Quantitative analysis of protein interaction network dynamics in yeast.

Area of Science:

• Molecular Biology
• Systems Biology
• Biochemistry

Background:

• Cellular functions rely on protein-protein interaction networks, which are dynamic and influenced by environmental conditions.
• Understanding these environment-dependent network dynamics is crucial for deciphering cellular mechanisms.
• Systematic measurement of protein interactions across various environments is needed to assess the relative importance of different regulatory mechanisms.

Purpose of the Study:

• To systematically measure in vivo protein complex abundance across diverse environments.
• To investigate the environment-dependent dynamics of protein-protein interaction networks.
• To provide a comprehensive resource of protein interaction data in Saccharomyces cerevisiae.

Main Methods:

• Employed a DNA-barcode-based multiplexed protein interaction assay.
• Measured the in vivo abundance of 1,379 binary protein complexes in Saccharomyces cerevisiae.
• Tested interactions across 14 distinct environmental conditions.

Main Results:

• 55% of measured binary protein complexes exhibited environment-dependent abundance.
• Transmembrane transporters were particularly involved in environment-dependent interactions.
• Network dynamics revealed prevalent concerted, protein-centered changes, especially around highly connected proteins.
• A mass-action model using mRNA levels accurately predicted complex abundance changes during a diauxic shift.

Conclusions:

• Protein-protein interaction networks are highly dynamic and significantly influenced by environmental factors.
• Concerted changes around highly connected proteins are a major feature of network dynamics.
• Relative mRNA levels can predict a substantial portion of protein complex abundance variance, particularly under specific metabolic shifts.
• The generated dataset serves as a valuable resource for studying cellular network mechanisms and dynamics.