Mode of regulation and the insulation of bacterial gene expression.

A gene can be said to be insulated from environmental variations if its expression level depends only on its cognate inducers, and not on variations in conditions. We tested the insulation of the lac promoter of E. coli and of synthetic constructs in which the transcription factor CRP acts as either an activator or a repressor, by measuring their input function-their expression as a function of inducers-in different growth conditions. We find that the promoter activities show sizable variation across conditions of 10%-100% (SD/mean). When the promoter is bound to its cognate regulator(s), variation across conditions is smaller than when it is unbound. Thus, mode of regulation affects insulation: activators seem to show better insulation at high expression levels, and repressors at low expression levels. This may explain the Savageau demand rule, in which E. coli genes needed often in the natural environment tend to be regulated by activators, and rarely needed genes by repressors. The present approach can be used to study insulation in other genes and organisms.

Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth.

When E. coli cells express unneeded protein, they grow more slowly. Such penalty to fitness associated with making proteins is called protein cost. Protein cost is an important component in the cost-benefit tradeoffs that underlie the evolution of protein circuits, but its origins are still poorly understood. Here, we ask how the protein cost varies during the exponential growth phase of E. coli. We find that cells growing exponentially following an upshift from overnight culture show a large cost when producing unneeded proteins. However, after several generations, while still in exponential growth, the cells enter a phase where cost is much reduced despite vigorous unneeded protein production. We find that this reduced-cost phase depends on the ppGpp system, which adjusts the amount of ribosomes in the cell and does not occur after a downshift from rich to poor medium. These findings suggest that protein cost is a transient phenomenon that happens upon an upshift in conditions and that cost is reduced when ribosomes and other cellular systems have increased to their appropriate steady-state level in the new condition.