title: The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology.
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.
authors.affiliation: J Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.
authors.forename: Seesandra V
authors.initials: SV
authors.lastname: Rajagopala
authors.forename: Natsuko
authors.initials: N
authors.lastname: Yamamoto
authors.forename: Adrienne E
authors.initials: AE
authors.lastname: Zweifel
authors.forename: Tomoko
authors.initials: T
authors.lastname: Nakamichi
authors.forename: Hsi-Kuang
authors.initials: HK
authors.lastname: Huang
authors.forename: Jorge David
authors.initials: JD
authors.lastname: Mendez-Rios
authors.forename: Jonathan
authors.initials: J
authors.lastname: Franca-Koh
authors.forename: Meher Preethi
authors.initials: MP
authors.lastname: Boorgula
authors.forename: Kazutoshi
authors.initials: K
authors.lastname: Fujita
authors.forename: Ken-ichirou
authors.initials: K
authors.lastname: Suzuki
authors.forename: James C
authors.initials: JC
authors.lastname: Hu
authors.forename: Barry L
authors.initials: BL
authors.lastname: Wanner
authors.forename: Hirotada
authors.initials: H
authors.lastname: Mori
authors.forename: Peter
authors.initials: P
authors.lastname: Uetz
mesh_terms: 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
chemical_list: D001426:Bacterial Proteins