I2BC Paris-Saclay

Photoenzyme Fatty Acid Photodecarboxylase (FAP) recently discovered in  microalgae is involved in light-driven generation of hydrocarbons from fatty  acids, a process that bears great promise for the production of biofuels and  the generation of high-value chemicals. The reaction mechanism has been  elucidated in great detail using a combination of biochemical, time-resolved spectroscopic and crystallographic methods and theoretical approaches.

More details here

Contact: pavel.muller@i2bc.paris-saclay.fr 

Escherichia coli acquires resistance to polymyxin B upon the activation of two-component systems, but this is at the expense of innate bile acid resistance. The lack of lipopolysaccharide phosphorylation accounts for bile susceptibility and impairs intestinal colonization in mice.

The surface properties of bacterial cells play a key role in resistance to various antimicrobial agents. Gram-negative bacteria expose lipopolysaccharides (LPS) on their surface, which can undergo different structural modifications. However, some of these modifications may be beneficial in some circumstances, but detrimental in others.

In this study, published in Frontiers in Microbiology, the team of Thierry Touzé, in collaboration with a team from Institut Pasteur, showed that Escherichia coli cells resist to cationic antimicrobial peptide polymyxin B, one last resort antibiotic, under conditions that simultaneously activate two-component regulatory systems PmrA/B and PhoP/Q. Among a set of modifications, they identified those responsible for this resistance, which occurs on the lipid A moiety (known as the endotoxin) from LPS. The acquisition of polymyxin B resistance came at the expense of loss of innate resistance to deoxycholate, a major component of bile. They provide evidences that bile susceptibility arises from the inhibition of LpxT-dependent modification, which consists in lipid A phosphorylation. Bile acids are abundant in the small intestine, where they modulate the commensal flora and the researchers further showed that the inactivation of lpxT impaired gut colonization in mice.

These results highlight the importance of lipid A decorations and their tight regulation in the lifestyle of E. coli and probably other Enterobacteriaceae that exhibit the same modifications

https://www.frontiersin.org/articles/10.3389/fmicb.2021.676596/full

Contact: thierry.touze@i2bc.paris-saclay.fr

We are glad to announce the opening of the microfabrication room in Gif-sur-Yvette (room 00-120, Bâtiment 23). This equipment was funded by “Région Ile de France” under the DIM ELICIT (Domaine d’Intérêt Majeur “Empowering LIfe sCiences with Innovative Technologies”)

Microfluidics is the science of fluids manipulation at the microscale using channels with dimensions of tens to hundreds of micrometers. It is also a technology called Lab-on-Chip used in Physics, Chemistry and Biology. The properties of flows at the microscale allow to work faster and cheaper with smaller sample volumes. The polymer used to produce microfluidics chip is transparent and biocompatible and provides access to time-lapse live imaging of biological systems on a microscope. It has many applications like cells sorting, encapsulation of drugs, DNA sequencing, micro-organisms swimming, mixing, etc.
The microfabrication plateform is a clean room fully equiped to make microfluidic chips from the mold design and its characterization, to the polymer microchip fabrication. It is managed by Jessica MARION et Vassanti AUDEMAR who handle the equipment :
- Clewin 5 : software to design the chip
- Laminator (Peak) or spin coater (Laurell) and UV exposer (Kloé) : to produce molds
- Profilometer (Filmetrics) : to characterize the mold
- Plasma cleaner (Harrick Plasma) : to seal the microfluidic chip
We will be happy to welcome you.
Contacts : Sébastien THOMINE (sebastien.thomine@i2bc.paris-saclay.fr), Jessica MARION ( jessica.marion@i2bc.paris-saclay.fr ), Vassanti AUDEMAR ( vassanti.audemar@i2bc.paris-saclay.fr )

Multiomic analysis of a suboptimal symbiotic interaction where a soybean nodulator (Bradyrhizobium diazoefficiens) faces NCR peptides in Aeschynomene afraspera and undergoes atypical terminal bacteroid differentiation

In the legume-rhizobium nitrogen-fixing symbiosis, some host plants produce antimicrobial peptides called NCR to control their bacterial partner and trigger its cellular differentiation. Consequently, intracellular bacteroids become polyploid, elongated and with a permeabilized membrane, collectively resulting in an altered bacterial viability. We call this phenomenon terminal bacteroid differentiation (TBD), which is associated to a higher return on investment to the host of the symbiotic process.

In the study by Nicoud et al. published in mSystems, we analyzed the physiology of Bradyrhizobium diazoefficiens USDA110 in symbiosis with its natural host soybean, which does not trigger TBD, and in interaction with Aeschynomene afraspera, a host producing NCR peptides and inducing TBD. To do so, we combined whole-nodule metabolomics, with bacterial transcriptomics and proteomics. We found that the maladapted symbiosis between Bradyrhizobium and Aeschynomene is suboptimal (reduced benefit to the host) and that bacteria undergo an intense stress. Finally, we characterized bacteroid differentiation by a combination of flow cytometry and image based morphometry and found a disconnection of the canonical features of TBD, with bacteroids that fail to elongate and endoreduplicate, while their membranes become preamble and their viability reduced.

https://doi.org/10.1128/mSystems.01237-20

Contact: benoit.alunni@i2bc.paris-saclay.fr

Mutations in DNA have large-ranging consequences, from evolution to disease. Many mechanisms contribute to mutational processes such as dysfunctions in DNA repair pathways and exogenous or endogenous mutagen exposures. Model organisms and mutation accumulation (MA) experiments are indispensable to study mutagenesis. Classical mutation accumulation experiments with the plate cell culture method are labour intensive and time consuming. To fill the need for more efficient approaches to characterize mutational profiles, the groups of F. Malloggi (NIMBE/LIONS, IRAMIS, CEA) and J. Soutourina (Genome biology/I2BC, CEA/CNRS/Paris-Saclay) have developed and validated an innovative microfluidic-based system for automatizing MA culturing over many generations in budding yeast. This unique experimental tool, coupled with high-throughput sequencing, significantly streamlines and speeds up genome-wide measurements of mutational profiles, while also parallelizing and simplifying the cell culture. Indeed, this approach allows replacing manual colony plating – which requires 800 Petri dishes and human intervention every 2 days for more than 6 months – with a single microfluidic chip that contains up to 8 MA lines operating in parallel for 1–3 months with limited intervention. This makes it possible to simultaneously compare, in an unbiased manner, many yeast strains to precisely decipher genome-wide mutational processes. To validate our approach, we performed microfluidic MA experiments on two different genetic backgrounds, a wild-type strain and a base-excision DNA repair ung1 mutant characterized by a well-defined mutational profile. Crucially, we have demonstrated that the microfluidic approach also results in mutation accumulation comparable to the traditional experiment on plate. Our microfluidic approach will significantly improve MA experiments to study mutagenesis. Mutation accumulation analysis in model organisms such as budding yeast, where changes in DNA transactions and effects of environmental conditions can be precisely controlled, is important to understand mutational processes in eukaryotic cells. As most cellular functions are conserved from yeast to human cells, this knowledge can help to understand mutational processes at the origin of many human diseases including cancers and developmental disorders. Our approach thus paves the way to massively-parallel MA experiments with minimal human intervention that can be used to investigate mutational processes at the origin of human diseases and to identify mutagenic compounds relevant for medical and environmental research.

More details here

Contact : julie.soutourina@cea.fr

In love with Integrative Structural Biology? The next @bsi2021 meeting is the PLACE-TO-BE from nov 29-dec 3 2021. Co-organized by @AFC_cristal and SFBiophys societies in Paris-Saclay campus. Please save the date, follow bsi2021, check http://bsi-2021.cnrs.fr, and RT!

The second French congress on Integrative Structural Biology (BSI), jointly organized by the Association Française de Cristallographie (AFC) and the Société Française de Biophysique (SFB), will take place on the Paris-Saclay campus from November 29 to December 3, 2021. The scientific program is available on the congress website. The congress can also be followed on twitter (@bsi2021). Structural biologists and biophysicists from I2BC (@I2BCParisSaclay), together with ENS-Paris-Saclay, Soleil, Ecole Polytechnic and ICSN are local organizers of the BSI202.

https://bsi-2021.cnrs.fr/

Contact: julie.menetrey@i2bc.paris-saclay.fr

Jeudi 11 mars 2021, l’ENS Paris-Saclay accueillait la finale Paris-Saclay du concours Ma Thèse en 180 seconde. Unique représentante de l'I2BC, Hélène BRET est arrivée deuxième. Bravo à elle et bonne chance pour la suite !

Quinze doctorants, issus d’une première sélection, ont présenté en 3 minutes leur sujet de thèse. Hélène Bret, étudiante dans l’équipe Assemblages macromoléculaires et intégrité des génomes (AMIG/I2BC) est arrivée deuxième de cette finale « régionale ».

Elle a d’abord expliqué très simplement pourquoi il était important de savoir prédire les interfaces entre deux protéines et la tâche immense que cela représentait devant les millions de paires de protéines qui existent et le petit nombre d’interfaces déjà déterminées expérimentalement grâce aux méthodes de biologie structurale. Pendant sa thèse, Hélène construit un programme informatique qui doit prédire où est l’interface pour un couple de protéines. Ce programme est un « réseau de neurones artificiels » qui apprend tout seul à partir des exemples obtenus en laboratoire. Et Hélène lui apprend à se tromper de moins en moins.

Hélène est ingénieur AgroParisTech spécialisée en science des données et apprentissage artificiel. Elle a obtenu en double diplôme un Master 2 ISI (Informatique : systèmes intelligents) de l'Université Paris-Dauphine. Elle est maintenant en deuxième année de thèse, co-encadrée par Raphaël Guérois et Jessica Andreani.

Revoir sa prestation ici.

En savoir plus à son sujet ici