The functional proteome landscape of Escherichia coli

Recent developments in high-throughput reverse genetics( 1,2 ) have revolutionized our ability to map gene function and interactions( 3–6 ). The power of these approaches lies on their ability to discover functionally-associated genes, which elicit similar phenotypic changes across multiple perturbations (chemical, environmental, or genetic) when knocked out( 7–9 ). However, due to the large number of perturbations, these approaches have been limited to growth or morphological readouts( 10 ). Here, we have used a high-content biochemical readout, thermal proteome profiling( 11 ), to measure proteome-wide abundance and thermal stability of 121 genetic perturbations in Escherichia coli. We observed that thermal stability, and therefore the state and interactions of essential proteins is commonly modulated, opening up the possibility to study a protein group that is particularly inaccessible to genetics. We show that functionally-associated proteins have coordinated abundance and thermal stability changes across perturbations, due to their co-regulation and physical interactions (with proteins, metabolites, or co-factors). Finally, we provide mechanistic insights into previously determined growth phenotypes( 12 ) that go beyond the deleted gene. These data, available at http://ecoliTPP.shiny.embl.de, represent a rich resource for inferring protein functions and interactions.