Genome-wide RNA-Seq of rRNA depleted total RNA from Arabidopsis thaliana WT (Col-0) and pumpkin mutant
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE121776 | GEO | 2019/10/01
REPOSITORIES: GEO
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Project description:Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare L). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identifications of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions, as well as opposite to annotated genes demonstrating the existence of numerous non-coding RNA candidates. dRNA-seq analysis of total RNA from green and white plastids of the barley mutant line albostrians
2011-11-23 | E-GEOD-33773 | biostudies-arrayexpress
Project description:Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare L). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identifications of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions, as well as opposite to annotated genes demonstrating the existence of numerous non-coding RNA candidates.
2011-11-23 | GSE33773 | GEO
Project description:RNA polymerases (RNAPs) transcribe DNA into RNA and are found in all living organisms with several degrees of complexity from single polypeptide chain to multimeric enzymes. In chloroplast of angiosperms, two RNAPs are involved in plastid gene transcription: the nuclear-encoded RNA polymerase (NEP) and the plastid-encoded RNA polymerase (PEP). The PEP is a prokaryotic-type multimeric RNAP found in different states depending on light stimuli and cell identity. One of these active states requires the assembly of nuclear-encoded proteins named PEP-Associated Proteins (PAPs) with the catalytic core, triggering the timely transcription of photosynthesis-associated plastid genes in cells acquiring their photosynthetic apparatus. A purification procedure was used to enrich native PEP from Sinapis alba chloroplasts. Crosslinking coupled to mass spectrometry provided initial structural information about the relative position of PEP subunits within the complex.
2022-09-12 | PXD032739 | Pride
Project description:RNA polymerases (RNAPs) transcribe DNA into RNA and are found in all living organisms with several degrees of complexity from single polypeptide chain to multimeric enzymes. In chloroplast of angiosperms, two RNAPs are involved in plastid gene transcription: the nuclear-encoded RNA polymerase (NEP) and the plastid-encoded RNA polymerase (PEP). The PEP is a prokaryotic-type multimeric RNAP found in different states depending on light stimuli and cell identity. One of these active states requires the assembly of nuclear-encoded proteins named PEP-Associated Proteins (PAPs) with the catalytic core, triggering the timely transcription of photosynthesis-associated plastid genes in cells acquiring their photosynthetic apparatus. A purification procedure was used to enrich native PEP from Sinapis alba chloroplasts. Mass spectrometry-based proteomic analysis of the obtained fraction identified the expected subunits, i.e. the core components and the PAPs as the most abundant proteins.
2022-09-12 | PXD032738 | Pride
Project description:We obtained an Arabidopsis mutant from the Arabidopsis Biological Resource Center stock collection and verified that it was homozygous for a T-DNA insertion in the first exon of ORRM1 (SALK_072648, designated here as orrm1). The homozygous mutant did not show any phenotypic defect when grown under growth room conditions. We examined the organelle transcriptome of the mutant for editing defects because other proteins carrying RIP domains have been shown to be editing factors. We analyzed the plastid RNA editing extent with a new methodology based on RNA-seq. Briefly, total RNA is isolated from leaves and RT-PCR products corresponding to known organelle genes are obtained by using gene-specific primers. The products are mixed in equimolar ratio, sheared, and used as templates to produce an Illumina TruSeq library. This RNA-seq analysis demonstrated that ORRM1 is a plastid editing factor; 12 among 34 plastid sites exhibit a severe reduction of editing extent in the mutant relative to the wild-type
2014-01-09 | E-MTAB-4378 | biostudies-arrayexpress
Project description:Genome wide quantitative trait loci (QTL) mapping was conducted in Arabidopsis thaliana using F2 mapping population (Col-0 × Don-0) and SNPs markers. A total of five linkage groups were obtained with number of SNPs varying from 45 to 59 per linkage group. The composite interval mapping detected a total of 36 QTLs for 15 traits and the number of QTLs ranged from one (root length, root dry biomass, cauline leaf width, number of internodes and internode distance) to seven (for bolting days). The range of phenotypic variance explained (PVE) and logarithm of the odds ratio of these 36 QTLs was found be 0.19-38.17% and 3.0-6.26 respectively. Further, the epistatic interaction detected one main effect QTL and four epistatic QTLs. Five major QTLs viz. Qbd.nbri.4.3, Qfd.nbri.4.2, Qrdm.nbri.5.1, Qncl.nbri.2.2, Qtd.nbri.4.1 with PVE > 15.0% might be useful for fine mapping to identify genes associated with respective traits, and also for development of specialized population through marker assisted selection. The identification of additive and dominant effect QTLs and desirable alleles of each of above mentioned traits would also be important for future research.
| S-EPMC7196571 | biostudies-literature
Project description:Plastids are endosymbiotic organelles containing their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid-encoded polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplasts DNA using ptChIP-seq. We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex pattern of binding to DNA with preferential association at genes encoding rRNA, tRNA and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with the levels of RNA accumulation, which allowed estimating the quantitative contribution of transcription to RNA accumulation.
2022-01-21 | GSE192568 | GEO
Project description:Autopolyploidy is a process whereby the chromosome set is multiplied and it is a common phenomenon in angiosperms. Autopolyploidy is thought to be an important evolutionary force that has led to the formation of new plant species. Despite its relevance, the consequences of autopolyploidy in plant metabolism are poorly understood. This study compares the metabolic profiles of natural diploids and artificial autotetraploids of Arabidopsis thaliana Col-0. Different physiological parameters are compared between diploids and autotetraploids using nuclear magnetic resonance (NMR), elemental analysis (carbon:nitrogen balance) and quantitative real-time PCR (qRT-PCR). The main difference between diploid and autotetraploid A. thaliana Col-0 is observed in the concentration of metabolites related to the tricarboxylic acid cycle (TCA) and ?-amino butyric acid (GABA) shunt, as shown by multivariate statistical analysis of NMR spectra. qRT-PCR shows that genes related to the TCA and GABA shunt are also differentially expressed between diploids and autotetraploids following similar trends as their corresponding metabolites. Solid evidence is presented to demonstrate that autopolyploidy influences core plant metabolic processes.
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Project description:GUN1 proteins controls protein homeostasis in chloroplast development in cotyledons of the model plant Arabidopsis thaliana, via coordination of nuclear encoded polymerase (NEP)-dependent chloroplast genes expression with plastid encoded polymerase (PEP)-dependent chloroplast genes expression. Lack of GUN1 leads to development of abnormal plastids and, consequently, accumulation of nuclear-encoded chloroplast-targeted (NECT) proteins which in many cases have been found still in their precursor form. Data dependent acquisition (DDA) mass spectrometry analysis of cotyledons soluble fractions, as well as targeted proteomics analysis of specific FtsH protease forms recognized by FtsH antibodies in western blotting, have been performed to identify peptides from the chloroplast transit peptide (cTP) of NECT in cotyledons extracts of wild type and GUN1 knocked-out mutant plants. The aim was to compare the number of cTPs found in 6 days after sowing (DAS) seedlings grown on plates with or without the inhibitor of plastid translation lincomycin.
2019-11-15 | PXD015078 | Pride
Project description:Plastid Encoded RNA Polymerase (PEP) is a bacterial type multisubunit RNA polymerase responsible for the bulk of transcription in chloroplasts. It contains four core subunits, which are orthologs of their cyanobacterial counterparts. In Arabidopsis thaliana PEP associates with 12 PEP-associated proteins (PAPs), which serve as peripheral subunits of the RNA polymerase. The exact contributions of PAPs to PEP function remain poorly understood. We show that a peripheral subunit of PEP, PAP1 (pTAC3), binds the same genomic loci as RpoB, a core subunit of PEP. PAP1 (pTAC3) and another peripheral PEP subunit, PAP7 (pTAC14), are required for RpoB binding to DNA. RpoB and another core PEP subunit, RpoC1, are expressed in pap1 (ptac3) and pap7 (ptac14) mutants. We propose that the peripheral subunits of PEP are required for the recruitment of core PEP subunits to DNA. pTAC3, binds the same genomic loci as RpoB, a core subunit of PEP. PAP1 pTAC3 and another peripheral PEP subunit, PAP7
2024-03-05 | GSE259283 | GEO