Biology subjects

Cornu, D.

Publications and source records attributed to Cornu, D..

5 recordsLinked to original sources

bioRxiv2023

The Ribosome Profiling landscape of yeast reveals a high diversity in pervasive translation

Pervasive translation is a widespread phenomenon that plays an important role in de novo gene birth; however, its underlying mechanisms remain unclear. Based on multiple Ribosome Profiling (Ribo-Seq) datasets, we investigated the RiboSeq landscape of coding and noncoding regions of yeast. Therefore, we developed a representation framework which allows the visual representation and rational classification of the entire diversity of Ribo-Seq signals that could be observed in yeast. We show that if coding regions are restricted to specific areas of the Ribo-Seq landscape, noncoding regions are associated with a wide diversity of translation signals and, conversely, populate the entire yeast Ribo-Seq landscape. Specifically, we reveal that noncoding regions are associated with canonical translation signals, but also with non-canonical ones absent from coding regions, and which appear to be a hallmark of pervasive translation. Notably, we report thousands of translated noncoding ORFs among which, 251 led to detectable products with Mass Spectrometry while being characterized by a wide range of translation specificities. Overall, we show that pervasive translation is not random with noncoding ORF translation signals being consistent across Ribo-Seq experiments. Finally, we show that the translation signal of noncoding ORFs is not explained by features related to the emergence of function, but rather determined by the translation start codon and the codon distribution in their two alternative frames. Overall, our results enable us to propose a topology of the pervasive Ribo-Seq landscape of a species, and open the way to future comparative analyses of this translation landscape under different conditions.

evolutionary biology↗

bioRxiv2023

TLN468 changes the pattern of tRNA used to readthrough premature termination codons in CFTR

Nonsense mutations account for 12% of cystic fibrosis (CF) cases. The presence of a premature termination codon (PTC) leads to gene inactivation, which can be countered by the use of drugs stimulating PTC readthrough, restoring production of the full-length protein. We recently identified a new readthrough inducer, TLN468, more efficient than gentamicin. We measured the readthrough induced by these two drugs with different cystic fibrosis transmembrane conductance regulator (CFTR) PTCs. We then determined the amino acids inserted at the S1196X, G542X, W846X and E1417X PTCs of CFTR during readthrough induced by gentamicin or TLN468. TLN468 significantly promoted the incorporation of one specific amino acid, whereas gentamicin did not greatly modify the proportions of the various amino acids incorporated relative to basal conditions. The function of the engineered missense CFTR channels corresponding to these four PTCs was assessed with and without potentiator. For the recoded CFTR, except for E1417Q and G542W, the PTC readthrough induced by TLN468 allowed the expression of CFTR variants that were correctly processed and had significant activity that was enhanced by CFTR modulators. These results suggest that it would be relevant to assess the therapeutic benefit of TLN468 PTC suppression in combination with CFTR modulators in preclinical assays.

molecular biology↗

bioRxiv2020

Glioma stem cells invasive phenotype at optimal stiffness is driven by MGAT5 dependent mechanosensing.

Glioblastomas stem-like cells (GSCs) by invading the brain parenchyma escape resection and radiotherapy. GSC invasion is associated with altered N-glycosylation pattern of integrins and other transmembrane proteins resulting in changed mechanosensing but details are elusive. Because the tumour microenvironment has an increased stiffness we studied the interaction between matrix stiffness, N-glycosylation and GSC migration. To mimic the fibrillar microenvironments, we designed 3D-ex-polyacrylonitrile nanofibers scaffolds (NFS) with adjustable stiffnesses by loading multiwall carbon nanotubes (MWCNT). We found that migration of GSCs was maximum at 166 kPa. Migration rate was correlated with cell shape, expression of focal adhesion (FA), Epithelial to Mesenchymal Transition (EMT) proteins and ({beta}1,6) branched N-glycan binding, galectin-3. Mutation of MGAT5 in GSC inhibited N-glycans ({beta}1-6) branching, suppressed the stiffness dependence of FA and EMT protein expression as well as migration on 166kPa NFS; underpinning the role of multibranched N-glycans as a critical regulator of mechanotransduction by GSC. Significance StatementDuring pathological processes in which cell migration is involved, cells undergo important functional changes in protein glycosylation and are responsive to environmental mechanical modifications. We addressed the question of the glycosylation role in mechanotransduction regulation of glioma stem cells. We created a bio-inspired 3D nanofiber scaffold (NFS) loaded with multiwall carbon nanotubes to obtain NFS of adjustable stiffness in physiological and pathological ranges. We highlighted and described a mechanism of fine mechanotransduction leading to a nonlinear migration response regarding to 3D microenvironment stiffness values. We show the importance to develop mechano-pharmacology as new therapeutic target by demonstrating the relationship existing between environmental stiffness and multibranched N-glycans catalysed by the MGAT5 enzyme to optimize directed migration.

cell biology↗

bioRxiv2020

A Phelipanche ramosa KAI2 Protein Perceives enzymatically Strigolactones and Isothiocyanates

Phelipanche ramosa is an obligate root-parasitic weed threatening major crops in central Europe. For its germination, it has to perceive various structurally diverging host-exuded signals, including isothiocyanates (ITCs) and strigolactones (SLs). However, the receptors involved are still uncharacterized. Here, we identified five putative SL receptors in P. ramosa, of which PrKAI2d3 is involved in seed germination stimulation. We established the high plasticity of PrKAI2d3, allowing interaction with different chemicals, including ITCs. The SL perception mechanism of PrKAI2d3 is similar to that of endogenous SLs in non-parasitic plants. We provide evidence that the PrKAI2d3 enzymatic activity confers hypersensitivity to SLs. Additionally, we demonstrated that methylbutenolide-OH binds PrKAI2d3 and stimulates P. ramosa germination with a bioactivity comparable to that of ITCs. This study highlights that P. ramosa has extended its signal perception system during evolution, a fact to be considered in the development of specific and efficient biocontrol methods.

plant biology↗

bioRxiv2019

Ubiquinone biosynthesis over the entire O2 range: characterization of a conserved, O2-independent pathway

Most bacteria can generate ATP by respiratory metabolism, in which electrons are shuttled from reduced substrates to terminal electron acceptors, via quinone molecules like ubiquinone. Dioxygen (O2) is the terminal electron acceptor of aerobic respiration and serves as a co-substrate in the biosynthesis of ubiquinone. Here, we characterize a novel, O2-independent pathway for the biosynthesis of ubiquinone. This pathway relies on three proteins UbiT (YhbT), UbiU (YhbU) and UbiV (YhbV). UbiT contains an SCP2 lipid-binding domain and is likely an accessory factor of the biosynthetic pathway, while UbiU-UbiV are involved in hydroxylation reactions and represent a novel class of O2-independent hydroxylases. We demonstrate that UbiU-UbiV form a heterodimer, wherein each protein binds a 4Fe-4S cluster via conserved cysteines that are essential for activity. The UbiT, -U, -V proteins are found in -, {beta}-, {gamma}-proteobacterial clades including several human pathogens, supporting the widespread distribution of a previously-unrecognized capacity to synthesize ubiquinone in the absence of O2. Together, the O2-dependent and O2-independent ubiquinone biosynthesis pathways contribute to optimize bacterial metabolism over the entire O2 range.\n\nIMPORTANCEIn order to colonize environments with large O2 gradients or fluctuating O2 levels, bacteria have developed metabolic responses that remain incompletely understood. Such adaptations have been recently linked to antibiotic resistance, virulence and the capacity to develop in complex ecosystems like the microbiota. Here, we identify a novel pathway for the biosynthesis of ubiquinone, a molecule with a key role in cellular bioenergetics. We link three uncharacterized genes of Escherichia coli to this pathway and show that the pathway functions independently from O2. In contrast, the long-described pathway for ubiquinone biosynthesis requires O2 as substrate. In fact, we find that many proteobacteria are equipped with the O2-dependent and O2-independent pathways, supporting that they are able to synthesize ubiquinone over the entire O2 range. Overall, we propose that the novel O2-independent pathway is part of the metabolic plasticity developed by proteobacteria to face varying environmental O2 levels.

microbiology↗