The temperature quickly modulates protein expression by Codon Usage in wheat filling grain
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap
ORGANISM(S): Triticum Aestivum (wheat)
TISSUE(S): Plant Cell, Kernel
SUBMITTER: 
Bingjin Wu
LAB HEAD: Bingjin Wu
PROVIDER: PXD021460 | Pride | 2021-03-24
REPOSITORIES: pride
Dataset's files
Similar Datasets
Project description:The protein content determines the cell state. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are still unknown. We quantified 47,535 mRNAs and 3,742 proteins in filling grain of wheat under two thermal environments. The impact of mRNA abundance and sequence features implicated in protein translation and degradation on protein expression were evaluated by regression analysis. Transcription, codon usage and amino acid frequency mainly affect protein expression, and their combined contribution explains 58.2% and 66.4% of protein abundance variation in two types of heat stresses. Of which, transcription contributes more to the protein expression under severe heat stress (31%) than to mild stress (6%). Codon usage plays a stable and powerful role in protein expression under heat stress, even surpassing transcription. What’s more, the usage of AAG is a key factor regulating rapid protein expression under heat stress. This study revealed the main factors affecting the changes of protein abundance in the early stage of heat stress, and explained the mystery that plants can express protein rapidly under heat stress.
2021-03-23 | GSE157909 | GEO
Project description:Alfalfa is the most produced perennial forage crop in Canada. Drought stress is a major form of abiotic stress, affecting its productivity and annual yield. A small RNA, miR156, plays a major role in drought tolerance by downregulating downstream SPL genes, but its effects at the proteome level are unknown. In this study, the protein level perturbations of miR156 overexpression (A8) and empty vector (EV) control genotypes were compared under drought stress. Using label-free quantification, 3,000 protein groups were identified, of which 68 were upregulated in A8 and 84 were downregulated relative to EV under control conditions. Conversely, under drought stress, 610 proteins were upregulated and only 52 proteins were downregulated in A8 relative to EV. Functional analysis using PlantRegMap showed that the enriched proteins are likely involved in biological and molecular processes including antioxidant response, response to stress, signal transduction and biosynthesis of secondary metabolites. These proteins/pathways might be involved in the enhancement of drought stress tolerance mediated by miR156. Protein groups related to signaling, such as MAP kinase, calcium-dependent protein kinase, protein phosphatase 2C, and transcriptional regulators including bZIP and zinc finger proteins were found to be differentially expressed when a search was conducted against a drought stress gene database. The proteomic dataset was validated by immunoblotting of selected proteins. The results of this study provide a better understanding and insight into the role of miR156 in drought stress tolerance in alfalfa at the proteomic level.
2023-10-19 | PXD028329 | Pride
Project description:Considering global climate changes, incidences of combined drought and heat stress are likely to increase in the future and will considerably influence plant-pathogen interactions. Until now, little is known about plants exposed to simultaneously occurring abiotic and biotic stresses. To shed some light on molecular plant responses to multiple stress factors, a versatile multi-factorial test system, allowing simultaneous application of heat, drought and virus stress, was developed. Comparative analysis of single, double and triple stress responses by transcriptome and metabolome analysis revealed that gene expression under multi-factorial stress is not predictable from single stress treatments. Hierarchical cluster and principal component analysis identified heat as the major stress factor clearly separating heat-stressed from non-heat stressed plants. We identified 11 genes differentially regulated in all stress combinations as well as 23 genes specifically-regulated under triple stress. Furthermore, we showed that virus treated plants displayed enhanced expression of defense genes, which was abolished in plants additionally subjected to heat and drought stress. Triple stress also reduced expression of genes involved in the R-mediated disease response and increased the cytoplasmic protein response which was not seen under single stress conditions. These observations suggested that abiotic stress factors significantly altered TuMV-specific signaling networks which lead to a deactivation of defense responses and a higher susceptibility of plants. Collectively, our transcriptome and metabolome data provide a powerful resource to study plant responses during multi-factorial stress and allows identifying metabolic processes and functional networks involved in tripartite interactions of plants with their environment. Stress induced gene expression in Arabidopsis leaves was measured after exposure to single and combined abiotic and biotic stress. Plants were grown on soil for 21 days till virus infection. Eight days later controlled drought stress was applied. At the end of the treatments heat was applied for three days. Four biological replicates have been hybridized for each treatment. Furthermore, Arabidopsis plants were exposed to a single severe heat stress (37°C day/33°C night) to mimic the severity of the triple stress experiment.
2013-06-10 | E-GEOD-46758 | biostudies-arrayexpress
Project description:To characterize plant heat stress-responsive genes and to clarify the heat stress-responsive transcription pathways, the transcriptome analysis of rice was conducted using microarray. Arabidopsis plants were grown in plastic pots filled with peat moss for 3 weeks (principal growth stage 1.07â1.08) under a 16 h light/8 h dark photoperiod (50 ± 10 μmol photons mâ2 sâ1) at 22°C, and were treated for 30 min at 37°C.
2017-02-28 | E-MTAB-4531 | biostudies-arrayexpress
Project description:BPMs are a family of E3 ubiquitin ligases. We identified BPM proteins as interactors of the Arabidopsis stress responsive transcription factor DREB2A. We found an increase in the accumulation level of the DREB2A protein under heat stress in transgenic Arabidopsis plants in which expression of six BPMs were suppressed by an amiRNA. In order to evaluate the impacts of the amiRNA on the gene expression under heat stress, transcriptomes were compared between these transgenic plants and vector control plants.
2018-11-01 | E-MTAB-5845 | biostudies-arrayexpress
Project description:Considering global climate changes, incidences of combined drought and heat stress are likely to increase in the future and will considerably influence plant-pathogen interactions. Until now, little is known about plants exposed to simultaneously occurring abiotic and biotic stresses. To shed some light on molecular plant responses to multiple stress factors, a versatile multi-factorial test system, allowing simultaneous application of heat, drought and virus stress, was developed. Comparative analysis of single, double and triple stress responses by transcriptome and metabolome analysis revealed that gene expression under multi-factorial stress is not predictable from single stress treatments. Hierarchical cluster and principal component analysis identified heat as the major stress factor clearly separating heat-stressed from non-heat stressed plants. We identified 11 genes differentially regulated in all stress combinations as well as 23 genes specifically-regulated under triple stress. Furthermore, we showed that virus treated plants displayed enhanced expression of defense genes, which was abolished in plants additionally subjected to heat and drought stress. Triple stress also reduced expression of genes involved in the R-mediated disease response and increased the cytoplasmic protein response which was not seen under single stress conditions. These observations suggested that abiotic stress factors significantly altered TuMV-specific signaling networks which lead to a deactivation of defense responses and a higher susceptibility of plants. Collectively, our transcriptome and metabolome data provide a powerful resource to study plant responses during multi-factorial stress and allows identifying metabolic processes and functional networks involved in tripartite interactions of plants with their environment. Stress induced gene expression in Arabidopsis leaves was measured after exposure to single and combined abiotic and biotic stress. Plants were grown on soil for 21 days till virus infection. Eight days later controlled drought stress was applied. At the end of the treatments heat was applied for three days. In parallel, a homozougus T-DNA insertion line SALK_021115C (N672283), located in the Arabidopsis gene At5g45000 has been exposed to the same stress conditions. Four biological replicates have been hybridized for each treatment.
2013-06-10 | E-GEOD-46759 | biostudies-arrayexpress
Project description:Considering global climate changes, incidences of combined drought and heat stress are likely to increase in the future and will considerably influence plant-pathogen interactions. Until now, little is known about plants exposed to simultaneously occurring abiotic and biotic stresses. To shed some light on molecular plant responses to multiple stress factors, a versatile multi-factorial test system, allowing simultaneous application of heat, drought and virus stress, was developed. Comparative analysis of single, double and triple stress responses by transcriptome and metabolome analysis revealed that gene expression under multi-factorial stress is not predictable from single stress treatments. Hierarchical cluster and principal component analysis identified heat as the major stress factor clearly separating heat-stressed from non-heat stressed plants. We identified 11 genes differentially regulated in all stress combinations as well as 23 genes specifically-regulated under triple stress. Furthermore, we showed that virus treated plants displayed enhanced expression of defense genes, which was abolished in plants additionally subjected to heat and drought stress. Triple stress also reduced expression of genes involved in the R-mediated disease response and increased the cytoplasmic protein response which was not seen under single stress conditions. These observations suggested that abiotic stress factors significantly altered TuMV-specific signaling networks which lead to a deactivation of defense responses and a higher susceptibility of plants. Collectively, our transcriptome and metabolome data provide a powerful resource to study plant responses during multi-factorial stress and allows identifying metabolic processes and functional networks involved in tripartite interactions of plants with their environment. Stress induced gene expression in Arabidopsis leaves was measured after exposure to single and combined abiotic and biotic stress. Plants were grown on soil for 21 days till virus infection. Eight days later controlled drought stress was applied. At the end of the treatments heat was applied for three days. Four biological replicates have been hybridized for each treatment.
2013-06-10 | E-GEOD-46757 | biostudies-arrayexpress
Project description:To gain insights into molecular mechanisms of tolerance to heat stress, we conducted a transcript profiling experiment to identify heat-responsive genes in contrasting peanut mini core accessions, either un-acclimated or acclimated to heat stress. Plants at reproductive stage were exposed to 28 °C (control), 45 °C for 15 d (un-acclimated) or 45 °C for 1 d followed by 7 d recovery and 15 d stress (acclimated). Two contrasting genotypes showing diverse response to stress were selected based on a bioassay involving chlorophyll fluorescence yield under elevated respiratory demand and membrane thermostability. Transcript profiling was performed using 8 x 15k custom oligo microarrays containing 15k peanut EST sequences. Gene enrichment analysis was performed using Blast2GO program and genes with homology to known proteins were categorized into detailed molecular functional groups. Majority of stress-responsive genes assigned to KEGG pathways belonged to starch, sucrose and galactose metabolism followed by aminoacid metabolism, and secondary metabolite biosynthesis. Differentially expressed transcripts from samples were validated in the samples from second year by quantitative real-time PCR. Transcripts of eight genes involved in terpenoid and flavanoid biosynthesis were induced after second and seventh day, respectively in leaves under heat stress. Metabolite analysis confirmed increases in metabolites of selected pathways under heat stress. The heat up-regulated genes in tolerant COC041 mini-core accession are potential candidate genes for engineering stress-tolerant peanuts and unraveling molecular mechanisms of peanut adaptation to heat stress. We used Agilent peanut microarrays to identify putative heat stress-responsive genes. Acclimated leaf tissues of the peanut genotypes COC041 (tolerant) and COC166 (susceptible) were used in the study. Three replications of microarray experiments were carried out by hybridizing the cRNA from different time points and stress conditions in a loop design on 8 x 15k microarray.
2010-06-30 | E-GEOD-18107 | biostudies-arrayexpress
Project description:To gain insights into molecular mechanisms of tolerance to heat stress, we conducted a transcript profiling experiment to identify heat-responsive genes in contrasting peanut mini core accessions, either un-acclimated or acclimated to heat stress. Plants at reproductive stage were exposed to 28 °C (control), 45 °C for 15 d (un-acclimated) or 45 °C for 1 d followed by 7 d recovery and 15 d stress (acclimated). Two contrasting genotypes showing diverse response to stress were selected based on a bioassay involving chlorophyll fluorescence yield under elevated respiratory demand and membrane thermostability. Transcript profiling was performed using 4 x 44k custom oligo microarrays containing 22k peanut EST sequences. The microarray analysis identified 710 stress-induced and 770 stress-repressed putative heat-responsive transcripts in the tolerant genotype. Gene enrichment analysis was performed using Blast2GO program and genes with homology to known proteins were categorized into detailed molecular functional groups. Majority of stress-responsive genes assigned to KEGG pathways belonged to starch, sucrose and galactose metabolism followed by amino acid metabolism, and secondary metabolite biosynthesis. Differentially expressed transcripts from samples obtained from first year’s experiment were validated in the samples from second year by quantitative real-time PCR. Transcripts of eight genes involved in terpenoid and flavanoid biosynthesis were induced after second and seventh day, respectively, in leaves under heat stress. Metabolite analysis confirmed increases in metabolites of selected pathways under heat stress. The heat up-regulated genes in tolerant COC041 mini-core accession are potential candidate genes for engineering stress-tolerant peanuts and unraveling molecular mechanisms of peanut adaptation to heat stress. We used Agilent peanut microarrays to identify putative heat stress-responsive genes. Directly heat-stressed leaf tissues of the peanut genotypes COC041 (tolerant) and COC166 (susceptible) were used in the study. Three replications of microarray experiments were carried out by hybridizing the cRNA from different time points and stress conditions in a loop design on 4 x 44k microarray.
2010-06-30 | E-GEOD-16492 | biostudies-arrayexpress