Similar Datasets
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:Plastid and cytoplasmic origins of 1O2-mediated gene responses
| PRJNA847965 | ENA
Project description:Purpose: In plants, chloroplasts not only fix energy through photosynthesis, but they synthesize numerous metabolites which can act as important growth regulators by impacting nuclear gene expression. Upon developmental and external stimuli, signaling between the nucleus and chloroplasts is essential for maintaining plant cellular homeostasis. In this study, we applied an Illumina HiSeq 2500 platform to investigate the transcriptome changes of 2 Arabidopsis thaliana mutant lines, a T-DNA knock out muant allele of DIFFERENTIAL AND GREENING-LIKE (DAL), termed dal-2, and a dexmathasone (Dex)-induced overexpression line of DAL-INTERACTING F-BOX (termed DIF-OX2). Methods: Total RNA was isolated from 12-d-old Col-0 (wild type control) and DIF-OX2 seedlings grown on Gamborg’s B-5 (GM) medium containing 1% sucrose (GM-Suc), with or without 10 μM Dex, and 20-d-old dal-2 plants also grown on GM-Suc medium, and deep sequenced as 100-mers using the Illumina HiSeq 2500 platform (DNA Sequencing Facility, University of Wisconsin Biotechnology Center). Raw image files for each library were converted to FASTQ files by the standard Illumina pipeline and processed for quality control by Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) to remove adapter and low quality sequences (phred=33, minimum length=36). Processed sequences were aligned to the A. thaliana Col-0 genomic sequence (from The Arabidopsis Information Resource (TAIR) version 10 at www.arabidopsis.org) via TOPHAT2 to identify accepted hits, which were then used to generate an absolute expression level (counts) of each locus by HTSeq (http://www-huber.embl.de/users/anders/HTSeq/). The resulting counts per locus were normalized to counts per million reads (CPM) among all 10 libraries and used to generate the list of differentially expressed (DE) genes between treatments or genotypes by edgeR (FDR < 5% or ABS[log2FoldChange (FC)] ≥ 1). Results: In total, 6,743 differentially expressed (DE) RNAs were identified using edgeR (FDR < 5%) in either dal-2 or DIF-OX2 (+Dex) seedlings, as compared to Dex-untreated or Dex-treated wild-type seedlings, respectively. Among these DE genes, the expression levels of 2,606 loci in dal-2 changed at a level greater than or equal to 2 fold compared to those in the Dex-untreated wild type control, but showed a strong positive correlation with their expression levels in DIF-OX2 (+Dex) (Spearman’s rank correlation rho = 0.72, p < 2.2e-16; Figure 5B-C). Conclusions: The similar transcriptome changes in both DIF-OX2 (+Dex) and dal-2 plants suggests that the DIF and DAL proteins are involved in the same pathway, which controls a retrograde signaling from chloroplasts to the nucleus, based on further biochemical analysis, cellular localization, and transcriptome comparisons with other public available microarray data from mutants impacting chloroplast retrograde signaling.
2018-12-31 | GSE84607 | GEO
Project description:cea10-02_light - photooxidative stress - To characterize the metabolic pathways implicated in oxidative stress responses and in acclimation mechanisms in the ch1 mutant - The extracts are carried out starting from sheets of Arabidopis thaliana having pushed on compost in controlled conditions (light: 250 µmol.m-2.s-1, temperature: 22°C day 18°C night, moisture: 55%, photoperiod: 8:00 jour/16h night) during 4 and 8 weeks for respectively the Col0 genotype and the mutant ch1. The acclimatization of the plants is done during 48 H under an average luminous intensity (450 µmol.m-2.s-1, photoperiod 8:00), whereas the stress requires a strong luminous intensity (900 µmol.m-2.s-1, photoperiod 8:00) and low temperature (10°C day, 14°C night) also during 48 hours.
2011-12-09 | GSE34247 | GEO
Project description:Canonical retrograde signalling comprises information transmission from organelles to the nucleus and in particular controls gene expression for organellar proteins. The need to re-assess this paradigm was suggested by discrepancies between de novo protein synthesis and transcript abundance in response to excess light. Here we uncover major components of a translation-dependent retrograde signalling pathway that first impacts translation and then transcription. The response realization depends on the kinases Mitogen-activated protein kinase 6 (MPK6) and Sucrose non-fermenting 1-related kinase (SnRK1) subunit, AKIN10. Global ribosome foot-printing revealed differential ribosome association of 951 transcripts within 10 min after transfer from low to high light. Despite predominant translational repression, 15 % of transcripts were increased in translation and enriched for chloroplast-localized photosynthetic proteins. About one third of these transcripts, including Stress associated proteins (SAP) 2 and 3, share regulatory motifs in their 5`-UTR that act as binding sites for glyceraldehyde-3-phosphate dehydrogenase (GAPC) and light responsive RNA binding proteins (RBPs). SAP2 and 3 are both translationally regulated and interact with the calcium sensor Calmodulin-like 49 (CML49), which promotes relocation to the nucleus inducing a translation-dependent nuclear stress response. Thus, translation-dependent retrograde signalling bifurcates to directly regulate a translational circuit of chloroplast proteins and simultaneously initiate a nuclear circuit synchronizing retrograde and anterograde response pathways, serving as a rapid mechanism for functional acclimation of the chloroplast CML49 KO and SAP3 KO 0' and 60' of low light (8µE) to high light (800µE) transfer in comparison to Col-0
2022-08-25 | GSE211805 | GEO
Project description:Protein acetylation is a key recurring co- and posttranslational modification. How different types of acetylation respond to the same environmental stress is unknown. A member of the newly discovered family of plastid acetyltransferases (GNAT2), which is featuring both lysine- and N-terminal acetyltransferase activity, was used in this study to obtain a holistic multi-omics acetylation-dependent view of the acclimation of plants to short-term light changes. Characterization of the N-terminal acetylome reveals that both its yield and coverage remain unchanged between WT and gnat2 knockout mutant lines when they are subjected for two hours to high-light or dark conditions. Similarly, no differences in their transcriptome or adenylate energy charge oscillations were observed under the tested light conditions between the genotypes. However, the GNAT2-associated lysine acetylome turned out to be sensitive to light changes. Our data suggests that the lysine acetylome marks on proteins change more rapidly allowing the acclimation to the environmental condition, while N-terminal acetylation changes are associated to long term responses. Taken together, our data reveals unique strategies of plant acclimation to the different treatments involving lysine but not N-terminal acetylation activities for the responses to environmental changes.
2024-08-19 | PXD040517 | JPOST Repository
Project description:Acetylation of amino groups is an important and recurrent protein modification in all eukaryotes. In plants, both lysine and N-terminal acetylation have additional important roles in protein regulation in chloroplasts. However, it is yet unclear how acetylation patterns respond to environmental stresses, and whether lysine or N-terminal modifications similarly contribute to the associated perturbations. A new family of plastid acetyltransferase, called GNATs, was recently discovered, which consists of closely related enzymes featuring both lysine- and N-terminal acetyltransferase activities often on the same polypeptide targets. Here, we take advantage of this unique characteristic of Arabidopsis GNAT2 to obtain a holistic multi-omics acetylation-dependent view during the acclimation of plants to short term changes in light. No substantial difference in transcriptome or adenylate energy charge oscillations were observed between WT and gnat2 knockout mutant lines when they were submitted for two hours to high-light or dark growth conditions. A detailed characterization of the N-terminal acetylome reveals that both its yield and coverage remain unchanged upon different light conditions in both genotypes. Unlike the N-terminal acetylome, the GNAT2-associated lysine acetylome is sensitive to the different light conditions used. In addition, a strong reduction in both types of acetylations on several plastid proteins was observed upon GNAT2 inactivation under all light conditions. Our data suggests that the lysine acetylome marks on proteins more rapidly fluctuate following acclimation to the environmental condition, while N-terminal acetylation changes are associated to longer term responses, like those promoted in the gnat2 background. Taken together, our data revealed unique strategies of plant acclimation to the different applied treatments involving specific PTMs and emphasizes distinct timescale responses of plastid lysine and N-terminal acetylomes to environmental changes.
2024-08-22 | PXD040235 | Pride
Project description:cea10-02_light - photooxidative stress - To characterize the metabolic pathways implicated in oxidative stress responses and in acclimation mechanisms in the ch1 mutant - The extracts are carried out starting from sheets of Arabidopis thaliana having pushed on compost in controlled conditions (light: 250 µmol.m-2.s-1, temperature: 22°C day 18°C night, moisture: 55%, photoperiod: 8:00 jour/16h night) during 4 and 8 weeks for respectively the Col0 genotype and the mutant ch1. The acclimatization of the plants is done during 48 H under an average luminous intensity (450 µmol.m-2.s-1, photoperiod 8:00), whereas the stress requires a strong luminous intensity (900 µmol.m-2.s-1, photoperiod 8:00) and low temperature (10°C day, 14°C night) also during 48 hours. 24 dye-swap - genotype comparison, treated vs untreated comparison
2011-12-09 | E-GEOD-34247 | biostudies-arrayexpress
Project description:Arabidopsis is a shade avioding plant. Under simulated shade light with reduced red-to-far red (R:FR) ratio around 0.7, hypocotyls of Arabidopsis seedlings elongate, which is one of the typical shade avoidance responses.We discovered that when the R:FR ratio further decreases to around 0.1 (strong shade), the shade-induced elongation of hypocotyl is abolished and phytochrome A (phyA) mediates this response.In this study, we aim to examine the difference between shade and strong shade treatment and uncover the role of phyA in regulating the shade avoidance responses.
2019-12-21 | GSE55899 | 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. Four biological replicates were grown separately under the same conditions. Arabidopsis seedlings were grown in the presence (+Lin) or absence (-Lin) of lincomycin in 0.5 µmol m-2 s-1 blue plus red (BR) light for 6 days. After 6 days of growth in 0.5 µmol m-2 s-1 of BR light, seedlings were transferred to 60 µmol m-2 s-1 BR light. 50-100 seedlings were collected before (0 h) and 0.5 h, 1 h, 4 h, and 24 h after the 0.5 to 60 µmol m-2 s-1 BR-fluence-rate shift for RNA extraction and hybridization on Affymetrix microarrays.
2012-03-02 | E-GEOD-24517 | biostudies-arrayexpress