Biology subjects

Dubois, G.

Publications and source records attributed to Dubois, G..

8 recordsLinked to original sources

bioRxiv2026

Feedback between PI4P signaling and ER-PM contact sites orchestrates polarized root hair growth

Eukaryotic cells are composed of different organelles that communicate with one another through direct contacts, which are necessary for a host of cellular reactions and for responding to different developmental and environmental changes. Plasma membrane (PM) forms extensive contacts with the endoplasmic reticulum (ER) at specific sites named ER-PM contact sites. These contacts play crucial functions in lipid homeostasis, Ca2+ regulation and signaling in all eukaryotes. However, the mechanisms by which plant ER-PM contact site proteins tether to the PM, as well as the dynamics of these contact sites, remain poorly understood. Here, we investigate the importance of phosphoinositides in the establishment and dynamics of ER-PM contact site proteins in plants. We found that phosphatidylinositol-4-phosphate (PI4P), rather than phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), is required for the association of ER-PM contact site proteins with the PM. Furthermore, we identified a PI4P phosphatase, SUPPRESSOR-OF-ACTIN7 (SAC7), that associates with the ER-PM contact site protein SYNAPTOTAGMIN1 (SYT1) and regulates its dynamic association with the PM. In particular, we found that in growing root hairs, a highly polarized cell type, SAC7 removes SYT1-containing contact sites at the growing tip. Consistently, optogenetic induction of ER-PM tethering reduced root hair elongation within minutes of blue light induction. Altogether, we propose a link between SAC7-mediated regulation of PI4P, dynamic ER-PM contact site establishment and polarized cell growth in plants.

Plant Biology↗

bioRxiv2024

Dual CRALBP isoforms unveiled: iPSC-derived retinal modelling and AAV2/5-RLBP1 gene transfer raise considerations for effective therapy

Inherited retinal diseases (IRDs) are clinically and genetically heterogeneous disorders characterised by progressive vision loss. Over 270 causative genes have been identified and variants within the same gene can give rise to clinically distinct disorders. Human induced pluripotent stem cells (iPSCs) have revolutionised disease modelling, by allowing pathophysiological and therapeutic studies in the patient and tissue context. The IRD gene RLBP1 encodes CRALBP, an actor of the rod and cone visual cycles in the retinal pigment epithelium (RPE) and Muller cells, respectively. Variants in RLBP1 lead to three clinical subtypes: Bothnia dystrophy, Retinitis punctata albescens and Newfoundland rod-cone dystrophy. We modelled RLBP1-IRD subtypes by patient-specific iPSC-derived RPE and identified pertinent therapeutic read-outs. We developed an AAV2/5-mediated gene replacement strategy and provided a proof-of-concept in the ex vivo human models that was validated in an in vivo Rlbp1-/- murine model. Most importantly, we identified a previously unsuspected smaller CRALBP isoform that is naturally and differentially expressed in both human and murine retina. The new isoform arises from an alternative methionine initiation site and plays a role in the visual cycle. This work provides novel insights into CRALBP expression and RLBP1-associated pathophysiology and raises important considerations for successful gene supplementation therapy.

molecular biology↗

bioRxiv2023

Plasmodesmata act as unconventional membrane contact sites regulating inter-cellular molecular exchange in plants

Membrane contact sites (MCS) are fundamental for intracellular communication, but their role in intercellular communication remains unexplored. We show that in plants, plasmodesmata communication bridges function as atypical endoplasmic reticulum (ER)-plasma membrane (PM) tubular MCS, operating at cell-cell interfaces. Similar to other MCS, ER-PM apposition is controlled by a protein-lipid tethering complex, but uniquely, this serves intercellular communication. Combining high-resolution microscopy, molecular dynamics, pharmacological and genetic approaches, we show that cell-cell trafficking is modulated through the combined action of Multiple C2 domains and transmembrane domain proteins (MCTP) 3, 4, and 6 ER-PM tethers, and phosphatidylinositol-4-phosphate (PI4P) lipid. Graded PI4P amounts regulate MCTP docking to the PM, their plasmodesmata localization and cell-cell permeability. SAC7, an ER-localized PI4P-phosphatase, regulates MCTP4 accumulation at plasmodesmata and modulates cell-cell trafficking capacity in a cell-type specific manner. Our findings expand MCSs functions in information transmission, from intracellular to intercellular cellular activities. In briefPlant intercellular communication is regulated via tubular membrane contact through PI4P binding-ER-PM tether MCTP proteins HighlightsO_LIPlasmodesmata are unconventional ER/PM tubular contact sites located at cell-cell interface C_LIO_LIPlasmodesmata operate as control valves, modulating ER-PM contacts to regulate transport C_LIO_LIMCTP3, MCTP4, MCTP6 and PI4P tethering elements act as valve regulators C_LIO_LISAC7 PI4P phosphatase controls plasmodesmata MCS in a cell-type-specific manner C_LI

plant biology↗

bioRxiv2023

Validation of Flavivirus Infectious Clones Carrying Fluorescent Markers for Antiviral Drug Screening and Replication Studies

Flaviviruses have emerged as major arthropod-transmitted pathogens and represent an increasing public health problem worldwide. High-throughput screening can be facilitated by the use of viruses that express easily detectable marker proteins. Developing molecular tools such as reporter-carrying versions of flaviviruses for studying viral replication and screening of antiviral compounds therefore represents a top priority. However, the engineering of flaviviruses carrying either fluorescent or luminescent reporters remains challenging due to the genetic instability caused by marker insertion; therefore, new approaches to overcome these limitations are needed. Here, we describe reverse genetic methods which includes design and validation of infectious clones of Zika, Kunjin and Dengue viruses harboring different reporter genes for infection, rescue, imaging and morphology using super-resolution microscopy. It was observed that for different flaviviruses constructs with identical design displayed strikingly different genetic stability while corresponding virions resembled wild-type virus particles in shape and size. A successful strategy was assessed to increase stability of rescued reporter virus and permit antiviral drug screening based on quantitative automated fluorescence microscopy and replication studies.

molecular biology↗

bioRxiv2022

Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?

AO_SCPLOWBSTRACTC_SCPLOWHuman-mediated introductions are reshuffling species distribution on a global scale. Consequently, an increasing number of allopatric taxa are now brought into contact, promoting introgressive hybridization between incompletely isolated species and new adaptive gene transfer. The broadcast spawning marine species, Ciona robusta, has been recently introduced in the native range of its sister taxa, Ciona intestinalis, in the English Channel and North-East Atlantic. These sea squirts are highly divergent, yet hybridization has been reported by crossing experiments and genetic studies in the wild. Here, we examined the consequences of secondary contact between C. intestinalis and C. robusta in the English Channel. We produced genomes phased by transmission to infer the history of divergence and gene flow, and analyzed introgressed genomic tracts. Demographic inference revealed a history of secondary contact with a low overall rate of introgression. Introgressed tracts were short, segregating at low frequency, and scattered throughout the genome, suggesting traces of past contacts during the last 30 ky. However, we also uncovered a hotspot of introgression on chromosome 5, characterized by several hundred kb-long C. robusta haplotypes segregating in C. intestinalis, that introgressed during contemporary times the last 75 years. Although locally more frequent than the baseline level of introgression, C. robusta alleles are not fixed, even in the core region of the introgression hotspot. Still, linkage-disequilibrium patterns and haplotype-based tests suggest this genomic region is under recent positive selection. We further detected in the hotspot an over-representation of candidate SNPs lying on a cytochrome P450 gene with a high copy number of tandem repeats in the introgressed alleles. Cytochromes P450 are a superfamily of enzymes involved in detoxifying exogenous compounds, constituting a promising avenue for functional studies. These findings support that introgression of an adaptive allele is possible between very divergent genomes and that anthropogenic hybridization can provide the raw material for adaptation of native lineages in the Anthropocene.

evolutionary biology↗

bioRxiv2020

Monitoring the microbiome for food safety and quality using deep shotgun sequencing

In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix filtering step that improved microbe detection specificity to >99.96% during in silico validation. The pipeline identified 119 microbial genera per HPP sample on average with 65 genera present in all samples. The most abundant of these were Bacteroides, Clostridium, Lactococcus, Aeromonas, and Citrobacter. We also observed shifts in the microbial community corresponding to ingredient composition differences. When comparing culture-based results for Salmonella with total RNA sequencing, we found that Salmonella growth did not correlate with multiple sequence analyses. We conclude that microbiome sequencing is useful to characterize complex food microbial communities, while additional work is required for predicting specific species viability from total RNA sequencing.

microbiology↗

bioRxiv2020

Only ten percent of the global terrestrial protected area network is connected via intact land

Land free of direct anthropogenic disturbance is considered essential for achieving biodiversity conservation outcomes but is rapidly eroding. In response, many nations are increasing their protected area estates but little consideration is given to the context of the surrounding landscape. This is despite the fact that connectivity between protected areas is critical in a changing climate and mandated in international protected area targets. By utilizing the latest human pressure assessment, which shows that [~]40% of the terrestrial planet is still intact, and a connectivity method, we found just 9.7% of Earths terrestrial protected network can be considered connected. On average, 11% of each nations protected area estate is connected via intact land. As the global community commits to bolder action on abating biodiversity loss, only an increased focus on landscape-scale habitat retention and restoration efforts will ensure those critical areas safeguarded for conservation outcomes will remain (or become) connected. One Sentence SummaryOnly 9.7% of the global protected area network can be considered connected by intact land.

ecology↗

bioRxiv2019

Land productivity dynamics in and around protected areas globally from 1999 to 2013

Tracking changes in total biomass production or land productivity is an essential part of monitoring land transformations and long-term alterations of the health and productive capacity of land that are typically associated with land degradation. Persistent declines in land productivity impact many terrestrial ecosystem services that form the basis for sustainable livelihoods of human communities. Protected areas (PAs) are a key strategy in global efforts to conserve biodiversity and ecosystem services that are critical for human well-being, and cover about 15% of the land worldwide. Here we globally assess the trends in land productivity in PAs of at least 10 km2 and in their unprotected surroundings (10 km buffers) from 1999 to 2013. We quantify the percentage of the protected and unprotected land that shows stable, increasing or decreasing trends in land productivity, quantified as long-term (15 year) changes in above-ground biomass derived from satellite-based observations with a spatial resolution of 1 km. We find that 44% of the land in PAs globally has retained the productivity at stable levels from 1999 to 2013, compared to 42% of stable productivity in the unprotected land around PAs. Persistent increases in productivity are more common in the unprotected lands around PAs (32%) than within PAs (18%) globally, which may be related to more active management and vegetation cover changes in some of these unprotected lands. About 14% of the protected land and 12% of the unprotected land around PAs has experienced declines in land productivity from 1999 to 2013 globally. Oceania has the highest percentage of land with stable productivity in PAs (57%) followed by Asia (52%). Europe is the continent with the lowest percentage of land with stable productivity levels in PAs (38%) and with the largest share of protected land with increasing land productivity (32%), which may be related to the high population density and share of agricultural land within PAs as well as to rural land abandonment processes in many regions of Europe. In conclusion, we provide a relevant indicator and assessment of land productivity dynamics that contributes to characterise the state, pressures and changes in and around protected areas globally. Further research may focus on more detailed analyses to disentangle the relative contribution of specific drivers (from climate change to land use change) and their interaction with land productivity dynamics and potential land degradation in different regions of the world.

ecology↗