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

Area of Science:

• Cell Biology
• Proteomics
• Systems Biology

Background:

• Cell cycle progression depends on dynamic changes in protein levels and locations within the cell.
• Understanding these proteome dynamics is crucial for deciphering fundamental biological processes.

Purpose of the Study:

• To comprehensively map proteome dynamics, including protein concentration and subcellular localization, throughout the yeast cell cycle.
• To investigate the distinct regulatory mechanisms controlling protein concentration versus localization during cell cycle progression.

Main Methods:

• Utilized two distinct convolutional neural networks (CNNs) to analyze images of millions of live yeast cells.
• Achieved high-resolution analysis of protein concentration and localization across approximately 20 subcellular compartments.
• Applied computational methods to identify cell cycle-periodic proteins and their regulatory patterns.

Main Results:

• Approximately 25% of the proteome exhibits cell cycle periodicity in either concentration or localization, but rarely both.
• Protein concentration changes primarily regulate cell cycle control, while localization changes implement the biophysical aspects of the cell cycle program.
• Identified distinct regulatory strategies for concentration and localization, highlighting their specialized roles.

Conclusions:

• Protein concentration and localization are differentially regulated during the cell cycle, serving distinct functional roles.
• This study provides a valuable resource for systems-level understanding of proteome dynamics and cell cycle control.
• The findings offer insights into the fundamental mechanisms governing cell division and cellular organization.