Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics
Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics
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DOI：
10.1074/jbc.m502332200
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发表时间：
2005-07-08
影响因子：
4.8
通讯作者：
Saito, K
中科院分区：
文献类型：
--
作者：
Hirai, MY;Klein, M;Saito, K
自模式生物基因组测序完成以来，未知基因的功能鉴定已成为生物学中的主要挑战。转录组学、蛋白质组学和代谢组学等后基因组学有望发现基因功能。这份报告概述了基因和代谢产物的基因网络的阐明，通过整合代谢组学与转录组学，并提出了一个新的基因功能的识别策略。结合硫胁迫下拟南芥的代谢组学和转录组学数据，采用批学习自组织映射方法进行分析。由相同机制调控的一组代谢物/基因聚集在一起。研究表明，硫代葡萄糖甙的代谢是受到协调调节的。三个未知的假定的磺基转移酶基因聚类在一起，已知的硫代葡萄糖苷生物合成基因参与生物合成的候选人。重组基因产物的体外酶促测定证实了它们作为硫代葡萄糖甙转移酶的功能。几个参与硫同化的基因与O-乙酰丝氨酸聚簇，O-乙酰丝氨酸被认为是这些基因的正调控因子。参与花色素苷生物合成的基因与编码特异性上调花色素苷生物合成基因的转录因子的基因聚簇。这些结果表明，调控代谢产物和转录因子基因可以通过这种方法来确定，基于假设，他们与下游基因，他们调节集群。该策略不仅适用于植物，也适用于其他生物，用于未知基因的功能阐明。
Since the completion of genome sequences of model organisms, functional identification of unknown genes has become a principal challenge in biology. Postgenomics sciences such as transcriptomics, proteomics, and metabolomics are expected to discover gene functions. This report outlines the elucidation of gene-to-gene and metabolite-to-gene networks via integration of metabolomics with transcriptomics and presents a strategy for the identification of novel gene functions. Metabolomics and transcriptomics data of Arabidopsis grown under sulfur deficiency were combined and analyzed by batch-learning self-organizing mapping. A group of metabolites/genes regulated by the same mechanism clustered together. The metabolism of glucosinolates was shown to be coordinately regulated. Three uncharacterized putative sulfotransferase genes clustering together with known glucosinolate biosynthesis genes were candidates for involvement in biosynthesis. In vitro enzymatic assays of the recombinant gene products confirmed their functions as desulfoglucosinolate sulfotransferases. Several genes involved in sulfur assimilation clustered with O-acetylserine, which is considered a positive regulator of these genes. The genes involved in anthocyanin biosynthesis clustered with the gene encoding a transcriptional factor that up-regulates specifically anthocyanin biosynthesis genes. These results suggested that regulatory metabolites and transcriptional factor genes can be identified by this approach, based on the assumption that they cluster with the downstream genes they regulate. This strategy is applicable not only to plant but also to other organisms for functional elucidation of unknown genes.