Similar Datasets
Project description:RNA polymerase II C-terminal domain (CTD) phosphorylation regulates transcription of both protein-coding mRNAs and non-coding RNAs (ncRNAs). However, understanding about CTD-phosphoregulation in plant ncRNA transcription is still obscure. Here we used Arabidopsis CTD phosphatase-like 4 knock-down lines (CPL4RNAi) and show that CPL4 functions in a genome-wide, conditional 3'-extensions of small nuclear RNA (snRNA) and biogenesis of novel snR-DPGs, which are protein-coding snRNA-mRNA fusion transcripts (snR-Downstream Protein-coding Gene). Production of snR-DPG is dependent on pol II snRNA promoter (PIIsnR), and CPL4RNAi promotes readthrough of snRNA 3’-end processing signal and pol II transcription downstream of snRNA. Also discovered was a novel unstable ncRNASSP14, which is driven by a PIIsnR and is conditionally 3'-extended to produce mRNA. In wild type, the snRNA-to-snR-DPG switching is induced by salt stress, and is associated with alteration of CTD phosphorylation status in the transcribing pol II complex. The snR-DPG transcripts occur widely in plants, suggesting that the transcriptional snRNA-to-snR-DPG switching is a previously unknown mechanism ubiquitous in plants to regulate gene expression in response to environmental stresses.
2018-02-16 | GSE98046 | GEO
Project description:RNA polymerase II C-terminal domain (CTD) phosphorylation regulates transcription of both protein-coding mRNAs and non-coding RNAs (ncRNAs). However, understanding about CTD-phosphoregulation in plant ncRNA transcription is still obscure. Here we used Arabidopsis CTD phosphatase-like 4 knock-down lines (CPL4RNAi) and show that CPL4 functions in a genome-wide, conditional 3'-extensions of small nuclear RNA (snRNA) and biogenesis of novel snR-DPGs, which are protein-coding snRNA-mRNA fusion transcripts (snR-Downstream Protein-coding Gene). Production of snR-DPG is dependent on pol II snRNA promoter (PIIsnR), and CPL4RNAi promotes readthrough of snRNA 3’-end processing signal and pol II transcription downstream of snRNA. Also discovered was a novel unstable ncRNASSP14, which is driven by a PIIsnR and is conditionally 3'-extended to produce mRNA. In wild type, the snRNA-to-snR-DPG switching is induced by salt stress, and is associated with alteration of CTD phosphorylation status in the transcribing pol II complex. The snR-DPG transcripts occur widely in plants, suggesting that the transcriptional snRNA-to-snR-DPG switching is a previously unknown mechanism ubiquitous in plants to regulate gene expression in response to environmental stresses.
2018-02-16 | GSE98045 | GEO
Project description:Salt-stress and CTD phosphatase-like 4 mediate switching of snRNA to mRNA transcription in Arabidopsis thaliana
| PRJNA383803 | ENA
Project description:The carboxy-terminal domain (CTD) of the large subunit of RNA polymerase II (Pol II) comprises multiple heptapeptide repeats of the consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Reversible phosphorylation of Ser2, Ser5, and Ser7 during the transcription cycle mediates the sequential recruitment of transcription/RNA processing factors. Phosphorylation of Ser7 is required for recruitment of the gene type-specific Integrator complex to the Pol II-transcribed small nuclear (sn)RNA genes. Here, we show that RNA Pol II-associated protein 2 (RPAP2) specifically recognizes the phospho-Ser7 mark on the Pol II CTD and also interacts with Integrator subunits. siRNA-mediated knockdown of RPAP2 and mutation of Ser7 to alanine cause similar defects in snRNA gene expression. In addition, we show that RPAP2 is a CTD Ser5 phosphatase. Taken together, our results indicate that during transcription of snRNA genes, Ser7 phosphorylation facilitates recruitment of RPAP2, which in turn both recruits Integrator and dephosphorylates Ser5.
| S-EPMC3262128 | biostudies-literature
Project description:Ferrochelatase-1 as a terminal enzyme of heme biosynthesis regulates many essential metabolic and physiological processes. Whether FC1 is involved in plant response to salt stress has not been described. This study shows that Arabidopsis overexpressing AtFC1 displays resistance to high salinity, whereas a T-DNA insertion knock-down mutant fc1 was more sensitive to salt stress than wild-type plants. AtFC1 conferred plant salt resistance by reducing Na+ concentration, enhancing K+ accumulation and preventing lysis of the cell membrane. Such observations were associated with the upregulation of SOS1, which encodes a plasma membrane Na+/H+ antiporter. AtFC1 overexpression led to a reduced expression of several well known salt stress-responsive genes such as NHX1 and AVP1, suggesting that AtFC1-regulated low concentration of Na+ in plants might not be through the mechanism for Na+ sequestration. To investigate the mechanism leading to the role of AtFC1 in mediating salt stress response in plants, a transcriptome of fc1 mutant plants under salt stress was profiled. Our data show that mutation of AtFC1 led to 490 specific genes up-regulated and 380 specific genes down-regulated in fc1 mutants under salt stress. Some of the genes are involved in salt-induced oxidative stress response, monovalent cation-proton (Na+/H+) exchange, and Na+ detoxification.
| S-EPMC5676718 | biostudies-literature
Project description:Salt stress is one of the major environmental threats to plant growth and development. However, the mechanisms of plants responding to salt stress are not fully understood. Through genetic screening, we identified and characterized a salt-sensitive mutant, ses5 (sensitive to salt 5), in Arabidopsis thaliana. Positional cloning revealed that the decreased salt-tolerance of ses5 was caused by a mutation in the transcription factor BP (BREVIPEDICELLUS). BP regulates various developmental processes in plants. However, the biological function of BP in abiotic stress-signaling and tolerance are still not clear. Compared with wild-type plants, the bp mutant exhibited a much shorter primary-root and lower survival rate under salt treatment, while the BP overexpressors were more tolerant. Further analysis showed that BP could directly bind to the promoter of XTH7 (xyloglucan endotransglucosylase/hydrolase 7) and activate its expression. Resembling the bp mutant, the disruption of XTH7 gave rise to salt sensitivity. These results uncovered novel roles of BP in positively modulating salt-stress tolerance, and illustrated a putative working mechanism.
| S-EPMC9866879 | biostudies-literature
Project description:Plant growth promoting rhizobacteria (PGPR) are a functionally diverse group of microbes having immense potential as biostimulants and stress alleviators. Their exploitation in agro-ecosystems as an eco-friendly and cost-effective alternative to traditional chemical inputs may positively affect agricultural productivity and environmental sustainability. The present study describes selected rhizobacteria, from a range of origins, having plant growth promoting potential under controlled conditions. A total of 98 isolates (ectophytic or endophytic) from various crop and uncultivated plants were screened, out of which four endophytes (n, L, K and Y) from Phalaris arundinacea, Solanum dulcamara, Scorzoneroides autumnalis, and Glycine max, respectively, were selected in vitro for their vegetative growth stimulating effects on Arabidopsis thaliana Col-0 seedlings with regard to leaf surface area and shoot fresh weight. A 16S rRNA gene sequencing analysis of the strains indicated that these isolates belong to the genera Pseudomonas, Bacillus, Mucilaginibacter and Rhizobium. Strains were then further tested for their effects on abiotic stress alleviation under both Petri-plate and pot conditions. Results from Petri-dish assay indicated strains L, K and Y alleviated salt stress in Arabidopsis seedlings, while strains K and Y conferred increases in fresh weight and leaf area under osmotic stress. Results from subsequent in vivo trials indicated all the isolates, especially strains L, K and Y, distinctly increased A. thaliana growth under both normal and high salinity conditions, as compared to control plants. The activity of antioxidant enzymes (ascorbate peroxidase, catalase and peroxidase), proline content and total antioxidative capacity also differed in the inoculated A. thaliana plants. Furthermore, a study on spatial distribution of the four strains, using either conventional Petri-plate counts or GFP-tagged bacteria, indicated that all four strains were able to colonize the endosphere of A. thaliana root tissue. Thus, the study revealed that the four selected rhizobacteria are good candidates to be explored as plant growth stimulators, which also possess salt stress mitigating property, partially by regulating osmolytes and antioxidant enzymes. Moreover, the study is the first report of Scorzoneroides autumnalis (fall dandelion) and Solanum dulcamara (bittersweet) associated endophytes with PGP effects.
| S-EPMC7391687 | biostudies-literature
Project description:Ubiquitination is an important post-translational protein modification that is known to play critical roles in diverse biological processes in eukaryotes. The RING E3 ligases function in ubiquitination pathways, and are involved in a large diversity of physiological processes in higher plants. The RING domain-containing E3 ligase AtRDUF1 was previously identified as a positive regulator of ABA-mediated dehydration stress response in Arabidopsis. In this study, we report that AtRDUF1 is involved in plant responses to salt stress. AtRDUF1 expression is upregulated by salt treatment. Overexpression of AtRDUF1 in Arabidopsis results in an insensitivity to salt and osmotic stresses during germination and seedling growth. A double knock-out mutant of AtRDUF1 and its close homolog AtRDUF2 (atrduf1atrduf2) was hypersensitive to salt treatment. The expression levels of the stress-response genes RD29B, RD22, and KIN1 are more sensitive to salt treatment in AtRDUF1 overexpression plants. In summary, our data show that AtRDUF1 positively regulates responses to salt stress in Arabidopsis.
| S-EPMC3741333 | biostudies-literature
Project description:Plants that can adapt their phenotype may be more likely to survive changing environmental conditions. Heritable epigenetic variation could provide a way to rapidly adapt to such changes. Here we tested whether environmental stress induces heritable, potentially adaptive phenotypic changes independent of genetic variation over few generations in Arabidopsis thaliana. We grew two accessions (Col-0, Sha-0) of A. thaliana for three generations under salt, heat and control conditions and tested for induced heritable phenotypic changes in the fourth generation (G4) and in reciprocal F1 hybrids generated in generation three. Using these crosses we further tested whether phenotypic changes were maternally or paternally transmitted. In generation five (G5), we assessed whether phenotypic effects persisted over two generations in the absence of stress. We found that exposure to heat stress in previous generations accelerated flowering under G4 control conditions in Sha-0, but heritable effects disappeared in G5 after two generations without stress exposure. Previous exposure to salt stress increased salt tolerance in one of two reciprocal F1 hybrids. Transgenerational effects were maternally and paternally inherited. Lacking genetic variability, maternal and paternal inheritance and reversibility of transgenerational effects together indicate that stress can induce heritable, potentially adaptive phenotypic changes, probably through epigenetic mechanisms. These effects were strongly dependent on plant genotype and may not be a general response to stress in A. thaliana.
| S-EPMC3621951 | biostudies-literature
Project description:Salt stress represents a significant abiotic stressor for plants and poses a severe threat to agricultural productivity. Glutaredoxins (GRXs) are small disulfide reductases that can scavenge cellular reactive oxygen species and are crucial for plant growth and development, particularly under stressful circumstances. Although CGFS-type GRXs were found to be involved in various abiotic stresses, the intrinsic mechanism mediated by LeGRXS14, a tomato (Lycopersicon esculentum Mill.) CGFS-type GRX, is not yet fully understood. We discovered that LeGRXS14 is relatively conserved at the N-terminus and exhibits an increase in expression level under salt and osmotic stress conditions in tomatoes. The expression levels of LeGRXS14 in response to osmotic stress peaked relatively rapidly at 30 min, while the response to salt stress only peaked at 6 h. We constructed LeGRXS14 overexpression Arabidopsis thaliana (OE) lines and confirmed that LeGRXS14 is located on the plasma membrane, nucleus, and chloroplasts. In comparison to the wild-type Col-0 (WT), the OE lines displayed greater sensitivity to salt stress, resulting in a profound inhibition of root growth under the same conditions. Analysis of the mRNA levels of the WT and OE lines revealed that salt stress-related factors, such as ZAT12, SOS3, and NHX6, were downregulated. Based on our research, it can be concluded that LeGRXS14 plays a significant role in plant tolerance to salt. However, our findings also suggest that LeGRXS14 may act as a negative regulator in this process by exacerbating Na+ toxicity and the resulting oxidative stress.
| S-EPMC10305512 | biostudies-literature