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

Aneta Ivanova, M. Lohse, B. Usadel, Harvey Millar, James Whelan

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Transcriptome and metabolite profiling of rice (Oryza sativa) embryo tissue during a detailed time course formed a foundationfor 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 g-aminobutyric acid. Later changes in the metabolome, including those involved incarbohydrate, amino acid, and cell wall metabolism, appeared to be driven by increases in transcript levels, given that the largegroup (over 6,000 transcripts) observed to increase from 12 HAI were enriched in metabolic functional categories. Analysis oftranscripts encoding proteins located in the organelles of primary metabolism revealed that for the mitochondrial gene set, agreater proportion of transcripts peaked early, at 1 or 3 HAI, compared with the plastid set, and notably, many of thesetranscripts encoded proteins involved in transport functions. One group of over 2,000 transcripts displayed a uniqueexpression pattern beginning with low levels in dry seeds, followed by a peak in expression levels at 1 or 3 HAI, beforemarkedly 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 transcriptsdisplaying similar changes in abundance identified a variety of common sequence motifs, potential binding sites fortranscription factors. Additionally, newly synthesized transcripts peaking at 3 HAI displayed a significant enrichment ofsequence elements in the 3# untranslated region that have been previously associated with RNA instability. Overall, theseanalyses reveal that during rice germination, an immediate change in some metabolite levels is followed by a two-step, largescalerearrangement of the transcriptome that is mediated by RNA synthesis and degradation and is accompanied by laterchanges in metabolite levels.
Original languageEnglish
Pages (from-to)961-980
JournalPlant Physiology
Volume149
Issue number2
DOIs
Publication statusPublished - 2009

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