Biology subjects

Delannoy, E.

Publications and source records attributed to Delannoy, E..

14 recordsLinked to original sources

bioRxiv2026

Translational profiling uncovers a tonoplast sugar transporter essential for vascular system development and cell wall composition

The inflorescence stem of Arabidopsis thaliana is a powerful model to study vascular development and carbon allocation, yet the translational landscape underlying xylem differentiation remains poorly defined. Here, we address this gap using tissue-specific Translating Ribosome Affinity Purification sequencing (TRAP-seq) to resolve the translatomes of xylem vessels, xylem parenchyma, and interfascicular fibers. We show that the very early stage of metaxylem differentiation involves coordinated activation of primary metabolism, plastid functions, and cell wall biosynthesis, supporting the metabolic demands of secondary wall formation. Xylem parenchyma displays enrichment in hormone signaling, stress, and immune pathways, consistent with a role in integrating environmental and metabolic cues. Interfascicular fibers exhibit increased translation of ribosomal proteins and spliceosome components, pointing to high translational activity and a role for alternative splicing during late development and programmed cell death. We further identify the tonoplast sugar transporter SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER 2 (SWEET2) as a key regulator of stem radial growth. Preferentially translated in early stage of metaxylem differentiation, SWEET2 acts as a rate-limiting component of vacuolar sugar exchange, controlling cytosolic hexose availability for secondary wall biosynthesis. By contrast, SWEET16 and SWEET17 exert more specialized, tissue-specific functions. Together, our findings establish subcellular sugar partitioning as a central determinant of vascular development and highlight the power of translatome profiling.

plant biology↗

bioRxiv2026

Development of a cost-effective Alveolus-on-Chip for studying Mycobacterium tuberculosis infection.

We developed a cost-effective human alveolus-on-chip based on 3D printing molds (3DP-Lung) to study early events of Mycobacterium tuberculosis (Mtb) infection in a physiologically human relevant microenvironment. This organ-on-chip platform is compatible with advanced imaging and recreates the alveolar-capillary interface by co-culturing primary human alveolar epithelial cells, endothelial cells and macrophages. We show that epithelial-only models display limited susceptibility to Mtb infection, whereas the integration of macrophages significantly enhances infection levels of the alveolar barrier and supports intracellular bacterial replication. Quantitative imaging reveals that macrophages act as a permissive niche, promoting Mtb infection of both epithelial and endothelial compartments. This accessible organ-on-chip platform enables robust modeling of early events of host-respiratory pathogen interactions and provides a valuable tool for studying tuberculosis pathogenesis in human-relevant conditions. More broadly, it lowers technical and economic barriers to accelerate the adoption of organ-on-chip technologies for studying human specific infection. SummaryA cost-effective human alveolus-on-chip enables physiologically relevant modeling of early host pathogen interaction and revealing a key role of macrophages in Mycobacterium tuberculosis infection

microbiology↗

bioRxiv2026

Defects in the Arabidopsis V-ATPase associated RAVE complex affects endosomal pH and triggers the onset of leaf cell clusters upon TOR inhibition

The TOR kinase is an important and conserved signaling hub in plants, as in other eukaryotes. However, the identification of the TOR pathway components and regulators in plants is still fragmentary. Using a genetic screen based on altered sensitivity to TOR inhibitors, we have selected an Arabidopsis mutant that develops leaf ectopic cell clusters of enlarged cells in a TOR-inhibition dependent manner. We have named this mutant loki (Localized growth depending on TOR Kinase Inhibition) and identified the causal mutation in a gene coding for the Arabidopsis homolog of the yeast Rav1 protein. This protein serves as the scaffold for the RAVE complex (Regulator of the ATPase of Vacuolar and Endosomal membranes), which regulates the V-ATPase activity in yeasts and animals. The overall V-ATPase activity is decreased in loki mutants and consistently the endosomal pH is increased. However, the vacuolar pH was found to be unaffected by this mutation. Interestingly, the det3 mutant, which is affected in the C subunit of the V-ATPase, also develops similar cell clusters. Finally, transcriptomic and metabolic analyses revealed that many pathways are affected by both the loki and det3 mutations, including cell wall integrity. This study establishes a new connection between the V-ATPase and the central TOR kinase in plants.

plant biology↗

bioRxiv2026

SAPTICoN, a robust no-code pipeline to analyze single cell transcriptomics data sets

Single-cell transcriptomic (SCT) analysis is essential for resolving cellular heterogeneity and uncovering the molecular foundations of development, physiology, and environmental responses. Despite its increasing importance, robust, reproducible, and broadly applicable SCT analytical tools remain largely restricted to well-annotated animal systems. This limitation poses significant challenges for biologists working on non-model species and poorly characterized tissues, where gene annotation is sparse and computational expertise is often limited. We developed a stable, end-to-end SCT analysis pipeline designed to be accessible to biologists with little training in bioinformatics and applicable to species and tissues with limited genomic annotation. Built on the Seurat framework and complemented with additional tools, the pipeline supports any organism by automatically generating R-compatible annotation packages from basic genome files. It integrates standardized workflows for data preprocessing, quality control, clustering, biomarker identification, and gene set enrichment analysis within a fixed Snakemake framework, ensuring high reproducibility. By minimizing coding requirements, the pipeline enables rigorous, biologically informed SCT analyses across diverse experimental systems.

bioinformatics↗

bioRxiv2025

The GT1 domain of RNase J ensures RNA quality control through dsRNA binding in Arabidopsis plastids

RNase J is a ribonuclease found in bacteria, archaea, and plant chloroplasts, and plays diverse roles in RNA maturation and stability. Chloroplast RNase J is encoded by the nuclear RNJ locus and is essential for embryo maturation. Arabidopsis or tobacco plants depleted for RNase J accumulate massive amounts of double-stranded RNA, which interferes with translation and causes chlorosis. Land plant RNase J uniquely contains a C-terminal GT1 domain, a DNA- binding motif found in transcription factors. Here, we have used complementation of an Arabidopsis rnj mutant with versions of RNase J with a mutated or deleted GT1 domain to investigate its role in RNase J function. We show that in vitro, the recombinant GT1 domain binds both double-stranded RNA and DNA, but not single-stranded nucleic acids, with no sequence specificity. Furthermore, while RNase J lacking GT1 binding complements the rnj mutant, these plants accumulate high levels of dsRNA as detected by immunolocalization and RNA-Seq. GT1 mutations also change RNase J solubility in vivo, suggesting that the GT1 domain is involved in localization within the plastid. Taken together, our results suggest that the GT1 domain plays a key role in dsRNA removal through localizing the enzyme and/or selectively binding the dsRNA substrate. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/682605v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@e5642borg.highwire.dtl.DTLVardef@136456org.highwire.dtl.DTLVardef@1205466org.highwire.dtl.DTLVardef@184f72b_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2025

Gut-on-Chip Methodology Based on 3D-Printed Molds: A Cost-Effective and Accessible Approach

1Gut-on-chips (GoC) represent a disruptive technology with great potential to understand the underlying mechanisms of gut health and pathology. Researchers who want to implement this approach, can either use expensive commercial microfluidic chips or build them from scratch in their lab. However, the design of such devices demands specific technical skills and expertise in computer assisted design (CAD). Additionally, the fabrication of the master molds for the chip production is very costly, time consuming and requires dedicated microfabrication facilities. Thus, the diffusion of these models in biology and health research laboratories remains limited due to this technological complexity and lack of affordability. In order to break these two bottlenecks, we present here the 3DP-{micro}Gut with open access designs and a simple fabrication approach based on a commercial 3D printer intended for general users. To ensure a good reproducibility with a sufficient number of available replicates for biological experiments, the method has been optimized to allow the production of multiple GoC per batch. The chips were also improved for confocal live imaging microscopy analyses. The chips are designed to be compatible with different types of microfluidics pumps, from stand-alone to completely integrated instrumentation. As a proof of concept, Caco-2 cells were seeded inside the fabricated GoC to validate their biocompatibility and functionality. After 7 days of maturation, cells self-differentiated in a 3D epithelium resembling in vivo expected structures. In summary we proposed a low-cost and open access GoC design and fabrication method with medium throughput. These results demonstrate the advantage of using 3D SLA printing to accelerate GoC implementation for gut physiopathology research.

bioengineering↗

bioRxiv2024

Early seedling development in dark conditions is directly controlled by plastids through the GUN1-dependent plastid retrograde pathway

In dark growth conditions, seedlings develop specific features such as an elongated hypocotyl, a tightly folded apical hook, and non-green cotyledons. This dark-specific process, known as skotomorphogenesis, relies primarily on mitochondria and eventually etioplasts for energy. Our previous research shows that skotomorphogenesis is reprogrammed in response to mitochondrial and plastidial dysfunction. Even though the direct link between mitochondria and skotomorphogenesis was described, the impact of plastid dysfunction on early development could not be separated from mitochondrial stress. In this study, we aim to determine the direct connection between plastid functionality and skotomorphogenic response. In this situation, we analyze the phenotypic, molecular, and metabolic effects of treating etiolated seedlings using lincomycin and spectinomycin, which target plastid translation. Our results with the lincomycin treatment highlight the direct role of plastids in the control of early development, even in dark growth conditions, in the absence of any photosynthetic activity, and without the involvement of mitochondrial intermediates. Additionally, our findings suggest that GUN1 plays a regulatory role in regulating nuclear gene expression in response to plastid translation inhibition. Thanks to our study, we can now build a more precise model proposing a straight link between the reprogramming of early development and the dysfunction of plastids in dark-growth conditions. Significance statementIn underground germination conditions, seedlings follow a dark-specific development program, called skotomorphogenesis, that is required for their efficient emergence from the soil. Our study demonstrates that plastids play a crucial role in controlling skotomorphogenesis, even in the absence of photosynthetic activity and without affecting mitochondrial function, and therefore we propose that regulation of etioplast functions might contribute to the adaptation of seedling development to constraining environmental conditions.

plant biology↗

bioRxiv2023

DiffSegR: An RNA-Seq data driven method for differential expression analysis using changepoint detection

To fully understand gene regulation, it is necessary to have a thorough understanding of both the transcriptome and the enzymatic and RNA-binding activities that shape it. While many RNA-Seq-based tools have been developed to analyze the transcriptome, most only consider the abundance of sequencing reads along annotated patterns (such as genes). These annotations are typically incomplete, leading to errors in the differential expression analysis. To address this issue, we present DiffSegR - an R package that enables the discovery of transcriptome-wide expression differences between two biological conditions using RNA-Seq data. DiffSegR does not require prior annotation and uses a multiple changepoints detection algorithm to identify the boundaries of differentially expressed regions in the per-base log2 fold change. In a few minutes of computation, DiffSegR could rightfully predict the role of chloroplast ribonuclease Mini-III in rRNA maturation and chloroplast ribonuclease PNPase in (3/5)-degradation of rRNA, mRNA, and tRNA precursors as well as intron accumulation. We believe DiffSegR will benefit biologists working on transcriptomics as it allows access to information from a layer of the transcriptome overlooked by the classical differential expression analysis pipelines widely used today. DiffSegR is available at https://aliehrmann.github.io/DiffSegR/index.html.

bioinformatics↗

bioRxiv2023

Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq.

Plant defense responses involve several biological processes that allow plants to fight against pathogenic attacks. How these different processes are orchestrated within organs and depend on specific cell types is poorly known. Here, using scRNA-seq technology on three independent biological replicates, we identified 10 distinct cell populations in wild-type Arabidopsis leaves inoculated with the bacterial pathogen Pseudomonas syringae DC3000. Among those, we retrieved major cell types of the leaves (mesophyll, guard, epidermal, companion and vascular S cells) to which we could associate characteristic transcriptional reprogramming and regulators, thereby specifying different cell-type responses to the pathogen. Further analyses of transcriptional dynamics, based on inference of cell trajectories, indicated that the different cell types, in addition to their characteristic defense responses, can also share similar modules of gene reprogramming, allowing for instance vascular S cells, epidermal cells and mesophyll cells to converge towards an identical cell fate, mostly characterized by lignification and detoxification functions. Moreover, it appeared that the defense responses of these three cell types can evolve along a second separate path. As this divergence does not correspond to the differentiation between immune and susceptible cells, we speculate that this might reflect the discrimination between cell-autonomous and non-cell-autonomous responses. Altogether our data provide an upgraded framework to describe, explore and explain the specialization and the coordination of plant cell responses upon pathogenic challenge.

plant biology↗

bioRxiv2022

Limiting etioplast gene-expression induces apical hook twisting during skoto-morphogenesis of Arabidopsis seedlings

When covered by a layer of soil, seedling development follows a dark-specific program (skoto-morphogenesis) consisting of small, non-green cotyledons, a long hypocotyl and an apical hook to protect meristematic cells. We recently highlighted the role played by mitochondria in the high energy-consuming reprogramming of Arabidopsis skoto-morphogenesis. Here, the role played by plastids, another energy supplying organelle, in skoto-morphogenesis is investigated. This study was conducted in dark conditions to exclude light signals so as to better focus on those produced by plastids. It was found that limitation of plastid gene-expression (PGE) induced an exaggerated apical hook bending. Inhibition of PGE was obtained at the level of transcription and translation using the antibiotics rifampicin and spectinomycin, respectively, as well as plastid RPOTP RNA polymerase mutants. Rifampicin-treated seedlings also showed expression induction of marker nuclear genes for mitochondrial stress, perturbation of the mitochondrial metabolism, increase of ROS levels and an augmented capacity of oxygen consumption by mitochondrial alternative oxidases (AOX). AOX enzymes act to prevent over-reduction of the mitochondrial electron transport chain. Previously, we reported that AOX1A, the main AOX isoform, was a key component in the developmental response to mitochondrial respiration deficiency. In this work, we suggest the involvement of AOX1A in the response to PGE dysfunction and propose the importance of signalling between plastids and mitochondria. Finally, it was found that seedling architecture reprogramming in response to rifampicin was independent of canonical organelle retrograde pathways and the ethylene signaling pathway. Significance statementIn underground germination conditions, seedling development follows a dark-specific program (skoto-morphogenesis) consisting of small and non-green cotyledons, a long hypocotyl and an apical hook to protect meristematic cells. We show that skoto-morphogenesis is reprogrammed when plastid gene expression is perturbed leading to an exaggeration of apical hook bending. We propose the involvement of the cooperation between plastids and mitochondria, the energy-supplying organelles of the cell.

plant biology↗

bioRxiv2022

TFIIF interacts with the Topoisomerase VI complex and selectively controls the expression of genes encoding PPR proteins involved in organellar RNA editing in Arabidopsis.

Communication between organelles and the nucleus is referred to as anterograde (nucleus to organelle) and retrograde (organelle to nucleus) signalling. In plants, the pentatricopeptide repeat (PPR) proteins represent a large family of nuclear-encoded proteins that are required for post-transcriptional control of chloroplast and mitochondria gene expression, and hence play a central role in the nuclear anterograde control of organelle genome expression. How PPR gene expression is controlled and regulated by retrograde signals is, however, still unknown. Here, we report a significant role for the general transcription factor TFIIF -subunit (TFIIF) in controlling PPR gene expression in Arabidopsis. First, we found that TFIIF interacts with the BIN4 subunit of the Topoisomerase VI (Topo VI). Transcriptome analysis of TFIIF and Topo VI mutant lines then revealed that many PLS-type PPR genes involved in RNA editing are reciprocally controlled by TFIIF and Topo VI. The misexpression of CLB19 and DYW1 genes in two allelic tfIIf mutants was associated with editing impairments in their plastid target RNAs rpoA and ndhD, respectively. Interestingly, we also detected a change in NDH activity in tfIIf plants. We also show that TFIIF and Topo VI coordinate the expression of NDH subunits encoded by the nuclear and plastid genomes. These results reveal the crucial role of the nuclear TFIIF and Topo VI complexes in controlling plastid genome expression at multiple levels of regulation, including the particular regulation of PPR gene expression.

plant biology↗

bioRxiv2021

Untargeted metabolomic analyses reveal the diversity and plasticity of the specialized metabolome in seeds of different Camelina sativa varieties

Despite the essential role of Specialized Metabolites (SMs) in the interaction of plants with the environment, studying the ability of crop seeds to produce these protective compounds has been neglected. Furthermore, seeds produce a myriad of SMs providing an interesting model to investigate their diversity and plasticity. Camelina sativa gained a lot of interest in the past few years as rustic oil seed crop. A characterization of seed SM landscapes in six camelina genotypes grown in the field and harvested during five growing seasons has been undertaken in this work. This allowed a comprehensive annotation of seed SMs combining analyses that cluster SMs based on their chemical structures and co-accumulation patterns. These data showed broad effects of the environment on the stimulation of the seed-specialized metabolome. Among well annotated compounds, flavonols were identified as the metabolic class characterised by high plasticity, revealing significant variable accumulation according to the year and/or the genotype. Lastly, a deeper characterisation of primary metabolites and lipids in two selected genotypes has been performed. We showed that, in addition to flavonols, alkaloids and glucosinolates displayed a higher phenotypic plasticity with respect to most of the primary metabolites, including some sugars and major storage compounds such as fatty acids, proteins and most lipid classes (e.g. DAG, TAG), but similar plasticity compared to free aminoacids and carboxylic acids. This work highlighted major and unexplored effects of the environment on the seed specialized metabolome demonstrating that seeds exhibit a dynamic and plastic metabolism, with an impact on seed quality. Significance statementSeeds produce a myriad of Specialized Metabolites (SMs) with an essential role in the interaction of plants with the environment. We characterized SM landscapes, primary metabolites and lipid composition in the seeds of camelina genotypes grown in the open field in five consecutive growing seasons. Our results showed the predominant effect of the environment on the regulation of the seed - specialized metabolome, with a potential impact on seed quality of camelina that may also occur in other oilseed crops.

plant biology↗

bioRxiv2020

The genomic impact of mycoheterotrophy: targeted gene losses but extensive expression reprogramming.

ABSTRACTMycoheterotrophic plants have lost the ability to photosynthesize and they parasitize their associated fungus to get the mineral and organic nutrients they need. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy to mycoheterotrophy occurred independently in almost all major lineages of land plants, but most often in Orchidaceae. Yet the molecular mechanisms underlying this shift are still poorly understood. The comparison of the transcriptomes of Epipogium aphyllum and Neottia nidus-avis, two mycoheterotrophic orchids, to other autotrophic and mycoheterotrophic orchids showed massive molecular function losses restricted to photosynthetic activities. In addition to these targeted losses, the analysis of their expression profiles showed that many orthologs had inverted root/shoot ratios compared to autotrophic species. Fatty acid and amino acid biosynthesis as well as primary cell wall metabolism were among the pathways most impacted by this expression reprogramming. Our study suggests that, while associated with function losses rather than metabolic innovations, the shift in nutritional mode from autotrophy to mycoheterotrophy remodeled the architecture of the plant metabolism.View Full Text

plant biology↗

bioRxiv2019

Two ecotype-related long non-coding RNAs in the environmental control of root growth

BackgroundRoot architecture varies widely between species and even between ecotypes of the same species despite the strong conservation of the protein-coding portion of their genomes. In contrast, non-coding RNAs evolved rapidly between ecotypes and may control their differential responses to the environment as several long non-coding RNAs (lncRNAs) can quantitatively regulate gene expression.\n\nResultsRoots from Columbia (Col) and Landsberg erecta (Ler) ecotypes respond differently to phosphate starvation. We compared complete transcriptomes (mRNAs, lncRNAs and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of new lncRNAs categorized as intergenic or antisense RNAs that were largely conserved at DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independently of the phosphate condition. These ecotype-related lncRNAs were characterized by analyzing their sequence variability among plants and their link with siRNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes including specific antisense RNAs targeting key regulators of root growth responses. Mis-regulation of several intergenic lncRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in Col.\n\nConclusionsThe in depth exploration of the non-coding transcriptome of two ecotypes identified thousands of new lncRNAs showing specific expression in root apexes. De-regulation of two ecotype-related lncRNAs revealed a new pathway involved in the regulation of primary root growth. The non-coding genome may reveal novel mechanisms involved in ecotype adaptation of roots to different soil environments.

plant biology↗