Because of its central position in the microbial research community, the Gram-negative bacterium Escherichia coli plays a leading role in investigations of the fundamental molecular biology of bacteria. This experimentally tractable microbe is a workhorse in basic and applied research aimed at elucidating the mechanistic basis of prokaryotic processes and traits, including those of pathogens. The ever-expanding availability of genomic resources makes E. coli particularly well-suited to systematic investigations of microbial protein components and functional relationships on a global scale. These include a genome-wide collection of single-gene deletion strains along with extensive knowledge of regulatory circuits and metabolic pathways. Yet despite being the most highly studied model bacterium, a recent comprehensive community annotation effort for the fully sequenced reference K-12 laboratory strains indicated that only half (54%) of the protein-coding gene products of E. coli currently have experimental evidence indicative of a biological role. The remaining genes have either only generic, homology-derived functional attributes (e.g. “predicted DNA-binding”) or no discernable physiological significance. Some of these functional “orphans” may have eluded characterization in part because they exhibit mild mutant phenotypes, are expressed at low or undetectable levels, or have limited homology to annotated genes.
One goal of modern biology is to chart groups of proteins that act together to perform biological processes via direct and indirect interactions. Such groupings are sometimes called functional modules. The types of protein interaction within modules include physical interactions that generate protein complexes and biochemical associations that make up metabolic pathways. Researchers have combined proteomic and bioinformatic tools and used them to decipher a large number of protein interactions, complexes and functional modules with high confidence. In addition, exploring the topology of the resulting interaction networks, they successfully predicted specific biological roles for a number of proteins with previously unknown functions, and identified some potential drug targets. Although their work is focused on E. coli, their phylogenetic projections suggest that a considerable fraction of observations and predictions can be extrapolated to many other bacterial taxa. As all the data derived from this study are publicly available (at eNet), others may build on this work for further hypothesis-driven studies of gene function discovery.
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol 7(4): e1000096
One-third of the 4,225 protein-coding genes of 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 to E. coli, including pathogenic strains. To elucidate the orphans’ biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a ‘‘systems-wide’’ functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.
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The PLoS ONE Prokaryotic Genome Collection is an attempt to present and highlight a number of important articles that describe whole genome sequence and/or comparative genomics of important prokaryotic organisms:
