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| Status |
Public on Sep 18, 2017 |
| Title |
Transcript and metabolite profiling indicate rapid regulation of the deacclimation process in cold acclimated Arabidopsis thaliana |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by array
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| Summary |
During low temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. During deacclimation in response to warm temperatures cold acclimated plants lose freezing tolerance and resume growth and development. While considerable effort has been directed toward understanding the molecular and metabolic basis of cold acclimation, much less information is available about the regulation of deacclimation. Here, we report metabolic (GC-MS) and transcriptional (microarrays, qRT-PCR) responses underlying deacclimation during the first 24 h after a shift of cold acclimated Arabidopsis thaliana (Columbia-0) plants to warm temperature. The data revealed a faster response of the transcriptome than of the metabolome and provided evidence for tightly regulated temporal responses at both levels. Metabolically deacclimation is associated with decreasing contents of sugars, amino acids and glycolytic and TCA cycle intermediates, indicating an increased need for carbon sources and respiratory energy production associated with growth resumption under warm temperature conditions. Deacclimation also involves extensive down-regulation of protein synthesis and changes in the metabolism of lipids and cell wall components. Altered hormonal regulation appears particularly important during deacclimation, with changes in the expression of genes related to auxin, gibberellin, brassinosteroid, jasmonate and ethylene metabolisms. Several transcription factor families controlling fundamental aspects of plant development are significantly regulated during deacclimation, emphasizing that loss of freezing tolerance and growth resumption are interrelated processes that are transcriptionally highly interrelated. Expression patterns of some clock oscillator components during deacclimation resembled those under warm conditions, indicating at least partial re-activation of the circadian clock. This study provide the first comprehensive analysis of the regulation of deacclimation in cold acclimated plants. The data indicate cascades of rapidly regulated genes and metabolites that underly the developmental switch resulting in reduced freezing tolerance and the resumption of growth. They constitute a reference dataset of genes, metabolites and pathways that are crucial during the first rapid phase of deacclimation and will be useful for the further analysis of this important but under-researched plant process.
We used whole genome microarrays to monitor changes in gene expression in the Arabidopsis thaliana accession Columbia-0 during the first 24 h after a shift of cold acclimated plants to warm temperature.
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| Overall design |
Plants from Arabidopsis thaliana accession Columbia-0 were cold acclimated at 4°C for three days. Plants were then deacclimation at 20°C for 24 h. Rosettes of non-acclimated and cold acclimated plants and plants deacclimated for 2 h, 4 h, 6 h, 12 h and 24 h were collected for RNA extraction and hybridization on Affymetrix Arabidopsis Gene 1.0 ST arrays in order to explore temporal transcriptome changes during deacclimation. For each sample total RNA was isolated from a pool of rosettes of 10 plants. The experiment was performed in three idenpendent biological replicates.
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| Contributor(s) |
Pagter M, Alpers J, Erban A, Kopka J, Zuther E, Hincha DK |
| Citation(s) |
28915789 |
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| Submission date |
Sep 14, 2016 |
| Last update date |
Sep 24, 2017 |
| Contact name |
Majken Pagter |
| E-mail(s) |
mp@bio.aau.dk
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| Phone |
+45 30229330
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| Organization name |
Aalborg University
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| Department |
Chemistry and Bioscience
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| Street address |
Fredrik Bajers Vej 7H
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| City |
Aalborg East |
| ZIP/Postal code |
9220 |
| Country |
Denmark |
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| Platforms (1) |
| GPL17416 |
[AraGene-1_0-st] Arabidopsis Gene 1.0 ST Array [transcript (gene) version] |
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| Samples (21)
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| Relations |
| BioProject |
PRJNA343034 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE86935_RAW.tar |
180.9 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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