RNA-seq analysis of the most basal half centimeter (dividing cells) of the fourth leaf of maize RIL89 plants, profiled at different time points after leaf appearance and with different watering conditions
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Zea mays
SUBMITTER: Dirk Inze
PROVIDER: E-MTAB-7749 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Detailed information: Rice (*Oryza sativa* L. cv. Nipponbare) is a drought-susceptible species which is well suited for studies of abiotic stress response because of the comprehensive bioinformatics resource available. By withholding water from the entire root system of young rice plants, or half the root system only, it was possible to infer the relative impact of signals arriving from roots growing in wet and dry soil on the shoot proteome. The global proteome of shoots had 685 proteins in common to all three drought treatments but there were major shifts in abundance of individual proteins within 16 functional categories. The dominant changes were analyzed more deeply. First, we investigated transport and cell component organization, where some proteins were up-regulated by drought but many more down-regulated. Proteins involved in protein metabolism were up-regulated in general by drought when they were responsible for protein degradation but those involved in protein synthesis were down-regulated when water was withheld. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soil. This suggests that drought signals are complex interactions and not simply the additive effect of water supply to the roots. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. Data analysis information: The result raw files were converted to mzXML format and processed through the global proteome machine (GPM) software (version 2.1.1) of the X!Tandem algorithm (freely available at http://www.thegpm.org). The 16 gel fractions were processed serially for each experiment and the output files were generated as non-redundant, merged files with protein identifications with log (e) values less than -1, for each individual gel fraction. A protein database compiled from NCBI *O*. *sativa* with 26938 protein sequences (August 2011) was used in GPM to search the tandem mass spectra; the database also included common trypsin and human peptide contaminants. False discovery rates (FDR) were evaluated by searching against a reversed sequence database. Search parameters included MS and MS/MS tolerances of +2 Da and +0.2 Da, carbamidomethylation of cysteine as fixed modifications, oxidation of methionine as variable modifications and tolerance of two missed tryptic cleavages and K/R-P cleavages.
2020-01-22 | PXD000319 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE29566: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue. GSE29567: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress during fibre development stages. Refer to individual Series
2012-06-03 | E-GEOD-29810 | biostudies-arrayexpress
Project description:Plants require a distinctive cohort of enzymes to coordinate division and cell expansion. Proteomic analysis now enables interrogation of immature leaf bases where these processes occur. Hence we investigated proteins in tissues sampled from leaves of a drought-tolerant rice (IAC1131) to provide insights into the effect of soil drying on gene expression when compared with the drought-sensitive Nipponbare. Shoot growth zones were dissected to count dividing cells and extract protein for subsequent Tandem Mass Tags (TMT) quantitative proteomic analysis. Gene Ontology (GO) annotations of differentially expressed proteins provided insights into responses of Nipponbare and IAC1131 to drought. Soil drying did not affect the proportion of mitotic cells in IAC1131. More than 800 proteins across most functional categories were up-regulated in drought (and down-regulated on re-watering) in IAC1131, including those involved in organization of the meristem and subsequent cell formation. On the other hand, the proportion of dividing cells in Nipponbare was severely impaired during drought and fewer than 200 proteins responded in abundance when the growing zones underwent a drying cycle. However, those proteins involved in oxidation state and response to external stimuli were more likely to be upregulated by drought, even in Nipponbare.
2019-03-26 | PXD008977 | Pride
Project description:Transcriptome analysis in cotton under drought stress. To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out in leaf tissue. Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Leaf samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. Gene expression profiles in drought induced and their respective control samples were analyzed using Affymertix cotton Genechip Genome arrays to study the global changes in the expression of genome. Total RNA was isolated from leaf tissue. Samples were collected from both drought induced and control plants. Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following the Affymetrix protocols. Three biological replicates were maintained.
2012-06-03 | E-GEOD-29566 | biostudies-arrayexpress
Project description:Switchgrass plants were grown in a Sandwich tube system to induce gradual drought stress by withholding watering. After 29 days, leaf photosynthetic rate decreased significantly, compared to the control plants which were watered regularly. The drought-treated plants recovered to the same leaf water content after three days of re-watering. Root tip (1cm basal fragment, designated as RT1 hereafter) and the elongation/maturation zone (the next upper 1 cm tissue, designated as RT2 hereafter) tissues were collected at the 29th day of drought stress treatment, (named SDT for severe drought treated), one (D1W) and three days (D3W) of re-watering. The tandem mass tags mass spectrometry-based quantitative proteomics analysis was performed to identify the proteomes, and drought-induced differentially expressed proteins (DEPs). From RT1 tissues, 6,156, 7,687 and 7,699 proteins were quantified, and 296, 535 and 384 DEPs were identified in the SDT, D1W and D3W samples, respectively. From RT2 tissues, 7,382, 7,255 and 6,883 proteins were quantified, and 393, 587 and 321 proteins DEPs were identified in the SDT, D1W and D3W samples. Between RT1 and RT2 tissues, very few DEPs overlapped at SDT, but the number of such proteins increased during the recovery phase. A large number of hydrophilic proteins and stress-responsive proteins were induced during SDT and remained at a higher level during the recovery stages. A large number of DEPs in RT1 tissues maintained the same expression pattern throughout drought treatment and the recovery phases. The DEPs in RT1 tissues were classified in cell proliferation, mitotic cell division, and chromatin modification, and those in RT2 were placed in cell wall remodeling and cell expansion processes. This study provided information pertaining to root zone-specific proteome changes during drought and recover phases, which will allow us to choose the proteins (genes) as better defined targets for developing drought tolerant plants.
2020-06-04 | PXD017441 | Pride
Project description:Genome-wide Transcriptional Analysis of Genes Associated with Drought Stress in Gossypium herbaceum root This experiment was designed to investigate the molecular mechanism associated with drought tolerance in root tissue of Gossypium herbaceum. The gene expression profiles of the root tissue using Affymetrix Cotton Genome Array were compared with drought tolerant and drought sensitive genotype of G.herbaceum under drought stress and watered condition. Many genes in various molecular function or biological processes were over- or under-represented between drought tolerant and sensitive genotype, suggesting various molecular mechanism and biochemical pathways are interlinked and tolerant genotype have developed multiple mechanisms as an adaptory behavior against drought stress. The transcriptional responses of root tissue in drought tolerant and sensitive genotype of Gossypium herbaceum under drought stress have been investigated. Physiological responses to drought stress, such as stomatal conductance, water use efficiency, root bending assay on different mannitiol concentration were also measured as indicators of imposed drought stress. Total RNA was isolated from root tissue from both genotype under drought stress and normal irrigated condition with three biological replicates
2012-03-28 | E-GEOD-36249 | biostudies-arrayexpress
Project description:Drought stress is a major problem around the world and although progress in understanding how vegetable crops and model plants adapt to drought have been made, there is still little information about how fruit crops deal with moderate drought stress. In this study, we investigated the response of two apple genotypes: a drought-sensitive genotype (M26) and a drought-tolerant genotype (MBB). Our results of the morphology, physiology and biochemistry under moderate drought stress, indicated that relative water content (RWC) and leaf area (LA) were not significant changes in two genotypes. However, it had larger leaf mass per area (LMA), and accumulated higher free proline (CFP), soluble sugars (CSS) and malonaldehyde (MDA) in the leaves. Thus, it appears that the MBB genotype could produce more osmosis-regulating substances. Phosphoproteomic was analyzed from leaves of both genotypes under moderate drought stress using the isobaric tags for relative and absolute quantification (iTRAQ) technology. A total of 595 unique phosphopeptides, 682 phosphorylated sites and 446 phosphoproteins were quantitatively analyzed in the two genotypes. Motif analyses of the phosphorylation sites showed that six motifs including [PxsP], [sP], [sD], [Rxxs], [sxP] and [sxs] were enriched. We identified 12 and 48 PLSC phosphoproteins in M26 and MBB, respectively. Among these, 9 PLSC phosphoproteins were common to both genotypes, perhaps indicating a partial overlaps of the mechanisms to moderate drought stress. Gene ontology analyses revealed that the PLSC phosphoproteins present a unique combination of metabolism, transcription, translation and protein processing, suggesting that the response in apple to moderate drought stress encompasses a new homeostasis of major cellular processes. The basic trend was an increase in protein abundance related to drought and organic substance upon moderate drought stress between two genotypes. These increases were higher in the drought-tolerant genotype (MBB) than in the drought-sensitive genotype (M26). The 23 differentially expressed mRNA encoding phosphoproteins were analysis by quantitative real-time PCR (qRT-PCR). Our study is the first to address the phosphoproteome of a major fruit crop, apple rootstocks, in response to moderate drought stress, and provide insights into the molecular regulation mechanisms of apple rootstock under moderate drought stress.
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
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Project description:DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses. In this study, we examined single-base resolution methylomes of Populus under control and drought stress conditions using high-throughput bisulfite sequencing for the first time. Our data showed methylation levels of methylated cytosines, upstream2kp, downstream2kb, and repeatitive sequences significantly increased after drought treatment in Populus. Interestingly, methylation in 100 bp upstream of the transcriptional start site (TSS) repressed gene expression, while methylations in 100 – 2000bp upstream of TSS and within the gene body were positively associated with gene expression. Integrated with the transcriptomic data, we found that all cis-splicing genes were non-methylated, suggesting that DNA methylation may not associate with cis-splicing. However, our results showed that 80% of trans-splicing genes were methylated. Moreover, we found 1156 transcription factors (TFs) with reduced methylation and expression levels and 690 TFs with increased methylation and expression levels after drought treatment. These TFs may play important roles in Populus drought stress responses through the changes of DNA methylation. Taken together, these findings may provide valuable new insight into our understanding of the interaction between gene expression and methylation of drought responses in Populus. Methylomes of Poplar response to drought
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Project description:Transcriptome analysis in cotton during fibre development stages. To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out at fibre development stages (0, 5, 10 and 20 dpa/Days post anthesis). Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. Gene expression profiles in drought induced and their respective control samples were analyzed using Affymertix cotton Genechip Genome arrays to study the global changes in the expression of genome. Total RNA was isolated from 0 dpa, 5 dpa, fibre bearing ovules of 10 dpa, and fibre bearing ovules of 20 dpa. Samples were collected from both drought induced and control plants. Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following the Affymetrix protocols. Three biological replicates were maintained.
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