Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods

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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).
Publisher
WILEY-BLACKWELL
Issue Date
2011-04
Language
English
Article Type
Article
Keywords

OUTER-MEMBRANE VESICLES; NADH-UBIQUINONE OXIDOREDUCTASE; CELL-DENSITY CULTIVATION; GRAM-NEGATIVE BACTERIA; P-TYPE ATPASE; RECOMBINANT PROTEINS; STRAINS REL606; PHOSPHOTRANSFERASE SYSTEM; SIGNAL PEPTIDES; FUSION PARTNER

Citation

PROTEOMICS, v.11, no.7, pp.1213 - 1227

ISSN
1615-9853
URI
http://hdl.handle.net/10203/98127
Appears in Collection
CBE-Journal Papers(저널논문)
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