Control of rRNA Synthesis in Escherichia coli : a Systems Biology Approach

Abstract

SUMMARY The first part of this review contains an overview of the various contributions and models relating to the control of rRNA synthesis reported over the last 45 years. The second part describes a systems biology approach to identify the factors and effectors that control the interactions between RNA polymerase and rRNA (rrn) promoters of Escherichia coli bacteria during exponential growth in different media. This analysis is based on measurements of absolute rrn promoter activities as transcripts per minute per promoter in bacterial strains either deficient or proficient in the synthesis of the factor Fis and/or the effector ppGpp. These absolute promoter activities are evaluated in terms of rrn promoter strength (V max/Km ) and free RNA polymerase concentrations. Three major conclusions emerge from this evaluation. First, the rrn promoters are not saturated with RNA polymerase. As a consequence, changes in the concentration of free RNA polymerase contribute to changes in rrn promoter activities. Second, rrn P2 promoter strength is not specifically regulated during exponential growth at different rates; its activity changes only when the concentration of free RNA polymerase changes. Third, the effector ppGpp reduces the strength of the rrn P1 promoter both directly and indirectly by reducing synthesis of the stimulating factor Fis. This control of rrn P1 promoter strength forms part of a larger feedback loop that adjusts the synthesis of ribosomes to the availability of amino acids via amino acid-dependent control of ppGpp accumulation.

Biochemical reactions in crowded environments: revisiting the effects of volume exclusion with simulations

“…These two reaction paradigms can be used to describe many different processes in cells, including some that are not enzymatic in a strict sense. An example for the latter is binding of RNA polymerase to a promoter and initiation of transcription, which can be described (within a minimal mathematical representation) by Michaelis-Menten kinetics with the promoter taking the role of the enzyme [39,40]. In the following, we will thus discuss some applications of these two elementary reactions to processes in gene expression.…”

A Proximal Promoter Element Required for Positive Transcriptional Control by Guanosine Tetraphosphate and DksA Protein during the Stringent Response

“…ribosomes) are in exceptionally high demand need to exhibit a high maximal clearing capacity. Indeed rrnB P1 exhibits an exceedingly high maximal velocity of expression and initiates transcription with one of the highest frequencies known (57)(58)(59). From this it follows that such promoters require a high RNAP concentration for saturation, and rrn promoters are, in this model, predicted to be favored by elevated levels of free RNAP.…”

Molecular crowding limits translation and cell growth

“…In the model organism Escherichia coli, over half of the biomass is protein (2), and protein synthesis accounts for more than two-thirds of the cell's ATP budget during rapid growth (3). Therefore, the machinery of protein synthesis, i.e., ribosomes, tRNAs, and ribosome-affiliated factors, plays a central role in maintaining exponential growth (1,4). This is manifested by an increased ribosome content in rapidly growing cells (2,5,6), by direct observations that protein synthesis is limited by the availability of free ribosomes (7), and by considerations that link evolutionary selective pressure to the cost of protein synthesis (8).…”