TY - JOUR
T1 - Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
AU - Lu, Peng
AU - Vogel, Christine
AU - Wang, Rong
AU - Yao, Xin
AU - Marcotte, Edward M.
N1 - Funding Information:
We thank John Prince and Aleksey Nakorchevskiy for valuable discussion and help with computational analysis of peptide fragmentation. This work was supported by grants from the Welch (F-1515) and Packard Foundations, the National Science Foundation and National Institutes of Health. C.V. acknowledges support by the International Human Frontier of Science Program.
PY - 2007/1/5
Y1 - 2007/1/5
N2 - We report a method for large-scale absolute protein expression measurements (APEX) and apply it to estimate the relative contributions of transcriptional- and translational-level gene regulation in the yeast and Escherichia coli proteomes. APEX relies upon correcting each protein's mass spectrometry sampling depth (observed peptide count) by learned probabilities for identifying the peptides. APEX abundances agree with measurements from controls, western blotting, flow cytometry and two-dimensional gels, as well as known correlations with mRNA abundances and codon bias, providing absolute protein concentrations across approximately three to four orders of magnitude. Using APEX, we demonstrate that 73% of the variance in yeast protein abundance (47% in E. coli) is explained by mRNA abundance, with the number of proteins per mRNA log-normally distributed about ∼5,600 (∼540 in E. coli) protein molecules/mRNA. Therefore, levels of both eukaryotic and prokaryotic proteins are set per mRNA molecule and independently of overall protein concentration, with >70% of yeast gene expression regulation occurring through mRNA-directed mechanisms.
AB - We report a method for large-scale absolute protein expression measurements (APEX) and apply it to estimate the relative contributions of transcriptional- and translational-level gene regulation in the yeast and Escherichia coli proteomes. APEX relies upon correcting each protein's mass spectrometry sampling depth (observed peptide count) by learned probabilities for identifying the peptides. APEX abundances agree with measurements from controls, western blotting, flow cytometry and two-dimensional gels, as well as known correlations with mRNA abundances and codon bias, providing absolute protein concentrations across approximately three to four orders of magnitude. Using APEX, we demonstrate that 73% of the variance in yeast protein abundance (47% in E. coli) is explained by mRNA abundance, with the number of proteins per mRNA log-normally distributed about ∼5,600 (∼540 in E. coli) protein molecules/mRNA. Therefore, levels of both eukaryotic and prokaryotic proteins are set per mRNA molecule and independently of overall protein concentration, with >70% of yeast gene expression regulation occurring through mRNA-directed mechanisms.
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U2 - 10.1038/nbt1270
DO - 10.1038/nbt1270
M3 - Article
C2 - 17187058
AN - SCOPUS:33846165487
SN - 1087-0156
VL - 25
SP - 117
EP - 124
JO - Nature Biotechnology
JF - Nature Biotechnology
IS - 1
ER -