Biology subjects

Boutet, E.

Publications and source records attributed to Boutet, E..

3 recordsLinked to original sources

bioRxiv2022

Shifted Reverse PAGE: a novel approach based on structure switching for the discovery of riboswitches and aptamers

Riboswitches are regulatory sequences composed of an aptamer domain capable of binding a ligand and an expression platform that allows the control of the downstream gene expression based on a conformational change. Current bioinformatic methods for their discovery have various limitations. To circumvent this, we developed an experimental technique to discover new riboswitches called SR-PAGE (Shifted Reverse Polyacrylamide Gel Electrophoresis). A ligand-based regulatory molecule is recognized by exploiting the conformational change of the sequence following binding with the ligand within a native polyacrylamide gel. Known riboswitches were tested with their corresponding ligands to validate our method. SR-PAGE was imbricated within an SELEX to enrich switching RNAs from a TPP riboswitch-based degenerate library to change its binding preference from TPP to thiamine. The SR-PAGE technique allows performing a large screening for riboswitches, search in several organisms and test more than one ligand simultaneously.

molecular biology↗

bioRxiv2022

Analysis of non-coding RNAs in Methylorubrum extorquens reveals a novel small RNA specific to Methylobacteriaceae

Methylorubrum extorquens metabolizes methanol, a cheap raw material that can be derived from waste. It is a facultative methylotroph, making it a model organism to study the metabolism of one carbon compounds. Despite a considerable interest to exploit this bacteria as a biotechnological tool in a methanol-based bioeconomy, little is known about its non-coding sRNA. Small RNAs play well-documented essential roles in Escherichia coli for post-transcriptional regulation; and have important functions in many bacteria, including other Alphaproteobacteria like Agrobacterium tumefaciens. M. extorquens is expected to contain many sRNAs, especially since it also encodes for the protein Hfq, a chaperone protein important in the interaction between sRNAs and their target, but also critical for the stabilization of sRNAs themselves. Few sRNAs are annotated in the genome of this Alphaproteobacteria and they were never validated. In this study, formerly annotated sRNAs ffh, CC2171, BjrC1505 were confirmed by Northern blot, validating the expression of sRNAs in M. extorquens. Moreover, analysis of RNA-sequencing data established a considerable list of potential sRNAs. Interesting candidates selected after bioinformatic analysis were tested by Northern blot, revealing a novel sRNA specific to Methylobacteriaceae, sRNA Met2624. Its expression patterns and genomic context were analyzed. This research is the first experimental validation of sRNAs in M. extorquens and paves the way for other sRNA discoveries.

molecular biology↗

bioRxiv2016

On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study

MOTIVATIONBiological knowledgebases, such as UniProtKB/Swiss-Prot, constitute an essential component of daily scientific research by offering distilled, summarized, and computable knowledge extracted from the literature by expert curators. While knowledgebases play an increasingly important role in the scientific community, the question of their sustainability is raised due to the growth of biomedical literature.\n\nRESULTSBy using UniProtKB/Swiss-Prot as a case study, we address this question by using different literature triage approaches. With the assistance of the PubTator text-mining tool, we tagged more than 10,000 articles to assess the ratio of papers relevant for curation. We first show that curators read and evaluate many more papers than they curate, and that measuring the number of curated publications is insufficient to provide a complete picture. We show that a large fraction of published papers found in PubMed is not relevant for curation in UniProtKB/Swiss-Prot and demonstrate that, despite appearances, expert curation is sustainable.\n\nAVAILABILITYUniProt is freely available at http://www.uniprot.org/.\n\nCONTACTsylvain.poux@sib.swiss

bioinformatics↗