Biology subjects

Sargueil, B.

Publications and source records attributed to Sargueil, B..

4 recordsLinked to original sources

bioRxiv2023

Designing molecular RNA switches with Restricted Boltzmann machines

Riboswitches are structured allosteric RNA molecules that change conformation upon metabolite binding, triggering a regulatory response. Here we focus on the de novo design of riboswitch-like aptamers, the core part of the riboswitch undergoing structural changes. We use Restricted Boltzmann machines (RBM) to learn generative models from homologous sequence data. We first verify, on four different riboswitch families, that RBM-generated sequences correctly capture the conservation, covariation and diversity of natural aptamers. The RBM model is then used to design new SAM-I riboswitch aptamers. To experimentally validate the properties of the structural switch in designed molecules, we resort to chemical probing (SHAPE and DMS), and develop a tailored analysis pipeline adequate for high-throughput tests of diverse sequences. We probe a total of 476 RBM-designed and 201 natural sequences. Designed molecules with high RBM scores, with 20% to 40% divergence from any natural sequence, display{approx} 30% success rate of responding to SAM with a structural switch similar to their natural counterparts. We show how the capability of the designed molecules to switch conformation is connected to fine energetic features of their structural components.

bioinformatics↗

bioRxiv2022

sRNA-controlled iron sparing response in Staphylococci

Staphylococcus aureus, a human opportunist pathogen, adjusts its metabolism to cope with iron deprivation within the host. We investigated the potential role of small non-coding RNAs (sRNAs) in dictating this process. A single sRNA, named here IsrR, emerged from a competition assay with tagged-mutant libraries as being required during iron starvation. IsrR is iron-repressed and predicted to target mRNAs expressing iron-containing enzymes. Among them, we demonstrated that IsrR down-regulates the translation of mRNAs of enzymes that catalyze anaerobic nitrate respiration. The IsrR sequence reveals three single-stranded C-rich regions (CRRs). Mutational and structural analysis indicated a differential contribution of these CRRs according to targets. We also report that IsrR is required for full lethality of S. aureus in a mouse septicemia model, underscoring its role as a major contributor to the iron-sparing response for bacterial survival during infection. IsrR is conserved among staphylococci, but it is not ortholog to the proteobacterial sRNA RyhB, nor to other characterized sRNAs down-regulating mRNAs of iron-containing enzymes. Remarkably, these distinct sRNAs regulate common targets, illustrating that RNA-based regulation provides optimal evolutionary solutions to improve bacterial fitness when iron is scarce.

microbiology↗

bioRxiv2020

IPANEMAP: Integrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles

The manual production of reliable RNA structure models from chemical probing experiments benefits from the integration of information derived from multiple protocols and reagents. However, the interpretation of multiple probing profiles remains a complex task, hindering the quality and reproducibility of modeling efforts. We introduce IPANEMAP, the first automated method for the modeling of RNA structure from multiple probing reactivity profiles. Input profiles can result from experiments based on diverse protocols, reagents, or collection of variants, and are jointly analyzed to predict the dominant conformations of an RNA. IPANEMAP combines sampling, clustering, and multi-optimization, to produce secondary structure models that are both stable and well-supported by experimental evidences. The analysis of multiple reactivity profiles, both publicly available and produced in our study, demonstrates the good performances of IPANEMAP, even in a mono probing setting. It confirms the potential of integrating multiple sources of probing data, informing the design of informative probing assays. AvailabilityIPANEMAP is freely downloadable at https://github.com/afafbioinfo/IPANEMAP Contactyann.ponty@lix.polytechnique.fr Supplementary information available at NAR online.

bioinformatics↗

bioRxiv2019

An epitranscriptomic switch at the 5′-UTR controls genome selection during HIV-1 genomic RNA packaging

During retroviral replication, the full-length RNA serves both as mRNA and genomic RNA (gRNA). While the simple retrovirus MLV segregates its full-length RNA into two functional populations, the HIV-1 full-length RNA was proposed to exist as a single population used indistinctly for protein synthesis or packaging. However, the mechanisms by which the HIV-1 Gag protein selects the two RNA molecules that will be packaged into nascent virions remain poorly understood. Here, we demonstrate that HIV-1 full-length RNA packaging is regulated through an epitranscriptomic switch requiring demethylation of two conserved adenosine residues present within the 5'-UTR. As such, while m6A deposition by METTL3/METTL14 onto the full-length RNA was associated with increased Gag synthesis and reduced packaging, FTO-mediated demethylation was required for the incorporation of the full-length RNA into viral particles. Interestingly, HIV-1 Gag associates with the RNA demethylase FTO in the nucleus and drives full-length RNA demethylation. Finally, the specific inhibition of the FTO RNA demethylase activity suppressed HIV-1 full-length RNA packaging. Together, our data propose a novel epitranscriptomic mechanism allowing the selection of the full-length RNA molecules that will be used as viral genomes.

molecular biology↗