Correlation between protein and mRNA abundance in yeast

We have determined the relationship between mRNA and protein expression lev els for selected genes expressed in the yeast Saccharomyces cerevisiae grow ing at mid-log phase. The proteins contained in total yeast cell lysate wer e separated by high-resolution two-dimensional (2D) gel electrophoresis. Ov er 150 protein spots were excised and identified by capillary liquid chroma tography-tandem mass spectrometry (LC-MS/MS). Protein spots were quantified by metabolic labeling and scintillation counting. Corresponding mRNA level s 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 mRN A data. Indeed, for some genes, while the mRNA levels were of the same valu e the protein levels varied by more than 20-fold. Conversely, invariant ste ady state levels of certain proteins were observed with respective mRNA tra nscript levels that varied by as much as 30-fold. Another interesting obser vation is that codon bias is not a predictor of either protein or mRNA leve ls. Our results clearly delineate the technical boundaries of current appro aches for quantitative analysis of protein expression and reveal that simpl e deduction from mRNA transcript analysis is Insufficient.