Nuclear gene expression in response to chloroplast division inhibition
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE20228 | GEO | 2010/04/20
SECONDARY ACCESSION(S): PRJNA124163
REPOSITORIES: GEO
Similar Datasets
Project description:The aim of this investigation is to analyse the effect on nuclear gene expression of inhibition of chloroplast division. Transgenic Arabidopsis lines (Ler) were generated that contained a chemically inducible promoter (XVE) upstream of AtMinD1. AtMinD1 encodes a product involved in chloroplast division; overexpression of AtMinD1 leads to chloroplast division inhibition. 6 samples were used in this experiment. Three treatments were performed: Treatment 1: Empty vector control seedlings (transformed with PER-10 only) were sown onto lehle, sprayed at 13 days old with 2uM 17-B-estradiol (inducer) and harvested 24 hours later. Treatment 2: Seeds were sown on lehle containing inducer and sprayed every 24 hours with 2uM inducer until harvested at 14 days old. Treatment 3: Seeds were sown on lehle plates, sprayed at 13 days old with 2uM inducer and harvested 24 hours later. For all three treatments, seedlings were grown in constant light conditions, and tissue was harvested from 14-day-old seedlings (4 rosette leaves) and snap frozen in liquid nitrogen before RNA preparation.
2010-04-28 | E-GEOD-20228 | biostudies-arrayexpress
Project description:Deep sequencing provided evidence that a novel subset of small RNAs were derived from the chloroplast genome of Chinese cabbage (Brassica rapa) and Arabidopsis (Ler). The chloroplast small RNAs (csRNAs) include those derived from mRNA, rRNA, tRNA and intergenic RNA. The rRNA-derived csRNA were preferentially located at the 3M-CM-"M-BM-^@M-BM-^Y-ends of the rRNAs, while the tRNA-derived csRNAs were mainly located at 5M-CM-"M-BM-^@M-BM-^Y-termini of the tRNAs. After heat treatment, the abundance of csRNAs decreased in chinese cabbage seedlings, except those of 24 nt in length. The novel heat-responsive csRNAs and their locations in the chloroplast were verified by Northern blotting. The regulation of some csRNAs to the putative target genes were identified by real-time PCR. Our results indicated that high temperature regulated the production of some csRNAs, which may have potential roles in transcriptional or post-transcriptional regulation, and affected putative target genes expression in chloroplast. Examination of two replicates of heat treated (HT) and control (MT) Chinese cabbage sample respectively, and one Arabidopsis (Ler) RNA sample.
2012-03-30 | E-GEOD-28281 | biostudies-arrayexpress
Project description:Deep sequencing provided evidence that a novel subset of small RNAs were derived from the chloroplast genome of Chinese cabbage (Brassica rapa) and Arabidopsis (Ler). The chloroplast small RNAs (csRNAs) include those derived from mRNA, rRNA, tRNA and intergenic RNA. The rRNA-derived csRNA were preferentially located at the 3â-ends of the rRNAs, while the tRNA-derived csRNAs were mainly located at 5â-termini of the tRNAs. After heat treatment, the abundance of csRNAs decreased in chinese cabbage seedlings, except those of 24 nt in length. The novel heat-responsive csRNAs and their locations in the chloroplast were verified by Northern blotting. The regulation of some csRNAs to the putative target genes were identified by real-time PCR. Our results indicated that high temperature regulated the production of some csRNAs, which may have potential roles in transcriptional or post-transcriptional regulation, and affected putative target genes expression in chloroplast.
2012-03-31 | GSE28281 | GEO
Project description:The experiment was conducted to examine the influence of non-chloroplast genomes rearangements on chloroplast transcription in cucumber
2011-09-10 | E-MEXP-3233 | biostudies-arrayexpress
Project description:The paired-end Illumina sequencing of total genomic DNA from Arabidopsis were performed to detect unique breakpoints consistent with rearrangements of chloroplast DNA.
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Project description:A transcription factor CYTOKININ-RESPONSIVE GATA FACTOR 1 (CGA1) regulates chloroplast development in rice (Oryza sativa) through modifying the expression of important nuclear expressed, chloroplast localized genes. A transcriptome analysis was done in wild type plants and transgenic rice over-expressing this OsCGA1 to identify the set of genes with altered expression.
2012-11-06 | GSE35630 | GEO
Project description:Autophagy is a conserved catabolic process that plays an essential role under nutrient starvation condition and influences different developmental processes. We observed that seedlings of autophagy mutants (atg2, atg5, atg7, and atg9) germinated in the dark showed delayed chloroplast development following illumination. The delayed chloroplast development was characterized by a decrease in photosynthetic and chlorophyll biosynthetic proteins, lower chlorophyll content, reduced chloroplast size, and increased levels of proteins involved in lipid biosynthesis. Confirming the biological impact of these differences, photosynthetic performance was impaired in autophagy mutants 12h post illumination. We observed that while gene expression for photosynthetic machinery during de-etiolation was largely unaffected in atg mutants, several genes involved in photosystem assembly were transcriptionally downregulated. We also investigated if the delayed chloroplast development could be explained by lower lipid import to the chloroplast or lower triglyceride (TAG) turnover. We observed that the limitations in the chloroplast lipid import imposed by trigalactosyldiacylglycerol1 are unlikely to explain the delay in chloroplast development. However, we found that lower TAG mobility in the triacylglycerol lipase mutant sugardependent1 significantly affected de-etiolation. Moreover, we showed that lower levels of carbon resources exacerbated the slow-greening phenotype whereas higher levels of carbon resources had an opposite effect. This work suggests a lack of autophagy machinery limits chloroplast development during de-etiolation, and this is exacerbated by limited lipid turnover (lipophagy) that physically or energetically restrains chloroplast development.
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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:Protein N-termini are prone to post translational modification and are major determinants of protein stability in bacteria, eukaryotes, and perhaps also in chloroplasts. Most chloroplast proteins undergo N-terminal maturation, but this is poorly understood due to insufficient experimental information and the N-termini of mature chloroplast proteins cannot be accurately predicted. This motivated an extensive characterization of chloroplast protein N-termini using terminal amine isotopic labeling of substrates (TAILS). Many nuclear-encoded plastid proteins accumulated with two or three different N-termini; we evaluated the significance of these different proteoforms. Ala, Val, Thr (often in N-Î? acetylated form) and Ser were the most frequently observed N-terminal residues, even after normalization for their frequency in the plastid proteome, while other residues were absent or highly under-represented. Plastid-encoded proteins showed a similar distribution of N-terminal residues, but with a higher frequency of Met. Infrequent residues such as Ile, Arg, Cys, Pro, Asp and Glu were observed for several abundant proteins likely reflecting functional regulation through their N-termini. In contrast, the thylakoid lumenal proteome showed a wide diversity of N-terminal residues, including those typically associated with instability (Asp, Glu, Leu, Phe). We propose that after cleavage of the chloroplast transit peptide by stromal processing peptidase, additional processing by unidentified peptidases occurs to avoid unstable or otherwise unfavorable N-terminal residues. The possibility of a chloroplast N-end rule is discussed. This work provides a baseline for understanding N-terminal processing and maturation of chloroplast proteins.
2017-11-14 | MSV000081716 | MassIVE
Project description:Identification of target transcripts for the putative chloroplast RNA binding protein CFM2 in Zea mays. CFM2 was immunoprecipitated from a chloroplast extract. Chloroplast extracts were prepared from WT tissue. RNA from the pellet and from the supernatant for each pulldown was labelled with different fluoro-dyes and hybridized onto an array covering the complete maize chloroplast genome. Messages enriched in the immunoprecipitate from WT tissue are likely targets for CFM2.
2006-09-01 | E-MEXP-743 | biostudies-arrayexpress