Oryza sativa Indica Group
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA211801 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR931847.fastq.gz | Fastqsanger.gz | |||
| SRR931848.fastq.gz | Fastqsanger.gz | |||
| SRR931849.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:Arsenic (As) contamination of rice grains affects millions of people worldwide. In this study, we found that sulfur application (20As+120S) decreased As concentration in rice grains by 44 % compared to grains without sulfur application (20As+0S). Importantly, sulfur application decreased arsenate [As(V)] and arsenite [As(III)] concentration in rice grains significantly, while there was no significant effect on dimethylarsenate (DMA) concentration. To elucidate the molecular basis of As accumulation in rice grains, we performed Illumina sequencing to acquire the differentially expressed genes induced by arsenate and sulfur treatments. By contrast with the control, the expression of 1,000 genes was found to be changed significantly, with 46 genes up-regulated and 954 genes down-regulated in grains grown in arsenate-contaminated soil (20As+0S). Between samples of control and arsenate together with sulfur treatment (20As+120S), 1,169 genes expressed significantly differently, with 16 genes up-regulated and 1,153 genes down-regulated. Sulfur application significantly changed the expression of genes involved in As metabolism in rice grains, significantly down-regulated phosphate transporter gene OsPT23 and aquaporin gene OsTIP4;2, while ABC transporter genes (OsABCG5, OsABCI7_2 and OsABC6) and phytochelatin synthase genes (OsPCS1, OsPCS3 and OsPCS13) were up-regulated. These results provide an insight into the molecular basis of how sulfur assimilation regulates As accumulation in rice grains.
2015-07-01 | GSE48799 | GEO
Project description:We performed Illumina sequencing to acquire the differentially expressed genes induced by arsenate and sulfur treatments. We found that sulfur (S) application reduced As concentration of rice grains harvested at 20 days after anthesis (DAA). By contrast with the control, the expression of 1001 genes were found to be significantly changed, 46 genes up-regulated and 954 genes down-regulated in the 20As grains. 1169 genes expressed significantly differently between the samples of control and 20As+120S, with 16 genes up-regulated and 1153 genes down-regulated. Among the differentially expressed genes (DEGs) regulated by As and S treatment, there were 10 DEGs encoding phosphate transporter, and 24 DEGs encoding aquaporin transporter. Some genes involved in As detoxification, such as ABC transporter, glutathione S-transferase and phytochelatin synthase were up-regulated by sulfur treatment. The results provide an insight into the molecular basis of how sulfur application regulates As accumulation in rice grains. Arsenic (As) was artificially added to soil with 20 mg/kg As (Na2AsO4.12H2O, 20As), another treatment was 20As+120S, sulfur (S) were supplied artificially with 120 mg/kg (Na2S2O3•5H2O) to the As-added soil (20As+120S).
2015-07-01 | E-GEOD-48799 | biostudies-arrayexpress
Project description:Rice (Oryza sativa L.) is the main staple food for nearly half of the world’s population. Cereals, especially rice is deficient in micronutrients such as Fe. However, rice genotypes differ in grain Fe concentration (Panda B, et.al. Am J Plant Sci. 2014;5:2829-41. doi: 10.4236/ajps.2014.518299). The present study is focused on identification of gene(s) involved in Fe accumulation in developing rice grain through high throughput RNA-seq technology and to understand the basis of differential Fe accumulation in developing rice grain. Two cultivars of rice viz. Sharbati (high Fe) and Lalat (low Fe) differing in grain iron concentration were used in the study. Root and grain transcriptome sequences of these two cultivars (at mid-grain filling stage) were generated using RNA-Seq (Illumina Hiseq 2000 platform). For each genotype, on an average 9.7 and 7 Gb data was generated for grain and root samples, respectively. The short reads were aligned against the Nipponbare reference genome (IRGSP build 5.0), thereby successfully mapping 95% and 67% of the reads from grain and root samples, respectively. Genes known to be involved in Fe metabolism were analyzed for expression. Among the genes coding for phytosiderophore synthesizing enzymes, OsNAS1 and OsNAAT2 showed higher expression in the grains of Sharbati while OsDMAS1 had higher expression in its root. Of the 18 yellow-stripe like (YSL) genes in rice, only 11 were found to be expressed in the two cultivars. Out of these, 2 (OsYSL2 and OsYSL 8) were up-regulated in the grains of Sharbati highlighting their importance in the uptake of Fe from soil and its accumulation in the developing grain. Two other genes (OsFRO1 and OsIRT1) known to be involved in Fe uptake by the root were also found to be highly expressed in the root of Sharbati. Our findings suggest that higher grain iron concentration of cv. Sharbati might be due to higher expression of key Fe transporters (viz. OsYSL2, OsYSL8 and OsITR1) and root membrane bound OsFRO1, which give an advantage in terms of absorption, transport and assimilation of Fe by this cultivar as compared to the low iron containing cultivar, Lalat.
2016-12-31 | GSE70093 | GEO
Project description:Rice grains are rich in starch but are deficient in proteins containing essential amino acids such as lysine and threonine. Therefore, efforts have been made to improve the nutritional value of rice by overexpressing the genes involved in lysine biosynthesis and/or suppression of lysine catabolism that led to the increased protein content in rice grains. Despite the economic and nutritional benefits rice, the protein accumulation mechanisms are largely elusive. Therefore, to explore the comprehensive proteome profiles, three different parts of rice grains including embryo, endosperm, bran were harvested from weedy rice cultivars (cv. Dharial) and its EMS mutant (DM) having 9.3 and 14.8% of protein content in rice grains, respectively. Here, we utilized a label-free quantitative proteomic analysis and this approach led to the identification of total 5,821 proteins. Of these, 322, 723, and 550 proteins revealed significant differences in their abundance in rice embryo, endosperm, and bran, respectively. Functional classification of identified proteins revealed that enrichment of proteins associated with nitrogen compound biosynthesis and transport, intracellular transport, localization, protein/amino acid synthesis, and photosynthesis, among others were observed in endosperm and bran of high protein mutant rice cultivar. Taken together, the current study uncovers the proteome changes and highlight the various functions of metabolic pathways associated with protein accumulation in rice.
2023-09-21 | PXD036806 | Pride
Project description:High temperature markedly reduces the yields and quality of rice grains. To identify the mechanisms underlying heat stress-induced responses in rice grains, proteomic technique was used. Khao Dawk Mali 105 rice grains at the milky, doughy, and mature stages of development after flowering were treated at 40 °C for 3 days. Aromatic compounds were decreased in rice grains under heat stress. The protein abundance involved in glycolysis and tricarboxylic acid cycle, including glyceraldehyde 3-phosphate dehydrogenase and citrate synthase, was changed in milky and doughy grains after heat treatment; however, no changes in mature grains. The abundance involved in amino acid metabolism was increased in doughy grains, but decreased in milky grains. In addition, the abundance involved in starch and sucrose metabolism, such as starch synthase, ADP-glucose pyrophosphorylase, granule-bound starch synthase, and alpha amylase, was decreased in milky grains, but increased in doughy grains. A number of redox homeostasis-related proteins, such as ascorbate peroxidase and peroxiredoxin, were increased in developing rice grains treated with heat stress. These results suggest that in response to heat stress, the abundance of numerous proteins involved in redox homeostasis and carbohydrate biosynthetic pathways may play a major role in the development of KDML105 rice grains.
2015-12-17 | PXD003156 | Pride
Project description:A Novel Regulatory Region for Amylose Synthesis in Rice Grains Identified by Systems Genetics Approach.
| PRJNA355111 | ENA
Project description:Arsenic is ubiquitously present in nature and various mechanisms have evolved enabling cells to evade toxicity and acquire tolerance. Herein, we explored how Saccharomyces cerevisiae (budding yeast) respond to trivalent arsenic (arsenite) by quantitative and kinetic transcriptome, proteome and sulfur metabolite profiling. Arsenite exposure affected transcription of genes encoding functions related to protein biosynthesis, arsenic detoxification, oxidative stress defense, redox maintenance and proteolytic activity. Importantly, enzymes involved in sulfate assimilation and glutathione biosynthesis were induced at both gene and protein levels. Kinetic metabolic profiling evidenced a significant increase in the pools of sulfur metabolites as well as elevated glutathione levels. Moreover, the flux in the sulfur assimilation pathway as well as the glutathione synthesis rate strongly increased with a concomitant reduction of sulfur incorporation into proteins. By combining comparative genomics and molecular analyses, we pin-pointed transcription factors that mediate thecore of the transcriptional response to arsenite. Taken together, our data reveals that arsenite-exposed cells channel a large part of assimilated sulfur into glutathione biosynthesis and we provide evidence that the transcriptional regulators Yap1p and Met4p control this response in concert. Keywords: stress
2007-10-18 | GSE6070 | GEO
Project description:Arsenic is ubiquitously present in nature and various mechanisms have evolved enabling cells to evade toxicity and acquire tolerance. Herein, we explored how Saccharomyces cerevisiae (budding yeast) respond to trivalent arsenic (arsenite) by quantitative and kinetic transcriptome, proteome and sulfur metabolite profiling. Arsenite exposure affected transcription of genes encoding functions related to protein biosynthesis, arsenic detoxification, oxidative stress defense, redox maintenance and proteolytic activity. Importantly, enzymes involved in sulfate assimilation and glutathione biosynthesis were induced at both gene and protein levels. Kinetic metabolic profiling evidenced a significant increase in the pools of sulfur metabolites as well as elevated glutathione levels. Moreover, the flux in the sulfur assimilation pathway as well as the glutathione synthesis rate strongly increased with a concomitant reduction of sulfur incorporation into proteins. By combining comparative genomics and molecular analyses, we pin-pointed transcription factors that mediate thecore of the transcriptional response to arsenite. Taken together, our data reveals that arsenite-exposed cells channel a large part of assimilated sulfur into glutathione biosynthesis and we provide evidence that the transcriptional regulators Yap1p and Met4p control this response in concert. Keywords: stress
2007-10-18 | GSE6072 | GEO
Project description:Arsenic is ubiquitously present in nature and various mechanisms have evolved enabling cells to evade toxicity and acquire tolerance. Herein, we explored how Saccharomyces cerevisiae (budding yeast) respond to trivalent arsenic (arsenite) by quantitative and kinetic transcriptome, proteome and sulfur metabolite profiling. Arsenite exposure affected transcription of genes encoding functions related to protein biosynthesis, arsenic detoxification, oxidative stress defense, redox maintenance and proteolytic activity. Importantly, enzymes involved in sulfate assimilation and glutathione biosynthesis were induced at both gene and protein levels. Kinetic metabolic profiling evidenced a significant increase in the pools of sulfur metabolites as well as elevated glutathione levels. Moreover, the flux in the sulfur assimilation pathway as well as the glutathione synthesis rate strongly increased with a concomitant reduction of sulfur incorporation into proteins. By combining comparative genomics and molecular analyses, we pin-pointed transcription factors that mediate thecore of the transcriptional response to arsenite. Taken together, our data reveals that arsenite-exposed cells channel a large part of assimilated sulfur into glutathione biosynthesis and we provide evidence that the transcriptional regulators Yap1p and Met4p control this response in concert. Keywords: stress, time course
2007-10-18 | GSE6068 | GEO
Project description:Arsenic is ubiquitously present in nature and various mechanisms have evolved enabling cells to evade toxicity and acquire tolerance. Herein, we explored how Saccharomyces cerevisiae (budding yeast) respond to trivalent arsenic (arsenite) by quantitative and kinetic transcriptome, proteome and sulfur metabolite profiling. Arsenite exposure affected transcription of genes encoding functions related to protein biosynthesis, arsenic detoxification, oxidative stress defense, redox maintenance and proteolytic activity. Importantly, enzymes involved in sulfate assimilation and glutathione biosynthesis were induced at both gene and protein levels. Kinetic metabolic profiling evidenced a significant increase in the pools of sulfur metabolites as well as elevated glutathione levels. Moreover, the flux in the sulfur assimilation pathway as well as the glutathione synthesis rate strongly increased with a concomitant reduction of sulfur incorporation into proteins. By combining comparative genomics and molecular analyses, we pin-pointed transcription factors that mediate thecore of the transcriptional response to arsenite. Taken together, our data reveals that arsenite-exposed cells channel a large part of assimilated sulfur into glutathione biosynthesis and we provide evidence that the transcriptional regulators Yap1p and Met4p control this response in concert. Keywords: stress
2007-10-18 | GSE6067 | GEO