Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Arabidopsis thaliana seedling in different development stages

ABSTRACT: Sample harvesting and preparation was conducted in 3 sets of 9 samples with each set encompassing the time points Day 0 to Day 8 after transfer to the growth room. We alternated tissue harvesting regimes to obtain sets of tissue for total RNA and metabolite extraction, thus corresponding tissue samples were used to compare metabolite and transcript profiles. A shelf in the growth room was divided into 3 sections and plates for each set were arranged horizontally around the shelf, such that each section contained an equal number of plates. Tissue was harvested each day at 09:00 h and only 1 sample per day was harvested resulting in 3 biological replicates for each time point. Each tissue sample consisted of pooled seedlings from an equal number of plates from each section. The total number of plates selected for each sample varied depending on the developmental stage. Each plate was examined under a microscope to ensure that seedlings were harvested at the required stage of development. Only those plates with greater than 95% of seedlings at the appropriate developmental stage were used.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Mark Hooks

PROVIDER: E-MEXP-2493 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:It has been strongly argued that plant cells should have a means of sensing sugars at the cell surface, so that extracellular and intracellular sugars can be sensed separately and their metabolism coordinated (Lalonde et al., Plant Cell, 11, 707-26, 2000). There is good evidence for an intracellular hexokinase-dependent pathway of hexose sensing in plants, but very little evidence for a hexokinase-independent signalling pathway, such as that provided by SNF3 or RGT2 in yeast. Many papers on sugar sensing in plants cite work from two laboratories as evidence for hexokinase-independent hexose signalling in plants. The first is that in which cell-wall invertase and sucrose synthase genes were induced by treatment of a Chenopodium suspension culture with 30 mM 6-Deoxyglucose (6DOG) for 24 h (Roitsch et al., Plant Physiol 108, 285-294, 1995; Godt et al., J. Plant Physiol 146, 231-238, 1995). The second is that in which a patatin transgene in Arabidopsis was shown to be weakly induced by growth over several days on a mixture of 30 mM glucose plus 30 mM 3-O-methylglucose (3OMG), but strongly induced by growth on 30 mM Glc plus 90 mM 3OMG (Martin et al., Plant J, 11, 53-62, 1997). We are not aware of any examples of Arabidopsis genes which respond to 6DOG or 3OMG yet this is an area of wide significance. Identification of such a gene would help to establish if a hexokinase-independent signalling system operates in plants, and would provide a basis for establishment of a genetic screen for mutants, using the gene promoter linked to a reporter such as luciferase. The aim of this proposal is to discover any genes which are either activated or repressed by glucose AND by 3OMG and/or 6DOG, but not by mannitol (an osmotic control). The use of both 3OMG and 6DOG will help to identify non-specific effects of either. All substrates will first be analysed by HPLC to confirm that they are pure. Arabidopsis Col-0 seedlings will be grown in vitro for 7 days in the absence of sugars, then treated with 30 mM glucose or glucose analogue for 8 h (these conditions are based on concentrations and time courses of Roitsch et al.). RNA will then be isolated from multiple independent plates to minimise biological variation.

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Transcription profiling of Arabidopsis thaliana seedling in different development stages

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