title: Global topology analysis of the Escherichia coli inner membrane proteome.
abstract: The protein complement of cellular membranes is notoriously resistant to standard proteomic analysis and structural studies. As a result, membrane proteomes remain ill-defined. Here, we report a global topology analysis of the Escherichia coli inner membrane proteome. Using C-terminal tagging with the alkaline phosphatase and green fluorescent protein, we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins. By constraining a topology prediction algorithm with this data, we derived high-quality topology models for the 601 proteins, providing a firm foundation for future functional studies of this and other membrane proteomes. We also estimated the overexpression potential for 397 green fluorescent protein fusions; the results suggest that a large fraction of all inner membrane proteins can be produced in sufficient quantities for biochemical and structural work.
authors.affiliation: Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
authors.forename: Daniel O
authors.initials: DO
authors.lastname: Daley
authors.forename: Mikaela
authors.initials: M
authors.lastname: Rapp
authors.forename: Erik
authors.initials: E
authors.lastname: Granseth
authors.forename: Karin
authors.initials: K
authors.lastname: Melén
authors.forename: David
authors.initials: D
authors.lastname: Drew
authors.forename: Gunnar
authors.initials: G
authors.lastname: von Heijne
mesh_terms: D000469:Alkaline Phosphatase / Q000032:analysis / Q000235:genetics; D002462:Cell Membrane / Q000737:chemistry*; D003001:Cloning, Molecular; D019295:Computational Biology; D003593:Cytoplasm / Q000737:chemistry; D004926:Escherichia coli / Q000737:chemistry* / Q000235:genetics / Q000648:ultrastructure; D029968:Escherichia coli Proteins / Q000032:analysis* / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D020440:Gene Duplication; D005798:Genes, Bacterial; D049452:Green Fluorescent Proteins / Q000032:analysis / Q000235:genetics; D008565:Membrane Proteins / Q000032:analysis* / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D019897:Periplasm / Q000737:chemistry; D017433:Protein Structure, Secondary; D020543:Proteome; D011993:Recombinant Fusion Proteins
chemical_list: D029968:Escherichia coli Proteins; D008565:Membrane Proteins; D020543:Proteome; D011993:Recombinant Fusion Proteins; D049452:Green Fluorescent Proteins; D000469:Alkaline Phosphatase