Dynamic allocation of proteomic resources by E. coli in rich and minimal media

Rapid adaptation to changing environment is central to bacterial fitness. In rich medium, Escherichia coli primarily direct gene expression towards ribosome biogenesis and cell growth. Upon transition to minimal medium, a large number of biosynthesis genes must be turned on before growth can resume. Quantitative proteomics reveals a hierarchy of growth bottlenecks in amino acid biosynthesis, establishing a simple positive relation between the onset time of many enzymes across biosynthesis pathways and the fractional “reserve” of these enzymes maintained while growing in rich medium when they are not needed. A coarse-grained kinetic model quantitatively captures the enzyme recovery kinetics across many pathways, based solely on snapshots of the proteome right before and long after the transition, without invoking any ad hoc fitting parameters. These results establish the adoption of an “as-needed” gene expression program across biosynthetic pathways and the simple regulatory strategies underlying this program.