Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

• DOI: 10.1371/journal.pbio.1000096
• Publication Date: 2009-04-21T17:19:05Z
• Authors: Pingzhao Hu; Sarath Chandra Janga; Mohan Babu; J. Javier Díaz-Mejía; Gareth Butland; Wenhong Yang; Oxana Pogoutse; Xinghua Guo; Sadhna Phanse; Peter Wong; Shamanta Chandran; Constantine Chris...; Anaies Nazarians-...; Negin Karimi Nasseri; Gabriel Musso; Mehrab Ali; Nazila Nazemof; Veronika Eroukova; Ashkan Golshani; Alberto Paccanaro; Jack F Greenblatt; Gabriel Moreno-Ha...; Andrew Emili
• Keywords: Proteome

One-third of the 4,225 protein-coding genes Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted E. coli, including pathogenic strains. To elucidate orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged strains and generated comprehensive genomic context inferences derive a high-confidence compendium for virtually entire proteome consisting 5,993 putative physical interactions 74,776 functional associations, most which are novel. Clustering respective probabilistic networks revealed orphan membership discrete multiprotein complexes modules together with annotated gene products, machine-learning strategy based on network integration implicated orphans specific processes. We provide additional experimental evidence supporting participation protein synthesis, amino acid metabolism, biofilm formation, motility, assembly bacterial cell envelope. This resource provides "systems-wide" blueprint model microbe, insights into evolutionary significance previously uncharacterized proteins.