For quantitative (phospho)proteomic experiments, E. coli cells were differentially labeled using the following stable isotope–labeled lysine derivatives: 4,4,5,5-D4 l-lysine (Lys4, medium-heavy lysine, K4, Cambridge Isotope Laboratories), 13C615N2 l-lysine (Lys8, heavy lysine, K8, Cambridge Isotope Laboratories), or l-lysine (Lys0, light lysine, K0, Sigma-Aldrich) (52). Both precultures and main cultures were grown in M9 minimal medium containing 0.0025% (w/v) Lys0, Lys4, or Lys8. The experimental design of all experiments is summarized in table S3.

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