Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1066297 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28738907.fastq.gz | Fastqsanger.gz | |||
| SRR28738908.fastq.gz | Fastqsanger.gz | |||
| SRR28738909.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Plastids communicate with the nucleus through retrograde signaling pathways that coordinate nuclear and plastid gene expression to support plant development and environmental adaptation. However, how plastid regulatory factors are dynamically controlled to modulate these signals remains largely unknown. Here we identify a proteostasis mechanism that regulates plastid retrograde signaling through the ubiquitin–26S proteasome system. We show that the nuclear-encoded plastid RNA-editing factor MULTIPLE ORGANELLAR RNA EDITING FACTOR 2 (MORF2) is targeted for degradation by a Skp1–Cullin1–F-box (SCF) ubiquitin ligase assembled with the MORF2-INTERACTING F-BOX (MIF) protein. MIF physically associates with MORF2 and promotes its ubiquitylation and proteasome-dependent turnover. Genetic and physiological analyses reveal that this pathway balances early plant development. MIF overexpression suppresses seedling growth and disrupts chloroplast structure and function, whereas mif null mutants or MORF2 overaccumulation retard seed germination and reduce photosynthetic efficiency. Transcriptomic profiling and RNA-editing analyses further demonstrate that MIF-dependent MORF2 turnover modulates plastid RNA editing and retrograde signaling pathways. Together, our results uncover a previously unrecognized cytoplasmic regulatory layer that links ubiquitin-mediated proteostasis to plastid RNA editing and retrograde signaling. This mechanism enables plants to coordinate seed germination and chloroplast development during early seedling establishment.
2026-04-16 | GSE325043 | 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:Retrograde signals emanate from the DNA-containing cell organelles (plastids and mitochondria) and control the expression of a large number of nuclear genes in response to environmental and developmental cues. Previous studies on retrograde signaling mainly analyzed the regulation of nuclear gene expression at the transcriptional level. To determine the contribution of post-transcriptional regulation to plastid retrograde signaling, we combined label-free proteomics with transcriptomic analysis of Arabidopsis thaliana seedlings and studied the response in whichto interference with the plastid gene expression (PGE) pathway of retrograde signaling.
2019-06-05 | PXD011759 | Pride
Project description:The CHLD and CHLM genes encode proteins involved in tetrapyrrole biosynthesis pathway. It was proposed that intermediates like magnesium protoporphyrin might play a role in retrograde plastid-to-nucleus signaling. In the present work we provide evidence that altered enzymes activity of the tetrapyrrole biosynthesis pathway are causing changes in gene expression of over 200 nuclear genes.
2013-04-01 | GSE41884 | GEO
Project description:Photoacclimation of unicellular algae allows for reversible changes in the number and/or effective absorption cross section of photosynthetic units on time scales of hours to days in response to changes in irradiance. The process involves an enigmatic signaling pathway from the plastid to the nucleus.Our results reveal, for the first time, a fundamental pathway of retrograde signal transduction in a eukaryotic photosynthetic alga.
2019-11-01 | GSE133301 | GEO
Project description:The CHLD and CHLM genes encode proteins involved in tetrapyrrole biosynthesis pathway. It was proposed that intermediates like magnesium protoporphyrin might play a role in retrograde plastid-to-nucleus signaling. In the present work we provide evidence that altered enzymes activity of the tetrapyrrole biosynthesis pathway are causing changes in gene expression of over 200 nuclear genes. The expression of the CHLD gene was diminished after inducing the RNAi system by spraying dexamethasone. The expression of the CHLM gene was increased after inducing the overexpressor system by spraying ß-estradiol.
2013-04-01 | E-GEOD-41884 | biostudies-arrayexpress
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:Signals originating within plastids modulate organelle differentiation by transcriptionally regulating nuclear-encoded genes. These retrograde signals are also integral regulators of plant development, including leaf morphology. The clb5 mutant displays severe leaf morphology defects due to Apocarotenoid Signal 1 (ACS1) accumulation in the developmentally arrested plastid. Transcriptomic analysis of clb5 validates ACS1 as a true retrograde signal impacting expression of hundreds of nuclear genes, including suppression of most genes encoding plastid ribosomal proteins.
2021-06-02 | GSE152252 | GEO
Project description:In the present study we investigated at the system level the proteome obtained from seedlings of Arabidopsis thaliana wild-type Col-0 and gun1-101 and gun1-102 mutant plants treated or not with lincomycin (Lin), a chloroplast translation inhibitor widely used to inhibit chloroplast biogenesis and to trigger the plastid-to-nucleus retrograde communication. Specifically, we attempted a description of cellular responses to Lincomycin in wild-type genetic background and in retrograde signaling-defective mutant gun1. Hypotheses and key players emerged by our holistic view were validated at the experimental level. Our findings suggest that, in the presence of Lincomycin, cell responses rely on the plastid compartment in a GUN1-dependent manner, while in the gun1-mutant background, the activity of extra-plastid compartments prevails. Moreover, results obtained by complementary approaches depict the Oxygen Evolving Complex subunit PsbO as an atypical Photosynthesis-related protein by accumulating in non-photosynthetic plastids and having a superhub role in modulating chloroplast dismantling upon impairment of plastid functions.
2025-07-14 | PXD051970 | Pride