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The yeast peroxisomal proteome at absolute quantitative scale.

Hirak Das1, Silke Oeljeklaus1, Renate Maier1

  • 1Biochemistry II, Theodor-Boveri-Institute, Faculty of Chemistry and Pharmacy, University of Würzburg, Am Hubland, 97094, Würzburg, Germany.

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Summary

Yeast peroxisomes significantly increase protein abundance during oleate growth, especially for beta-oxidation enzymes, showcasing organelle adaptation. This study quanties the peroxisomal proteome changes under different metabolic conditions.

Keywords:
Saccharomyces cerevisiaeAbsolute quantificationMass spectrometryPeroxisomesProtein copy numbersProteomic ruler

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Area of Science:

  • Cell Biology
  • Biochemistry
  • Proteomics

Background:

  • Peroxisomes are crucial for lipid metabolism and redox balance.
  • Protein expression in yeast peroxisomes is metabolically regulated.
  • Understanding peroxisomal proteome dynamics is key to cellular function.

Purpose of the Study:

  • To quantify the yeast peroxisomal proteome under oleate and glucose conditions.
  • To investigate the adaptive changes in peroxisomal protein abundance.
  • To provide a quantitative resource for peroxisome biology research.

Main Methods:

  • Label-free mass spectrometry for absolute protein quantification.
  • Analysis of Saccharomyces cerevisiae proteome under distinct metabolic states (oleate vs. glucose).
  • Determination of protein copy numbers for peroxisomal and associated proteins.

Main Results:

  • Overall peroxisomal proteome is ~3-fold higher on oleate (2.8%) vs. glucose (0.8%).
  • Core peroxisomal proteins show a 9-fold increase on oleate, supporting fatty acid beta-oxidation.
  • Metabolic enzymes like beta-oxidation and glyoxylate cycle enzymes increased >500-fold; import machinery showed moderate changes (2-8 fold).

Conclusions:

  • Yeast peroxisomes undergo significant remodeling in response to metabolic cues.
  • The organelle exhibits remarkable adaptive flexibility, particularly in metabolic enzyme content.
  • This quantitative proteomic dataset serves as a valuable resource for studying peroxisome function and adaptation.