BLADE : Bacterial Adaptation, Diversity and Engineering(EAD4)

Research activities in the field of integrative physiology to decipher metabolic regulation in prokaryotes

 

In the last few years, the scientific strategy and composition of the team EAD4 have evolved:

  • The main objective of the team is to improve the performance of bacterial metabolism. It is divided into two distinct missions: to describe / understand and then to control /exploit the regulations by which bacteria reprogram their metabolic network enabling dynamic adaptation to the environment. To do this, the team has developed an original multi-scale approach to integrate genome-wide analyses of the different intracellular regulatory levels (mRNA, protein, metabolites, etc.) to macroscopic phenotypic characterization (physiological or metabolic). This systems biology-based approach is used to identify bottlenecks of bacterial adaptation and novel targets for reprogramming bacteria with improved characteristics, notably for synthetic biology applications.
  • After a long period of constant effectives, the number of team members has sharply increased, from only 3 researchers and a part-time technician in 2005, to reach nowadays around 20 persons (7 scientists, 3 research engineers, 1 technician and 1 technical assistant plus doctoral and post-doctoral fellows). The multidisciplinary team was constructed to facilitate close collaboration with mathematicians, physicists and recently reinforced with the recruitment of an engineer in bio-statistics and modeling. To enhance the multi-level competence of the team, two microbiologists, experts in genome and biodiversity analysis, were recruited in 2014.

A multi-scale and systemic approach on two model bacteria

  • The team is world-renowned for its expertise in lactic acid bacteria. The systemic approach was developed to understand the metabolic adaptation of Lactococcus lactis, the model of lactic acid bacteria, largely employed in the food industry (found in dairy products) and one of the most ingested bacteria in humans. This approach gradually evolved from biochemical pathway analysis to whole genome level molecular phenomena. Today, this integrative approach has been extended to the model bacterium Escherichia coli, comprising both commensal strains encountered in the gut and pathogenic strains. Introduction of this model in the team has led to an enlarged spectrum of academic collaborations and reinforced our application domains in Agro-Food industry and Nutrition, Human Health and White Biotechnology.
  • Multidisciplinary methods and approaches were developed (in-house and through collaborations) to better understand the dynamics of bacterial metabolic adaptation. Phenotype characterization generally begins with genotypic and phenotypic screenings. These approaches are based on our established skill-base to explore microbial biodiversity using molecular genomic techniques (high throughput sequencing, PFGE, MLST, CGH, etc.). Phenotypes are then analyzed through a multi-scale strategy combining macro-kinetic characterization (extracellular metabolome measurements, microbial engineering, biophysics, etc.) and systemic techniques to analyze at the molecular level, the different steps of the cellular process (in-house transcriptomics, collaborative proteomic and intracellular metabolomics, enzymatic activities, etc.). We have developed original biological methods such as the stabilome (stabilities of RNA molecules present in the cell), the translatome (number of ribosomes loaded on each messenger RNA) but also mathematical methods to integrate large datasets in order to better understand the dynamics of RNA expression and its consequences on cellular adaptation. In recent years, this analysis was supported by physico-chemical characterization of cells (size, hydrophobicity, adhesion, etc.) through the combination of biophysical tools (shear stress flow chamber, optical tweezer, fluorescence multiple particle tracking, AFM, FISH, etc.).

Relevant academic collaborations and partnerships to face industrial demands

  • The team EAD4 has developed a collaborative strategy with complementary national and international academic partners (Switzerland, Poland, Italy, Portugal and Estonia):
  • in molecular microbiology, with well-known groups for their expertise in the field of RNA regulation (LMGM-Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse and ITQB-Instituto de Tecnologia Quimica e Biologica, Lisbon, Portugal).
  • in biochemistry and fermentation (IBB-Institute of Biochemistry and Biophysics, Warsaw, Poland, Università degli Studi di Torino, Turin, Italy; CCFFT-Competence Center of Food and Fermentation Technology, Tallinn, Estonia).
  • in mathematics and physics with world-renowned groups in modeling (EPFL-École Polytechnique Fédérale de Lausanne, Switzerland ; INRIA-Institut National de Recherche en Informatique et en Automatique, Grenoble ; LAAS-Laboratoire d'Analyse et d'Architecture des Systèmes, Toulouse) and in bioinformatics and statistics (MIAT-Unité de Mathématiques et Informatique Appliquées de Toulouse, IMT-Institut de Mathématiques de Toulouse).
  • The team benefits from the technical support of local technology platforms (Genopole Toulouse Midi-Pyrénées).
  • The team exploits its expertise through collaborations with industrial partners, mainly in the Agro-Food domain (Danone, Soredab / Bongrain, Lactalis, Yoplait…), in the pharmaceutical industry (Sanofi Pasteur, Tolerys) and for biotechnology applications (GTP-Technology, Carbios).

 

 Examples of projects

  • The core project of the team federating all the researchers of the group aims at understanding in E. coli and L. lactis the dynamics of gene expression and its consequences on bacterial adaptation. In this context, the RNA is considered as a system. Generally, transcription is viewed as the only factor for variation in intracellular messenger concentration. The team provides an original approach integrating transcription with post-transcriptional regulations (degradation and translation of mRNA). In E. coli, the group mainly focuses on the role of a global post-transcriptional regulatory system, CSR (Carbon Storage Regulator) in metabolic adaptation. This innovative and federative project on the dynamics of bacterial gene expression benefits from the support of several platforms in Toulouse, from collaborations with other research groups within LISBP and from national and international academic partnerships. It has received public and private financial supports (PhD grants PRES-Région and INRA-INRIA, ANR white program, Toulouse White Biotechnology pre-competitive program, etc).
  • The main application of our investigations is in the food-chain, from the utilization of bacteria in food processes until their ingestion and interaction within the intestinal tract. In the dairy and cheese industry, several projects explore lactic acid bacteria metabolism in the context of fermented dairy products (notably in collaboration with Yoplait) while in the gut context we intend to better define probiotic bacteria (Syndifrais project). Moreover, a project in the field of industrial biotechnology exploiting our knowledge of lactic acid bacteria adaptation is currently carried out in the team. It is part of the activities of Toulouse White Biotechnology and its goal is to produce biodegradable plastics from biomass.
  • In parallel, we have constantly and successfully transferred our metabolic knowledge from strains having potential applications in industrial biotechnology to pathogenic bacteria interesting the pharmaceutical companies. Industrial collaborations and a European Union financed project have concerned different pathogenic species (Streptococcus pneumoniae, Corynebacterium diphteriae and Haemophilus influenzae and today Bordetella pertussis causing whooping cough). In these projects, our investigations have provided a better knowledge of the bacterial behavior allowing the general link between virulence and metabolic fitness to be explored to optimize productivity and quality of tomorrow’s vaccines.