Transcriptome response study of arabidopsis wild type (Col6-3), gun1-9 mutant and MORF2 overexpression lines to norflurazon treatment in retrograde signaling
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PROVIDER: PRJNA432917 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of transcriptome response of norflurazon treated or untreated 5-day old whole seedlings with genotypes: Col6-3 (wild type), gun1-9 and MORF2 overexpression lines. GUN1 and MORF2 are involved in chloroplast-to-nucleus retrograde signaling. Results provide insight into the nuclear genes expression profile under control of GUN1 retrograde pathways and the regulation similarity between gun1-9 and MORF2 overexpression lines.
2019-05-02 | GSE110125 | GEO
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. GENOMES UNCOUPLED1 (GUN1) participating in multiple retrograde signaling pathways that collectively regulate the nuclear transcriptome. We used microarrays to further investigate the regulation of nuclear gene expression by PGE retrograde signals mediated by GUN1.
2019-06-05 | GSE122667 | GEO
Project description:Distinct retrograde signaling pathways have been identified for several cellular organelles. These pathways are important to maintain the function of these organelles in response to organelle-specific stress. Using Caenorhabditis elegans, we show for the first time that such a retrograde signaling also exists for peroxisomes. Analysis of the C. elegans transcriptome revealed that peroxisomal import stress caused by the knock-down of the peroxisomal matrix protein import receptor prx-5/PEX5 induces the compensatory up-regulation of genes involved in defense response and lipid metabolic processes, especially peroxisomal beta oxidation. We, therefore, propose that the peroxisomal retrograde signaling participates in the maintenance of peroxisomal function in response to peroxisomal import stress.
2020-12-19 | GSE156318 | GEO
Project description:Peroxisomal retrograde signaling in C. elegans
| PRJNA657442 | ENA
Project description:Transcriptome profile of Arabidopsis wild-type (Col-0) and mutants of the plastidic retrograde signalling pathway (gun1-1,gun4-1, gun5-1) germinated in the presence of 5µM Norflurazon for 5d in continious light (100µE). Analysis was performed on biological triplicates of total leaf RNA using paired-end Illumina Hi/MiSeq technology.
2019-10-18 | GSE104868 | GEO
Project description:Chloroplast-nuclear retrograde signaling is viewed as a mechanism for inter-organelle communication. Here we show the SAL1-PAP (3′-phosphoadenosine 5′- phosphate) retrograde pathway functions more broadly in guard cells, interacting with abscisic acid (ABA) signaling at least in part via exoribonucleases. Unexpectedly, PAP bypasses the canonical signaling components ABA Insensitive 1 (ABI1) and Open Stomata 1 (OST1) by priming an alternative pathway that restores ABA-responsive gene expression, ROS bursts, ion channel function and stomatal closure in ost1-2. This alternative pathway up-regulates lowly expressed Calcium Dependent Protein Kinases (CDPKs) which have the capacity to activate the key slow anion channel SLAC1 in response to ABA-mediated and ost1-2 independent calcium release. The role of PAP in priming an alternative pathway to bypass components previously considered essential for stomatal closure demonstrates how a chloroplast signal can have broader roles as a secondary messenger to directly intersect with and tune hormone signaling.
2017-03-21 | GSE84997 | 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:While retrograde signalling pathways have been identified for several organelles, the existence of such a pathway for peroxisomes remains elusive. We identified a peroxisomal retrograde signalling (PRS) in C. elegans, which is activated in response to peroxisomal import stress. We analyzed the PRS using a proteomic approach.
2021-01-11 | PXD014720 | Pride
Project description:GUN1 integrates retrograde signals in the chloroplast but the underlying mechanism is elusive. FUG1, a chloroplast translation initiation factor, and GUN1 are co-expressed at the transcript level, and FUG1 co-immunoprecipitates with GUN1. We used mutants of GUN1 (gun1-103) and FUG1 (fug1-3) to analyse their functional relationship at the physiological and systems-wide level, the latter including transcriptome and proteome analyses. Absence of GUN1 aggravates the effects of decreased FUG1 levels on chloroplast protein translation, resulting in transient additive phenotypes with respect to photosynthesis, leaf coloration, growth and cold acclimation. Variegation of the var2 mutant is enhanced by gun1-103 in terms of increasing the fraction of white sectors, in contrast to fug1-3 that acts as suppressor. The transcriptomes of fug1-3 and gun1-103 are very similar, but absence of GUN1 alone has almost no effects on protein levels, whereas chloroplast protein accumulation is markedly decreased in fug1-3. In gun1 fug1 double mutants, effects on transcriptomes and particularly proteomes are enhanced. Our results show that GUN1 function becomes critical when chloroplast proteostasis is perturbed by decreased translation (fug1) or degradation (var2) of chloroplast proteins. The functions of FUG1 and GUN1 appear to be related, corroborating the view that GUN1 operates in chloroplast proteostasis.
2019-04-23 | GSE123583 | GEO
Project description:The mitochondrial and nuclear genomes contribute to mitochondrial function, and when mitochondrial function is compromised, mitochondrial retrograde signaling alters nuclear gene expression. We performed gene expression profiling of engineered cells that had mitochondria containing a disease-associated mutation that causes mitochondrial dysfunction. By generating networks of transcription factors that targeted these genes, the authors revealed putative mitochondrial retrograde signaling pathways. One such pathway involved retinoic acid receptor alpha (RXRA), the mRNA for which was reduced in the mutant cells. Network analysis and experiments in cells suggested that mitochondrial dysfunction caused by the mutation initiated a positive feedback loop that aggravated mitochondrial dysfunction: Reduced RXRA abundance further compromised expression of genes encoding products involved in mitochondrial function and translation. This gene-transcription factor mapping-network approach may reveal targets for therapeutic intervention of diseases associated with mitochondrial dysfunction. To investigate retrograde signaling pathways induced by the mitochondrial dysfunction caused by the mt3243 mutation, we generated the three types of cybrid cells using a mitochondria-mediated transformation method. Cells lacking mtDNA (rho0) were fused with mtDNAs with the mt3243 mutation isolated from platelets of a diabetic patient with sensorineural hearing loss. We then isolated three types of cybrid cells: W cells had wild-type mtDNA (3243A homoplasmy), H cells had both the mutant and wild-type mtDNA (3243A/G heteroplasmy) with 70% of the mtDNA containing 3243G, and M cells with only mutant mtDNA (3243G homoplasmy). Gene expression profiles of cybrid cells were generated using Illumina HumanHT-12-v3-BeadChip (Illumina, San Diego, CA), which includes 49,896 probes corresponding to 25,202 annotated genes. According to the Illumina protocols, three biological triplicates of each type of cybrid cells were analyzed. Total RNA (500ng) was isolated from cybrid cells using RNeasy Mini Kit (Qiagen, GmbH, Germany). RNA integrity number (RIN) was in the range of RIN = 9.2 and 10 when measured with an Agilent 2100 Bioanalyzer. RNA was reversely transcribed and amplified using IlluminaTotalPrep RNA amplification kit (Ambion, Austin, TX). In vitro transcription was then carried out to prepare cRNA. The cRNAs were hybridized to the array and then labeled with Cy3-streptavidin (Amersham Bioscience, Little Chalfont, UK). The fluorescent signal on the array was measured with a BeadStation 500 System (Illumina, San Diego, CA).
2013-02-12 | E-GEOD-27545 | biostudies-arrayexpress