Howell Katharine A, Narsai Reena, Carroll Adam, Ivanova Aneta, Lohse Marc, Usadel Björn, Millar A Harvey, Whelan James
Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia.
Plant Physiol. 2009 Feb;149(2):961-80. doi: 10.1104/pp.108.129874. Epub 2008 Dec 12.
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.
在一个详细的时间进程中对水稻（Oryza sativa）胚组织进行转录组和代谢物谱分析，为研究萌发过程中的转录和转录后过程奠定了基础。吸胀1小时后（HAI），与转录水平的变化无关，代谢发生了快速变化，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，包括那些参与碳水化合物、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 HAI开始增加的大量基因（超过6000个转录本）在代谢功能类别中富集。对编码位于初级代谢细胞器中的蛋白质的转录本分析表明，对于线粒体基因集，与质体基因集相比，更大比例的转录本在早期（1或3 HAI）达到峰值，值得注意的是，这些转录本中有许多编码参与运输功能的蛋白质。一组超过2000个转录本表现出独特的表达模式，在干种子中水平较低，随后在1或3 HAI时表达水平达到峰值，然后在后期时间点显著下降。该组在转录因子和信号转导成分中富集。通过公开可用的水稻芯片数据进一步研究了这些瞬时表达的转录因子的一个子集，表明其中一些仅在萌发过程中表达。对丰度变化相似的转录本的1 kb上游区域进行分析，确定了多种常见的序列基序，即转录因子的潜在结合位点。此外，在3 HAI达到峰值的新合成转录本在3'非翻译区显示出与RNA不稳定性相关的序列元件的显著富集。总体而言，这些分析表明，在水稻萌发过程中，一些代谢物水平立即发生变化，随后是转录组的两步大规模重排，这是由RNA合成和降解介导的，并伴随着代谢物水平的后期变化。
