Overexpression of a Medicago truncutula homeodomain finger protein, MtPHD6, enhances drought tolerance in Arabidopsis
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PROVIDER: PRJNA556865 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: We aimed to dissect function of Medicago truncutula homeodomain finger protein, MtPHD6 in Arabidopsis Methods: A total amount of 3 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0). Results:In total, four samples with three biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis revealed different networks which were modulated by drought stress and MtPHD6 transgene in Arabidopsis seedlings
2020-01-08 | GSE134945 | GEO
Project description: Not available
| S-EPMC6916436 | biostudies-literature
Project description:Molecular Elasticity and Adjustment of Drought Recovery Dynamics of 14N- and 15N-fertilized Legume Medicago truncatula. Climate change in conjunction with population growth necessitates a systems biology approach to characterize plant drought response and a more thorough understanding of the underlying molecular mechanisms. During drought stress and recovery, the metabolome and proteome regulate and are regulated through diverse mechanisms including synthesis and degradation. In order to study this complex regulation network, a front-end multilevel analysis is presented for the first time, investigating protein turnover, regulatory classes of proteins and metabolites as well as post translational ubiquitination of a target set of proteins during a severe stress and recovery scenario in the model legume Medicago truncatula. Evidence for enhanced translational proteome regulation was observed during drought recovery and functional clusters of differentially dynamic phases during the course of recovery were defined. The data give novel insights into molecular elasticity that enable recovery of drought stressed plants. Additionally, these results offer putative targets and metabolic pathways for future plant-bioengineering towards enhanced drought stress tolerance.
2016-03-29 | PXD001728 | Pride
Project description:Medicago truncatula (Medicago) flowering is promoted by winter cold (vernalization) followed by long day photoperiods (VLD). By analysing a Tnt1 insertion mutant and 17 CRISPR-Cas9 gene-edited lines with delayed flowering, we identified INHIBITOR OF GROWTH (ING) 2 (MtING2) encoding a plant homeodomain (PHD) zinc finger and predicted H3K4me2/3 epigenome reader in Medicago. There are two ING genes in most plants, but their physiological role has not been described. Mting2 mutants had many developmental abnormalities including delayed flowering particularly in VLD, compact architecture, abnormal leaves with extra leaflets but no trichomes and smaller seeds and seed barrels. RNA-Seq experiments indicated that >7000 genes are mis-expressed in the Mting2 mutant consistent with its strong mutant phenotypes. Mting2 did not show reduced accumulation of the strong floral promoter FLOWERING LOCUS T-LIKE gene, MtFTa1, but did have increased expression of MtTFL1c, consistent with the delayed flowering of the mutant. ChIP-Seq analysis identified >5000 novel H3K4me3 locations in the genome of Mting2-1 mutant compared to wild type, which overlapped with some differentially expressed genes. Overall, our study has uncovered an important physiological role of a plant ING gene in development, flowering and gene expression, which likely involves an epigenetic mechanism.
2022-11-10 | GSE189301 | GEO
Project description:Medicago truncatula (Medicago) flowering is promoted by winter cold (vernalization) followed by long day photoperiods (VLD). By analysing a Tnt1 insertion mutant and 17 CRISPR-Cas9 gene-edited lines with delayed flowering, we identified INHIBITOR OF GROWTH (ING) 2 (MtING2) encoding a plant homeodomain (PHD) zinc finger and predicted H3K4me2/3 epigenome reader in Medicago. There are two ING genes in most plants, but their physiological role has not been described. Mting2 mutants had many developmental abnormalities including delayed flowering particularly in VLD, compact architecture, abnormal leaves with extra leaflets but no trichomes and smaller seeds and seed barrels. RNA-Seq experiments indicated that >7000 genes are mis-expressed in the Mting2 mutant consistent with its strong mutant phenotypes. Mting2 did not show reduced accumulation of the strong floral promoter FLOWERING LOCUS T-LIKE gene, MtFTa1, but did have increased expression of MtTFL1c, consistent with the delayed flowering of the mutant. ChIP-Seq analysis identified >5000 novel H3K4me3 locations in the genome of Mting2-1 mutant compared to wild type, which overlapped with some differentially expressed genes. Overall, our study has uncovered an important physiological role of a plant ING gene in development, flowering and gene expression, which likely involves an epigenetic mechanism.
2022-11-10 | GSE189617 | GEO
Project description:For transcript analysis of aluminum tolerance responses in Medicago truncatula we compared transcripts from 2.5 µM Al-treated and control (-Al) root tips corresponding to 12 and 48 h after Al treatment in Al-tolerant (T32) and Al-sensitive (S70) lines. Keywords: 2 time points and 2 lines
2007-02-08 | GSE6946 | GEO
Project description:For transcript analysis of aluminum tolerance responses in Medicago truncatula (A17) we compared transcripts from 2.5 µM Al-treated and control (-Al) root tips corresponding to 12 h after Al treatment. Keywords: One time point and one genotype
2007-02-22 | GSE7066 | GEO
Project description: Not available
| S-EPMC5787828 | biostudies-other
Project description:Background Maintaining global food security in the context of climate changes is an important challenge in the next century. Improving abiotic stress tolerance of major crops, like wheat, can contribute to this goal. Therefore, new genes improving tolerance to abiotic stresses, like drought, are needed to support breeding programs aimed at producing more adapted cultivars. Recently, we screened five wheat Zinc Finger Proteins (TaZFPs) and identified TaZFP13D as a new gene improving water-stress tolerance. However, a more detailed characterization of this gene is required to better evaluate its potential in drought tolerance and to decipher the underlying molecular basis. Results We used the Barley Stripe Mosaic Virus to up- or down-regulate TaZFP13D expression in wheat. Overexpression of TaZFP13D under well-watered conditions enhances growth as indicated by improved biomass. Exposing plants to a severe drought stress revealed that TaZFP13D strongly increases survival rate and stress recovery. In addition, TaZFP13D reduces drought-induced oxidative damages, at least in part by improving key antioxidant enzymes activity. Conversely, down-regulation of TaZFP13D decreases drought tolerance and protection against drought-induced oxidative damages. RNA-seq-based transcriptome analysis showed that many genes regulated by TaZFP13D were previously shown to improve drought tolerance, while many others are related to the photosynthetic electron transfer chain and are proposed to improve photosynthesis efficiency and chloroplast protection against ROS damages. Conclusion This study highlights the important role of TaZFP13D in wheat drought tolerance, contributes to unravel the complex regulation governed by TaZFPs, and provides a useful marker to select more drought tolerant wheat cultivars.
2023-03-08 | GSE226842 | GEO
Project description:Drought is a major environmental constraint affecting physiological, biochemical and molecular changes of crops, causing loss in crop productivities. Understanding the molecular mechanisms of drought tolerance is important for crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain-leucine zipper class IV transcription factor gene, Rice outermost cell-specific gene 10 (Roc10), improves drought tolerance and grain yield by increasing lignin accumulation in ground tissues of rice plants. Overexpression of Roc10 significantly enhanced drought tolerance of transgenic rice plants at the vegetative stages of growth with highly effective photosystem and reduction of water loss rate as compared with non-transgenic control and RNAi plants. More importantly, Roc10 overexpression plants had higher drought tolerance at the reproductive stage of growth with higher grain yield over controls under field-drought conditions. We identified downstream and putative target genes of Roc10 by using RNA-seq and ChIP-seq data of rice shoots. Roc10 overexpression elevated the expression levels of lignin biosynthetic genes in shoots with a concomitant increase in accumulation of lignin. The overexpression and RNAi lines showed opposite patterns of lignin accumulation. The Roc10 is mainly expressed in the outer cell layers including epidermis and vasculature of shoots that coincides with areas of increased lignification. Furthermore, the Roc10 was found to directly bind to the promoter of PEROXIDASEN/PEROXIDASE38, a key gene in lignin biosynthesis. Together, our findings suggested that the Roc10 confers drought stress tolerance by enhancing lignin biosynthesis in ground tissues of rice plants.
2018-01-06 | GSE93287 | GEO