Project description:To compare the genome-wide transcriptional effect of ABA and iCB in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 10 uM iCB-treated plants. Differential gene expression analysis between mock- and ABA-treated or iCB-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iCB upregulated and downregulated genes represent almost all the ABA-responsive genes, which reflects the activation of PYL1-like and PYL4-like and PYL8-like ABA receptors in tomato seedlings.
Project description:To compare the genome-wide transcriptional effect of ABA and iSB09 in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 20 uM iSB09-treated plants. Differential gene expression analysis between mock- and ABA-treated or iSB09-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iSB09 upregulated and downregulated genes represent a subset of the ABA-responsive genes, which reflects the activation of PYL1-like and PYL4-like ABA receptors in tomato seedlings. Additionally, to compare the genome-wide transcriptional effect of ABA and iCB in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 10 uM iCB-treated plants. Differential gene expression analysis between mock- and ABA-treated or iCB-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iCB mimics ABA transcriptional response through activation of the three subfamilies of ABA receptors.
Project description:Analysis of abscisic acid (ABA) perception and signaling in crops is complicated by the multigenic nature of the PYR/PYL/RCAR ABA receptor family and the reported functional redundancy, which is a formidable challenge, particularly in polyploid plants. Therefore, few molecular genetics studies have been performed in crop species to study the contribution of ABA signaling to balance plant growth and adaptation to the environment. Our data reveal ABA-responsive genes in Nicotiana benthamiana, an allotetraploid biotech crop, and provide a molecular framework for gene expression analyses aimed at optimizing plant growth and environmental adaptation in agriculture. To obtain the genome-wide transcriptional effect of ABA in Nb WT plants, we performed RNA-seq studies as described in experimental procedures. Differential gene expression analysis between mock- and ABA-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected
Project description:In Arabidopsis, protein kinases from SnRK2 subclass I and III are considered to be mainly osmotic- and ABA- responsive, respectively. In this work we shed light on the role of SnRK2.4 kinase, a member of subclass I, in shaping the plant root architecture in response to exogenous ABA. We showed that SnRK2.4 is active in control conditions and upon ABA treatment, with a higher ABA sensitivity than SnRK2.2 and SnRK2.3 from class III concerning lateral root inhibition and root primordia emergence. To get insights into the molecular substrates of SnRK2.4, we compared the transcriptome, the proteome and phosphoproteome of wild-type plant to that of snrk2.4 mutants in control conditions and after 1 µM ABA treatment. Our phosphoproteomic analysis, that described 3858 unique phosphopeptides corresponding to 1820 phosphoproteins, revealed that 186 and 277 proteins were under phosphorylated in snrk2.4 mutants, in control conditions and upon ABA treatment, respectively. A regulation by SnRK2.4 of membrane transporters and cell-to-cell communication was highlighted in both conditions. By contrast, in response to ABA, SnRK2.4 specifically induced a decreased cellular abundance of RNA-helicases, thus, putatively interfering with mRNA splicing. It also modulated the phosphorylation of proteins putatively involved in the attenuation of ABA signaling, in lipid signaling and in cell wall biosynthesis, via an intricate PKs cascade mainly including members of CDPKs. This work pinpoints SnRK2.4 as an atypical ABA responsive SnRK2 involved in fundamental aspects of cell physiology.
Project description:In this study, we have identified genes that are respectively activated and repressed by the low concentration of ABA and show that ROP10 gates a specific subset of genes that are responsive only to a low ABA concentration. Keywords: Whole seedlings of wild-type (Ws) and the mutant (rop10-1) treated with or without ABA
Project description:To expore whether UV-B induce the expression of ABA-responsive genes, we compared transcriptomes of 10-d-old Col-0 and uvr8 seedlings ± 50 uM ABA treatment and 3-h exposure to 5 mol m–2 s–1 UV-B or white-light control.
Project description:Non-inflamed (cold) tumors such as leiomyosarcoma (LMS) do not benefit from immune checkpoint blockade (ICB) monotherapy. Combining ICB with angiogenesis-, or poly-ADP ribose polymerase (PARP) inhibitors may increase tumor immunogenicity by altering the immune cell composition of the tumor microenvironment (TME). The DAPPER phase II study evaluated the safety, immunologic, and clinical activity of ICB-based combinations in pre-treated LMS patients.