Yannis-Nicolas François

All living beings use ribosomes to synthesize proteins from α-amino acids. Inherited from our common ancestor, a few universally conserved ribosome biogenesis steps, introducing essential ribosomal RNA modifications, have survived to our days. However, it was unknown whether similar primordial core mechanisms could also target ribosomal proteins. Here we show that the assembly and the function of ribosomes depend on the installation of an unusual β-amino acid, isoaspartate, within the ribosomal protein uS11. In bacteria, mitochondria, and plastids, this modification is catalyzed by the metzincin-like hydrolase YbeY, whereas in archaea and eukaryotes, it is introduced by the atypical kinase Fap7. The formation of this strategically positioned isoaspartate enables correct maturation of the small ribosomal subunit to support protein synthesis and normal cell physiology.

Antibody–drug conjugates (ADCs) are composed of a tumor-targeting mAb conjugated to a cytotoxic payload to enable the selective delivery of the cytot

We report the design and synthesis of ratiometric ¹⁹F‐ATCUN (Xxx‐Zzz‐His) peptide probes for the selective and reversible detection of Ni²⁺ and Cu²⁺ by ¹⁹F NMR spectroscopy. In contrast to fluorescence‐based approaches, ¹⁹F NMR enables background‐free detection in biological media, due to the absence of fluorine in native biomolecules. The probes remain stable and functional in complex cell media (DMEM), enabling the detection of Cu²⁺ and Ni²⁺ by ¹⁹F NMR with a limit of detection (LOD) of 4 µM and quantification (LOQ) of 10 µM, relevant for studying copper‐related pathologies.

Bioaerosols are of great health and environmental concern. Current techniques for their characterization are generally designed to detect individual species or oppositely unspecific molecular tracers. Metaproteomics on the other hand features the possibility to cover a broad range of taxonomies in a single analysis. This work presents a successful application of metaproteomics to characterize the biological fraction of airborne particulate matter (PM). A bottom-up proteomic strategy was employed, including protein extraction by ultrasonication in aqueous buffer, in-solution tryptic digestion, and nanoflow liquid chromatography-high-resolution mass spectrometry analysis. Extraction parameters were optimized to enhance proteins' recovery. The method was validated on Escherichia coli extracts before its application on ambient PM₁₀ samples collected over 12 weeks in Strasbourg, France. A total of 1,087 peptides were detected across all samples, with a weekly average of 223 ± 104 peptides corresponding to 111 ± 40 proteins. Peptides from species belonging to animals, plants, fungi, bacteria, and archaea kingdoms were inventoried. Many of them proved to be very relevant, as they were related to human allergens and pathogens, plant pathogens, or ecological indicators. In this work, the major benefits of metaproteomics, yet rather unexploited, as well as its pitfalls and challenges for a broader application in atmospheric chemistry, are discussed.

Monoclonal antibody (mAbs) therapeutics cannot evade the occurrence of adverse effects. Thus, mAbs are commonly triggering immune responses corresponding to the expression of antidrug antibodies. Antidrug antibodies can neutralize mAbs, leading to their inhibition and hasten clearance, which dramatically hampers their therapeutic effects. Therefore, studies concerning the affinity between a mAbs and the corresponding antidrug antibody are demonstrating a growing interest to further understand the outcome of biotherapeutics after administration. We describe a novel analytical approach for the determination of the dissociation constant (K_d) between a mAb and an antidrug antibody using capillary electrophoresis coupled to mass spectrometry (CE-MS/MS). The CE-MS/MS method employs a competitive assay, followed by the quantification of the residual amount of the active mAbs. The methodology allowed for the measurement of K_d using serum samples without the implementation of immobilization to achieve protein-protein interaction. This characteristic enabled us to generate the interaction in conditions reflecting the physiological environment. A mathematical treatment was developed to calculate K_d from MS/MS data, taking into account the stoichiometry of the mAbs/antidrug antibody complex and the bivalent properties of the two immunoglobulins. Prior to CE-MS/MS analysis, the interaction of the two proteins was studied by using mass photometry (MP) to determine equilibrium conditions and complexation stoichiometry. CE-MS/MS was used to investigate the interaction between infliximab and a neutralizing anti-infliximab antibody. Results allowed to measure a K_d of 14.4 ± 2.9 nM. MS instrumentation sensitivity and specificity showed to be relevant to achieve accurate and robust K_d measurements for strong interactions in the nanomolar range.

As RNA post-transcriptional modifications are of growing interest, several methods were developed for their characterization. One of them established for their identification, at the nucleosidic level, is the hyphenation of separation methods, such as liquid chromatography or capillary electrophoresis, to tandem mass spectrometry. However, to our knowledge, no software is yet available for the untargeted identification of RNA post-transcriptional modifications from MS/MS data-dependent acquisitions. Thus, very long and tedious manual data interpretations are required. To meet the need of easier and faster data interpretation, a new user-friendly search engine, called Nucleos'ID, was developed for CE-MS/MS and LC-MS/MS users. Performances of this new software were evaluated on CE-MS/MS data from nucleoside analyses of already well-described Saccharomyces cerevisiae transfer RNA and Bos taurus total tRNA extract. All samples showed great true positive, true negative, and false discovery rates considering the database size containing all modified and unmodified nucleosides referenced in the literature. The true positive and true negative rates obtained were above 0.94, while the false discovery rates were between 0.09 and 0.17. To increase the level of sample complexity, untargeted identification of several RNA modifications from Pseudomonas aeruginosa 70S ribosome was achieved by the Nucleos'ID search following CE-MS/MS analysis.