About Synthetic Biology in Bordeaux (SB2)

In December 2013, with the help of the Regional Government, the first meeting on Synthetic Biology has held in Aquitaine. The event gathered over 200 participants from the industry and academia. Academics have then decided to structure the Synthetic Biology community in Bordeaux. This initiative is encouraged and financially supported by the University of Bordeaux. In 2014, thanks to a first financial support of the University, SB2 launched several actions : organizing an international Symposium, a call for projects (2 projects were supported) and supporting the Bordeaux i-GEM team. Since 2015, we are one of the four “Action Thématique Transversale” financially supported by the “Sciences du Vivant et de la Santé” Research Department of the University.

3 research programmes

Stabilisers for water-in-fluorinated-oil dispersions: key properties for microfluidic applications

Colonies of Mycoplasma hominis (x70, H. Renaudin)

Synthetic biology approaches for seamless deletions of MCS encoding genes in M. capricolum

Polymeresomes

Genomes, minimal cells and organisms, genomic engineering

By combining different approaches, the main goal of RP1 is to develop a number of minimal systems either micmicking the cells (protocells) or engineering minimal cells by starting with mycoplasmas.

Bioinformatics

Visualization of a sRNA predicted targets network. The validated are in yellow.

Biodiversity, metabolic engineering

The goal of metabolic engineering is to produce added-value molecules in a cost effective manner for industrial applications. In Bordeaux, host platforms not only include model organisms such E. coli and S. cerevisiae, but also higher organisms such as algae and higher plants like the high-throughput Nicotiana benthamiana transient leaf assay or genetically modified oilseed crops. Metabolism modelling is performed at different levels, from molecular to the cellular level.

Example of a G-quadruplex structure formed with a sequence found in the HIV-1 virus (Amrane, JACS 2014)

Protein-inspired nanostructures :Electron density surronding hydrophobic side chains in the crystal sructure of a helix bundle formed by a water soluble foldamer

Protein-inspired nanostructures: Crystal structure of a channel-type assembly with a water filled pore formed from helical oligourea foldamers

A protein dimer mediated by foldamer-protein, foldamer-foldamer and protein-protein interactions

Supramolecular Chemistry – Non covalalent intermolecular interactions

A Z33-yellow fluorescent protein fusion is adsorbed on a virus surface by mean of an antibody recognizing the virus major coat protein

Biomimetism, orthogonal biosystems, bionanoscience for synthetic biology

The goal of this research programme is to improve our current understanding of biological systems through molecular mimicry and to create bioinspired architectures mimicking biopolymers (task 1), to interface these new molecules with biomolecular components and to produce bio-orthogonal systems with new functions (task 2), and finally to use this molecular toolbox either for bottom up assemblies of artificial lab on a chip or to direct the “in cell” organization of complex functional macromolecular networks.

5 technology platforms

Organized within a common structure (CGFB), technological platforms are dedicated to the study of living organisms at cellular and molecular level. They are dedicated to the study of DNA, genes and byproducts (Genome-Transcriptome), proteins and protein modification (Proteome), metabolites and enzyme activities (Metabolome), cell imaging (BIC), biomacromolecules, proteins and nucleic acid complexes (BioPhysicoChemistry).

Cell imaging (BIC)

BioPhysicoChemistry

DNA, genes and byproducts

Proteome

Metabolites and enzyme activities

26 research teams

The research teams involved in SB2 are listed below. Note the teams are not UMR structures, but project teams.

Jean-Jacques Toulmé

Aptamères

Martin Teichman

Transcription Maturation et Structures

Jean-Louis Mergny

OLIFANS

Ivan Huc

Chimie supramoléculaire biomimétique

Gilles Guichard

Chimie Peptidomimétique

Dereck McCusker

Dynamics of Cell Growth and Division

Alain Blanchard

Mollicutes

Thierry Michon

Virus Nanotechnology

Michel Hernould

Biologie Synthétique Végétale

Jean-Paul di Rago

Molecular genetics of mitochondrial systems

Jean-Pierre Mazat

Virtual mitochondrion

Valérie Gabelica

BiophyMS

Fredéric Domergue

Surface Lipids

Fabien Darfeuille

Petits ARN non codant

Vincent Arondel

Biosynthèse de l’huile chez les plantes

Florence Corellou

Signalisation & régulation de la fluidité des membranes

Cécile Bébéar

IHMC

Isabelle Bestel

Molecular modeling for (bio)molecule engineering

Olivier Lambert

Architecture de complexes membranaires et processus cellulaires

Jean-Christophe Baret

Soft Micro Systems

Jean-Paul Salvetat

Microscopie des nanostructures

Isabelle Dutour

Modèles et Algorithmes pour la Bioinformatique et la Visualisation

Pascal Durrens

PLEIADE

Sébastien Lecommandoux

Auto-assemblages polymères et sciences du vivant

Frédéric Bringaud

Intermediate metabolism of Trypanosomes

Laurence Navailles

Matière molle : structure et dynamique