Rice whole transcriptome differences at two temperature levels surveyed by RNA-Seq
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Indica Group
PROVIDER: GSE42096 | GEO | 2012/11/07
SECONDARY ACCESSION(S): PRJNA179127
REPOSITORIES: GEO
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Project description:We report that TOG1 coordinates global changes of gene expression upon high temperature to support rice thermotolerant growth. We performed gene ontology (GO) enrichment analysis of the differentially expressed genes in rice seedlings grown at 25 ℃ and 30 ℃ and found that when temperature increases, wild-type dramatically adjusts the expression level of hundreds of genes in GO terms polysaccharide metabolic process, carbohydrate metabolic process, glucan metabolic process, carbon fixation, response to stimulus and organic substance metabolic process required for growth. However, in a tog1 mutant, the differentially expressed genes in response to the temperature increase significantly enriched in GO terms response to stimulus, response to oxidative stress and response to stress, whereas the coordination of primary metabolic processes and carbon fixation were largely impaired or undetectable. Differentially expressed mRNA profiles of 22-day-old wild type (WT) and tog1 rice upon a temperature difference were generated by deep sequencing
2012-11-07 | E-GEOD-42096 | biostudies-arrayexpress
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2024-03-28 | GSE249345 | GEO
Project description:Background: Drought stress is the major environmental stress that affects plant growth and productivity. It triggers in plants a wide range of responses detectable at different scales: molecular, biochemical and physiological levels. At the molecular level the response to drought stress results in the differential expression of several metabolic pathways. For this reason, explore the subtle differences existing in gene expression of drought sensitive and drought tolerant genotypes allows to identify drought-related genes that could be used for selection of drought tolerance traits. Genome-wide RNA-Seq technology was used to compare the drought response of two sorghum genotypes characterized by contrasting water use efficiency. Results: the physiological measurements carried out confirmed the drought sensitivity of IS20351 and the drought tolerance of IS22330 previously studied. The expression of drought-related genes was more abundant in the sensitive genotype IS20351 compared to the tolerant IS22330. The Gene Ontology enrichment highlighted a massive increase in transcript abundance in “response to stress” and “abiotic stimulus”, “oxidation-reduction reaction” in the sensitive genotype IS20351 under drought stress. “Antioxidant” and “secondary metabolism”, “photosynthesis and carbon fixation process”, “lipids” and “carbon metabolism” were the pathways most affected by drought in the sensitive genotype IS20351. The sensitive genotype IS20351 showed under well-watered conditions a lower constitutive expression level of “secondary metabolic process” (GO:0019748) and “glutathione transferase activity” (GO:000004364). Conclusions: RNA-Seq analysis revealed to be a very useful tool to explore differences between sensitive and tolerant sorghum genotypes. The transcriptomic results supported all the physiological measurements and were crucial to clarify the tolerance of the two genotypes studied. The connection between the differential gene expression and the physiological response to drought states unequivocally the drought tolerance of the genotype IS22330 and the strategy adopted to cope with drought stress.
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Project description:Most significantly affected GOs by TST stress include Cellular localization, transport and migration such as Cellular macromolecule localization (GO:0070727), Intracellular transport (GO:0046907) and Intracellular protein transport (GO:0006886), metabolic processes such as Small molecule metabolic process (GO:0044281), Cellular amide metabolic process (GO:0043603) and Lipid metabolic process (GO:0006629), neuronal cell population differentiation and proliferation such as Neurogenesis (GO:0022008), Neuron differentiation (GO:0030182), Glial cell differentiation (GO:0010001), Central nervous system development (GO:0007417), Astrocyte differentiation (GO:0048708) and Gliogenesis (GO:0042063), and cell signaling such as G-protein-coupled receptor signaling pathway (GO:0007186), Negative regulation of signaling (GO:0023057), Positive regulation of signaling (GO:0023056), Response to endogenous stimulus (GO:0009719) and Regulation of intracellular signal transduction (GO:1902531). Peptide metabolic process (GO:0006518), Peptidyl amino acid modification (GO:0018193), Regulation of steroid biosynthetic process (GO:0050810) were also significantly enriched in the TST stress-induced mice brain. Top significantly enriched Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways by the stress response related DEGs between high-dose RE vs TST include mitogen-activated protein kinase (MAPK) signaling pathway, Chemokine signaling pathway, Neurotrophin signaling pathway, Cytokine-cytokine receptor interaction, GnRH signaling pathway, ErbB signaling pathway, Toll-like receptor signaling pathway, T cell receptor signaling pathway, B cell receptor signaling pathway, vascular endothelial growth factor (VEGF) signaling pathway, Long-term depression, NOD-like receptor signaling pathway, Insulin signaling pathway, Jak-STAT signaling pathway, Apoptosis, and mTOR signaling pathway.
2021-07-29 | GSE180884 | GEO
Project description:To understand the molecular mechanisms underlying chilling tolerance in rice, transcriptomic deep sequencing was performed to reveal the differentially expressed genes between chilling tolerance chromosome substitution line (CSL), DC90 and its chilling-sensitive recurrent parent 9311 under early chilling stress events. Our results revealed a set of DEGs with higher basal expression in DC90 by comparison with 9311. They were functionally enriched in GO terms, such as, response to stress, response to stimulus, and response to abiotic stimulus, suggesting their positive role in intrinsic chilling tolerance. Common up-regulated and down-regulated DEGs were enriched in 26 and 34 GO terms, including response to stimulus, response to stress, and response to abiotic stimulus, respectively. Furthermore, comparative transcriptomic analysis between DC90 and 9311 in response to early chilling stress revealed 502 DEGs specifically identified in DC90. Most of gene loci were located beyond introgressed regions, implying that the introgression led to reprogramming of transcriptome in response to early chilling stress. CARMO platform analysis of these DEGs presented a complex regulatory network, including phytohormone signaling, photosynthesis pathway, that coordinately involved in chilling tolerance response of DC90. Here, the unveiled molecular regulatory network shed light on deep understanding the mechanisms of rice chilling tolerance. As well, chilling tolerant-QTLs and co-localized DEGs in introgressed fragments, will be focused for further functional investigation of the molecular mechanisms of early chilling stress response in rice.
2017-06-25 | GSE76415 | GEO
Project description:Straw return is crucial for the sustainable development of rice planting. To investigate the response of rice leaves to rice straw return, we analyzed the physiological index of rice leaves and measured differentially expressed protein (DEPs) and differentially expressed metabolites (DEMs) levels in rice leaves by the use of proteomics and metabolomics approaches. The results showed that, compared with no rice straw return, rice straw return significantly decreased the dry weight of rice plants and nonstructural carbohydrate contents and destroyed the chloroplast ultrastructure. In rice leaves under rice straw return, 329 DEPs were upregulated, 303 DEPs were downregulated, 44 DEMs were upregulated, and 71 DEMs were downregulated. These DEPs and DEMs were mainly involved in various molecular processes, including photosynthesis, carbon fixation in photosynthetic organisms, glycolysis, and the citric acid cycle. Rice straw return promoted the accumulation of osmotic adjustment substances, such as organic acids, amino acids, and other substances, and reduced the material supply and energy production of carbon metabolism, thus inhibiting the growth of rice.
2022-09-12 | PXD035835 | Pride
Project description:We characterized and compared the biological and molecular functions of HRE1α and HRE1β, two alternative splicing variants of HRE1, a AP2/ERF transcription factor in Arabidopsis. To compare the downstream regulatory mechanisms of HRE1α and HRE1β, Quant-Seq analysis was carried out. The experiment was designed to identify and compare differentially expressed genes (DEGs) between WT and HRE1α-overexpressing transgneic plants (OXs) and WT and HRE1β OXs grown for 14 days under SD conditions. We analyzed the biological process gene ontology (GO) annotation categories of the DEGs in HRE1α OXs and HRE1β OXs. The genes upregulated in HRE1α OXs, but not in HRE1β OXs, were enriched in the regulation of biological processes such as flower development, shoot system development, circadian rhythms, gene expression, response to gibberellin, nitrogen compound metabolic process, and aromatic compound biosynthetic processes. However, the genes up-regulated in HRE1β OXs, but not in HRE1α OXs, were enriched in the regulation of the following processes: response to toxic substances, secondary metabolic processes, response to biotic stimulus, glutathione metabolic process, response to reactive oxygen species, cell wall organization, DNA replication, response to salicylic acid, lipid localization, response to oxidative stress, carbohydrate metabolic process, photosynthesis, mitotic cell cycle process, response to osmotic stress, and response to abscisic acid. The genes upregulated in both HRE1α OXs and HRE1β OXs were enriched in biological processes involved in response to abiotic stimulus, response to light stimulus, response to endogenous stimulus, response to oxygen-containing compound, and response to lipid. In addition, we investigated the biological function of AtRH17, a DEAD-box RNA helicase gene in Arabidopsis, in salt stress response. To investigate the downstream regulatory mechanisms of AtRH17, Quant-Seq analysis was carried out. The experiment was designed to identify DEGs between WT and AtRH17 OXs grown for 14 days under SD conditions. GO annotation enrichment and KEGG pathway analysis showed that the upregulated and downregulated genes are involved in various biological functions including secretion, signaling, detoxification, metabolic pathways, catabolic pathways, and biosynthesis of secondary metabolites as well as in stress responses. Genevestigator analysis of the upregulated genes showed that nine genes, namely, LEA4‐5, GSTF6, DIN2/BGLU30, TSPO, GSTF7, LEA18, HAI1, ABR, and LTI30, were upregulated in Arabidopsis under salt, osmotic, and drought stress conditions. In particular, the expression levels of LEA4‐5, TSPO, and ABR were higher in AtRH17 OXs than in WT under salt stress condition.
2020-09-23 | GSE152166 | GEO
Project description:Seven carbon autotrophic fixation pathways were described so far. However, it is not common to find the co-existence of more than one cycle in a single cell. Here, we describe a thermophilic bacterium Carbonactinospora thermoautotrophica StC with a unique and versatile carbon metabolism. StC was isolated from a consortium found in a burning organic pile that exhibits an optimal growth temperature between 55° and 65° C. The genome analyses suggested that the strain StC potentially performs two-carbon fixation pathways, Calvin-Benson-Bassham (CBB) cycle and the Reductive citrate cycle (rTCA) and preserve a microcompartment related with CO2 concentration. To better understand the carbon fixation in StC strain, the expression of the genes of bacterial cells grown autotrophically and heterotrophically were analyzed. For our surprise the data showed the co-existing of the both carbon fixation pathways - CBB and rTCA cycles - in a cultivable thermophilic chemoautotrophic bacterium Carbonactinospora thermoautotrophica strain StC, based on integrated omics of genomics, transcriptomics, and proteomics. These two cycles working together may help microorganisms to improve the CO2 fixation. The knowledge about the co-occurrence of carbon cycle in a single cell leads open a question ‘why microorganisms use multiple pathways to fix carbon and what the advantage for this strategy?’. Advancing on this is a key to better understand the biological carbon fixation mechanism in thermophiles and prospecting the repurposing of enzymes in synthetic biology for biotechnological applications.
2024-04-09 | GSE263135 | GEO
Project description:To understand molecular pathogenesis of chemical induced contact dermatitis, cultured normal human epidermal keratinocytes (NHKCs) were treated with sub-cytotoxic concentration of sodium lauryl sulfate (SLS, 10 microM) and urushiol (1 microM). In analysis, 259 genes were selected as up-regulated DEGs in the SLS-treated NHKCs and 193 genes as down-regulated DEGs. In urushiol-treated NHKCs, 173 up-regulated and 124 down-regulated DEGs were identified. Gene Ontology (GO) biological process (BP) in the SLS-induced upregulated DEGS in NHKCs were inflammation-associated biological processes, such as inflammatory response (GO:0006954), cellular response to calcium ion (GO:0071277), immune response (GO:0006955) and cellular response to lipopolysaccharide (GO:0071222) and in urushiol-induced upregulated DEGs were inflammation-associated biological processes such as cytokine-mediated signaling pathway (GO:0019221) and inflammatory response (GO:0006954). SLS downregulated proteins in chemotaxis (GO:0006935), oxidation-reduction process (GO:0055114), cornification (GO:0070268), G1/S transition of mitotic cell cycle (GO:0000082), keratinization (GO:0031424) and cellular protein metabolic process (GO:0044267) and urushiol downregulated proteins in nervous system development (GO:0007399), positive regulation of cell proliferation (GO:0008284) and cellular protein metabolic process (GO:0044267) significantly.
2019-11-01 | GSE126354 | GEO
Project description:Background: Low temperature (LT) often occurs at the seedling stage in the early rice-growing season, especially for direct seeded early-season indica rice, and using flooding irrigation can mitigate LT damage in rice seedlings. The molecular mechanism by which flooding mitigates the damage induced by LT stress has not been fully elucidated. Thus, LT stress at 8C, LT accompanied by flooding (LTF) and CK (control) treatments were established for three days to determine the transcriptomic, proteomic and physiological response in direct seeded rice seedlings at the seedling stage. Results: LT damaged chloroplasts, and thylakoid lamellae, and increased osmiophilic bodies and starch grains compared to CK, but LTF alleviated the damage to chloroplast structure caused by LT. The physiological characteristics of treated plants showed that compared with LT, LTF significantly increased the contents of rubisco, chlorophyll, PEPCK, ATP and GA3 but significantly decreased soluble protein, MDA and ABA contents. 4D-label-free quantitative proteomic profiling showed that photosynthesis-responsive proteins, such as phytochrome, as well as chlorophyll and the tricarboxylic acid cycle were significantly downregulated in LT/CK and LTF/CK comparison groups. However, compared with LT, phytochrome, chlorophyllide oxygenase activity and the glucan branching enzyme in LTF were significantly upregulated in rice leaves. Transcriptomic and proteomic studies identified 72818 transcripts and 5639 proteins, and 4983 genes that were identified at both the transcriptome and proteome levels. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were significantly enriched in glycine, serine and threonine metabolism, biosynthesis of secondary metabolites, glycolysis/gluconeogenesis and metabolic pathways. Conclusion: Through transcriptomic, proteomic and physiological analyses, we determined that a variety of metabolic pathway changes were induced by LT and LTF. GO and KEGG enrichment analyses demonstrated that DEGs and DEPs were associated with photosynthesis pathways, antioxidant enzymes and energy metabolism pathway-related proteins. Our study provided new insights for efforts to reduce the damage to direct seeded rice caused by low-temperature stress and provided a breeding target for low temperature flooding-resistant cultivars. Further analysis of translational regulation and metabolites may help to elucidate the molecular mechanisms by which flooding mitigates low-temperature stress in direct seeded early indica rice at the seedling stage.
2021-09-10 | PXD024034 | Pride