The proteome of a cell determines its structural and functional features and needs to be tightly regulated to maintain proper cellular function. The level of each protein in a cell is set by its rate of synthesis and decay. The interplay between these rates determines protein turnover, which can vary strongly between different cell types. These rates exhibit intrinsic variability in vivo and fluctuate according to nutriment availability and other environmental cues. It is known that the inhibition of protein decay and the subsequent accumulation of misfolded proteins triggers the Integrated Stress Response that ultimately represses protein expression. Meanwhile, much less is known about how a change in protein synthesis impacts protein decay in mammalian cells.

This PhD thesis aims to quantitatively demonstrate and dissect the coordination of protein synthesis and decay in mammalian cells. To this end, we utilize well-controlled cellular and perturbation models, state-of-the-art quantitative live-cell imaging techniques and analysis pipelines, a novel Bayesian inference algorithm, and dynamic SILAC. To comprehensively address the research question, we have introduced a novel theoretical understanding of the concept of protein turnover, proposed new analytical tools, and demonstrated how this novel approach may lead to a reconsideration of previously published data and results.

We show that the adaptation of the protein decay to a change in protein synthesis is primarily mediated by a core passive adaptation mechanism unable to maintain protein levels, yet buffering them. Using a simple mathematical model, we were able to quantitatively predict this protein turnover adaptation and protein level fold-change at steady-state. We demonstrate that protein decay adapts to protein synthesis in the 5-10 hours timescale. Moreover, we find that in mouse embryonic stem cells, a facultative mTOR-mediated adaptation adds up to the core passive adaptation, ensuring protein level maintenance.

This work shed light on the dynamic and the intertwining of protein synthesis and protein decay. It also highlights the impossibility of fully disentangling these two fundamental processes of cell biology.