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, 149 (2):
961-80 (February 2009)Howell, Katharine A Narsai, Reena Carroll, Adam Ivanova, Aneta Lohse,
Marc Usadel, Bjorn Millar, A Harvey Whelan, James Research Support,
Non-U.S. Gov't United States Plant physiology Plant Physiol. 2009
Feb;149(2):961-80. Epub 2008 Dec 12..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.