Journal
PLOS BIOLOGY
Volume 7, Issue 4, Pages 929-947Publisher
PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pbio.1000096
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Funding
- Canadian Institutes of Health Research [MOP-77639]
- Ontario Research and Development Challenge Fund, Genome Canada
- Ontario Genomics Institute
- Natural Sciences and Engineering Research Council of Canada
- BBSRC [BB/F00964X/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/F00964X/1] Funding Source: researchfish
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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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