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 depends on their ability to identify functionally associated genes, which elicit similar phenotypic changes across several perturbations (chemical, environmental or genetic) when knocked out 7 – 9 . However, owing to the large number of perturbations, these approaches have been limited to growth or morphological readouts 10 . Here we use a high-content biochemical readout, thermal proteome profiling 11 , to measure the proteome-wide protein abundance and thermal stability in response to 121 genetic perturbations in Escherichia coli . We show that thermal stability, and therefore the state and interactions of essential proteins, is commonly modulated, raising the possibility of studying a protein group that is particularly inaccessible to genetics. We find that functionally associated proteins have coordinated changes in abundance and thermal stability across perturbations, owing to their co-regulation and physical interactions (with proteins, metabolites or cofactors). Finally, we provide mechanistic insights into previously determined growth phenotypes 12 that go beyond the deleted gene. These data represent a rich resource for inferring protein functions and interactions. Thermal proteome profiling combined with a reverse genetics approach provides insights into the abundance and thermal stability of the global proteome of Escherichia coli .