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Submitted on August 8, 2002
Vet Preclinical Sciences, University of Liverpool, Liverpool, Merseyside L697ZJ
Corresponding Author: r.beynon{at}liv.ac.uk
Functional genomics experiments frequently involve a comparison of the levels of gene expression between two or more genetic, developmental, or physiological states. Such comparisons can be carried out at either the RNA (transcriptome) or protein (proteome) level, but there is often a lack of congruence between parallel analyses using these two approaches. In order to fully interpret protein abundance data from proteomics experiments, it is necessary to understand the contributions made by the opposing processes of synthesis and degradation to the transition between the states compared. Thus, there is a need for reliable methods to determine the rates of turnover of individual proteins at amounts comparable to those obtained in proteomics experiments. Here, we show that stable-isotope-labelled amino acids can be used to define the rate of breakdown of individual proteins by inspection of mass shifts in tryptic fragments. The approach has been applied to an analysis of abundant proteins in glucose-limited yeast cells grown in aerobic chemostat culture at steady state. The average rate of degradation of 50 proteins was 2.2 %/h, although some proteins were turned over at imperceptible rates, and others had degradation rates of almost 10 %/h. This range of values suggests that protein turnover is a significant missing dimension in proteomics experiments and needs to be considered when assessing protein abundance data and comparing it to the relative abundance of cognate mRNA species.
Revised on August 27, 2002
Accepted on August 28, 2002
Dynamics of protein turnover, a missing dimension in proteomics
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