使用基因敲除文库和表型芯片组合对1440个大肠杆菌基因进行功能分析。

Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays.

作者信息

Ito Mikito, Baba Tomoya, Mori Hirotada, Mori Hideo

机构信息

Biofrontier Laboratories, Kyowa Hakko Kogyo Co. Ltd., Tokyo 194-8533, Japan.

出版信息

Metab Eng. 2005 Jul;7(4):318-27. doi: 10.1016/j.ymben.2005.06.004.

DOI:10.1016/j.ymben.2005.06.004

PMID:16095938

Abstract

Escherichia coli is one of the best elucidated organisms. However, about 40% of E. coli genes have not been assigned to their function yet. We analyzed 1440 single gene knock-out mutants using the GN2-MicroPlate, which permits assay of 95 carbon-source utilizations simultaneously. In the knock-out library there are 1044 of so called y-genes with no apparent function. The raw dataset was analyzed and genes were interrelated by the clustering method of the GeneSpring software. In the resulted dendrogram of genes, a group of genes with known and related function tended to be assembled into a cluster. Our clustering method would be useful for functional assignment of so called y-genes with no apparent function, since the resulted dendrogram could connect y-genes to phenotype and function of well-studied genes.

摘要

大肠杆菌是研究得最为透彻的生物之一。然而，约40%的大肠杆菌基因尚未明确其功能。我们使用GN2微孔板分析了1440个单基因敲除突变体，该微孔板可同时检测95种碳源的利用情况。在敲除文库中，有1044个所谓的y基因，其功能尚不明确。我们对原始数据集进行了分析，并通过GeneSpring软件的聚类方法将基因相互关联起来。在生成的基因树状图中，一组具有已知相关功能的基因倾向于聚集在一起。我们的聚类方法对于确定那些功能尚不明确的所谓y基因的功能很有用，因为生成的树状图可以将y基因与已深入研究的基因的表型和功能联系起来。