J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
BMC Genomics. 2010 Aug 11;11:470. doi: 10.1186/1471-2164-11-470.
Systems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames (ORFs) have been made for about a dozen bacterial species and allow researchers to express and study complete proteomes in a high-throughput fashion.
We have constructed an open reading frame (ORFeome) collection of 3974 or 94% of the known Escherichia coli K-12 ORFs in Gateway entry vector pENTR/Zeo. The collection has been used for protein expression and protein interaction studies. For example, we have compared interactions among YgjD, YjeE and YeaZ proteins in E. coli, Streptococcus pneumoniae, and Staphylococcus aureus. We also compare this ORFeome with other Gateway-compatible bacterial ORFeomes and show its utility for comparative functional genomics.
The E. coli ORFeome provides a useful resource for functional genomics and other areas of protein research in a highly flexible format. Our comparison with other ORFeomes makes comparative analyses straighforward and facilitates direct comparisons of many proteins across many genomes.
系统生物学和功能基因组学需要全基因组数据集和资源。大约十几个细菌物种已经构建了完整的克隆开放阅读框（ORF）集，允许研究人员以高通量的方式表达和研究完整的蛋白质组。
我们构建了一个含有 3974 个或 94%的大肠杆菌 K-12 已知 ORF 的开放阅读框（ORFeome）集合，这些 ORF 都位于 Gateway 入口载体 pENTR/Zeo 中。该集合已被用于蛋白质表达和蛋白质相互作用研究。例如，我们比较了大肠杆菌、肺炎链球菌和金黄色葡萄球菌中 YgjD、YjeE 和 YeaZ 蛋白之间的相互作用。我们还将这个 ORFeome 与其他兼容 Gateway 的细菌 ORFeome 进行了比较，并展示了它在比较功能基因组学方面的实用性。
大肠杆菌 ORFeome 为功能基因组学和蛋白质研究的其他领域提供了一个高度灵活的资源。我们与其他 ORFeome 的比较使得比较分析变得简单，并促进了许多蛋白质在许多基因组中的直接比较。
