Apero Talks

JSM3 AperoTalks are informal and educational scientific presentations where all students and young researchers of the IM2B can meet. Everybody can present their research topic in a 30-minute presentation in order to initiate scientific discussions.

Seminars are usually followed by an "apéro" that allows everyone to share ideas & opinions, form networks and friendships either by just having a beer or by other themed-nights, such as games nights or similiar events.


April 18th, 2024 Camille Herrou (LCB, LISM) and Ludovic Dubard (BIP)

Camille Herrou Molecular and structural basis of the mechanism of type IVa pili machinery activation in Myxococcus xanthus. 

In all living organisms, cell movements are essential for primordial processes such as environmental exploration or multicellular development. In bacteria, one of the main motility systems, used to move on surfaces, are type IV pili (Tfp). Tfp are filamentous nanomachines, widespread in bacteria and archaea, mediating functions as diverse as adhesion to biotic/abiotic surfaces, formation of microcolonies and biofilms, twitching mechanosensing, and DNA. Tip-based motility relies on cycles of extension of pilin fibres, their binding of substrates and their retraction to pull the bacteria forward. Nevertheless, these simple cycles are not sufficient and Tfp-based motility is actually mediated by the coordinated activation of multiple Tfp machineries at one side of the cell. My PhD project aims, using a multi-scale approach, to decipher the molecular and structural basis of the mechanism allowing activation of type IV pili in the bacterial model Myxococcus xanthus.

Ludovic Dubard Copper- Ligand complexes, a new way to use copper toxicity?

Copper's antimicrobial properties find diverse applications in healthcare, anti-fouling coatings, and agriculture. However, the long standing use of CuSO4 (Bordeaux mixture) as a fungicide in vineyard and fruit production has raised environmental concerns. The accumulation of copper in soils has detrimental effects on crop yields and biodiversity. Recent advances in chemistry have led to the synthesis of chemical ligands capable of forming copper ligand (Cu-L) complexes. These complexes have emerged as an interesting alternative strategy to maximize the efficiency of copper toxicity while limiting the quantities of copper to be applied. In this study, we focused on two different Cu-L complexes. A concentration of Cu-L complexes 60 times lower than that of CuSO4 inhibits bacterial growth effectively. To elucidate mechanism of action of Cu-L, we studied their impact at different scales. Overall, our research provides new insights into the toxicity mechanisms of CuSO4 and Cu-L complexes, which will be of interest for the development of new antibiotics and in minimizing soil contamination.

March 21th, 2024 Alex Lutz and Lucas Dupuis (BIP)

Alex Lutz FlrA, a FleQ-like protein used as a bait to learn more about Shewanella oneidensis biofilms formation. 

Biofilm is the predominant lifestyle in nature, and this fortress is effective both in adapting to environmental stimuli, and during infections by some pathogens. So, it's important to understand how this biofilm is formed in bacteria, and whether there are common mechanisms/patterns between bacteria in this processus. In the pathogen Pseudomonas aeruginosa, whose biofilm is fairly well studied, FleQ a transcriptional regulator, regulates the transition between the planktonic and sessile lifestyle of the bacterium. In the presence of low levels of intracellular c-di-GMP, FleQ promotes the expression of flagellum genes and represses the expression of biofilm genes, and vice versa in the presence of intracellular c-di-GMP. Most Gammaproteobacteria have a FleQ homologue, and this could be an interesting starting point to learn more about biofilm formation in other bacteria. In my PhD project, I am interested in the bacterium Shewanella oneidensis MR1-R, which displays interesting bioremediation abilities through the formation of its biofilms. FlrA protein, which is a FleQ homologue, is known to be a master regulator of motility in S. oneidensis, and we believe it is also involved in the bacterium's biofilm formation. Thus, we aim to use FlrA, a FleQ-like protein, as a bait, to fish out biofilm formation mechanisms in S. oneidensis


Lucas Dupuis Role of the Tat system for copper resistance in Pseudomonas aeruginosa.

The opportunistic pathogen Pseudomonas aeruginosa can cause acute or chronic infections by using a whole arsenal of systems allowing its virulence. For example, the Tat system, allowing the export of substrate proteins from the cytoplasm to the periplasm, is essential for the virulence of P. aeruginosa. Previous studies have shown that this system gives to P. aeruginosa a better tolerance to copper. Copper is an essential element for bacteria but can become toxic in high concentration. This metal is used by macrophages as an antimicrobial agent and copper resistance could be a virulence issue. The aim of my thesis is to better understand the role of the Tat system and its substrates in copper tolerance in P. aeruginosa. Among the 34 known P. aeruginosa Tat substrates, we identified 2 candidates, and described (physiologically and biochemically) two distinct copper resistance mechanisms.

February 15th, 2024 Aude Béranger and Juliette Patricio (Laboratoire de Chimie Bactérienne)

Aude Béranger Phenotypic heterogeneity as a strategy for metabolic adaptation in Lactococcus cremoris.

Although Lactococcus cremoris is a fermenting bacterium, it harbors an electron transport chain (ETC), which, when functional, leads to higher biomass and robustness of the cells. This simple ETC is composed of a single primary dehydrogenase, menaquinones and a single terminal oxidase, a cytochrome bd oxidase (CydAB), that requires heme, a molecule L. cremoris is auxotroph for, to be functional. Surprisingly, the genes encoding the main actors of the ETC are poorly regulated in response to O2 and heme, despite the substantial cost of their production, especially in non-respiration-permissive conditions when they are not used. Our hypothesis is the occurrence of variations in the quantity of ETC proteins between cells, that could lead to variations in respiration capacity. This strategy, defined as phenotypic heterogeneity, could be used by L. cremoris to adapt to changing environments, allowing the population to undergo respiration immediately after the apparition of heme and O2 in the environment, without an excessive loss of energy. To address this question, we produced a translational CydB-GFP fusion and used fluorescence microscopy to show that CydB is heterogeneously present in the membrane of cells grown under low tensions of O2 after 24h of culture. Furthermore, using oxygraphy, we showed that L. cremoris O2 consumption rate increases immediately after addition of heme in the medium, indicating that L. cremoris is readily able to respire upon restoration of CydB activity. Our results show that heterogeneity might be one driver of metabolic adaptation in L. cremoris


Juliette Patricio Polysaccharides utilization by Gram-positive bacteria: from genome mining to biochemical characterization.

Bacterial communities are ubiquitous and play pivotal roles in the carbon cycle and life processes, particularly through the degradation of polysaccharides. Investigating these communities enhances our understanding of their function within animal microbiota and allows for the exploration of biotechnological applications, such as biofuel production and probiotic development. The study of Carbohydrate-Active EnZymes (CAZymes), cataloged in the CAZy database, offers insights into polysaccharide degradation mechanisms. This research has been extensively conducted on Bacteroidetes, highlighting Polysaccharide Utilization Loci (PULs) that encompass genes for glycan sensing, transport, depolymerization and regulation. Recent discoveries reveal that Ruminiclostridium cellulolyticum, along with other Firmicutes, possesses similar genomic regions that are yet to be thoroughly examined. My doctoral project is structured into three major parts: a bioinfomatics study to identify these mechanisms, followed by proteomic and transcriptomic analyses for model validation, and concluding with biochemical experiments to determine the specificity of transporters and CAZymes activities.

January 11th, 2024 Emma Forest (MCT) & Barbara Cardoso-Domingues (MCT)

Emma Forest Antibiotic enhancers: A New Approach to Fight Antibiotic Resistance

With close to 5 million deaths associated with antimicrobial resistance (AMR) in 2019, bacteria sensitivity to antibiotics is a major health issue. To overcome AMR, several strategies can be considered: In this project, we focus on the use of potentiators, or antibiotic enhancers, and multitarget inhibitors. Those two strategies have proven to be effective in several cases and are both clinically relevant. We chose to use NV716, a polyaminoisoprenyl compound that permeates Gram negative membranes and inhibits active efflux mechanisms, in combination with two families of Ser/Cys-based enzyme inhibitors, the oxadiazolone-core derivatives (OX) and analogs of Cyclophostins and Cyclipostins (CyC). Those two families are multi-target inhibitors with good antimicrobial activity against Mycobacteria, but are inefficient against Gram-negative and Gram-positive bacteria. The aim of this project is to potentiate OX/CyC compounds against the largest pool of bacteria and identify our hit compounds targets to better understand their mode of action. Ultimately, this could lead to promising ways to tackle AMR by developing new multipurpose treatments of bacterial infections. 


Barbara Cardoso-Domingues Degradable synthetic antibacterial copolymers for therapeutic applications

Bacterial infections currently rank as the second leading cause of global mortality due to the development and spread of resistant bacteria. Consequently, there is a need for the development of new antimicrobial therapies. Among them, synthetic amphiphilic copolymers (sACs), emerge as promising candidates with their high antibacterial activity, coupled with low toxicity and lack of existing resistance. However, their potential is limited by their non-degradability. The COPOTIC project aims to develop a broad collection of degradable sACs and test their antibacterial activity against ESKAPEE group bacteria. Degradable sACs were synthesized and their activity was assessed by determining the minimum inhibitory concentration (MIC). Hemolysis and toxicity tests on cells were conducted to evaluate copolymer toxicity. The results show that the antimicrobial activity of sACs varies depending on the compound and bacterial strain. Acinetobacter baumannii, Staphylococcus aureus, and Klebsiella aerogenes are the most sensitive strains. Among these sACs, some of them exhibited low toxicities with minimal hemolytic capacity. Additionally, a test conducted with one copolymer demonstrated that degradation products are inactive against bacterial growth. These initial findings allows the preselection of sACs for membrane activity studies and appear promising for future in vivo investigations.

November 23th, 2023 Nil Gaudu (BIP) & Varun Ravishankar (BIP/LISM)

 VARUN RAVISHANKAR Understanding the interactions between the mitochondrial VDAC2 and pro-apoptotic proteins

Apoptosis is a tightly regulated form of cell death observed in all eukaryotic cells due to various forms of cellular stress. It involves a whole ensemble of proteins, of which the effector molecules BID and BAX play a crucial role in the final step, the permeabilization of the outer mitochondrial membrane. BAX forms large oligomers on the mitochondrial membrane, but the activation steps that lead to this are still not very well known. Recently, protein knockout studies _in vivo_ have shown the potential association of the mitochondrial ion channel VDAC2 with these pro-apoptotic proteins, but the data are confusing and often, contradictory. We aim to explore these interactions and the possible conformational changes arising due to such interactions _in vitro_, primarily using EPR. A better understanding of the associations between these molecules on the surface of the mitochondrion would be crucial in devising drug targets in cases where apoptosis is misregulated, for instance in neurodegenerative diseases and in cancer.


NIL GAUDU Synthesis of mineral-decorated liposomes as minimal cells for exploring the basics of chemo-osmosis at the emergence of life

Looking at the emergence of life as the common denominator of living we observe one feature shared among most current living organisms : the use of electron transport chains to produce chemical energy (i.e. ATP) thanks to the mechanism of chemo-osmosis. This involves transmembrane metallo-enzymes able to transform a redox desiquilibrium across the membrane into a proton-motive force subsequently powering the synthesis of ATP. The iron double hydroxide mineral called "green rust" is thought to be an inorganic precursor of such transmembrane metallo-enzymes, given the resemblance of their metal-bound catalytic sites. Then, we can imagine that this mineral could have played a role in the first inorganic bioenergetic system at the emergence of life by catalyzing the same reactions as these enzymes. To explore this hypothesis, the capacity of this mineral to generate a transmembrane proton-gradient in response to a given redox disequilibrium can be tested by incorporating it in a liposome membrane an measure the formation of a cross membrane pH gradient. To build such a novel and never seen mineral-liposome bioenergetic system, numerous properties of the mineral should be improved to make it analogous to current transmembrane proteins. This will be the topic of my presentation and will leads us to explore other questions such as the specific redox reactivity of the crystal or its electrochemical behaviour.