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Published on December 12, 2008; 10.1104/pp.108.129874

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Received September 12, 2008
Accepted December 3, 2008

Mapping metabolic and transcript temporal switches during germination in Oryza sativa highlights specific transcription factors and the role of RNA instability in the germination process

Katharine A. Howell , Reena Narsai , Adam Carroll , Aneta Ivanova , Marc Lohse , Bjorn Usadel , A. Harvey Millar , and James Whelan *

ARC Centre of Excellence in Plant Energy Biology, MCS Building M316 University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia; Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany

* Corresponding author; email: seamus{at}cyllene.uwa.edu.au.

Transcriptome and metabolite profiling of rice embryo tissue during a detailed time course formed a foundation for examining transcriptional and post-transcriptional processes during germination. One hour after imbibition (HAI), independent of changes in transcript levels, rapid changes in metabolism occurred, including increases in hexose phosphates, TCA cycle intermediates and GABA. Later changes in the metabolome, including those involved in carbohydrate, amino acid and cell wall metabolism, appeared to be driven by increases in transcript levels, given that the large group (over 6,000 transcripts) observed to increase from 12 HAI were enriched in metabolic functional categories. Analysis of transcripts encoding proteins located in the organelles of primary metabolism revealed that for the mitochondrial gene set a greater proportion of transcripts peaked early, at 1 or 3 HAI, compared to the plastid set, and notably, many of these transcripts encoded proteins involved in transport functions. One group of over 2,000 transcripts displayed a unique expression pattern beginning with low levels in dry seeds, followed by a peak in expression levels at 1 or 3 HAI before markedly declining at later time points. This group was enriched in transcription factors and signal transduction components. A subset of these transiently expressed transcription factors, were further interrogated across publicly available rice array data, indicating that some were only expressed during the germination process. Analysis of the 1 kb upstream regions of transcripts displaying similar changes in abundance identified a variety of common sequence motifs, potential binding sites for transcription factors. Additionally, newly synthesised transcripts peaking 3 HAI displayed a significant enrichment of sequence elements in the 3' UTR that have been previously associated with RNA instability. Overall, these analyses reveal that during rice germination, an immediate change in some metabolite levels is followed by a two-step, large-scale re-arrangement of the transcriptome which is mediated by RNA synthesis and degradation and is accompanied by later changes in metabolite levels.




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R. Narsai, K. A. Howell, A. Carroll, A. Ivanova, A. H. Millar, and J. Whelan
Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings
Plant Physiology, September 1, 2009; 151(1): 306 - 322.
[Abstract] [Full Text] [PDF]


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