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Molecular and Cellular Biology, March 1999, p. 1720-1730, Vol. 19, No. 3
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

Correlation between Protein and mRNA Abundance in Yeast

Steven P. Gygi, Yvan Rochon, B. Robert Franza, and Ruedi Aebersold*

Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195-7730

Received 5 October 1998/Returned for modification 11 November 1998/Accepted 2 December 1998

We have determined the relationship between mRNA and protein expression levels for selected genes expressed in the yeast Saccharomyces cerevisiae growing at mid-log phase. The proteins contained in total yeast cell lysate were separated by high-resolution two-dimensional (2D) gel electrophoresis. Over 150 protein spots were excised and identified by capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS). Protein spots were quantified by metabolic labeling and scintillation counting. Corresponding mRNA levels were calculated from serial analysis of gene expression (SAGE) frequency tables (V. E. Velculescu, L. Zhang, W. Zhou, J. Vogelstein, M. A. Basrai, D. E. Bassett, Jr., P. Hieter, B. Vogelstein, and K. W. Kinzler, Cell 88:243-251, 1997). We found that the correlation between mRNA and protein levels was insufficient to predict protein expression levels from quantitative mRNA data. Indeed, for some genes, while the mRNA levels were of the same value the protein levels varied by more than 20-fold. Conversely, invariant steady-state levels of certain proteins were observed with respective mRNA transcript levels that varied by as much as 30-fold. Another interesting observation is that codon bias is not a predictor of either protein or mRNA levels. Our results clearly delineate the technical boundaries of current approaches for quantitative analysis of protein expression and reveal that simple deduction from mRNA transcript analysis is insufficient.

* Corresponding author. Mailing address: Department of Molecular Biotechnology, Box 357730, University of Washington, Seattle, WA 98195-7730. Phone: (206) 221-4196. Fax: (206) 685-7301. E-mail: ruedi{at}u.washington.edu.

Molecular and Cellular Biology, March 1999, p. 1720-1730, Vol. 19, No. 3
0270-7306/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


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