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Using microorganisms for bioproduction requires the reorientation of metabolic fluxes from biomass synthesis to the production of compounds of interest. We previously engineered a synthetic growth switch in Escherichia coli based on inducible expression of the β‐ and β′‐subunits of RNA polymerase. Depending on the level of induction, the cells stop growing or grow at a rate close to that of the wild‐type strain. This strategy has been successful in transforming growth‐arrested bacteria into biofactories with a high production yield, releasing cellular resources from growth towards biosynthesis. However, high selection pressure is placed on a growth‐arrested population, favoring mutations that allow cells to escape from growth control. Accordingly, we made the design of the growth switch more robust by building in genetic redundancy. More specifically, we added the rpoA gene, encoding for the α‐subunit of RNA polymerase, under the control of a copy of the same inducible promoter used for expression control of ββ′. The improved growth switch is much more stable (escape frequency <10−9), while preserving the capacity to improve production yields. Moreover, after a long period of growth inhibition the population can be regenerated within a few generations. This opens up the possibility to alternate biomass accumulation and product synthesis over a longer period of time and is an additional step towards the dynamical control of bioproduction. [ABSTRACT FROM AUTHOR]

The ability to control growth is essential for fundamental studies of bacterial physiology and biotechnological applications. We have engineered an Escherichia coli strain in which the transcription of a key component of the gene expression machinery, RNA polymerase, is under the control of an inducible promoter. By changing the inducer concentration in the medium, we can adjust the RNA polymerase concentration and thereby switch bacterial growth between zero and the maximal growth rate supported by the medium. We show that our synthetic growth switch functions in a medium-independent and reversible way, and we provide evidence that the switching phenotype arises from the ultrasensitive response of the growth rate to the concentration of RNA polymerase. We present an application of the growth switch in which both the wild-type E. coli strain and our modified strain are endowed with the capacity to produce glycerol when growing on glucose. Cells in which growth has been switched off continue to be metabolically active and harness the energy gain to produce glycerol at a twofold higher yield than in cells with natural control of RNA polymerase expression. Remarkably, without any further optimization, the improved yield is close to the theoretical maximum computed from a flux balance model of E. coli metabolism. The proposed synthetic growth switch is a promising tool for gaining a better understanding of bacterial physiology and for applications in synthetic biology and biotechnology. [ABSTRACT FROM AUTHOR]

Gene expression is controlled by the joint effect of (i) the global physiological state of the cell, in particular the activity of the gene expression machinery, and (ii) DNA-binding transcription factors and other specific regulators.We present a model-based approach to distinguish between these two effects using time-resolved measurements of promoter activities.We demonstrate the strength of the approach by analyzing a circuit involved in the regulation of carbon metabolism in E. coli. Our results show that the transcriptional response of the network is controlled by the physiological state of the cell and the signaling metabolite cyclic AMP (cAMP). The absence of a strong regulatory effect of transcription factors suggests that they are not the main coordinators of gene expression changes during growth transitions, but rather that they complement the effect of global physiological control mechanisms. This change of perspective has important consequences for the interpretation of transcriptome data and the design of biological networks in biotechnology and synthetic biology. [ABSTRACT FROM AUTHOR]

Deals with transcriptional activation in prokaryotes. Modulation of overall geometry of DNA; Architectural protein integration host factor (IHF) of Escherichia coli; Effect of a DNA-bending protein on transcription; Generation of transcriptionally up mutants; Characterization of the mutant IHF proteins.

Focuses on participation of a heterodimeric DNA-binding and -bending protein in the regulation of a promoter. Stimulation of transcription by integration host factor (IHF); Correct phasing of the promoter with the IHF binding site; Importance of a flexible DNA joint between the sites bound by IHF and by RNA polymerase.