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Dumas, B.

Publications and source records attributed to Dumas, B..

3 recordsLinked to original sources

A DEAD BOX RNA helicase from Medicago truncatula is hijacked by an RNA-binding effector from the root pathogen Aphanomyces euteiches to facilitate host infection

Microbial effectors from plant pathogens are molecules that target host components to facilitate colonization. While eukaryotic pathogens are virtually able to produce hundreds of effectors, the molecular mechanisms allowing effectors to promote infection are still largely unexplored. Here we show that the effector AeSSP1256 from the soilborne oomycete pathogen Aphanomyces euteiches is able to interact with plant RNA. Heterologous expression of AeSSP1256 delays Medicago truncatula host roots development and facilitate pathogen colonization. Transcriptomic analyses of AeSSP1256-expressing roots show a downregulation of genes implicated in ribosome biogenesis pathway. A yeast-two hybrid approach reveals that AeSSP1256 associates with a nucleolar L7 ribosomal protein and a M. truncatula RNA helicase (MtRH10) orthologous to the Arabidopsis RNA helicase RH10. Association of AeSSP1256 with MtRH10 impaired the capacity of MtRH10 to bind nucleic acids. Promoter:GUS composite plants revealed that MtRH10 is expressed preferentially in the meristematic root cells. Missense MtRH10 plants displayed shorter roots with developmental delay and are more susceptible to A. euteiches infection. These results show that the effector AeSSP1256 facilitates pathogen infection by causing stress on plant ribosome biogenesis and by hijacking a host RNA helicase involved in root development and resistance to root pathogens.

plant biology

MS-CleanR: A feature-filtering approach to improve annotation rate in untargeted LC-MS based metabolomics

Untargeted metabolomics using liquid chromatography-mass spectrometry (LC-MS) is currently the gold-standard technique to determine the full chemical diversity in biological samples. This approach still has many limitations, however; notably, the difficulty of estimating accurately the number of unique metabolites being profiled among the thousands of MS ion signals arising from chromatograms. Here, we describe a new workflow, MS-CleanR, based on the MS-DIAL/MS-FINDER suite, which tackles feature degeneracy and improves annotation rates. We show that implementation of MS-CleanR reduces the number of signals by nearly 80% while retaining 95% of unique metabolite features. Moreover, the annotation results from MS-FINDER can be ranked with respect to database chosen by the user, which improves identification accuracy. Application of MS-CleanR to the analysis of Arabidopsis thaliana grown in three different conditions improved class separation resulting from multivariate data analysis and lead to annotation of 75% of the final features. The full workflow was applied to metabolomic profiles from three strains of the leguminous plant Medicago truncatula that have different susceptibilities to the oomycete pathogen Aphanomyces euteiches; a group of glycosylated triterpenoids overrepresented in resistant lines were identified as candidate compounds conferring pathogen resistance. MS-CleanR is implemented through a Shiny interface for intuitive use by end-users (available at: https://github.com/eMetaboHUB/MS-CleanR).

bioinformatics

Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations

Microsatellite expansions are the cause of more than 20 neurological or developmental human disorders. Shortening expanded repeats using specific DNA endonucleases may be envisioned as a gene editing approach. Here, a new assay was developed to test several CRISPR-Cas nucleases on microsatellites involved in human diseases, by measuring at the same time double-strand break rates, DNA end resection and homologous recombination efficacy. Broad variations in nuclease performances were detected on all repeat tracts. Streptococcus pyogenes Cas9 was the most efficient of all. All repeat tracts did inhibit double-strand break resection. We demonstrate that secondary structure formation on the guide RNA was a major determinant of nuclease efficacy. Using deep sequencing, off-target mutations were assessed genomewide. Out of 221 CAG/CTG or GAA/TTC trinucleotide repeats of the yeast genome, three were identified as carrying statistically significant low frequency mutations, corresponding to off-target effects.

genetics