Microarray analysis of Indian mustard plants subjected to arsenate stress
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ABSTRACT:
ORGANISM(S): Brassica juncea
PROVIDER: GSE66464 | GEO | 2015/03/04
SECONDARY ACCESSION(S): PRJNA277020
REPOSITORIES: GEO
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Project description:In this study, time dependent (4 h to 96 h) transcriptome changes in roots and shoots of Brassica juncea were analyzed under arsenate (AsV) stress by using Agilent platform. A total of 1285 genes showed significant change in expression pattern upon arsenate (AsV) exposure. The genes belonged to various signaling pathways including hormones (jasmonate, abscisic acid (ABA), auxin and ethylene) and kinases. Significant effects were also noticed on genes of sulfur, nitrogen, CHO, and lipid metabolisms along with photosynthesis. These studies indicated interconnections among sulfur metabolism, jasmonate and kinase signaling pathways. Transcriptome results and biochemical analyses highlight that signaling and metabolic pathways work in a dynamic coordination to perceive and respond to the stress. A set of 53939 sequences, which include EST and nucleotide sequences of Brassica sp., were downloaded from GenBank. These sequences were subjected to clustering and analyzed using CAP3/tgicl program and other in-house tools. A set of 26881 non-redundant sequences was created, which was used for probe design. This set included 1720 Brassica juncea, 15259 Brassica napus and 5075 Brassica rapa sequences; and 6456 from other species. Probes were designed for the non-redundant sequences using Agilent eArray tool. Best probe composition algorithm with the option to design multiple probes for each sequence was the main criteria used for the probe design. AgilentM-bM-^@M-^Ys 4x44 array was selected to print the oligos. A set of positive and negative controls were also added on to the microarray chip. A set of replicate probes were also added for calculating the intra-array reproducibility. The quantity and purity of the RNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. Each of the total RNA preparations was individually assessed for RNA quality based on the 28S/18S ratio and RIN measured on an Agilent 2100 Bioanalyzer system using the RNA 6000 Nano LabChip Kit .With the use of AgilentM-bM-^@M-^Ys 1-Color Quick Amp Labeling Kit, 500 ng of high quality total RNA was denatured in the presence of a T7 promoter primer and a 1-Color RNA Spike-In Kit. Reverse transcriptase was used to reverse-transcribe the mRNA. cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3-labeled CTP. Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer. With the use of AgilentM-bM-^@M-^Ys Gene Expression Hybridization Kit, 1.65 M-BM-5g of cyanine 3-labeled linearly amplified cRNA was added to a hybridization cocktail and then fragmented. The hybridization cocktail was then dispensed into the wells of gasket slides on top of which a Brassica 4x44K Gene Expression Microarray was placed. This microarray M-bM-^@M-^\sandwichM-bM-^@M-^] was then sealed in a hybridization chamber. The microarrays were hybridized at 65M-BM-0C rotating at 10 RPMs for 17 hours. Slides were washed in AgilentM-bM-^@M-^Ys Gene Expression Wash Buffers according to manufacturer specifications. The microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction and analysis was performed using Agilent Technologies Feature Extraction software version 10.7.3.1.Microarray data quality was evaluated by reviewing ten standard QC metrics generated by the Feature Extraction Software [Consult the Agilent Technologies Feature Extraction Software version 10.7.3.1 reference guide for a full explanation of the QC metrics]. To determine if there was a large hybridization, staining, or wash artifacts, a visual examination of each array was performed by loading the array image into Feature Extraction Software. Microarrays were determined to be free of any large artifacts (M-bM-^IM-% 10% of total surface area) that could have affected the quality of the data.
2015-03-04 | E-GEOD-66464 | biostudies-arrayexpress
Project description:Stress constantly challenges plant adaptation to the environment. Of all stress types, arsenic was a major threat during the early evolution of plants. The most prevalent chemical form of arsenic is arsenate, whose similarity to phosphate renders it easily incorporated into cells via the phosphate transporters. Here we found that arsenate stress provokes a notable transposon burst in plants, in coordination with arsenate/phosphate transporter repression, which immediately restricts arsenate uptake. This repression was accompanied by delocalization of the phosphate transporter from the plasma membrane. When arsenate was removed, the system rapidly restored transcriptional expression and membrane localization of the transporter. We identify WRKY6 as an arsenate-responsive transcription factor that mediates arsenate/phosphate transporter gene expression and restricts arsenate-induced transposon activation. Plants therefore have a dual WRKY-dependent signaling mechanism that modulates arsenate uptake and transposon expression, providing a coordinated strategy for arsenate tolerance and transposon gene silencing.
2014-04-25 | GSE49037 | GEO
Project description:Stress constantly challenges plant adaptation to the environment. Of all stress types, arsenic was a major threat during the early evolution of plants. The most prevalent chemical form of arsenic is arsenate, whose similarity to phosphate renders it easily incorporated into cells via the phosphate transporters. Here we found that arsenate stress provokes a notable transposon burst in plants, in coordination with arsenate/phosphate transporter repression, which immediately restricts arsenate uptake. This repression was accompanied by delocalization of the phosphate transporter from the plasma membrane. When arsenate was removed, the system rapidly restored transcriptional expression and membrane localization of the transporter. We identify WRKY6 as an arsenate-responsive transcription factor that mediates arsenate/phosphate transporter gene expression and restricts arsenate-induced transposon activation. Plants therefore have a dual WRKY-dependent signaling mechanism that modulates arsenate uptake and transposon expression, providing a coordinated strategy for arsenate tolerance and transposon gene silencing. Three biological replicates were performed for each sample type. Single channel hybridizations were carried-out using either Affymetrix ATH1 platform or Nimblegen Gene Expression 12x135K platform (Arabidopsis thaliana).
2014-04-25 | E-GEOD-49037 | biostudies-arrayexpress
Project description:We advance a three gene model of arsenate tolerance in rice based on testing root growth of 108 recombinant inbred lines (RILs) of the Bala x Azucena population. Marker genotype at 3 loci determined arsenate tolerance in 99% of RILs tested. Interestingly, plants must inherit 2, but any two alleles from the tolerant parent (Bala) to have the tolerant phenotype. Challenging the Affymetrix GeneChip Rice Genome array with Azucena and Bala RNA isolated from control and arsenate treated plants revealed 592 genes 2 fold-upregulated by arsenate and 696 downregulated. The array data was also used to identify which genes are expressed within the three target loci. We used microarrays to detail the gene expression at three locations in the rice genome termed AsTol6.1, AsTol6.2 and AsTol10 in response to 1ppm arsenate. The data was also used to study the global gene expression of the two varieties of rice, Azucena and Bala, in the presence of 1ppm arsenate. Keywords: Hydroponics, 0 and 1ppm sodium arsenate, Rice varieties Azucena and Bala
2006-03-16 | GSE4471 | GEO
Project description:Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars, B. juncea and B. nigra, for salinity tolerance. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52. We report transcriptome sequencing of two-weeks-old seedlings of B. juncea var. CS52 under normal growth conditions (CTRL) and in response to salinity stress (SS) using Illumina paired-end sequencing
2015-02-28 | E-GEOD-66389 | biostudies-arrayexpress
Project description:Wild type (BY4741) Saccharomyces cerevisiae strains and their isogenic slt2 deficient counterparts, were treated for 2 hours with sodium arsenate 100 micromolar. Control (untreated) cells were also collected. Total RNA was extracted and analyzed by microarray hybridization. The data obtained from these experiments allows to determine those genes that are regulated by Slt2 activity after arsenate treatment.
2010-07-25 | GSE17364 | GEO
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:Arsenic metalloid is a double-edge sword. On the one hand it is a very toxic and powerful carcinogen, and on the other it has been successfully used in the treatment of acute promyelocytic leukemia. In order to prevent the deleterious effects caused by arsenic compounds, almost all living organisms have developed mechanisms to eliminate it. In this study genome-wide response of S. cerevisiae to arsenic shows that this metal interferes with genes involved in the iron homeostasis including those encoding proteins that function in iron uptake, incorporation into Fe–S clusters, and more. In addition our data indicate that Yap1 transcriptionally controls the iron homeostasis regulator AFT2 as well as its direct target, MRS4. Most importantly in response to arsenate exposure Yap1 strongly regulates the expression of several genes involved in the Fe-S proteins biosynthesis, namely NBP35 and YFH1. Interestingly mRNA levels encoding Fet3, Ferro-O2-oxidoreductase required for high-affinity iron uptake, are drastically destabilized upon arsenic exposure. Such destabilization is due to the 5’ to 3’ exonuclease Xrn1 localized in the P Bodies. Moreover FET3 mRNA decay is not mediated by Cth2 and is independent on the formation of ROS responsible for the toxic effects of arsenic compounds. Strikingly, in presence of arsenate fet3 mutant shows resistance over the wild-type which leads us to suggest that Fet3 has a role in arsenic toxicity. Unexpectedly arsenic treatment seems to activate the non-reductive iron uptake in order to maintain the cellular iron homeostasis. Furthermore our genetic, biochemical, and physiological analysis demonstrate that aft1 mutant is sensitive to arsenic compounds and such phenotype is reversible upon addition of iron. We also show that arsenic exposure induces iron deficiency in aft1 mutant. In conclusion this work shows for the first time that arsenic, a chemotherapy drug used to treat a specific type of acute promyelocytic leukemia (APL), disrupts iron homeostasis and our results suggest that this disruption is independent on ROS generation. Finally we provide preliminary data confirming that such disruption also takes place in mammalian cells, an observation that can be very relevant in term of clinical applications. yap1yap8 mutant cells independently transformed with pRS416 and YcpLac111, YcpLac111-YAP1, or pRS416-YAP8 were grown in triplicates in SC-URA-LEU containing 2mM of AsV until exponential growth phase, and RNA was extracted, labeled, and hybridized to Affymetrix Yeast Genome S98 arrays.
2011-11-04 | E-GEOD-33427 | biostudies-arrayexpress
Project description:We performed two dimensional thermal proteome profiling (2D-TPP) of deletion mutants of Vibrio cholerae to study their function upon exposure to arsenate.
2022-07-11 | PXD035237 | Pride
Project description:Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars, B. juncea and B. nigra, for salinity tolerance. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52.
2015-02-28 | GSE66389 | GEO