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

Mee Jung Han, Hongseok Yun, Jeong Wook Lee, Yu Hyun Lee, Sang Yup Lee, Jong Shin Yoo, Jin Young Kim, Jihyun F. Kim, Cheol Goo Hur

Research output: Contribution to journalArticle

12 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1213-1227
Number of pages15
JournalProteomics
Volume11
Issue number7
DOIs
Publication statusPublished - 2011 Apr 1

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Proteome
Computational methods
Escherichia coli
Genes
Genome
Membranes
Proteins
Open Reading Frames
Industrial applications

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology

Cite this

Han, Mee Jung ; Yun, Hongseok ; Lee, Jeong Wook ; Lee, Yu Hyun ; Lee, Sang Yup ; Yoo, Jong Shin ; Kim, Jin Young ; Kim, Jihyun F. ; Hur, Cheol Goo. / Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods. In: Proteomics. 2011 ; Vol. 11, No. 7. pp. 1213-1227.
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Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods. / Han, Mee Jung; Yun, Hongseok; Lee, Jeong Wook; Lee, Yu Hyun; Lee, Sang Yup; Yoo, Jong Shin; Kim, Jin Young; Kim, Jihyun F.; Hur, Cheol Goo.

In: Proteomics, Vol. 11, No. 7, 01.04.2011, p. 1213-1227.

Research output: Contribution to journalArticle

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