Biology subjects

Rubio, B.

Publications and source records attributed to Rubio, B..

7 recordsLinked to original sources

bioRxiv2025

Esca Disease triggers local transcriptomic response and systemic DNA methylation changes in grapevine

Woody plants such as grapevine are vulnerable to trunk diseases caused by pathogens that colonize the wood, disrupt vascular function, and induce recurrent leaf symptoms associated with major metabolic disturbances and canopy decline. Over time, these diseases can irreversibly alter plant physiology and phenotype, ultimately reducing vine longevity. One of the most predominant of such diseases is esca, which is a major cause of vineyard dieback, with rising incidence worldwide over the past decade. However, the molecular mechanisms underlying esca symptom development remain unclear. In this study, we leveraged the heterogeneous expression of esca-symptoms within individual grapevines to investigate molecular responses in both symptomatic and asymptomatic leaf tissues. By combining metabolite profiling, RNA-seq and whole genome bisulfite sequencing, we show that metabolic alterations and extensive transcriptomic reprogramming are restricted to symptomatic leaves and are partially associated with local changes in DNA methylation. Asymptomatic leaves display distinct DNA methylation changes, some of which are shared with symptomatic tissues, suggesting a systemic response to the disease at the epigenetic level. Notably, subset of these methylation marks are observable prior to symptom emergence, highlighting the potential of epigenetic biomarkers for the early detection of trunk diseases in perennial plants.

plant biology↗

bioRxiv2025

Loss of the alternative calcineurin variant CnAβ1 enhances brown adipocyte differentiation and drives metabolic overactivation through FoxO1 activation

The alternative calcineurin A variant CnA{beta}1 has a unique C-terminal domain that provides it with distinct subcellular localization and mechanism of action different from other calcineurin isoforms. Here, we used mice lacking CnA{beta}1s C-terminal domain (CnA{beta}1{Delta}i12) to show that the absence of this specific isoform strongly reprograms metabolism. CnA{beta}1{Delta}i12 mice on a high-fat diet showed reduced body weight, white adipose tissue (WAT) mass, and circulating triglycerides, together with enhanced insulin sensitivity. In brown adipose tissue (BAT), CnA{beta}1 deficiency increased mitochondrial content and upregulated fatty acid oxidation and thermogenic proteins, improving cold resistance. Conversely, under starvation, CnA{beta}1{Delta}i12 mice experienced rapid fat depletion and hypothermia. Importantly, BAT-specific FoxO1 knockout in CnA{beta}1{Delta}i12 mice reduced catabolism-related gene expression and partially reversed the metabolic phenotypes, increasing body weight and WAT mass. Our findings reveal a relevant role for CnA{beta}1 in orchestrating BAT metabolism, highlighting its potential as a therapeutic target for obesity and metabolic syndrome.

physiology↗

bioRxiv2024

Grapevine cell response to carbon deficiency requires transcriptome and methylome reprogramming

Sugar limitation has dramatic consequences on plant cells, which include a profound reorganization of the cell metabolism, transcriptional reprogramming, and the recycling of cellular components to maintain fundamental cell functions. There is so far no description of the possible contribution of epigenetic regulations in the adaptation of plant cells to limited carbon availability. We investigated this question using non-photosynthetic grapevine cells (Vitis vinifera, cv Cabernet Sauvignon) cultured in vitro with contrasted glucose concentrations. As expected, limited sugar availability in the culture medium led to a rapid cell growth arrest. This was associated with a major metabolic shift characterized by depletion in soluble sugar and total amino acids, an increase in malate content and changes in the cell redox status. Consistently, flux modeling showed a dramatic slowdown of many pathways required for biomass accumulation such as cell wall polymers and total protein content. In contrast, anaplerotic fluxes, the synthesis of some amino acids, redox and polyamine metabolism were enhanced. Carbon deprivation also resulted in a major transcriptional reprogramming characterized by the induction of genes involved in photosynthesis, and the repression of those related to sucrose mobilization or cell cycle control. Similarly, the epigenetic landscape was deeply modified. Glucose-depleted cells showed a higher global DNA methylation level than those grown with glucose. Changes in DNA methylation mainly occurred at transposable elements, but also at genes including differentially expressed genes, suggesting that DNA methylation could participate in the adaptation of cells to limited sugar availability. In addition, genes encoding histone modifiers were differentially expressed suggesting that additional epigenetic mechanisms may be at work during the response of plant cells to carbon shortage.

plant biology↗

bioRxiv2023

Species-specific epigenetic responses to drought stress of two sympatric oak species reflect their ecological preferences.

O_LIIn a context of climate change, it is necessary to decipher the strategies established by plants to cope with limited water supply. C_LIO_LITranscriptome, methylome and small RNA data were generated for two oak species with contrasting levels of drought tolerance (Quercus robur and Quercus petraea), under control and drought stress conditions C_LIO_LIAll data are in line with a species-specific response to drought stress consistent with their ecological preferences. The biological processes associated with genomic regions identified in all datasets were mainly associated with parietal processes in Q. petraea, which may explain in part its better tolerance to water deprivation. C_LIO_LIA significant proportion of DNA methylation differences observed in control conditions between the two oak species were maintained during DS which may constitute a pool of epigenetic markers discriminating these two oak species. These markers were enriched in highly differentiated SNPs suggesting that some of them may be associated both with the ecological differences or intrinsic barriers to reproduction between the two species. C_LIO_LIAn integrative approach of the three datasets revealed genomic co-locations of potential importance for forest three adaptation to drought stress. C_LI

genomics↗

bioRxiv2023

The functionally plastic rod photoreceptors in the simplex retina of Little skate (Leucoraja erinacea) exhibit a hybrid rod-cone morphology and enhanced synaptic connectivity.

The retinas of the vast majority of vertebrate species are termed "duplex" - that is, they contain both rod and cone photoreceptor neurons in different ratios. The retina of Little skate (Leucoraja erinacea) is a rarity among vertebrates because it contains only rod photoreceptors and is thus "simplex". This unique retina provides us with an important comparative model and an exciting opportunity to study vertebrate rod circuitry within the context of a functional, evolutionarily optimized system, all without the concern about artifacts from genetically modified rod-only mouse models. Perhaps even more importantly, the Leucoraja retina is able to function under both scotopic and photopic ranges of illumination with a single complement of photoreceptors. It is currently unknown what structural characteristics mediate this remarkable functional plasticity. To address this question, we performed serial block-face electron microscopy imaging and examined the structure of rods and their post-synaptic partners. We find that skate rods exhibit ultrastructural characteristics that are either common to rods or cones in other vertebrates (e.g., outer segment architecture, synaptic ribbon number, terminal extensions), or are uniquely in-between those of a typical vertebrate rod or cone (e.g., number of invaginating contacts, clustering of multiple ribbons over a single synaptic invagination). We therefore hypothesize that the unique hybrid rod-cone structure of skate rods and their post-synaptic partners is correlated with the ability of the skate visual system to function across scotopic and photopic ranges of illumination. These findings have the potential to reveal as yet undescribed principles of vertebrate retinal design. Significance statementThe vast majority of vertebrate retinas are duplex and have mixed rod-cone populations of photoreceptors in varying ratios. The processing of visual information in a duplex retina tends to be separated between rod and cone systems, which mediate function under scotopic and photopic lighting conditions, respectively. However, the cartilaginous fish Little skate (Leucoraja erinacea) has a simplex retina, comprised solely of rod photoreceptors. Skate rods are also unusual because they have the ability to retain function over a full range of lighting conditions. We have little knowledge about the ultrastructural anatomy of the skate retina, and we hypothesize that this functional plasticity can be traced back to morphological adaptations at the level of individual photoreceptors and the downstream retinal circuitry, thus illuminating new pathways for the processing of visual information among vertebrates.

neuroscience↗

bioRxiv2020

Metabolic profile discriminates and predicts Arabidopsis susceptibility to virus under field conditions

As obligatory parasites, plant viruses alter host cellular metabolism. There is a lack of information on the variability of virus-induced metabolic responses among genetically diverse plants in a natural context with daily changing conditions. To decipher the metabolic landscape of plant-virus interactions in a natural setting, one hundred and thirty-two and twenty-six accessions of Arabidopsis thaliana were inoculated with Turnip mosaic virus (TuMV), in two field experiments over 2 years. The accessions were phenotyped for viral accumulation, above-ground biomass, targeted and untargeted metabolic profiles. The accessions revealed quantitative response to the virus, from susceptibility to resistance. Susceptible accessions accumulate primary and secondary metabolites upon infection, at the cost of hindered growth. Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA) revealed that the primary metabolites sucrose, glucose and glutamate discriminate susceptible and resistant accessions. Twenty-one metabolic signatures were found to significantly accumulate in resistant accessions whereas they maintained their growth at the same level as mock-inoculated plants without biomass penalty. Metabolic content was demonstrated to discriminate and to be highly predictive of the susceptibility of inoculated Arabidopsis. The PLS coefficient estimated in the training data set reveals, after cross-validation, a correlation of 0.61 between predicted and true viral accumulation. This study is the first to describe the metabolic landscape of plant-virus interactions in a natural setting and its predictive link to susceptibility. It reveals that, in this undomesticated species and in ecologically realistic conditions, growth and resistance are in a permanent conversation and provides new insights on plant-virus interactions.

plant biology↗

bioRxiv2019

De novo phased assembly of the Vitis riparia grape genome

Grapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American native Vitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained from Vitis riparia resulting in a 225X depth of coverage. We generated a genome assembly of the V. riparia grape de novo using the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species.

genomics↗