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RNA-sequencing of GmWRKY54 over-expression and null plants

ABSTRACT: WRKY transcriptional factors play important roles in response to various abiotic stresses. In this study, we demonstrate that inserting a copy of soybean WRKY54 driven by a constitutive promoter of CMP (cestrum yellow leaf curling virus) or a drought induced promoter of RD29a, improves drought tolerance in transgenic soybean plants. GmWRKY54 is a transcriptional activator and regulates expressions of large numbers of stress-related genes. Using a GO enrichment toolkit, we found that GmWRKY54 up-regulated GO terms related to transcriptional regulator and gene expression and down-regulated GO terms related to photosynthesis and membrane. Using a co-expression network analysis, we find that dozens of genes are negatively co-expressing with photosynthetic genes. These genes are related to ABA signaling pathway, Ca2+ signaling pathway and transcriptional factors. Transgenic plants confer drought tolerance through improving stomatal closure, reducing transpiration rate and reducing membrane damage during water deficit. GmWRKY54 activates expression of these ABA or Ca2+ signaling-related genes, which finally regulates stomatal aperture. GmWRKY54 binds to the promoter regions of genes encoding an ABA receptor (PYL8-1), two calcium dependent protein kinase (CPK3-1 and CPK3-2), a CBL (Calcineurin B-like protein) interacting protein kinase (CIPK11-2), a SnRK family protein kinase and a ferritin, suggesting that they are the direct targets of GmWRKY54. Our study reveals that GmWRKY54 significantly improves drought tolerance in soybean and regulates expression of large numbers of drought-related genes, suggesting that GmWRKy54 maybe a master regulator of drought response.

ORGANISM(S): Glycine max

PROVIDER: GSE98958 | GEO | 2018/05/31

REPOSITORIES: GEO

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Project description:External application of acetic acid has been recently reported to enhance the survival to drought in plants such as Arabidopsis, rapeseed, maize, rice and wheat, but the effects of acetic acid application on increased drought tolerance in woody plants such as a tropical crop “cassava” remain elusive. A molecular understanding of acetic acid-induced drought avoidance in cassava will contribute to the development of technology that can be used to enhance drought tolerance without resorting to transgenic technology or advancements in cassava cultivation. In the present study, morphological, physiological and molecular responses to drought were analyzed in cassava after the treatment with acetic acid. Results indicated that the acetic acid-treated cassava plants had a higher level of drought avoidance than water-treated, control plants. Specifically, higher leaf relative water content, and chlorophyll and carotenoid levels were observed as soils dried out during the drought treatment. Leaf temperatures in acetic acid-treated cassava plants were higher relative to leaves on plants pretreated with water and the increase of ABA content was observed in leaves of acetic acid-treated plants, suggesting that stomatal conductance and the transpiration rate in leaves of acetic acid-treated plants decreased to maintain relative water contents and avoid drought. Transcriptome analysis revealed that the acetic acid treatment increased the expression of ABA signaling-related genes, such as OPEN STOMATA 1　(OST1) and protein phosphatase 2C; as well as drought response and tolerance-related genes, such as outer membrane tryptophan-rich sensory protein (TSPO), and heat shock proteins. Collectively, the external application of acetic acid enhances drought avoidance in cassava through the upregulation of ABA signaling pathway genes and several stress response- and tolerance-related genes. These data support the idea that adjustments of the acetic acid application to plants is useful to enhance drought tolerance in order to minimize the growth inhibition in the agricultural field.

Project description:Transgenic Arabidopsis plants with constitutively low inositol (1,4,5) triphosphate exhibit an increased tolerance to water stress by an ABA-independent pathway; The phosphoinositide pathway and inositol (1,4,5) trisphopsphate (InsP3) are implicated in plant responses to stress. In order to manipulate the pathway and determine the downstream consequences of altered InsP3-mediated signaling, we generated transgenic Arabidopsis plants expressing the mammalian type I inositol polyphosphate 5-phosphatase, an enzyme that specifically hydrolyzes the soluble inositol phosphates and terminates the signal. Transgenic plants have no morphological differences compared to wild type; however, rapid transient Ca2+ responses to a cold or salt stimulus are reduced by ~ 30%. To further understand the role of InsP3-mediated signaling in plant stress responses we focused on drought stress. Surprisingly, the InsP 5-ptase plants lose less water and exhibited an increased tolerance to drought. Stomatal bioassays showed that transgenic guard cells are less responsive to the inhibition of opening by ABA but show an increased sensitivity to ABA-induced closure. The onset of the drought stress is delayed in the transgenic plants and ABA levels did not increase as much as in the wild type. Transcript profiling has revealed that DREB2A and a subset of DREB2A regulated genes are basally up regulated in the InsP 5-ptase plants. These results indicate that the drought tolerance of the InsP 5-ptase plants is mediated in part via an ABA-independent pathway. The constitutive dampening of the InsP3 signal in this system has uncovered novel regulation and cross talk between signaling pathways. Experiment Overall Design: In order to compare global expression profiles between wild type and transgenic plants in response to water stress we harvested leaves for transcript profiling at day 0 (well watered) and at day 7 when the transgenic plants were still at an RWC of >85% and the wild type and vector control plants were at an RWC of ~ 50 -60% . Leaves were harvested and pooled from ~ 10 plants of each line/time point and three independent biological replicates were carried out with wild type (WT) and 2 independent transgenic lines (T6 and T8). The vector control line (C2) was used as an additional control.

Project description:Systems responses of mature leaves from 4 reference cultivars of a larger collection of European potato cultivars (Solanum tuberosum L.) are investigated by metabolome profiling and RNA-Sequencing. The chosen reference cultivars, Milva, Alegria, Desiree, and Saturna, vary in ascending order in regard to drought tolerance. Systems analyses are based on 3 independent field trials and 3 paralleled greenhouse trials. Robust responses across all cultivars and conditions to natural seasonal drought stress comprise proline, raffinose, galactinol, arabitol, arabinonic acid, chlorogenic acid, and 102 transcripts which consist to a high proportion of heat shock proteins and genes with signaling or regulatory functions, such as a homolog of abscisic acid receptor PYL4. Constitutive differences of the tolerant cultivars, Desiree and Saturna, compared to the sensitive cultivars include arbutin (hydroquinone-beta-D-glucopyranoside), octopamine (p-hydroxyphenylethanolamine), ribitol and 248 differential transcripts. Many of these transcripts are disease related, receptor kinases, or regulatory genes, for example a homolog of the Arabidopsis FOUR LIPS MYB-regulator of stomatal cell proliferation. Functional enrichment analyses imply that heat stress is a major acclimation component of potato leaves to agronomical relevant drought stress. Enhanced leaf heat stress is a result of drought caused by loss of transpiration cooling. This effect and CO2-limitation are the main dilemmas of drought- or ABA-induced stomatal closure. Constitutive differences between tolerant and sensitive cultivars indicate partially synergistic interactions of drought and biotic stress responses. We suggest that drought tolerance of the potato reference cultivars may be caused by general resistance mechanisms which are part of previously selected pathogen tolerance. Transcriptome profiling by RNA-sequencing of 48 leaf samples from 4 potato cultivars grown under control or drought stress conditions in 6 independent experiments

Project description:Pokhilko2013 - TOC1 signalling in Arabidopsis circadian clock In this model, Pokhilko et al. has incorporated the negative transcriptional regulations of the core clock genes by TOC1 and the up-regulation of TOC1 expression by ABA signalling, to their previous model BIOMD0000000412 This model is described in the article: Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. Pokhilko A, Mas P, Millar AJ. BMC Syst Biol 2013; 7: 23 Abstract: BACKGROUND: 24-hour biological clocks are intimately connected to the cellular signalling network, which complicates the analysis of clock mechanisms. The transcriptional regulator TOC1 (TIMING OF CAB EXPRESSION 1) is a founding component of the gene circuit in the plant circadian clock. Recent results show that TOC1 suppresses transcription of multiple target genes within the clock circuit, far beyond its previously-described regulation of the morning transcription factors LHY (LATE ELONGATED HYPOCOTYL) and CCA1 (CIRCADIAN CLOCK ASSOCIATED 1). It is unclear how this pervasive effect of TOC1 affects the dynamics of the clock and its outputs. TOC1 also appears to function in a nested feedback loop that includes signalling by the plant hormone Abscisic Acid (ABA), which is upregulated by abiotic stresses, such as drought. ABA treatments both alter TOC1 levels and affect the clock's timing behaviour. Conversely, the clock rhythmically modulates physiological processes induced by ABA, such as the closing of stomata in the leaf epidermis. In order to understand the dynamics of the clock and its outputs under changing environmental conditions, the reciprocal interactions between the clock and other signalling pathways must be integrated. RESULTS: We extended the mathematical model of the plant clock gene circuit by incorporating the repression of multiple clock genes by TOC1, observed experimentally. The revised model more accurately matches the data on the clock's molecular profiles and timing behaviour, explaining the clock's responses in TOC1 over-expression and toc1 mutant plants. A simplified representation of ABA signalling allowed us to investigate the interactions of ABA and circadian pathways. Increased ABA levels lengthen the free-running period of the clock, consistent with the experimental data. Adding stomatal closure to the model, as a key ABA- and clock-regulated downstream process allowed to describe TOC1 effects on the rhythmic gating of stomatal closure. CONCLUSIONS: The integrated model of the circadian clock circuit and ABA-regulated environmental sensing allowed us to explain multiple experimental observations on the timing and stomatal responses to genetic and environmental perturbations. These results crystallise a new role of TOC1 as an environmental sensor, which both affects the pace of the central oscillator and modulates the kinetics of downstream processes. This model is hosted on BioModels Database and identified by: BIOMD0000000445. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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RNA-sequencing of GmWRKY54 over-expression and null plants

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