Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle

Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ~20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. Distinct levels of protein regulation are preferentially utilized for different aspects of the cell cycle, with changes in protein concentration being mostly involved in cell cycle control, while changes in protein localization in the biophysical implementation of the cell cycle program. We present a resource for exploring global proteome dynamics during the cell cycle, which will aid in understanding a fundamental biological process at a systems level. Overall design: To understand how periodicity in protein concentration emerges during the cell cycle, we generated cell cycle-specific ribosome profiling and RNA-seq datasets in duplicate. Briefly, we synchronized cells in G1 phase with alpha factor, and isolated cells at five time-points after release into fresh medium, corresponding to the phases used for in silico synchrony of our proteomics data (G1 Post-Start; S/G2; Metaphase; Anaphase and Telophase; G1 Pre-Start was excluded due to the method of synchrony).