Metabolomics-based post-genome science in plants

基于代谢组学的植物后基因组科学

• 批准号: 15201045
• 负责人: SAITO Kazuki
• 金额: $ 26.79万
• 依托单位: Chiba University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (A)
• 财政年份: 2003
• 资助国家: 日本
• 起止时间: 2003 至 2006
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-15201045/
• 关键词: metabolomics; transcriptomics; functional genomics; metabolism; Arabidopsis thaliana; 多変量解析; 自己組織化マップ; 栄養ストレス; アントシアニン; アルカロイド; メタボローム; 機能ゲノミクス; グルコシノレート; DNAマイクロアレイ; フラボノイド

Integrated analysis of omics can provide the clues for identification of gene function and precise information about gene-to-metabolite and/or metabolite-to-metabolite networks. We ran the functional genomics project combining metabolome and transcriptome in Arabidopsis thaliana. Nutritional stress of nitrogen and sulfur resulted in global change of metabolome that could be correlated with the modulation of gene expression, indicating the presence of gene-to-metabolite networks, in particular, in glucosinolate biosynthesis. The comprehensive gene expression and metabolite profiles of anthocyanin overproducing Arabidopsis lines revealed the function of novel genes that are responsible for modification and storage of anthocyanins. The function of those genes was identified by analysis of the T-DNA insertion lines and recombinant proteins. By expanding this strategy, we used a transcriptome database publicly available for functional identification of unknown genes and networks. Upon these co-expression analyses, the models of co-expressed genes in particular metabolic pathways were constructed, leading to speculation of functions of those genes followed by confirmation with reverse genetics strategy. Extensive metabolic profiling of the knockout mutants of genes of interest was performed by a metabolome-analytical platform employing mass spectrometry. Detailed metabolite analysis of the mutants revealed the changes in metabolo-types, indicating the gene functions. This strategy of integrated analysis of metabolome and transcriptome is applicable to decipher the function of genes not only for a model plant A. thaliana but also for unexplored plants expected rich with a variety of phychemicals.

组学综合分析可以为基因功能鉴定和基因-代谢物和/或代谢物-代谢物网络的精确信息提供线索。我们在拟南芥中进行了结合代谢组和转录组的功能基因组计划。氮和硫的营养胁迫导致了代谢组分的全球变化，这可能与基因表达的调控有关，表明基因到代谢物网络的存在，特别是在硫代葡萄糖苷的生物合成中。花青素高产拟南芥品系的全面基因表达和代谢产物谱揭示了负责花青素修饰和储存的新基因的功能。通过对T-DNA插入线和重组蛋白的分析，鉴定了这些基因的功能。通过扩展这一策略，我们使用了一个公开可用的转录组数据库，用于未知基因和网络的功能鉴定。在这些共表达分析的基础上，构建了共表达基因的模型，特别是代谢途径，从而推测这些基因的功能，然后用反向遗传学策略进行验证。利用代谢组分析平台利用质谱仪对感兴趣基因的敲除突变体进行广泛的代谢谱分析。对突变体的详细代谢物分析揭示了代谢物类型的变化，表明了基因功能。这种代谢组和转录组的综合分析策略不仅适用于模式植物拟南芥的基因功能破译，也适用于预计富含多种植物化学物质的未知植物。

项目成果

Mami Yamazaki, Yukiko Makita, Karin Springob, Kazuki Saito: "Regulatory mechanisms for anthocyanin biosynthesis in chemotypes of Perilla Frutescens var. crispa"Biochemical Engineering Journal. 14. 191-197 (2003)

Mami Yamazaki、Yukiko Makita、Karin Springob、Kazuki Saito：“紫苏化学型花青素生物合成的调节机制”生化工程杂志。

Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor

• DOI: 10.1111/j.1365-313x.2005.02371.x
• 发表时间: 2005-04-01
• 期刊: PLANT JOURNAL
• 影响因子: 7.2
• 作者: Tohge, T;Nishiyama, Y;Saito, K
• 通讯作者: Saito, K

Post-genomics approaches for the elucidation of plant adaptive mechanisms to sulphur deficiency

• DOI: 10.1093/jxb/erh184
• 发表时间: 2004-08-01
• 期刊: JOURNAL OF EXPERIMENTAL BOTANY
• 影响因子: 6.9
• 作者: Hirai, MY;Saito, K
• 通讯作者: Saito, K

メタボロミクスにおけるデータベースと研究例

代谢组学的数据库和研究实例

• 发表时间: 2005
• 期刊: 化学と生物 43・3
• 作者: 草野 都;斉藤 和季
• 通讯作者: 斉藤 和季

Integrated data mining of transcriptome and metabolome based on BL-SOM.

基于BL-SOM的转录组和代谢组集成数据挖掘。

• 发表时间: 2006
• 期刊: J. Comp. Aid. Chem. 7
• 作者: Mitsuru Yano;Shigehiko Kanaya;Md.Altaf-Ul-Amin;Ken Kurokawa;Masami Yokota Hirai;Kazuki Saito
• 通讯作者: Kazuki Saito