Section: New Results

Models of carbon metabolism in bacteria

All free-living bacteria have to adapt to a changing environment. Specific regulatory systems respond to particular stresses, but the most common decision bacteria have to make is the choice between alternative carbon sources, each sustaining a specific, maximal growth rate. Many bacteria have evolved a strategy that consists in utilizing carbon sources sequentially, in general favouring carbon sources that sustain a higher growth rate. As long as a preferred carbon source is present in sufficient amounts, the synthesis of enzymes necessary for the uptake and metabolism of less favourable carbon sources is repressed. This phenomenon is called Carbon Catabolite Repression (CCR) and the most salient manifestation of this regulatory choice is diauxic growth, a phenomenon discovered by Jacques Monod more than 70 years ago. Although this system is one of the paradigms of the regulation of gene expression in bacteria, the underlying mechanisms remain controversial. CCR involves the coordination of different subsystems of the cell - responsible for the uptake of carbon sources, their breakdown for the production of energy and precursors, and the conversion of the latter to biomass.

The complexity of this integrated system, with regulatory mechanisms cutting across metabolism, gene expression, signaling and subject to global physical and physiological constraints, has motivated important modeling efforts over the past four decades, especially in the enterobacterium Escherichia coli. Different hypotheses concerning the dynamic functioning of the system have been explored by a variety of modeling approaches. In an article in Trends in Microbiology [19] , which was initiated during the sabbatical of Andreas Kremling in Grenoble in 2013, we have reviewed these studies and summarized their contributions to the quantitative understanding of CCR, focusing on diauxic growth in E. coli. Moreover, we have proposed a highly simplified representation of diauxic growth that makes it possible to bring out the salient features of the models proposed in the literature and confront and compare the explanations they provide. In parallel, specific aspects of CCR, in particular a better understanding of the role of the signalling molecule cyclic adenosine monophosphate (cAMP) in the dynamic regulation of promoters during growth transitions in E. coli, have been studied in the context of the PhD thesis of Valentin Zulkower, using both models and experimental data.

Beside CCR and the multiple regulatory systems controlling the metabolism of E. coli, the involvement of post-transcriptional regulation is uncertain. The post-transcriptional factor CsrA is stated as being the only regulator essential for the use of glycolytic substrates, but its impact on the functioning of central carbon metabolism has not been demonstrated. In the framework of the PhD thesis of Manon Morin, supported by a Contrat Jeune Scientifique INRA-Inria, the collaboration of Delphine Ropers, Muriel Cocaign-Bousquet and Brice Enjalbert from LISBP at INSA Toulouse has resulted in a multi-scale analysis of a wild-type strain and its isogenic mutant attenuated for CsrA. A variety of experimental data has been acquired for these two strains in relevant conditions, including growth parameters, gene expression levels, metabolite pools, enzyme activities and metabolic fluxes. Data integration, metabolic flux analysis and regulation analysis revealed the pivotal role of post-transcriptional regulation for reshaping carbon metabolism. In particular, the work has shed light on csrA essentiality and has provided an explanation for the glucose-phosphate stress observed in the mutant strain. A paper summarizing the work has been submitted for publication in a microbiology journal.