The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology
- Equal contributors
1 J Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, MD 20850, USA
2 Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
3 Dept. of Biochemistry and Biophysics, Texas A & M University, College Station, TX 77843-2128, USA
4 National Institute of Technology and Evaluation, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
5 Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
6 Institute for Advanced Biosciences, Keio University, Tsuruoka City, Yamagata, Japan
7 Proteros Biostructures, Martinsried, Germany
BMC Genomics 2010, 11:470 doi:10.1186/1471-2164-11-470Published: 11 August 2010
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.