Projects

Reallocation of cellular ressources for the heterologous protein production in Bacillus subtilis

In collaboration with V. Fromion (MAiAGE, INRA), the project focuses on the study of the effect of the production of heterologous production on the growth rate. This is part of an ITN project : http://proteinfactory-msca-itn.eu/

Transcription termination factor Rho and microbial phenotypic heterogeneity

Fluctuations in gene expression (noise) at the level of transcription initiation largely contribute to cell-to-cell variability within population. We study the regulatory role of the multi-functional transcription termination factor Rho, the major inhibitor of pervasive transcription in bacteria and the emerging global regulator of gene expression. We propose that termination activity of Rho might be among the mechanisms by which cells manage the intensity of transcriptional noise, thus affecting population heterogeneity.

Division of labor for production of natural products in synthetic bacterial communities

We build and analyze the functioning of complex synthetic consortia to decipher natural phenomena and for applications in biotechnology. The systemic characterization of the designed synthetic consortia will allow a better understanding of social interactions through global and targeted analyses of gene expression. The interest of such an approach is to be able to complexify the production pathways and optimize the production yields of compounds of interest.

Gene expression in the Gram positive bacterium B. subtilis

The aim of this project is to decipher the rules driving gene expression in the gram positive bacterium Bacillus subtilis.

We developed a knowledge-based mathematical model of translation that we experimentally validated. We identified a unique global regulation, which is growth rate dependent and that apply to all proteins constitutive or not, and which is independent of any dedicated transcriptional regulators. In light of evolutionary constraints, we do believe that such global regulations are shaped to minimize cost in bacterial resources allocation.

Genome engineering

Synthetic biology enables advances in chassis design for biotechnologies. Bacillus subtilis is a GRAS bacteria (Generally Recognized as Safe) of industrial interest. The genome engineering development for Escherichia coli has no equivalent in B. subtilis. This project therefore proposes to develop new methodologies for B. subtilis, based on CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat / CRISPR-associated protein 9) and recombineering (recombination mediated genetic engineering) to enable specific and controlled genome editing.

Minimal genome

This project was started with Philippe Noirot in 2013 and will soon be published ....

We have first identified the chromosomal dispensable regions allowing the genome reduction and the reduced strains have then been characterized. We were able to combine unmarked deletions / insertions and have engineered the chromosome of Bacillus subtilis at large scale. 

Tools development for the construction of chassis strains for biotechnology

Synthetic genetic circuits often fail to function as designed because of unwanted interactions between circuit components and the host system. A promising strategy to foster innovation in biotechnology relies on the construction of adequately streamlined host strains. In collaboration with Carol Lartigue (BFP, UMR 1332 INRA / Bordeaux Univ, Villenave d'Ornon).

Cell free

We are currently developping cell free systems. Cell-free synthetic biology emerges as a powerful and flexible enabling technology. Cell free systems activates biological machinery without the use of living cells, and allows direct control of transcription, translation and metabolism in an open environment.

Protein secretion

Bacillus subtilis is a model organism for Gram-positive bacteria and a workhorse for secreted enzyme production in the industry. Secretory and membrane proteins are translocated through the Sec Pathway. Although this highly conserved pathway has been extensively studied, there is a lack of knowledge about the protein interactions and complexes involved in this mechanism.Through the combination of techniques, mainly tandem affinity purification coupled to mass spectrometry and Blue Native PAGE, we studied the protein interactions within the (holo)translocon as well as with the accessory proteins. This is part of an ITN project named ProteinFactory: http://proteinfactory-msca-itn.eu/

Flavonoids: microbial production and mode of action

Part of an ANR project in collaboration with J.L Faulon (BioRetroSynth, INRA), we aim at developing efficient production strains for flavonoids. Our study focuses also on the understanding of their mode of action on Gram positive bacteria.

Bacillus subtilis engineering for the production of glucansucrases and glucopolymers in Bacillus subtilis

This project aims to develop a platform for the production of glucansucrases and glucopolymers by genome engineering and optimization of the culture conditions of Bacillus subtilis, an industrial bacterium with GRAS status. In collaboration with G. Véronèse (LISBP, Toulouse), and TWB.

Orthogonal Transcription

We aim to engineer systems to efficiently produce protein. Therefore, parallel and independent systems, as orthogonal expression systems, appear as useful tools to minimize undesired crosstalk between specific protein expression and cellular machinery. We will develop in Bacillus subtilis an orthogonal transcription system based on heterologous sigma factors.

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