Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. Export

@article{citeulike:4462926, abstract = {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.}, author = {Hu, Pingzhao and Janga, Sarath Chandra C. and Babu, Mohan and D\'{\i}az-Mej\'{\i}a, Javier J. and Butland, Gareth and Yang, Wenhong and Pogoutse, Oxana and Guo, Xinghua and Phanse, Sadhna and Wong, Peter and Chandran, Shamanta and Christopoulos, Constantine and Nazarians-Armavil, Anaies and Nasseri, Negin Karimi K. and Musso, Gabriel and Ali, Mehrab and Nazemof, Nazila and Eroukova, Veronika and Golshani, Ashkan and Paccanaro, Alberto and Greenblatt, Jack F. and Moreno-Hagelsieb, Gabriel and Emili, Andrew}, citeulike-article-id = {4462926}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pbio.1000096}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19402753}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19402753}, day = {28}, doi = {10.1371/journal.pbio.1000096}, issn = {1545-7885}, journal = {PLoS biology}, keywords = {ecoli, network\_biology}, month = {April}, number = {4}, pages = {e1000096+}, posted-at = {2009-05-05 03:54:06}, priority = {2}, publisher = {Public Library of Science}, title = {Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.}, url = {http://dx.doi.org/10.1371/journal.pbio.1000096}, volume = {7}, year = {2009} }

TY - JOUR ID - citeulike:4462926 L3 - citeulike-article-id:4462926 N2 - 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. IS - 4 JF - PLoS biology SN - 1545-7885 TI - Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PB - Public Library of Science VL - 7 SP - e1000096 KW - ecoli KW - network_biology AU - Hu, Pingzhao AU - Janga, Sarath Chandra AU - Babu, Mohan AU - Díaz-Mejía, Javier AU - Butland, Gareth AU - Yang, Wenhong AU - Pogoutse, Oxana AU - Guo, Xinghua AU - Phanse, Sadhna AU - Wong, Peter AU - Chandran, Shamanta AU - Christopoulos, Constantine AU - Nazarians-Armavil, Anaies AU - Nasseri, Negin Karimi AU - Musso, Gabriel AU - Ali, Mehrab AU - Nazemof, Nazila AU - Eroukova, Veronika AU - Golshani, Ashkan AU - Paccanaro, Alberto AU - Greenblatt, Jack AU - Moreno-Hagelsieb, Gabriel AU - Emili, Andrew PY - 2009/04/28/ UR - http://dx.doi.org/10.1371/journal.pbio.1000096 ER -