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

Cited 12 time in scopus
Metadata Downloads
Title
Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods
Author(s)
M J Han; H Yun; J W Lee; Y H Lee; S Y Lee; J S Yoo; J Y Kim; Jihyun Kim; Cheol-Goo Hur
Bibliographic Citation
Proteomics, vol. 11, no. 7, pp. 1213-1227
Publication Year
2011
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.
Keyword
Computational predictionEscherichia coli BMicrobiologySubcellular localization
ISSN
1615-9853
Publisher
Wiley
DOI
http://dx.doi.org/10.1002/pmic.201000191
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
Files in This Item:
  • There are no files associated with this item.


Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.