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  9.2 ), 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 this year [18] . In this publication, which is based on the PhD thesis of Jérôme Izard and post-doctoral work of Cindy Gomez Balderas, we describe 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. We have shown that our synthetic growth switch functions in a medium-independent and reversible way, and we have provided evidence that the switching phenotype arises from the ultrasensitive response of the growth rate to the concentration of RNA polymerase. In parallel, Delphine Ropers in collaboration with Jean-Luc Gouzé and Stefano Casagrande of the BIOCORE team are developing a quantitative model of the gene expression machinery to account for this surprising observation.

The publication in Molecular Systems Biology also presents a biotechnological 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 synthetic growth switch is thus a promising tool for gaining a better understanding of bacterial physiology and for applications in synthetic biology and biotechnology. We submitted a patent for such applications at the European Patent Office.

Whereas the synthetic growth switch has been designed for biotechnological purposes, the question can be asked how resource allocation is organized in wild-type strains that have naturally evolved. Recent work has shown that coarse-grained models of resource allocation can account for a number of empirical regularities relating the the macromolecular composition of the cell to the growth rate. Some of these models hypothesize control strategies enabling microorganisms to optimize growth. While these studies focus on steady-state growth, such conditions are rarely found in natural habitats, where microorganisms are continually challenged by environmental fluctuations. The aim of the PhD thesis of Nils Giordano is to extend the study of microbial growth strategies to dynamical environments, using a self-replicator model. In a recently submitted paper, we have formulated dynamical growth maximization as an optimal control problem that can be solved using Pontryagin’s Maximum Principle. We compare this theoretical gold standard with different possible implementations of growth control in bacterial cells. This study has been carried out in collaboration with Jean-Luc Gouzé and Francis Mairet of the BIOCORE project-team.