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  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, K. A., Narsai, R., Carroll, A., Ivanova, A., Lohse, M., Usadel, B., et al. (2009). 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 Physiology, 149(2), 961-980. doi:10.1104/pp.108.129874.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-25A8-D Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-25A9-B
Genre: Journal Article

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 Creators:
Howell, K. A.1, Author
Narsai, R.1, Author
Carroll, A.1, Author
Ivanova, A.1, Author
Lohse, M.2, Author              
Usadel, B.2, Author              
Millar, A. H.1, Author
Whelan, J.1, Author
Affiliations:
1External Organizations, ou_persistent22              
2Integrative Carbon Biology, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753329              

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Free keywords: genome-wide analysis messenger-rna arabidopsis-thaliana seed-germination gene-expression database protein tool sequences dormancy
 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.

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Language(s): eng - English
 Dates: 2008-12-172009
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: ISI: ISI:000263129400032
DOI: 10.1104/pp.108.129874
ISSN: 0032-0889 (Print) 0032-0889 (Linking)
URI: ://000263129400032 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633829/pdf/pp1490961.pdf?tool=pmcentrez
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Title: Plant Physiology
Source Genre: Journal
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Pages: - Volume / Issue: 149 (2) Sequence Number: - Start / End Page: 961 - 980 Identifier: -