title: Interaction network containing conserved and essential protein complexes in Escherichia coli.
abstract: Proteins often function as components of multi-subunit complexes. Despite its long history as a model organism, no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames (approximately 23% of the genome). A total of 857 proteins, including 198 of the most highly conserved, soluble non-ribosomal proteins essential in at least one bacterial species, were tagged successfully, whereas 648 could be purified to homogeneity and their interacting protein partners identified by mass spectrometry. An interaction network of protein complexes involved in diverse biological processes was uncovered and validated by sequential rounds of tagging and purification. This network includes many new interactions as well as interactions predicted based solely on genomic inference or limited phenotypic data. This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.
authors.affiliation: Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada.
authors.forename: Gareth
authors.initials: G
authors.lastname: Butland
authors.forename: José Manuel
authors.initials: JM
authors.lastname: Peregrín-Alvarez
authors.forename: Joyce
authors.initials: J
authors.lastname: Li
authors.forename: Wehong
authors.initials: W
authors.lastname: Yang
authors.forename: Xiaochun
authors.initials: X
authors.lastname: Yang
authors.forename: Veronica
authors.initials: V
authors.lastname: Canadien
authors.forename: Andrei
authors.initials: A
authors.lastname: Starostine
authors.forename: Dawn
authors.initials: D
authors.lastname: Richards
authors.forename: Bryan
authors.initials: B
authors.lastname: Beattie
authors.forename: Nevan
authors.initials: N
authors.lastname: Krogan
authors.forename: Michael
authors.initials: M
authors.lastname: Davey
authors.forename: John
authors.initials: J
authors.lastname: Parkinson
authors.forename: Jack
authors.initials: J
authors.lastname: Greenblatt
authors.forename: Andrew
authors.initials: A
authors.lastname: Emili
mesh_terms: D000483:Alleles; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D019143:Evolution, Molecular; D005798:Genes, Bacterial / Q000235:genetics; D020043:Genes, Essential / Q000235:genetics; D023281:Genomics; D013058:Mass Spectrometry; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D011485:Protein Binding; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: D029968:Escherichia coli Proteins; D046912:Multiprotein Complexes; D011993:Recombinant Fusion Proteins