Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26798402_1.fastq.gz | Fastqsanger.gz | |||
| SRR26798402_2.fastq.gz | Fastqsanger.gz | |||
| SRR26798403_1.fastq.gz | Fastqsanger.gz | |||
| SRR26798403_2.fastq.gz | Fastqsanger.gz | |||
| SRR26798404_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The regulator for chloroplast biogenesis (rcb) mutant was identified as a mutant defective in phytochrome-mediated chloroplast biogenesis. The rcb mutant has long hypocotyl and albino phenotypes. RCB initiates chloroplast biogenesis in the nucleus by promoting the degradation of the master repressors for chloroplast biogenesis, the PIFs (Phytochrome Interacting Factors). To understand how RCB regulates the expression of PIF-regulated genes, we performed genome-wide expression analysis of RCB-dependent genes using a rcb-10 null allele.
2019-06-20 | GSE122351 | GEO
Project description:For establishing the photosynthetic apparatus plant cells must orchestrate the expression of genes encoded in both nucleus and chloroplast. Therefore a crosstalk between the two compartments is necessary. We employed a trivalent gene expression profiling approach in order to elucidate the changes in gene expression that occur during the early steps of light-induced chloroplast biogenesis.
2017-12-01 | GSE88988 | GEO
Project description:The transition of chloroplast function from biogenesis to degeneration upon leaf senescence is critical for a plant’s fitness, as nutrient relocation from leaves to reproductive organs is achieved through this process. The optimal timing of transition should be regulated by tight coordination between chloroplast and nucleus, but the underlying mechanisms remain elusive. Here, we describe the regulatory mechanism of this transition. Chloroplast-Related LONG NONCODING RNA 1 (CHLORELLA1) is highly co-expressed with genes coding for chloroplast functionality during leaf development. Leaves of chlorella exhibit precocious senescence symptoms and a decline in the expression of chloroplast-associated genes, indicating that CHLORELLA1 plays a role in maintaining chloroplast function. Mechanistically, nucleus-encoded CHLORELLA1 transcripts are translocated into the chloroplast and contribute to the assembly of the plastid-encoded RNA polymerase (PEP) complex. At aged leaves, decreased expression of CHLORELLA1 attenuates PEP complex assembly and transcription of photosynthesis genes, possibly triggering leaf senescence. Moreover, CHLORELLA1 is directly activated by GLK1/2, master regulators of chloroplast maintenance. Our study unravels a new layer of the regulation via chloroplast-targeted lncRNA as an anterograde signal in timely decision of leaf senescence.
2025-08-16 | GSE255867 | GEO
Project description:Chloroplast biogenesis, essential for photosynthesis, depends on the import of nuclear-encoded proteins through TOC (Translocon at the Outer Envelope of Chloroplasts) complexes. Despite its significance, the mechanisms regulating this process remain largely elusive. We identify CTR1 (Constitutive Triple Response 1), a RAF-like kinase known for its role in ethylene signaling, as a key regulator of Toc33, a core TOC component. CTR1 phosphorylates and stabilizes Toc33 by preventing its ubiquitination and degradation independently of the ethylene signaling pathway. Disruption of Toc33 phosphorylation impairs its stability and photosynthetic protein import, which consequently affects chloroplast structural integrity and biogenesis. Our findings underscore the essential role of CTR1-mediated TOC phosphorylation in chloroplast biogenesis, revealing an unexpected link between an ethylene signaling component and organelle development.
2026-01-13 | PXD059681 | JPOST Repository
Project description:Chloroplast biogenesis represents a crucial step in seedling development, and is essential for the transition to autotrophic growth in plants. This light-controlled process relies on the transcription of nuclear and plastid genomes that drives the effective assembly and regulation of the photosynthetic machinery. Here we reveal a novel regulation level for this process by showing the involvement of chromatin remodelling in the coordination of nuclear and plastid gene expression for proper chloroplast biogenesis and function. The two Arabidopsis homologs of the yeast EPL1 proteins, core components of the NuA4 histone acetyl-transferase complex, are essential for the correct assembly and performance of chloroplasts. EPL1 proteins are necessary for the coordinated expression of nuclear genes encoding most of the components of chloroplast transcriptional machinery, specifically promoting H4K5Ac deposition in these loci. These data unveil a key participation of epigenetic regulatory mechanisms in the coordinated expression of the nuclear and plastid genomes.
2022-07-26 | GSE180614 | GEO
Project description:Photosynthetic capacity is the result of chloroplast biogenesis, but whether photosynthesis itself is required for chloroplast biogenesis has not been investigated. In this study we use 680nm red light to overexcite Photosystem II to disrupt photosynthesis in two conditional mutants (var2 and abc1k1) and demonstrate that this arrests chloroplast biogenesis. During their biogenesis, chloroplasts import the majority of proteins associated with photosynthesis and some are transported further across the thylakoid membrane by the evolutionarily conserved SEC (Secretory) and TAT (Twin Arginine Translocation) pathways, energized by ATP and the proton gradient, respectively. Most luminal thylakoid proteins are synthesized in the cytoplasm with bi-partite, cleavable targeting sequences (first for the chloroplast envelope, second for the thylakoid membrane). Two-step cleavage of these peptides is essential for chloroplast biogenesis. Linked to the photosynthetic defect in var2 and abc1k1 under red light, six incompletely cleaved essential proteins at the thylakoid lumen side of Photosystems I and II accumulated to high levels in the mutants. In summary, the results show that the processing of a specific module of photosynthesis-associated proteins and concomitantly progression of chloroplast biogenesis depend on photosynthesis at the earliest stages of seedling development.
2024-12-13 | PXD050814 | Pride
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:The studies were performed using Arabidopsis thaliana: wt Col (N6000) and SALK_116579 (geralt, GERMINATION ALBINO TRANSIENT) mutant. At2g47590 gene encodes GERALT protein. This protein was not characterized so far. It is localized in chloroplasts, influences chloroplast biogenesis and chlorophyll biosynthesis and its role decreases with the plant age.
2025-09-18 | GSE271033 | 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:Upon exposure to light, plant cells quickly acquire photosynthetic competence by converting pale etioplasts into green chloroplasts. This developmental transition involves the de novo biogenesis of the thylakoid system, and requires reprogramming of metabolism and gene expression. Etioplast-to-chloroplast differentiation involves massive changes in plastid ultrastructure, but how these changes are connected to specific changes in physiology, metabolism and expression of the plastid and nuclear genomes is poorly understood. Here a new experimental system in the dicotyledonous model plant tobacco (Nicotiana tabacum) that allows us to study the leaf de-etiolation process at the systems level. We have determined the accumulation kinetics of photosynthetic complexes, pigments, lipids and soluble metabolites, and recorded the dynamic changes in plastid ultrastructure and in the nuclear and plastid transcriptomes. Our data describe the greening process at high temporal resolution, resolve distinct genetic and metabolic phases during de-etiolation, and reveal numerous candidate genes that may be involved in light-induced chloroplast development and thylakoid biogenesis.
2019-03-09 | GSE128049 | GEO