Economics of the Bacterial Proteome
Extension of our quantitative mass spectrometry methods to study the entire E. coli proteome allows us to precisely quantify protein levels of > 800 proteins that account for ~95% of the proteome by mass. The ribosomal proteins represent a large sector of the proteome, and the abundance of these proteins is strongly linked to the growth rate of the cell, since the production of ribosomes determines the overall protein synthesis capacity for the cell.
In collaboration with the laboratory of Professor <Terry Hwa at UCSD>, we have developed a quantitative framework that describes the coarse-grained behavior of the proteome as a function of growth rate, in response to different nutrient limitations. Key sectors are “CARUSO”, which respond to Carbon-limitation, Ammonia-limitation, Ribosome-limitation, Unlimited, S-limitated (both C- and A-limitation), and O (unchanged). Remarkably, these sectors respond in a linear way as the growth rate changes, and these linear responses can be characterized by a small number of adjustable parameters. The slopes of the growth rate dependencies correspond to the “cost” of synthesizing the proteins that carry a particular metabolic flux. Thus, the bulk behavior of the proteome can be accurately modeled based on the change price of limiting nutrients in a macroeconomic model.