Our favorite tools
Getting started with iTP-Seq
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itpseq Python module and command-line tool
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Case studies
iTP-Seq
Developed in our group, inverse toeprinting coupled to next-generation sequencing (iTP-Seq) is a scalable in vitro profiling method designed to map bacterial translation landscapes with codon resolution (Seip et al., (2018) Life Sci Alliance).
iTP-Seq can be used on any custom-made mRNA library, including random libraries whose sequence content is not known in advance. As a result, it can be used to precisely probe how translation is modulated by mRNA sequence context, without being limited to sequences found in a given genome.
To date, we have used iTP-Seq (1) to investigate how ribosome-targeting antibiotics exert context-dependent effects (Leroy et al. (2023) Nat Chem Biol) — an important step towards deciphering their detailed mechanisms of action, and (2) to perform in-depth characterizations of arrest-inducing sequences, such as the leader peptides of antibiotic resistance genes (Beckert et al. (2021) Nat Commun).
iTP-Seq's adaptability and scalability make it a powerful tool for studying how protein synthesis is regulated beyond antibiotic action or arrest peptides. For example, we are now using iTP-Seq in collaboration with the Balíková-Novotná (BIOCEV, Prague) and Boël (IBPC, Paris) groups to dissect the mechanisms of action of antibiotic resistance (ARE) and translational ABC-F proteins, respectively.
Single Particle Cryo-EM
To gain structural insights into ribosome function, we use single particle cryo-EM for high-resolution structural analysis of ribosomal complexes.
We benefit from privileged access to the cryo-EM facility at the European Institute of Chemistry and Biology (IECB) in Bordeaux, featuring a 200 kV Glacios transmission electron microscope equipped with a Falcon IV camera and a Selectris energy filter, as well as a dedicated cluster for data processing.
Droplet microfluidics
In collaboration with the Baret group (CNRS - CRPP), our lab has established a state-of-the-art microfluidics platform, incorporating precision pressure controllers, a high-voltage amplifier for droplet pico-injection and sorting, and three independent lasers for multi-channel fluorescence detection.
This platform enables the parallel interrogation of millions of individual bacterial cultures encapsulated in picoliter-sized droplets, opening the door to efficient and scalable antimicrobial discovery and characterization.
Droplet generation
Droplet
pico-injection
Fluorescent
bacteria in
droplets