12026415_1.fastq.gz | Fastqsanger.gz | |||
| SRR12026415_2.fastq.gz | Fastqsanger.gz | |||
| SRR12026416_1.fastq.gz | Fastqsanger.gz | |||
| SRR12026416_2.fastq.gz | Fastqsanger.gz | |||
| SRR12026417_1.fastq.gz | Fastqsanger.gz |
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Project description:Adverse environmental conditions, such as salinity, heat waves, or water scarcity have a devastating impact on plant productivity. In nature, multiple abiotic stresses occur simultaneously and plants evolved unique responses to cope against combination stress that are not induced under a single stress condition. Here we coupled genome-wide transcriptional profiling and untargeted metabolomics with physiological and biochemical analyses to characterize the effect of salinity and heat applied jointly in the metabolism of tomato plants. Our results demonstrate that combination of salinity and heat causes unique reprogramming of tomato metabolic pathways, including changes in the expression of 1,388 genes and accumulation of 568 molecular features. Pathway enrichment analysis of transcript and metabolite data indicated that the proline and ascorbate pathways act synchronously to maintain cellular redox homeostasis, which was supported by measurements of enzymatic activity and oxidative stress markers. We also identified key transcription factors from the basic Leucine Zipper Domain (bZIP), Zinc Finger Cysteine-2/Histidine-2 (C2H2) and Trihelix families that are likely regulators of the identified up-regulated genes under salinity and heat combination. Our results expand the current understanding of how plants acclimate to environmental stresses in combination and unveiled the synergism between key cellular metabolic pathways for effective reactive oxygen species detoxification. Our study opens the door to elucidating the different signaling mechanisms for stress tolerance.
2021-09-01 | GSE152620 | GEO
Project description:To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNA. Keywords = abiotic stress Keywords: repeat sample
2005-03-02 | GSE2211 | GEO
Project description:Ascorbate (vitamin C) is an important antioxidant in leaves with multiple functions in photosynthesis and its levels are tightly regulated by light quality. The majority of work to date has focussed on regulation of ascorbate levels via biosynthesis. However, the pathway of ascorbate degradation, which is localised in the apoplast may additionally play a significant role. The degradative pathway begins with ascorbate oxidation by the enzyme ascorbate oxidase (AO) and hence we have examined the impact of manipulation of ascorbate oxidase activity on the content of ascorbate and the acclimation of photosynthesis to changing light levels. Leaf ascorbate content was highly light dependent in Nicotiana tobaccum being double in high compared with low light conditions. In contrast ascorbate oxidase activity was not altered by changing light levels. Transgenic tobacco lines with reduced or enhanced AO activity exhibited no morphological phenotype and photosynthesis under high light was similarly impaired irrespective of the measured AO activity. However further investigation between AO activity and leaf acclimation to changing light intensity revealed a suite of metabolic and transcriptome changes indicating a role for the apoplastic ascorbate pool in chloroplast to nucleus communication. In all genotypes, transcripts associated with ascorbate synthesis and recycling were less abundant following transition from high to low light. However transcripts associated with glutathione recycling, light harvesting, reaction centre function and the Calvin cycle were all increased in abundance. Following the transition from high to low light increases in leaf threonate, an ascorbate degradation product, were proportional to AO activity. A number of chloroplast synthesised amino acids were significantly increased both during high light and following transfer back to LL for 12 h. Similarly, several primary carbohydrates and TCA intermediates were significantly enhanced following high light treatment. In addition to light effects, AO activity had a significant impact on ï¢-alanine, aspartate and threonine. Intriguingly, a large number of fatty acids were reduced in antisense AO and wild-type plants immediately after high light stress however the content of these compounds were significantly increased in overexpressing sense lines. We conclude that AO mediated turnover plays an important role in adjusting cellular ascorbate content to photosynthetic need in a fluctuating light environment and that light mediated signals rapidly adjust that the apoplastic ascorbate pool.
2017-03-01 | E-MTAB-4816 | biostudies-arrayexpress
Project description:Plant basic helix-loop-helix (bHLH) transcription factors are involved in physiological and developmental processes, and also play essential roles in abiotic stresses. However, their exact roles in abiotic stress are still need to be elucidated, and most of bHLHs have not been functionally characterized. In the present study, we characterized the functional role of AtbHLH112 in response to abiotic stresses. AtbHLH112 is a nuclear-localized protein, and its nuclear-localization is induced by salt, drought and ABA. Besides binding to E-box motif, AtbHLH112 is found to bind to a novel motif with the sequence “GG[GT]CC[GT][GA][TA]C” (GCG-box), and the binding affinity is induced by salt and ABA. Gain- and loss-of-function analyses showed that the transcript level of AtbHLH112 is positively correlated with salt and drought tolerance. AtbHLH112 mediates stress tolerance by upregulating the expression of P5CS genes and decreasing the expression of P5CDH and PRODH genes to increase proline levels, and via enhancing the expression of POD and SOD genes to improve ROS scavenging ability. All data together suggested that AtbHLH112 regulates the expression of genes through binding to GCG-box and E-box to mediate the physiological stress responses, including proline biosynthesis and ROS scavenging pathways to enhance stress tolerance.
2014-08-09 | GSE60260 | GEO
Project description:The l-galactose (Smirnoff-Wheeler) pathway represents the major route to l-ascorbic acid (vitamin C) biosynthesis in plants. Arabidopsis thaliana VTC2 and its paralogue VTC5 function as GDP-l-galactose phosphorylases converting GDP-l-galactose to l-galactose-1-P, thus catalyzing the first committed step in the biosynthesis of l-ascorbate. Here we report that the l-galactose pathway of ascorbate biosynthesis described in higher plants is conserved in green algae. The Chlamydomonas reinhardtii genome encodes all the enzymes required for vitamin C biosynthesis via the Smirnoff-Wheeler pathway. We have characterized recombinant C. reinhardtii VTC2 as an active GDP-l-galactose phosphorylase. C. reinhardtii cells exposed to oxidative stress show increased VTC2 mRNA and l-ascorbate levels. We have also shown that enzymatic components of the ascorbate-glutathione system (e.g. ascorbate peroxidase, Mn superoxide dismutase, dehydroascorbate reductase) are up-regulated in response to increased oxidative stress. These results indicate that C. reinhardtii VTC2, like its plant homologs, is a key enzyme in ascorbate biosynthesis in green algae and together with components of the ascorbate recycling system represents the major route in providing protective levels of ascorbate in oxidatively stressed algal cells. Our results suggest that C. reinhardtii cells exposed to oxidative stress conditions produce more ascorbate both by de novo synthesis (Smirnoff-Wheeler pathway) and by recycling via the ascorbate-glutathione cycle.
2012-05-03 | GSE34826 | GEO
Project description:The l-galactose (Smirnoff-Wheeler) pathway represents the major route to l-ascorbic acid (vitamin C) biosynthesis in plants. Arabidopsis thaliana VTC2 and its paralogue VTC5 function as GDP-l-galactose phosphorylases converting GDP-l-galactose to l-galactose-1-P, thus catalyzing the first committed step in the biosynthesis of l-ascorbate. Here we report that the l-galactose pathway of ascorbate biosynthesis described in higher plants is conserved in green algae. The Chlamydomonas reinhardtii genome encodes all the enzymes required for vitamin C biosynthesis via the Smirnoff-Wheeler pathway. We have characterized recombinant C. reinhardtii VTC2 as an active GDP-l-galactose phosphorylase. C. reinhardtii cells exposed to oxidative stress show increased VTC2 mRNA and l-ascorbate levels. We have also shown that enzymatic components of the ascorbate-glutathione system (e.g. ascorbate peroxidase, Mn superoxide dismutase, dehydroascorbate reductase) are up-regulated in response to increased oxidative stress. These results indicate that C. reinhardtii VTC2, like its plant homologs, is a key enzyme in ascorbate biosynthesis in green algae and together with components of the ascorbate recycling system represents the major route in providing protective levels of ascorbate in oxidatively stressed algal cells. Our results suggest that C. reinhardtii cells exposed to oxidative stress conditions produce more ascorbate both by de novo synthesis (Smirnoff-Wheeler pathway) and by recycling via the ascorbate-glutathione cycle. Sampling of Chlamydomonas 2137 exposed to hydrogen peroxide
2012-05-02 | E-GEOD-34826 | biostudies-arrayexpress
Project description:Plant basic helix-loop-helix (bHLH) transcription factors are involved in physiological and developmental processes, and also play essential roles in abiotic stresses. However, their exact roles in abiotic stress are still need to be elucidated, and most of bHLHs have not been functionally characterized. In the present study, we characterized the functional role of AtbHLH112 in response to abiotic stresses. AtbHLH112 is a nuclear-localized protein, and its nuclear-localization is induced by salt, drought and ABA. Besides binding to E-box motif, AtbHLH112 is found to bind to a novel motif with the sequence M-bM-^@M-^\GG[GT]CC[GT][GA][TA]CM-bM-^@M-^] (GCG-box), and the binding affinity is induced by salt and ABA. Gain- and loss-of-function analyses showed that the transcript level of AtbHLH112 is positively correlated with salt and drought tolerance. AtbHLH112 mediates stress tolerance by upregulating the expression of P5CS genes and decreasing the expression of P5CDH and PRODH genes to increase proline levels, and via enhancing the expression of POD and SOD genes to improve ROS scavenging ability. All data together suggested that AtbHLH112 regulates the expression of genes through binding to GCG-box and E-box to mediate the physiological stress responses, including proline biosynthesis and ROS scavenging pathways to enhance stress tolerance. Differentially expression genes of AtbHLH112-overexpression plants, mutant (SALK_033618C) plants and wild type of Columbia Arabidopsis thaliana were measured under salt stressed and normal condition for 3 hours, respectively. Three independent experiments were performed at each treatment using different plants for each experiment.
2014-08-09 | E-GEOD-60260 | biostudies-arrayexpress
Project description:Plants will meet various abiotic stresses during their growth and development. One of the important strategies for plants to deal with the stress is involved in metabolic regulation, causing the dramatic changes of metabolite profiles. Metabolomic studies have been intensively conducted to reveal the responses of plants to abiotic stress, but most of them were limited to one or at most two abiotic stresses in a single experiment. In this study, we compared the metabolite profiles of barley seedlings exposed to seven abiotic stresses simultaneously, including drought, salt stress, aluminum (Al), cadmium (Cd), deficiency of nitrogen (N), phosphorus (P) and potassium (K). The results showed that metabolite profiles of barley under these stresses could be classified into three types: osmotic stresses (drought and salt); metal stresses (Al and Cd) and nutrient deficiencies (N, P and K deficiencies). Compared with the control, some metabolites (including polyamines, raffinose and piperonic acid) in plants exposed to all abiotic stresses changed significantly, while some other metabolites showed the specific change only under a certain abiotic stress, such as proline being largely increased by osmotic stress (drought and salinity), the P-containing metabolites being largely decreased under P deficiency, some amino acids (lysine, tyrosine, threonine, ornithine， glutamine and so on) showing the dramatic reduction in the plants exposed to N deficiencies, respectively. The current meta-analysis obtained a comprehensive view on the metabolic responses to various abiotic stress, and improved the understanding of the mechanisms for tolerance of barley to abiotic stress.
2021-01-07 | ST001648 | MetabolomicsWorkbench
Project description:Plant basic helix-loop-helix (bHLH) proteins play essential roles in physiological and developmental processes and are also involved in abiotic stresses. However, their exact roles in abiotic stress are still not fully understood, and most of them have not been functionally characterised. In the present study, we characterised the functional role of AtbHLH112 in response to abiotic stress. A WRKY gene, AtWRKY66, can regulate the expression of the AtbHLH112 via binding to W-box motifs present in its promoter. AtbHLH112 is a nuclear-localised protein, and its nuclear localisation is increased upon exposure to NaCl, mannitol and ABA. In addition to binding to the G-box motif, AtbHLH112 is found to bind to a novel motif M-bM-^@M-^\GGGCCGGTCM-bM-^@M-^] (named the GCG-box) to regulate gene expression. Gain- and loss-of-function analyses showed that the transcript level of AtbHLH112 is positively correlated with tolerance to salt and drought. AtbHLH112 can confer stress tolerance via enhanced expression of POD and SOD genes to improve ROS scavenging ability and via upregulated expression of P5CS genes and decreased expression of P5CDH and PRODH genes to improve proline levels. Our data suggested that AtbHLH112 regulates the expression of genes via binding to the G-box and the GCG-box to improve stress-related pathways, such as ROS scavenging and proline biosynthesis. Differentially expression genes of AtbHLH112-overexpression plants and mutant (SALK_033618C) plants of Arabidopsis thaliana were measured under salt stressed and normal condition for 3 hours, respectively. Three independent experiments were performed at each treatment using different plants for each experiment.
2013-11-14 | E-GEOD-52326 | biostudies-arrayexpress
Project description:Plant basic helix-loop-helix (bHLH) proteins play essential roles in physiological and developmental processes and are also involved in abiotic stresses. However, their exact roles in abiotic stress are still not fully understood, and most of them have not been functionally characterised. In the present study, we characterised the functional role of AtbHLH112 in response to abiotic stress. A WRKY gene, AtWRKY66, can regulate the expression of the AtbHLH112 via binding to W-box motifs present in its promoter. AtbHLH112 is a nuclear-localised protein, and its nuclear localisation is increased upon exposure to NaCl, mannitol and ABA. In addition to binding to the G-box motif, AtbHLH112 is found to bind to a novel motif “GGGCCGGTC” (named the GCG-box) to regulate gene expression. Gain- and loss-of-function analyses showed that the transcript level of AtbHLH112 is positively correlated with tolerance to salt and drought. AtbHLH112 can confer stress tolerance via enhanced expression of POD and SOD genes to improve ROS scavenging ability and via upregulated expression of P5CS genes and decreased expression of P5CDH and PRODH genes to improve proline levels. Our data suggested that AtbHLH112 regulates the expression of genes via binding to the G-box and the GCG-box to improve stress-related pathways, such as ROS scavenging and proline biosynthesis.
2013-11-14 | GSE52326 | GEO