Open Access Highly Accessed Research article

The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology

Seesandra V Rajagopala1, Natsuko Yamamoto2, Adrienne E Zweifel3, Tomoko Nakamichi2, Hsi-Kuang Huang1, Jorge David Mendez-Rios1, Jonathan Franca-Koh1, Meher Preethi Boorgula1, Kazutoshi Fujita4, Ken-ichirou Suzuki4, James C Hu3, Barry L Wanner5, Hirotada Mori26* and Peter Uetz17*

Author Affiliations

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

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BMC Genomics 2010, 11:470  doi:10.1186/1471-2164-11-470

Published: 11 August 2010

Abstract

Background

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.

Results

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.

Conclusions

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.