A chemostat array enables the spatio-temporal analysis of the yeast proteome

Area of Science:

• Cell biology
• Proteomics
• Microbial systems

Background:

• Understanding cellular responses to environmental changes is crucial for biological hypothesis testing.
• High-throughput methods are needed to analyze proteome dynamics at the single-cell level.

Purpose of the Study:

• To develop and utilize a microchemostat platform for large-scale, high-resolution analysis of yeast proteomes.
• To systematically investigate protein abundance and localization changes in response to various cellular perturbations.

Main Methods:

• A massively parallel microchemostat array was employed to culture and observe 1,152 yeast-green fluorescent protein (GFP)-tagged strains.
• Single-cell measurements of protein abundance, localization, cell size, and growth were performed with 20-minute resolution.
• Over 10,000 experiments were conducted across multiple conditions, including methyl methanesulfonate and UV irradiation, with deletion strains.

Main Results:

• Rapid and synchronous formation of processing bodies was observed upon UV irradiation.
• Four gene disruptions were identified that cause abnormal ribonucleotide-diphosphate reductase (Rnr4) localization.
• A systematic view of the yeast proteome in flux was generated, detailing protein dynamics.

Conclusions:

• The microchemostat platform enables large-scale interrogation of proteomes under dynamic conditions.
• Concurrent observation of multiple cellular parameters at the single-cell level provides comprehensive insights into cellular responses.
• This approach facilitates the discovery of genes involved in critical cellular processes like protein localization.