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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
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Quantitative analysis of chaperone network throughput in budding yeast.

Philip Brownridge1, Craig Lawless, Aishwarya B Payapilly

  • 1Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.

Proteomics
|February 20, 2013
PubMed
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Molecular chaperones are crucial for protein folding in yeast. This study quantifies chaperone abundance and reveals their workload, efficiency, and target preferences, showing they handle the majority of cellular protein flux.

Area of Science:

  • Proteomics
  • Molecular Biology
  • Yeast Genetics

Background:

  • Molecular chaperones are essential for protein folding and stress response in eukaryotes.
  • The budding yeast Saccharomyces cerevisiae has a well-characterized chaperone network with 63 annotated chaperones.
  • Previous studies used affinity purification and MS/MS to identify chaperone targets.

Purpose of the Study:

  • To quantify the absolute abundance (copies per cell) of yeast chaperones using QconCAT methodology and SRM-MS.
  • To compare these quantitative estimates with existing data and analyze the relationship between chaperone abundance and their targets.
  • To characterize chaperone 'throughput' and protein flux on a proteome-wide scale in an unstressed model eukaryote.

Main Methods:

  • Application of the QconCAT methodology for absolute quantification of yeast chaperones.

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  • Selected Reaction Monitoring Mass Spectrometry (SRM MS) for direct quantification.
  • Integration of quantitative data with interactome data to analyze chaperone-target relationships.

    • Main Results:

    • Direct quantification of yeast chaperones in absolute terms (copies per cell).
    • Comparison of QconCAT results with existing quantitative estimates, highlighting methodological differences.
    • Demonstration of a distinct relationship between chaperone abundance and their targets.
    • Characterization of chaperone class specializations regarding workload, efficiency, and subcellular localization.
    • Estimation of protein flux through molecular chaperones, revealing they handle ~62% of total cellular protein flux.

    Conclusions:

    • Molecular chaperones are critical for managing the majority of protein flux in eukaryotic cells.
    • Chaperone classes exhibit specialized roles, workloads, and localization preferences.
    • The study provides novel insights into chaperone function and importance by integrating quantitative proteomics with interactome data.