Bacteria are extremely adaptable and able adjust their lifestyle very quickly when these changes occur. One dramatic illustration of this capacity is the spread of antibiotic resistance among bacterial pathogens. During the last decade, the emergence of multi-resistant bacteria, which are resistant to several treatments, led to increase mortality caused by common infections. The 2014 report on antimicrobial resistance from the World Health Organization warns against the beginning of a “post-antibiotic” era, when most of the bacterial pathogens will become resistant to all treatments available.
In this context, it is crucial to fully understand the molecular mechanism of bacterial adaptability to ultimately target and limit this ability. To survive in a changing environment, bacteria have to resist to stresses induced by these changes and ultimately to adapt their lifestyle if these changes persist. These two processes are almost contradictory since the first aims at maintaining cell integrity while the second allows long term variability through the acquisition of new traits.
For 10 years, we engaged several lines of research on this topic in the lab, first at institut Pasteur and from 2016 within the MFP unit and at the Institut Européen de Chimie et Biologie (IECB) in Bordeaux. Over the last 5 years, we focused our research on the main projects listed below. Our lab has also been instrumental in setting up a state of the art cryo-electron microscopy (CryoEM) facility at IECB. We have several on-going collaborations related to our expertise in CryoEM. We are also involved in technological development projects such as the implementation of super-resolution correlative microscopy in cryo conditions.
The bacterial Type 6 secretion (T6S) system is one of the key players for microbial competition, as well as an important virulence determinant during bacterial infections. It assembles a nano-crossbow-like structure that propels an arrow made of Hcp tube and VgrG spike into the cytoplasm of the attacker cell and punctures the prey’s cell wall. The nano-crossbow is stably anchored to the cell envelope of the attacker by a membrane core complex. In collaboration with Eric Cascales’ laboratory in Marseille (France), we recently have shown that this membrane complex is assembled by the sequential addition of three proteins -TssJ, TssM and TssL- and presented a structure of the fully assembled complex (Nature 2015). Since our arrival at IECB and MFP, we solved the cryoEM structure of this complex (EMBO J. 2019). We also solved the cryoEM structure of another key element of the T6S system, the baseplate (Nature microbiology 2018) and of the T6SS substrate from pathogenic Escherichia coli in complex with the T6SS spike (EMBO J. 2020).
We want to understand how DNA can be uptaken and recombined in the bacterial genome during bacterial transformation. Natural genetic transformation, first discovered in Streptococcus pneumoniae by F. Griffith in 1928, is observed in many Gram-negative and Gram-positive bacteria. This process promotes genome plasticity and adaptability. In particular, it enables many human pathogens such as Streptococcus pneumonia, Neisseria gonorrhoeae or Vibrio Cholerae to acquire resistance to antibiotics and/or to escape vaccines through the binding and incorporation of new genetic material. While it is well established that this process requires the binding, internalization of external DNA and its recombination in the bacterial genome, the molecular details of these steps are unknown. In this project, we aim at acquiring a detailed understating of each of these steps. We discovered a new appendage at the surface of S. pneumoniae cells and showed that this appendage is similar in morphology and composition to appendages called Type IV pili commonly found in Gram-negative bacteria. We demonstrated that this new pneumococcal pilus is essential for transformation and that it directly binds DNA (PLOS Pathogens 2013 and 2015). We are also actively studying the DNA translocation apparatus. Finally, we identified a new key ATPase involved in the recombination process. We determined the crystal structure of this protein and identified its function in vitro and in vivo in collaboration with Patrice Polard’s team in Toulouse (France) (Nature Commun. 2017)
Acetaldehyde–alcohol dehydrogenase (AdhE) enzymes are a key metabolic enzyme in bacterial physiology and pathogenicity. They convert acetyl-CoA to ethanol via an acetaldehyde intermediate during ethanol fermentation in an anaerobic environment. This two-step reaction is associated to NAD+ regeneration, essential for glycolysis. The bifunctional AdhE enzyme is conserved in all bacterial kingdoms but also in more phylogenetically distant microorganisms such as green microalgae. It is found as an oligomeric form called spirosomes, for which the function remains elusive. We used cryo-electron microscopy to obtain structures of E. coli spirosomes in different conformational states. We showed that spirosomes contain active AdhE monomers, and that AdhE filamentation is essential for its activity in vitro and function in vivo. The detailed analysis of these structures provides insight showing that AdhE filamentation is essential for substrate channeling within the filament and for the regulation of enzyme activity. This work was published in Nature communications in 2020.