Rice Plastid Assembly
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ABSTRACT:
PROVIDER: PRJEB19309 | ENA |
REPOSITORIES: ENA
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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: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: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
Project description:Porcine 60K BeadChip genotyping arrays (Illumina) are increasingly being applied in pig genomics to validate SNPs identified by re-sequencing or assembly-versus-assembly method. Here we report that more than 98% SNPs identified from the porcine 60K BeadChip genotyping array (Illumina) were consistent with the SNPs identified from the assembly-based method. This result demonstrates that whole-genome de novo assembly is a reliable approach to deriving accurate maps of SNPs.
2016-07-05 | GSE83910 | GEO
Project description:We investigated changes in gene expression in rice plants exposed to RDV to gain some insight into the fundamental physiological and biochemical changes that are induced by viral infection, in the hope of finding clues that might help to control the viral disease. An analysis, using microarrays, of gene expression in rice plants infected with Rice dwarf virus revealed significant decreases in levels of expression of genes that are involved in the formation of cell walls, reflecting the stunted growth of diseased plants. The expression of plastid-related genes was also suppressed, as anticipated from the white chlorotic appearance of infected leaves. By contrast, the expression of defense- and stress-related genes was enhanced after viral infection. Keywords: disease state analysis
2007-03-14 | GSE5286 | GEO
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:In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample. We collected seedlings of three rice cultivars subjected to control (kept in water), desiccation (transferred on folds of tissue paper) and salinity (transferred to beaker containing 200 mM NaCl solution) treatments. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to Japonica reference genome using Tophat software. Cufflinks was used for reference-based assembly and differential gene expression was studied using cuffdiff software. The differentially expressed genes during various abiotic stress conditions were identified.
2015-12-31 | E-GEOD-60287 | biostudies-arrayexpress
Project description:Biogenesis of plastid ribosomes is facilitated by auxiliary factors which process and modify ribosomal RNAs (rRNA) or are involved in ribosome assembly. In comparison to their bacterial and mitochondrial counterparts, the biogenesis of plastid ribosomes is less well understood and few auxiliary factors have been described so far. In this study, we report the functional characterization of CGL20 (CONSERVED ONLY IN THE GREEN LINEAGE20) in Arabidopsis thaliana (AtCGL20) a small, proline-rich protein which is targeted to mitochondria and chloroplasts. In Arabidopsis, CGL20 is encoded by segmentally duplicated genes of high similarity (AtCGL20A and AtCGL20B), and inactivation of both in the atcgl20ab mutant leads to a visible virescent phenotype, and growth arrest at low temperature. The chloroplast proteome, thylakoid complex abundance and pigment composition are significantly affected in atcgl20ab mutants, resulting in a combined proton gradient regulation (pgr) and chlororespiratory reduction (crr) phenotype. Loss of AtCGL20 alters plastid rRNA ratios, perturbs the formation of a hidden break in 23S rRNA and causes abnormal accumulation of 50S ribosomal subunits in the high-molecular-mass fraction of chloroplast stromal extracts. Moreover, AtCGL20A-eGFP fusion proteins comigrate with 50S ribosomal subunits in sucrose density gradients, even after RNase treatment of stromal extracts. Therefore, we propose that AtCGL20 participates in late stages of the biogenesis of 50S ribosomal subunits in plastids – a role which presumably evolved in the green lineage as a consequence of structural divergence of plastid ribosomes.
2020-03-16 | GSE134415 | GEO
Project description:In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.
2015-12-31 | GSE60287 | GEO
Project description:Zebra leaf is a special phenotype of variegated leaf in monocotyledonous plant. Here, we characterized a mutant zebra10 (zb10) in maize, which displays defective chloroplast development in white section of leaves at the seedling stage and pale-white kernels. Map based cloning revealed that ZB10 encodes plastid terminal oxidase (ZmPTOX) which is localized in chloroplasts. ZmPTOX protein is highest expressed in leaves and also highly expressed in endosperm. Expression and metabolism analysis showed that function-loss of PTOX interferes with carotenoid synthesis and chloroplast biogenesis by affecting phytoene desaturase activity. In-depth observation showed that crossband formation of zebra leaf could be related to photoperiodic rhythm, and expression of alternative oxidases 2 (ZmAOX2) could be regulated by circadian rhythm and light intensity in zb10. Further studies revealed ectopic expression of ZmAOX2 protein can function in chloroplasts and rescue the defective phenotype of im. We conclude that ZmPTOX plays an vital role in carotenoid synthesis and plastid biogenesis in maize. ZmAOX2 involve in formation of zebra crossbands with diurnal rhythm and green-revertible process of leaves in zb10.
2024-03-01 | GSE259213 | GEO