Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA327795 | ENA |
REPOSITORIES: ENA
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Project description:Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). There is increasing evidence for the translation of these sORFs into bioactive peptides. Yet only a few small peptides are annotated in the model organism Arabidopsis thaliana. To aid the functional annotation of small peptides, we have developed ARA-PEPs, a repository and webserver of putative peptides encoded by sORFs in the Arabidopsis genome from in house Tiling arrays, RNA sequencing and from publicly available datasets. In order to identify novel oxidative stress-induced peptides in Arabidopsis thaliana a tiling array analysis (GeneChip® Arabidopsis Tiling 1.0R Arrays ) was performed on mRNA extracted from leaves inoculated with Botrytis cinerea (BC). Normalized log signals were obtained using the Affymetrix Tiling Analysis Software - Version 1.1, Build 2. ON and OFF probes were selected using a threshold, based on positive controls. Next, groups of 4-13 successive ON probes were combined into short TARs and a selection was made of TARs having an average signal intensity at least 2.6-fold higher after BC treatment compared to the control treatment, resulting in 195 BC induced TARs.
2016-12-23 | GSE84002 | GEO
Project description:We present a functional characterisation of two members of the IDA-LIKE (IDL) peptide family in Arabidopsis thaliana, IDL6 and IDL7. They are processed both C- and N-terminally to produce active peptides. Structure analyses of synthesized IDL6 and IDL7 peptides indicate that they lack secondary structure elements. Localisation studies suggest that the peptides require a signal peptide and C-terminally processing to be correctly transported out of the cell. Treatment of plants with synthetic IDL6 and IDL7 peptides resulted in down-regulation of a broad range of stress-responsive genes, including early stress-responsive transcripts, dominated by a large group of ZINC FINGER PROTEINS (ZFPs), WRKYs and genes encoding calcium-dependent proteins. idl6 and idl7 mutants were more tolerant to salt, whereas the respective overexpression lines displayed increased sensitivity to both salt and oxidative stress. Taken together, our results suggest that the putative peptide ligands IDL6 and IDL7 act as suppressors of abiotic stress responses in Arabidopsis.
2016-03-31 | GSE77467 | GEO
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:Proteomic investigation of Arabidopsis thaliana ftsH12 - ftsH12 is one of 17 genes of the FtsH metallo-protease family encoded within the A. thaliana genome.
2020-11-09 | PXD010619 | Pride
Project description:The mitochondrial CLPXP complex supports the coordination and assembly of mitochondrial and nuclear encoded protein complexes in Arabidopsis thaliana. Protein labeling using iTRAQ reagents and application of optimized ChaFRADIC technology to enrich N-Terminal peptides.
2020-09-14 | PXD016263 | Pride
Project description:We present a functional characterisation of two members of the IDA-LIKE (IDL) peptide family in Arabidopsis thaliana, IDL6 and IDL7. They are processed both C- and N-terminally to produce active peptides. Structure analyses of synthesized IDL6 and IDL7 peptides indicate that they lack secondary structure elements. Localisation studies suggest that the peptides require a signal peptide and C-terminally processing to be correctly transported out of the cell. Treatment of plants with synthetic IDL6 and IDL7 peptides resulted in down-regulation of a broad range of stress-responsive genes, including early stress-responsive transcripts, dominated by a large group of ZINC FINGER PROTEINS (ZFPs), WRKYs and genes encoding calcium-dependent proteins. idl6 and idl7 mutants were more tolerant to salt, whereas the respective overexpression lines displayed increased sensitivity to both salt and oxidative stress. Taken together, our results suggest that the putative peptide ligands IDL6 and IDL7 act as suppressors of abiotic stress responses in Arabidopsis. Two weeks old seedlings were treated either with 100 nM IDL6 or IDL7 peptide (treated) or 100 nM mock peptide (control) and whole rosettes were harvested 2 hours after treatment. 4 biological replicaes per treatment. Two color microarray. Biological replicas are dye-swapped between slides.
2016-03-31 | E-GEOD-77467 | biostudies-arrayexpress
Project description:Transcriptional profiling of Arabidopsis thaliana 12-days old seedlings comparing Col-0 wild type with transgenic plants with altered expression of dual-targetting plastid/mitochondrial organellar RNA-polymerase RPOTmp. Transgenic plants used for experiment were: overexpressor plants obtained by transformation of Col-0 WT plants with genetic constructs created in [Tarasenko et al., 2016] contained catalytic part of RPOTmp enzyme with transit peptides of RPOTm (mitochondrial) and RPOTp (plastid) by agrobacterial transformation; plants with complementation of RPOTmp functions in mitochondria or chloroplasts obtained from transformation of GABI_286E07 rpotmp knockout-mutant plants with genetic constructs created in [Tarasenko et al., 2016]. Goal was to determine the effects of RPOTmp knockout/overexpression on global Arabidopsis thaliana gene expression.
2023-12-25 | GSE251661 | GEO
Project description:Proteogenomics is an emerging research field yet lacking a standard method of analysis. In this article, we demonstrate the strength of proteogenomic analysis specific for N-terminal data that aims at the discovery of novel translational start sites. In summary, unidentified spectra were matched to a specific N-terminal peptide library encompassing all theoretical protein N-termini encoded in the genome. Gene prediction suggested 81 protein-coding models, of which several alternative proteoforms with unannotated protein starts. Next to the proteomic data, complementary ribosome footprinting data was generated from Arabidopsis thaliana cell cultures. Translation initiation site mapping by the ribosome footprinting data provided orthogonal evidence for 14 novel peptides identified by our proteogenomics pipeline.
2016-11-25 | GSE88790 | GEO
Project description:Mitochondria are known to be functional organelles, but their role as a signaling unit is increasingly being appreciated. The recent identification of a short open reading frame (sORF) in the mitochondrial DNA (mtDNA) that encodes a signaling peptide, humanin, suggests the possible existence of additional sORFs in the mtDNA that yield bioactive peptides. Here we report the identification of a sORF within the mitochondrial 12S rRNA encoding a 16-amino-acid peptide named MOTS-c (mitochondrial open-reading-frame of the twelve S rRNA -c) that regulates insulin sensitivity and metabolic homeostasis. MOTS-c is detected in various tissues and in circulation in an age-dependent manner. Its primary target organ appears to be the skeletal muscle and its cellular actions inhibit the folate cycle and its tethered de novo purine biosynthesis, causing a significant accumulation of AICAR levels concomitantly with AMPK activation. MOTS-c treatment in mice prevented age-dependent and high-fat diet-induced insulin resistance, as well as diet-induced obesity. These results suggest that mitochondria may be more actively engaged in regulating metabolic homeostasis than previously recognized, through the production of peptides encoded within its genome that act at the cellular and organismal level.
2015-03-07 | GSE65068 | GEO
Project description:Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana
| PRJNA149671 | ENA