Biology subjects

Tocquin, P.

Publications and source records attributed to Tocquin, P..

5 recordsLinked to original sources

bioRxiv2026

Zinc and iron homeostatic interactions in a mutant lacking nicotianamine vacuolar storage and citrate xylem loading

Metal homeostasis in plants relies on coordinated uptake, chelation, and transport mechanisms involving, but not limited to, citrate and nicotianamine (NA). In Arabidopsis (Arabidopsis thaliana), disruption of the citrate exporter FRD3 (FERRIC REDUCTASE DEFECTIVE 3) causes constitutive Fe deficiency responses, altered iron (Fe), manganese (Mn) and zinc (Zn) distribution, with Fe accumulation in the root cell wall. This ultimately results in oxidative and biotic stress responses, and impaired root development, phenotypes that are partially alleviated by Zn excess. In this study, we investigated the consequences of impairing both citrate loading into xylem vessels and NA partitioning within cells. The frd3 zif1 double mutant exhibits enhanced sensitivity to Zn excess, severe defects in root system architecture and meristem maintenance, persistent oxidative stress, and compromised reproductive development. These phenotypes correlate with sustained activation of Fe deficiency signaling and marked defects in root-to-shoot metal translocation. Our findings reveal that coordinated citrate export and NA compartmentation form an integrated buffering strategy required to maintain metal homeostasis and partitioning, as well as redox balance and proper development, including root plasticity and seed yield, under fluctuating metal availability.

plant biology↗

bioRxiv2022

AURTHO: autoregulation as facilitator of cis-acting element discovery of orthologous transcription factors

Transcriptional regulation is key in bacteria for providing an adequate response in time and space to changing environmental conditions. However, despite decades of research, the binding sites and therefore the target genes and the function of most transcription factors (TFs) remain unknown. Filling this gap in knowledge through conventional methods represents a colossal task which we demonstrate here can be significantly facilitated by a widespread feature in transcriptional control: the autoregulation of TFs implying that the yet unknown transcription factor binding site (TFBS) is neighbouring the TF itself. In this work, we describe the "AURTHO" methodology (AUtoregulation of oRTHOlogous transcription factors), consisting of analyzing upstream regions of orthologous TFs in order to uncover their associated TFBSs. AURTHO enabled the de novo identification of novel TFBSs with an unprecedented improvement in terms of quantity and reliability. DNA-protein interaction studies on a selection of candidate cis-acting elements yielded an >90% success rate, demonstrating the efficacy of AURTHO at highlighting true TF-TFBS couples and confirming the identification in a near future of a plethora of TFBSs across all bacterial species. Key pointsO_LITranscription factor (TF) autoregulation implies that their binding site (TFBS) is in their close vicinity C_LIO_LIWe developed and assessed the AURTHO methodology (AUtoregulation of oRTHOlogous TFs) for TFBS discovery C_LIO_LIOur results shows that AURTHO greatly facilitates the identification of highly reliable novel TFBSs C_LI

bioinformatics↗

bioRxiv2020

LED light gradient as a screening tool for light quality responses in model plant species

Current developments in light-emitting diodes (LEDs) technologies have opened new perspectives for sustainable and highly efficient indoor cultivation. The introduction of LEDs not only allows a reduction in the production costs on a quantitative level, it also offers opportunities to manipulate and optimise qualitative traits. Indeed, while plants respond strongest to red and blue lights for photosynthesis, the whole light spectrum has an effect on plant shape, development, and chemical composition. In order to evaluate LEDs as an alternative to traditional lighting sources, the species-specific plant responses to distinct wavelengths need to be evaluated under controlled conditions. Here, we tested the possibility to use light composition gradients in combination with semi-automated phenotyping to rapidly explore the phenotypic responses of different species to variations in the light spectrum provided by LED sources. Plants of seven different species (Arabidopsis thaliana, Ocimum basilicum, Solanum lycopersicum, Brachypodium distachyon, Oryza sativa, Euphorbia peplus, Setaria viridis) were grown under standard white fluorescent light for 30 days, then transferred to a Red:Blue gradient for another 30 days and finally returned to white light. In all species, differences in terms of dimension, shape, and color were rapidly observed across the gradient and the overall response was widely species-dependent. The experiment yielded large amounts of imaging-based phenotypic data and we suggest simple data analysis methods to aggregate the results and facilitate comparisons between species. Similar experimental setups will help achieve rapid environmental optimization, screen new crop species and genotypes, or develop new gene discovery strategies.

plant biology↗

bioRxiv2017

Contribution of the β-glucosidase BglC to the Onset of the Pathogenic Lifestyle of Streptomyces scabies

Common scab disease on root and tuber plants is caused by Streptomyces scabies and related species which use the cellulose synthase inhibitor thaxtomin A as main phytotoxin. Thaxtomin production is primarily triggered by the import of cello-oligosaccharides. Once inside the cell, the fate of the cello-oligosaccharides is dichotomized into i) fueling glycolysis with glucose for the saprophytic lifestyle through the action of {beta}-glucosidase(s) (BG), and ii) eliciting the pathogenic lifestyle by inhibiting the CebR-mediated transcriptional repression of thaxtomin biosynthetic genes. Here we investigated the role of scab57721 encoding a putative BG (BglC) in the onset of the pathogenicity of S. scabies. Enzymatic assays showed that BglC was able to release glucose from cellobiose, cellotriose and all other cello-oligosaccharides tested. Its inactivation resulted in a phenotype opposite to what was expected as we monitored reduced production of thaxtomin when the mutant was cultivated on media containing cello-oligosaccharides as unique carbon source. This unexpected phenotype could be attributed to the highly increased activity of alternative intracellular BGs, probably as a compensation of bglC inactivation, which then prevented cellobiose and cellotriose accumulation to reduce the activity of CebR. In contrast, when the bglC null mutant was cultivated on media devoid of cello-oligosaccharides it instead constitutively produced thaxtomin. This observed hypervirulent phenotype does not fit with the proposed model of the cello-oligosaccharide-mediated induction of thaxtomin production and suggests that the role of BglC in the route to the pathogenic lifestyle of S. scabies is more complex than currently presented.

microbiology↗

bioRxiv2016

PREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool

In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their expression. To this end, we have developed an improved and online version of the PREDetector software aimed at identifying putative transcription factor-binding sites (TFBS) in bacterial genomes. The original philosophy of PREDetector 1.0 is maintained, i.e. to allow users to freely fix the DNA-motif screening parameters, and to provide a statistical means to estimate the reliability of the prediction output. This new version offers an interactive table as well as graphics to dynamically alter the main screening parameters with automatic update of the list of identified putative TFBS. PREDetector 2.0 also has the following additional options: (i) access to genome sequences from different databases, (ii) access to weight matrices from public repositories, (iii) visualization of the predicted hits in their genomic context, (iv) grouping of hits identified in the same upstream region, (v) possibility to store the performed jobs, and (vi) automated export of the results in various formats. PREDetector 2.0 is available at http://predetector.fsc.ulg.ac.be/.

bioinformatics↗