title: Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods.
abstract: Escherichia coli K-12 and B strains have most widely been employed for scientific studies as well as industrial applications. Recently, the complete genome sequences of two representative descendants of E. coli B strains, REL606 and BL21(DE3), have been determined. Here, we report the subproteome reference maps of E. coli B REL606 by analyzing cytoplasmic, periplasmic, inner and outer membrane, and extracellular proteomes based on the genome information using experimental and computational approaches. Among the total of 3487 spots, 651 proteins including 410 non-redundant proteins were identified and characterized by 2-DE and LC-MS/MS; they include 440 cytoplasmic, 45 periplasmic, 50 inner membrane, 61 outer membrane, and 55 extracellular proteins. In addition, subcellular localizations of all 4205 ORFs of E. coli B were predicted by combined computational prediction methods. The subcellular localizations of 1812 (43.09%) proteins of currently unknown function were newly assigned. The results of computational prediction were also compared with the experimental results, showing that overall precision and recall were 92.16 and 92.16%, respectively. This work represents the most comprehensive analyses of the subproteomes of E. coli B, and will be useful as a reference for proteome profiling studies under various conditions. The complete proteome data are available online (http://ecolib.kaist.ac.kr).
authors.affiliation: Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), BioProcess Engineering Research Center, and Institute for the BioCentury, KAIST, Yuseong-gu, Daejeon, Republic of Korea.
authors.forename: Mee-Jung
authors.initials: MJ
authors.lastname: Han
authors.forename: Hongseok
authors.initials: H
authors.lastname: Yun
authors.forename: Jeong Wook
authors.initials: JW
authors.lastname: Lee
authors.forename: Yu Hyun
authors.initials: YH
authors.lastname: Lee
authors.forename: Sang Yup
authors.initials: SY
authors.lastname: Lee
authors.forename: Jong-Shin
authors.initials: JS
authors.lastname: Yoo
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Kim
authors.forename: Jihyun F
authors.initials: JF
authors.lastname: Kim
authors.forename: Cheol-Goo
authors.initials: CG
authors.lastname: Hur
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002462:Cell Membrane / Q000235:genetics / Q000378:metabolism; D002853:Chromatography, Liquid; D003593:Cytoplasm / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D015180:Electrophoresis, Gel, Two-Dimensional; D004926:Escherichia coli / Q000166:cytology / Q000235:genetics* / Q000378:metabolism; D005110:Extracellular Space / Q000235:genetics / Q000378:metabolism; D016680:Genome, Bacterial; D013058:Mass Spectrometry; D008432:Mathematical Computing; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D019897:Periplasm / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000235:genetics* / Q000378:metabolism; D012107:Research Design; D013045:Species Specificity; D013347:Subcellular Fractions / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins; D020543:Proteome