Integrative Analysis of Sorghum Bicolor Green Prop Roots Under Elevated CO2 and Water Deficit Conditions
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ABSTRACT:
PROVIDER: PRJNA742236 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14935703_1.fastq.gz | Fastqsanger.gz | |||
| SRR14935703_2.fastq.gz | Fastqsanger.gz | |||
| SRR14935704_1.fastq.gz | Fastqsanger.gz | |||
| SRR14935704_2.fastq.gz | Fastqsanger.gz | |||
| SRR14935705_1.fastq.gz | Fastqsanger.gz |
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Project description:Elevated CO2 (E[CO2]) improves the biomass and yield when combined with water-stress in C4 plants. Although several studies described the molecular response of the C4 plant Sorghum bicolor during drought exposure, none reported its combinatorial effect with E[CO2] in the roots. We decided to perform a molecular analysis using green prop roots, the portion of the radicular system photosynthetically active and more sensible to drought. Whole-transcriptome analysis identified 394 up- and 1,471 down-regulated genes. Among the E[CO2] induced pathways, photosynthesis stood out. Carbon fixation, phenylpropanoid, phenolic compounds, and fatty acid biosynthesis-related pathways were repressed. Protein family analysis showed induction of chlorophyll a-b binding protein family, and repression of glutathione-related enzymes. Protein-protein interaction networks exhibited well-defined clusters, including genes related to cell organization and biogenesis, oxireduction process, and photosynthesis being induced. The findings suggest that the E[CO2] mitigates the water deficit by antioxidant and osmoregulation activity, as well as by accumulation of sugaralcohols in the green prop roots, which may be responsible by the increase in biomass together with the cell proliferation. The higher carbon uptake explains the increase in photosynthetic and primary metabolism activities. Our data revealed that green prop roots present an intriguing metabolism under water deficit and E[CO2], showing its crucial role in the drought tolerance acquisition in a predicted future global atmosphere.
2021-06-30 | GSE179109 | GEO
Project description:The effects of elevated CO2 (hypercapnia) on organisms are not well known, nor are the molecular pathways by which organisms sense CO2. We have performed microarray analysis on Drosophila in order to develop a genetic model for better understanding the effects of CO2.
2009-09-30 | GSE17444 | GEO
Project description:Plant respiration responses to elevated growth [CO2] are key uncertainties in predicting future crop and ecosystem function. In particular, the effects of elevated growth [CO2] on respiration over leaf development are poorly understood. This study tested the prediction that, due to greater whole-plant photoassimilate availability and growth, elevated [CO2] induces transcriptional reprogramming and a stimulation of nighttime respiration in leaf primordia, expanding leaves, and mature leaves of Arabidopsis thaliana. In primordia, elevated [CO2] altered transcript abundance, but not for genes encoding respiratory proteins. In expanding leaves, elevated [CO2] induced greater glucose content and transcript abundance for some respiratory genes, but did not alter respiratory CO2 efflux. In mature leaves, elevated [CO2] led to greater glucose, sucrose and starch content, plus greater transcript abundance for many components of the respiratory pathway, and greater respiratory CO2 efflux. Therefore, growth at elevated [CO2] stimulated dark respiration only after leaves transitioned from carbon sinks into carbon sources. This coincided with greater photoassimilate production by mature leaves under elevated [CO2] and peak respiratory transcriptional responses. It remains to be determined if biochemical and transcriptional responses to elevated [CO2] in primordial and expanding leaves are essential prerequisites for subsequent alterations of respiratory metabolism in mature leaves.
2014-04-04 | GSE56480 | GEO
Project description:The effects of elevated CO2 (hypercapnia) on organisms are not well known, nor are the molecular pathways by which organisms sense CO2. We have performed microarray analysis on Drosophila in order to develop a genetic model for better understanding the effects of CO2. Equal numbers of 5-day old male and female flies (at least 40 total) were exposed to 13% CO2 or air for 24h and RNA extracted. Gene expression changes in CO2 compared with air were analyzed. Experiments were performed in triplicate and the 3 separate microarray experiments are included.
2010-06-25 | E-GEOD-17444 | biostudies-arrayexpress
Project description:The transcript responses of both growing, trifoliate 6 and fully expanded, trifoliate 4 soybean leaves to elevated CO2 was investigated. We also compared the transcriptome of fully expanded vs. developing leaves in both ambient and elevated CO2. Keywords = soybean Keywords = elevated carbon dioxide Keywords = global change Keywords = leaf growth Keywords = plant Keywords: soybean leaf comparisons
2006-08-23 | GSE5573 | GEO
Project description:Background: The unprecedented rise in atmospheric CO2 concentration and injudicious fertilization or heterogeneous distribution of Mg in the soil warrant further research to understand the synergistic and holistic mechanisms involved in the plant growth regulation. The objective of this work is to understand responses in plants along with interactive effect of elevated CO2 and Mg levels by comparing data on single stress with that of combined stresses. Results: This study investigated the influence of elevated CO2 (800 μL L−1) on physiological and transcriptomic profiles in Arabidopsis cultured in hydroponic media treated with 1 μM (low), 1000 μM (normal) and 10000 μM (high) Mg2+. Following 7-d treatment, elevated CO2 increased the shoot growth and chlorophyll content under both low and normal Mg supply, whereas root growth was improved exclusively under normal Mg nutrition. Notably, the effect of elevated CO2 on mineral homeostasis in both shoots and roots was less than that of Mg supply. Irrespective of CO2 treatment, high Mg increased leaf number but decreased root growth and absorption of P, K, Ca, Fe and Mn whereas low Mg increased the concentration of P, K, Ca and Fe in leaves. Elevated CO2 decreased the expression of genes related to cadmium response, cell redox homeostasis and lipid localization, but enhanced photosynthesis, signal transduction, protein phosphorylation, NBS-LRR disease resistance proteins and subsequently programmed cell death in low-Mg shoots. By comparison, elevated CO2 enhanced the response of lipid localization (mainly LTP transfer protein/protease inhibitor), endomembrane system, heme binding and cell wall modification in high-Mg roots. Some of these transcriptomic results are substantially in accordance with our physiological and/or biochemical analysis. Conclusions: Contrasting changes were found between roots and shoots with the shoot transcriptome being more severely affected by low Mg while the root transcriptome more affected by high Mg. Elevated CO2 had a greater effect on transcript response in low Mg-fed shoots as well as in high Mg-fed roots. The present findings broaden our current understanding on the interactive effect of elevated CO2 and Mg levels in the Arabidopsis, which may help to design the novel metabolic engineering strategies to cope with Mg deficiency/excess in crops under elevated CO2.
2015-05-01 | GSE64501 | GEO
Project description:Transcriptomic profiling of the diatom Thalassiosira pseudonana at normal and elevated CO2 levels and at normal and elevated light levels. Common reference total RNA (Agilent Quick-Amp Cy3-labeled) was used in all arrays as an internal standard.
2015-11-06 | GSE57737 | GEO
Project description:Plant respiration responses to elevated growth [CO2] are key uncertainties in predicting future crop and ecosystem function. In particular, the effects of elevated growth [CO2] on respiration over leaf development are poorly understood. This study tested the prediction that, due to greater whole-plant photoassimilate availability and growth, elevated [CO2] induces transcriptional reprogramming and a stimulation of nighttime respiration in leaf primordia, expanding leaves, and mature leaves of Arabidopsis thaliana. In primordia, elevated [CO2] altered transcript abundance, but not for genes encoding respiratory proteins. In expanding leaves, elevated [CO2] induced greater glucose content and transcript abundance for some respiratory genes, but did not alter respiratory CO2 efflux. In mature leaves, elevated [CO2] led to greater glucose, sucrose and starch content, plus greater transcript abundance for many components of the respiratory pathway, and greater respiratory CO2 efflux. Therefore, growth at elevated [CO2] stimulated dark respiration only after leaves transitioned from carbon sinks into carbon sources. This coincided with greater photoassimilate production by mature leaves under elevated [CO2] and peak respiratory transcriptional responses. It remains to be determined if biochemical and transcriptional responses to elevated [CO2] in primordial and expanding leaves are essential prerequisites for subsequent alterations of respiratory metabolism in mature leaves. Arabidopsis plants were grown in either ambient (370 ppm) or elevated (750 ppm) CO2. Leaf number 10 was harvested when it was a primordia, expanding, or mature in each of the CO2 treatments.
2014-04-04 | E-GEOD-56480 | biostudies-arrayexpress
Project description:Diatoms are responsible for ~40% of marine primary productivity1, fueling the oceanic carbon cycle and contributing to natural carbon sequestration in the deep ocean2. Diatoms rely on energetically expensive carbon concentrating mechanisms (CCMs) to fix carbon efficiently at modern levels of CO23–5. How diatoms may respond over the short and long-term to rising atmospheric CO2 remains an open question. Here we use nitrate-limited chemostats to show that the model diatom Thalassiosira pseudonana rapidly responds to increasing CO2 by differentially expressing gene clusters that regulate transcription and chromosome folding and subsequently reduces transcription of photosynthesis and respiration gene clusters under steady-state elevated CO2. These results suggest that exposure to elevated CO2 first causes a shift in regulation and then a metabolic rearrangement. Genes in one CO2-responsive cluster included CCM and photorespiration genes that share a putative cyclic-AMP responsive cis-regulatory sequence, implying these genes are co-regulated in response to CO2 with cAMP as an intermediate messenger. We verified cAMP-induced down-regulation of CCM gene δ-CA3 in nutrient-replete diatom cultures by inhibiting the hydrolysis of cAMP. These results indicate an important role for cAMP in down-regulating CCM and photorespiration genes under elevated CO2 and provide insights into mechanisms of diatom acclimation in response to climate change.
2015-04-17 | GSE67971 | GEO
Project description:There are seedling samples (high CO2 exposure of 0h, 2h, 6h, 12h, 1d, 3d, 7d, 14d) with duplicates in two chambers. Arabidopsis WT (Col-0) seeds were plated on Murashige and Skoog plates and placed at 4°C in darkness for at least 2 d to synchronize germination. Plants were grown at 22C under long-day conditions (16-h light and 8-h dark) in two atmospheric CO2 environments: ambient (CO2: 390 μmol molâ??1) or elevated (CO2: 780 μmol molâ??1). Plants were grown in ambient atmospheric CO2 concentration and then exposed to elevated CO2 for 0 h, 2 h, 6 h, 12 h, 1 d, 3 d, 7 d and 14 d. 14-d-old seedlings were sampled at the same time. Treatments for elevated CO2 were carried out two times using two different chambers. Duplicate samples were collected from each chamber experiment. Totally, four biologically replicates were prepared in each condition.
2015-12-31 | E-GEOD-49960 | biostudies-arrayexpress