Computational and experimental approaches to chart theEscherichia colicell-envelope-associated proteome and interactome

Abstract

The bacterial cell-envelope consists of a complex arrangement of lipids, proteins and carbohydrates that serves as the interface between a microorganism and its environment or, with pathogens, a human host. Escherichia coli has long been investigated as a leading model system to elucidate the fundamental mechanisms underlying microbial cell-envelope biology. This includes extensive descriptions of the molecular identities, biochemical activities and evolutionary trajectories of integral transmembrane proteins, many of which play critical roles in infectious disease and antibiotic resistance. Strikingly, however, only half of the c. 1200 putative cell-envelope-related proteins of E. coli currently have experimentally attributed functions, indicating an opportunity for discovery. In this review, we summarize the state of the art of computational and proteomic approaches for determining the components of the E. coli cell-envelope proteome, as well as exploring the physical and functional interactions that underlie its biogenesis and functionality. We also provide a comprehensive comparative benchmarking analysis on the performance of different bioinformatic and proteomic methods commonly used to determine the subcellular localization of bacterial proteins.

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

“…Six of the seven orphans of this particular neighborhood are predicted to localize to the E. coli inner membrane [38]. We found that deletion of these orphans results in hypersensitivity to an otherwise exported drug, similar to that observed upon loss of the annotated components (Figure 7E), suggesting equal participation in the maintenance of cell homeostasis.…”

“…For the negative gold standards, we compiled pairs of proteins annotated with different subcellular localizations (i.e., one cytoplasmic, the other periplasmic or outer membrane-bound [38]. …”

Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies

“…The study identified 263 novel proteins potentially associated with the Symbiosis Interactome, and the topology of the Symbiosis Interactome was used to guide experimental techniques attempting to validate novel proteins involved in different stages of symbiosis. The second approach is proteomic analysis of the protein complexes, typically performed using affinity tag/pull-down of large protein complexes and then MS/MS characterization at a proteome level (Butland et al, 2005;Gingras et al, 2005;Krogan et al, 2006;Díaz-Mejía et al, 2009). Using this approach, some subsets of the interactomes, such as cell-envelopeassociated proteome and interactome in Escherichia coli, have been studied .…”

Global landscape of cell envelope protein complexes in Escherichia coli

“…Knowledge of cell envelope protein–protein interactions (cePPIs) and their physical and functional organization into multiprotein complexes (MPCs) therefore provides critical information into the basic systems governing prokaryotic physiology, which in turn is essential to combat infections by antibiotic-resistant pathogens. Yet while previous small-scale investigations in E. coli have identified certain MPCs required for peptidoglycan synthesis, chemotaxis, lipopolysaccharide (LPS) export and envelope assembly 2,4,5 , experimental data concerning the binding partners and functions of most bacterial CEPs are still lacking 6 .…”