Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process
Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process
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DOI：
10.1104/pp.108.129874
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发表时间：
2009-02-01
期刊：
影响因子：
7.4
通讯作者：
Whelan, James
中科院分区：
文献类型：
--
作者：
Howell, Katharine A.;Narsai, Reena;Whelan, James
水稻（Oryza sativa）胚组织在一个详细的时间过程中的转录组和代谢产物谱形成了研究萌发过程中的转录和转录后过程的基础。吸胀（HAI）后1小时，独立于转录水平的变化，代谢发生快速变化，包括磷酸己糖、三羧酸循环中间体和γ-氨基丁酸的增加。代谢组的后期变化，包括参与碳水化合物、氨基酸和细胞壁代谢的变化，似乎是由转录水平的增加驱动的，因为观察到从12个HAI增加的大组（超过6，000个转录物）富含代谢功能类别。位于初级代谢的细胞器中的蛋白质编码的转录本的分析表明，线粒体基因组，更大比例的转录本达到峰值早，在1或3 HAI，与质体集相比，值得注意的是，许多这些转录本编码的蛋白质参与运输功能。一组超过2，000个转录物显示出独特的表达模式，开始于干种子中的低水平，随后在1或3 HAI时表达水平达到峰值，然后在稍后的时间点显著下降。这一组富含转录因子和信号转导成分。这些瞬时表达的转录因子的一个子集在公开的水稻阵列数据中进一步询问，表明一些转录因子仅在萌发过程中表达。分析的1-kb的上游区域的转录本显示类似的变化丰度确定了各种常见的序列基序，潜在的结合位点的转录因子。此外，在3 HAI处达到峰值的新合成的转录物显示出3'非翻译区中序列元件的显著富集，所述序列元件先前与RNA不稳定性相关。总的来说，这些分析表明，在水稻萌发过程中，一些代谢物水平的立即变化，随后是一个两步，大规模的重排的转录组介导的RNA合成和降解，并伴随着后来的代谢物水平的变化。
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.