Plastid and cytoplasmic origins of 1O2-mediated gene responses
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA847965 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19619800.fastq.gz | Fastqsanger.gz | |||
| SRR19619777.fastq.gz | Fastqsanger.gz | |||
| SRR19619778.fastq.gz | Fastqsanger.gz | |||
| SRR19619779.fastq.gz | Fastqsanger.gz | |||
| SRR19619780.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:Effect of low and high light in Arabidopsis Ch1 mutant
2022-11-02 | GSE205861 | GEO
Project description:The reactive oxygen species singlet oxygen, 1O2, has an extremely short half-life, yet is intimately involved with stress signalling in the cell. We previously showed that the effects of 1O2 on the transcriptome are highly correlated with 80S ribosomal arrest due to oxidation of guanosine residues in mRNA. Here, we show that dysregulation of chlorophyll biosynthesis in the flu mutant or through feeding by δ-aminolevulinic acid can lead to accumulation of photoactive chlorophyll intermediates in the cytoplasm, which generates 1O2 upon exposure to light and causes the oxidation of RNA, eliciting 1O2-responsive genes. In contrast, transcriptomes derived from DCMU treatment, or the Ch1 mutant under moderate light conditions display commonalties with each other but do not induce 1O2 gene signatures. Comparing 1O2 related transcriptomes to an index transcriptome induced by cycloheximide inhibition enables distinction between 1O2 of cytosolic or of plastid origin. These comparisons provide biological insight to cases of mutants or environmental conditions that produce 1O2.
| S-EPMC9676463 | biostudies-literature
Project description:We report that phosphatidylglycerol (PG) biosynthesis in plastid is required for plastid gene expression mediated by plastid-encoded RNA polymerase and light-induced expression of nuclear-encoded photosynthesis-associated genes. A transcription factor GOLDEN-LIKE1 was also found to be involved in the downregulation of nuclear photosynthesis genes in responce to PG deficiency.
2022-07-15 | GSE180205 | GEO
Project description:Retrograde signaling from the chloroplast to the nucleus is necessary to regulate the chloroplast proteome during development and fluctuating environmental conditions. Although the specific chloroplast process(es) that must occur and the nature of the signal(s) that exits the chloroplast are not well understood, previous studies using drug inhibitors of chloroplast biogenesis have revealed that normal chloroplast development is required to express Photosynthesis Associated Nuclear Genes (PhANGs). In an attempt to determine which specific steps in chloroplast development are involved in retrograde signaling, we analyzed Arabidopsis mutants defective in the six genes encoding sigma factor (Sig) proteins that are utilized by the plastid-encoded RNA polymerase to transcribe specific sets of plastid genes. Here, we demonstrate that both Sig2 and Sig6 have partially redundant roles in not only plastid transcription, but also tetrapyrrole synthesis and retrograde signaling to control PhANG expression. Normal PhANG expression can be partly restored in the sig2 mutant by increasing heme synthesis. Furthermore, there is a genetic interaction between Sig and GUN (genomes uncoupled) genes to generate chloroplast-retrograde signals. These results demonstrate that defective plastid transcription is the source of at least two retrograde signals to the nucleus; one involving tetrapyrrole synthesis and the other involving the accumulation of an unknown plastid transcript. We also propose that the study of sig mutants (with defects in the expression of specific plastid genes) provides a new genetic system, which avoids the use of harsh inhibitors and their potential side effects, to monitor developmental retrograde signaling and to elucidate its mechanisms.
2012-09-18 | E-MTAB-4338 | biostudies-arrayexpress
Project description:Plants adapt to environmental changes by adjusting growth and defense, and the role of epigenetic modifications in this process is unclear. Sensing and adjusting to environmental changes are more important in certain tissues such as epidermis, vasculature, meristem, and reproductive tissues. These tissues possess sensory plastids that are specialized in environmental sensing. We show perturbation of four sensory plastid proteins MSH1, PPD3, CUE1, and SAL1 induce gene expression and DNA methylation changes targeted to networks associated to environmental sensing, with significant overlap with hda6-induced CHG hypermethylated genes at 12-hr daylength. At 16-hr daylength, hda6 loses CHG hypermethylation in gene body, and sensory plastid mutants have weaker phenotypes and DNA methylation- and gene expression- associated gene networks. We show daylength-responsive epistatic interaction between sensory plastid mutants with hda6. We also show that hda6 mutation confers daylength memory and, with msh1, enhanced tolerance to heat stress and biotic stress. These results suggest that HDA6 mediates programmed adjustments in plant phenotype triggered by sensory plastid-to-nucleus retrograde signaling in response to daylength and environmental cues.
2024-06-20 | GSE270059 | GEO
Project description:Plants adapt to environmental changes by adjusting growth and defense, and the role of epigenetic modifications in this process is unclear. Sensing and adjusting to environmental changes are more important in certain tissues such as epidermis, vasculature, meristem, and reproductive tissues. These tissues possess sensory plastids that are specialized in environmental sensing. We show perturbation of four sensory plastid proteins MSH1, PPD3, CUE1, and SAL1 induce gene expression and DNA methylation changes targeted to networks associated to environmental sensing, with significant overlap with hda6-induced CHG hypermethylated genes at 12-hr daylength. At 16-hr daylength, hda6 loses CHG hypermethylation in gene body, and sensory plastid mutants have weaker phenotypes and DNA methylation- and gene expression- associated gene networks. We show daylength-responsive epistatic interaction between sensory plastid mutants with hda6. We also show that hda6 mutation confers daylength memory and, with msh1, enhanced tolerance to heat stress and biotic stress. These results suggest that HDA6 mediates programmed adjustments in plant phenotype triggered by sensory plastid-to-nucleus retrograde signaling in response to daylength and environmental cues.
2024-06-20 | GSE270032 | GEO
Project description:Shortly after the release of singlet oxygen (1O2), drastic changes in nuclear gene expression occur in the conditional flu mutant of Arabidopsis that reveal a rapid transfer of signals from the plastid to the nucleus. In contrast to retrograde control of nuclear gene expression by plastid signals described earlier, the primary effect of 1O2 generation in the flu mutant is not the control of chloroplast biogenesis but the activation of a broad range of signaling pathways known to be involved in biotic and abiotic stress responses. This activity of a plastid-derived signal suggests a new function of the chloroplast, namely that of a sensor of environmental changes that activates a broad range of stress responses. Inactivation of the plastid protein EXECUTER1 attenuates the extent of 1O2-induced up-regulation of nuclear gene expression, but it does not fully eliminate these changes. A second related nuclear-encoded protein, dubbed EXECUTER2, has been identified that is also implicated with the signaling of 1O2-dependent nuclear gene expression changes. Like EXECUTER1, EXECUTER2 is confined to the plastid. Inactivation of both EXECUTER proteins in the ex1/ex2/flu triple mutant is sufficient to suppress the up-regulation of almost all 1O2-responsive genes. Retrograde control of 1O2-responsive genes requires the concerted action of both EXECUTER proteins within the plastid compartment. Keywords: biotic and abiotic stress response, nuclear gene expression, plastid-derived signal, Col-0 ecotype, continuous light and then dark-incubated plants
2008-02-14 | GSE10509 | GEO
Project description:Plastids emit signals that broadly affect cellular processes. Based on previous genetic analyses, we propose that plastid signaling regulates the downstream components of a light signaling network and that these interactions coordinate chloroplast biogenesis with both the light environment and development by regulating gene expression. We tested these ideas by analyzing light-regulated and plastid-regulated transcriptomes. We found that the plastid is a major regulator of light signaling, attenuating the expression of more than half of all light-regulated genes in our dataset and changing the nature of light regulation for a smaller fraction of these light-regulated genes. Our analyses provide evidence that light and plastid signaling are interactive processes and are consistent with these interactions serving as major drivers of chloroplast biogenesis and function.
2012-03-02 | GSE24517 | GEO
Project description:During vertebrate embryogenesis, hematopoietic stem and progenitor cell (HSPC) production through endothelial-to-hematopoietic transition requires suitable developmental signals, but how these signals are accurately regulated remains incompletely understood. Cytoplasmic polyadenylation, which is one of the posttranscriptional regulations, plays a crucial role in RNA metabolism. Here, we report that Cpeb1b-mediated cytoplasmic polyadenylation is important for HSPC specification by translational control of Hedgehog (Hh) signaling during zebrafish early development. Cpeb1b is highly expressed in notochord and its deficiency results in defective HSPC production. Mechanistically, Cpeb1b regulates hemogenic endothelium specification by the Hedgehog–Vegf–Notch axis. We demonstrate that the cytoplasmic polyadenylation element motif-dependent interaction between Cpeb1b and shha messenger RNA (mRNA) in the liquid-like condensates, which are induced by Pabpc1b phase separation, is required for cytoplasmic polyadenylation of shha mRNA. Intriguingly, the cytoplasmic polyadenylation regulates translation but not stability of shha mRNA, which further enhances the Shha protein level and Hh signal transduction. Taken together, our findings uncover the role of Cpeb1b-mediated cytoplasmic polyadenylation in HSPC development and provide insights into how posttranscriptional regulation can direct developmental signals with high fidelity to translate them into cell fate transition.
2023-02-06 | GSE207906 | GEO
Project description:Cytoplasmic UHRF1 restrains MHC-I-mediated anti-tumor immune response
| PRJNA1085386 | ENA