Section: New Results

Growth control in bacteria and biotechnological applications

The ability to experimentally control the growth rate is crucial for studying bacterial physiology. It is also of central importance for applications in biotechnology, where often the goal is to limit or even arrest growth. Growth-arrested cells with a functional metabolism open the possibility to channel resources into the production of a desired metabolite, instead of wasting nutrients on biomass production. The objective of the RESET project, supported in the framework of the Programme d'Investissements d'Avenir (Section 8.2), is to develop novel strategies to limit or completely stop microbial growth and to explore biotechnological applications of these approaches.

A foundation result for growth control in bacteria was published in the journal Molecular Systems Biology at the end of 2015 [6]. In that publication, we described an engineered E. coli strain where 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. The publication also presented a biotechnological application of the synthetic growth switch in which both the wild-type E. coli strain and our modified strain were 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. This work has been continued in several directions in the context of the RESET project by Célia Boyat. Moreover, extending work on self-replicator models of bacterial growth, we have studied the production of metabolites by means of the growth switch from an optimal control perspective, in a paper that is currently being prepared for publication.

In a review published in Trends in Microbiology this year [19], we have put the scientific results mentioned above in a broader context. As illustrated by the synthetic growth switch, reengineering the gene expression machinery allows modifying naturally evolved regulatory networks and thereby profoundly reorganizing the manner in which bacteria allocate resources to different cellular functions. This opens new opportunities for our fundamental understanding of microbial physiology and for a variety of applications. We describe how recent breakthroughs in genome engineering and the miniaturization and automation of culturing methods have offered new perspectives for the reengineering of the transcription and translation machinery in bacteria as well as the development of novel in vitro and in vivo gene expression systems. In our paper, we review different examples from the unifying perspective of resource reallocation, and discuss the impact of these approaches for microbial systems biology and biotechnological applications.