Coordination of protein synthesis and decay in mammalian cells

Protein synthesis and decay rates must be tightly coordinated to ensure proteome homeostasis. How this coordination is established is unknown. Here we use quantitative live cell imaging combined with computational inference and proteomics to determine how changes in global protein synthesis rates alter protein decay rates. A passive adaptation of protein degradation and dilution rates operates in cells tightly coupling proliferation rate to protein synthesis rates, allowing to partially buffer changes in proteome concentrations with increased loss of short-lived proteins. In contrast, the proliferation rate of Mus musculus embryonic stem cells (mESCs) is hyposensitive to moderate changes in protein synthesis. mESCs uncouple protein degradation and dilution rates and robustly maintain their protein levels. Finally, we also show that terminally differentiated human glial cells strongly adapt protein degradation rates to altered protein synthesis. Our work illuminates the complex interplay between protein synthesis, degradation, and cell division to regulate proteome homeostasis. Overall design: We performed RNAseq to investigate the early transcriptomic response of NIH/3T3 and mESC to protein synthesis inhibition mediated by CHX treatment. The experiment was performed in triplicate for each cell line. A timecourse was performed and samples were collected after 0 h, 1 h, 2 h, 5 h, or 48 h of CHX treatment. Differential expression analysis with respect to the initial timepoint (0 hours) was then performed for each timepoint of each cell line.