The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology.
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.
Rajagopala
Seesandra V
SV
J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
Yamamoto
Natsuko
N
Zweifel
Adrienne E
AE
Nakamichi
Tomoko
T
Huang
Hsi-Kuang
HK
Mendez-Rios
Jorge David
JD
Franca-Koh
Jonathan
J
Boorgula
Meher Preethi
MP
Fujita
Kazutoshi
K
Suzuki
Ken-ichirou
K
Hu
James C
JC
Wanner
Barry L
BL
Mori
Hirotada
H
Uetz
Peter
P
D001426:Bacterial Proteins / Q000378:metabolism; D048168:Escherichia coli K12 / Q000235:genetics*; D016680:Genome, Bacterial; D016366:Open Reading Frames; D017422:Sequence Analysis, DNA; D013211:Staphylococcus aureus / Q000235:genetics; D013296:Streptococcus pneumoniae / Q000235:genetics
D001426:Bacterial Proteins