Plant Physiol. 2009 Feb;149(2):961-80. doi: 10.1104/pp.108.129874. Epub 2008 Dec 12.

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

Howell KA, Narsai R, Carroll A, Ivanova A, Lohse M, Usadel B, Millar AH, Whelan J.

Source

Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia.

Abstract

Transcriptome and metabolite profiling of rice (Oryza sativa) embryo tissue during a detailed time course formed a foundation for examining transcriptional and posttranscriptional processes during germination. One hour after imbibition (HAI), independent of changes in transcript levels, rapid changes in metabolism occurred, including increases in hexose phosphates, tricarboxylic acid cycle intermediates, and gamma-aminobutyric acid. 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 with 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 synthesized transcripts peaking at 3 HAI displayed a significant enrichment of sequence elements in the 3' untranslated region 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 rearrangement of the transcriptome that is mediated by RNA synthesis and degradation and is accompanied by later changes in metabolite levels.

PMID:: 19074628; [PubMed - indexed for MEDLINE]
PMCID:: PMC2633829

Free PMC Article

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Figure 2.

Profiles of known metabolites and hierarchical clustering of differentially expressed genes during rice germination. A, Changes in the levels of all identified metabolites were calculated as fold changes relative to the 0-HAI time point and log transformed. Changes are represented as a false color heat map where the color saturates at a log₂ false color (FC) value of 5 (i.e. a 32-fold change). Data from a study performed using whole Arabidopsis seeds (Fait et al., 2006) are included for comparison, where I represents seeds imbibed for 72 h at 4°C in the dark relative to dry seeds and G indicates a comparison of seeds imbibed for 72 h at 4°C in the dark followed by 24 h of growth under germinative conditions (21°C in the light) relative to dry seeds. White coloring indicates no significant change, and gray coloring indicates that a metabolite was not measured. The fold changes for all metabolites detected and associated P values are shown in Supplemental Table S2B. B, From microarray analysis, all probe sets that were called present at a minimum of one time point were normalized to the highest level of expression over the time course of the study and hierarchically clustered using average linkage based on Euclidian distance. Four primary clusters were defined: cluster 1 (green), transcripts that increased in abundance over the time period examined; cluster 2 (black), transcripts that were low or absent at 0 HAI, peaked at 1 or 3 HAI, and then declined in abundance; cluster 3 (pink), transcripts that declined in abundance over the time period examined; cluster 4 (blue), transcripts that displayed relatively stable levels of abundance throughout the time course. Subclusters of clusters 1 and 3 are defined by differences in the time points at which changes in transcript levels occurred. For all clusters, a graph showing the average expression level is presented. Fold changes and their associated P values for all probe sets can be found in Supplemental Table S1.

Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process

Plant Physiol. 2009 February;149(2):961-980.