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.
Date of this Version
8-11-2010
DOI
10.1186/1471-2164-11-470
Recommended Citation
Rajagopala, Seesandra V.; Yamamoto, Natsuko; Zweifel, Adrienne E.; Nakamichi, Tomoko; Huang, Hsi-Kuang; Mendez-Rios, Jorge David; Franc-Koh, Jonathan; Boorgula, Meher Preethi; Fujita, Kazutoshi; Suzuki, Ken-ichirou; Hu, James C.; Wanner, Barry L.; Mori, Hirotada; and Uetz, Peter, "The Escherichia Coli K-12 ORFeome: a Resource for Comparative Molecular Microbiology" (2010). Department of Biological Sciences Faculty Publications. Paper 11.
http://dx.doi.org/10.1186/1471-2164-11-470
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.