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 knownEscherichia 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.

Comments

This is the publisher pdf of Seesandra V Rajagopala, Natsuko Yamamoto, Adrienne E Zweifel, Tomoko Nakamichi, Hsi-Kuang Huang, Jorge Mendez-Rios, Jonathan Franca-Koh, Meher Boorgula, Kazutoshi Fujita, Ken-ichirou Suzuki, James C Hu, Barry L Wanner, Hirotada Mori, Peter Uetz. The Escherichia Coli K-12 ORFeome: a Resource for Comparative Molecular Microbiology. BMC Genomics 2010, 11:470 (11 August 2010) and is available at: 10.1186/1471-2164-11-470.

Date of this Version

8-11-2010

DOI

10.1186/1471-2164-11-470

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