Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA255000 | ENA |
REPOSITORIES: ENA
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Project description:Background Protein synthesis is a highly energy demanding process and is regulated according to energy availability in plant cells. Light and sugar availability affect mRNA translation but the specific roles of these factors remain unclear. In this study, sucrose was applied to Arabidopsis seedlings kept in the light or in the dark, in order to distinguish sucrose and light effects on transcription and translation. These were studied using microarray analysis of steady state mRNA and mRNA bound to translating ribosomes. Results Steady state mRNA levels were affected differently by sucrose in the light and in the dark but general translation increased to a similar extend in both conditions. Alterations in polysomal mRNA association closely followed the changes induced on the transcript level. However, for 243 mRNAs, a change in ribosome occupancy was observed after sucrose treatment in the light, but not in the dark condition. Many of these mRNAs are annotated as encoding ribosomal proteins, supporting specific translational regulation of this group of transcripts. Unexpectedly, the numbers of ribosomes bound to each mRNA decreased for mRNAs with increased ribosome occupancy. Conclusions Our results suggest that sucrose regulate translation of these 243 mRNAs but specifically in the light, through a novel regulatory mechanism. Our data sows that increased polysomal association is not necessarily leading to more ribosomes per transcript, suggesting a mechanism of translational induction not solely dependent on increased translation initiation rates.
2015-01-28 | GSE59306 | GEO
Project description:Background Protein synthesis is a highly energy demanding process and is regulated according to energy availability in plant cells. Light and sugar availability affect mRNA translation but the specific roles of these factors remain unclear. In this study, sucrose was applied to Arabidopsis seedlings kept in the light or in the dark, in order to distinguish sucrose and light effects on transcription and translation. These were studied using microarray analysis of steady state mRNA and mRNA bound to translating ribosomes. Results Steady state mRNA levels were affected differently by sucrose in the light and in the dark but general translation increased to a similar extend in both conditions. Alterations in polysomal mRNA association closely followed the changes induced on the transcript level. However, for 243 mRNAs, a change in ribosome occupancy was observed after sucrose treatment in the light, but not in the dark condition. Many of these mRNAs are annotated as encoding ribosomal proteins, supporting specific translational regulation of this group of transcripts. Unexpectedly, the numbers of ribosomes bound to each mRNA decreased for mRNAs with increased ribosome occupancy. Conclusions Our results suggest that sucrose regulate translation of these 243 mRNAs but specifically in the light, through a novel regulatory mechanism. Our data sows that increased polysomal association is not necessarily leading to more ribosomes per transcript, suggesting a mechanism of translational induction not solely dependent on increased translation initiation rates. Four different samples groups were used: Control, Darkness, Sucrose, Simultaneous Darkness and sucrose treatments. All sample groups was represented by both total mRNA hybridization and of mRNAs from polysomal enrichment. All sample groups were represented by three biological replicates.
2015-01-28 | E-GEOD-59306 | biostudies-arrayexpress
Project description:To understand the contribution of the RPL24B protein, a component of the large 60S ribosomal subunit, to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and the rpl24b/stv1-1 T-DNA insertion mutant. RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays. Each plant sample was analyzed for the mRNA abundance in total mRNA, polysomal mRNA, and nonpolysomal mRNA. Three biological replicates were collected. The rpl24b mutant was compared with wild type.
2014-01-01 | E-GEOD-51474 | biostudies-arrayexpress
Project description:To understand the contribution of the poly(A)binding protein to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and pab2 pab8 double mutant seedlings. The mutants continue to express the PAB4 paralog of PABP. RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.
2014-01-01 | GSE51480 | GEO
Project description:To understand the contribution of the RPL24B protein, a component of the large 60S ribosomal subunit, to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and the rpl24b/stv1-1 T-DNA insertion mutant. RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.
2014-01-01 | GSE51474 | GEO
Project description:To understand the contribution of the poly(A)binding protein to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and pab2 pab8 double mutant seedlings. The mutants continue to express the PAB4 paralog of PABP. RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays. Each plant sample was analyzed for the mRNA abundance in total mRNA (T), polysomal mRNA (PL), and nonpolysomal mRNA (NP). Four biological replicates were collected for polysomes and three for total RNA. The pab2 pab8 double mutant was compared with wild type.
2014-01-01 | E-GEOD-51480 | biostudies-arrayexpress
Project description:To understand the role of GCN2 in regulating translation, we compared the polysome loading state and overall transcript level between Arabidopsis thaliana wild type (ecotype Landsberg erecta) and gcn2 (Genetrap line GT8359, Cold Spring Harbor Laboratory) seedlings with or without herbicide chlorosufuron treatment RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.
2015-12-01 | GSE52116 | GEO
Project description:To understand the role of GCN2 in stress response, the total transcript and translation state were compared between Arabidopsis thaliana wild type (ecotype Landsberg erecta) and gcn2 (Genetrap line GT8359, Cold Spring Harbor Laboratory) seedlings with or without herbicide chlorosufuron treatment RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.
2015-12-01 | GSE52117 | GEO
Project description:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. The presented model is a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. The Petri net formalism was used to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs were applied. Based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism, the core metabolism of Arabidopsis thaliana was formulated. Each reaction (transition) is experimentally proven. The complete Petri net model consists of 134 metabolites, represented by places, and 243 reactions, represented by transitions. Places and transitions are connected via 572 edges.
2020-04-09 | MODEL1801090001 | BioModels
Project description:VC109+111 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings
| PRJNA91029 | ENA