Biology subjects

Vicente, J.

Publications and source records attributed to Vicente, J..

13 recordsLinked to original sources

bioRxiv2026

Functional diversification of UBP6 in plant immunity through N-degron pathway regulation

Deubiquitylases are key proteolytic regulators of ubiquitin-dependent cellular processes, catalyzing the removal or remodelling of ubiquitin modifications on substrate proteins, including those targeted for proteasomal degradation. UBIQUITIN PROTEASE (UBP)6 is a deubiquitylase that promotes the abundance of NONEXPRESSOR OF PATHOGENESIS RELATED GENES (NPR)1, a conserved master regulator of plant immunity. Here, we show that the Arabidopsis thaliana protease METACASPASE (MC)9 site-specifically processes UBP6, generating the E157-UBP6 proteoform, whose stability is controlled by the Arginyl-transferase (ATE) N-degron pathway. We observed that pathogen recognition both triggers UBP6 cleavage and leads to conditional stabilisation of E157 UBP6, which is enhanced as the defence response intensifies. Our data suggest that E157 UBP6, which lacks deubiquitylating activity, may induce inhibition of the proteasome, elevating NPR1 levels and enhancing salicylic acid (SA) induced gene activation, all of which collectively contribute to restricting pathogen growth. Thus, UBP6 cleavage and N-degron pathway regulation provide distinct proteoforms of UBP6 with specific effects on the immune processes.

plant biology↗

bioRxiv2026

Combined impacts of invasive alien species and fire on ecosystems are complex, mostly negative, and understudied: a global review

Invasion-fire interactions can negatively impact ecosystems by driving biodiversity loss, altering ecological processes, modifying habitat structure, and compromising ecosystem functioning. Understanding how this interaction operates is essential to design effective management strategies that are successful in controlling both invasive alien species (IAS) and fire. Therefore, the present literature review aims to synthesize the current knowledge on invasion-fire interaction and its impacts on ecosystems, as well as identify knowledge gaps in the field. The review included 464 studies, from which information on context, species and fire characteristics, interaction outcomes, and research approaches was extracted. Fire generally promotes IAS, although studies on invasive animals are limited and no research has examined the effects of fire on fungi. Management through prescribed fire showed significantly better outcomes than wildfires in suppressing IAS, yet positive impacts still outnumbered the negative ones. In turn, IAS can change fire regimes causing regime shifts, but this direction of interaction is much less studied. Combined impacts of fire and IAS on ecosystems are predominantly negative, although interactions are complex and not always synergistic. Key knowledge gaps include geographic regions with known Invasion-fire interactions that remain underreported, a lack of broad-scale studies, limited management interventions, understudied taxa, and limited understanding of the combined effects on ecosystems. Remote sensing and laboratory experiments, which have been rarely used, could address some of these gaps.

ecology↗

bioRxiv2026

Conditional stability of HY5 through the ATE N-degron pathway regulates environmental responses in Arabidopsis thaliana

The N-degron pathways of ubiquitin mediated proteolysis target proteins for degradation dependent on their amino terminal residue, often produced after protease activity. Very few substrates have been identified in plants even though enzymes of these pathways are highly conserved in eukaryotes. Here we identify ELONGATED HYPOCOTYL5 (HY5), an important transcriptional regulator involved in many aspects of plant development, as a target for the endopeptidase METACASPASE (MC)9, producing the carboxy-terminal protein fragment (proteoform) E59-HY5. E59-HY5 is shown to be a substrate of the arginyl transferase (ATE) N-degron pathway, and influences physiological processes known to be controlled by HY5, including photomorphogenesis and the unfolded protein response. Conditional stability of E59-HY5 was shown to result from environmentally controlled ATE function, which may highlight a general mechanism for N-degron pathway regulation of proteoform and proteome function during growth and development.

plant biology↗

bioRxiv2025

How big is enough? Movement-informed zoning for African swine fever mitigation

O_LIAfrican swine fever (ASF) poses a serious threat to domestic pigs and wild boar populations. Wild boar can disperse the virus, making effective containment crucial. One of the main control strategies involves establishing restricted zones around detected cases, i.e., areas with temporary restrictions on access and hunting; however, determining the appropriate size of these zones remains a major challenge. C_LIO_LITo inform the size of restricted zones, we analyzed GPS data from 527 wild boar across 46 European study sites using a two-step approach combining first-passage time analysis and survival modelling to quantify the risk of wild boar leaving areas of different radii (i.e., spatial scales). We investigated how the risk of leaving varied over time and across environmental gradients. To go further, we used our model findings to develop an online application that generates predictive maps of optimal buffer sizes for ASF management at the European scale, based on a given risk threshold (the maximum acceptable probability that a wild boar leaves the area). C_LIO_LIWe found that the relationship between radius and the risk of leaving is negative exponential, and the risk of leaving increased over time, with a more rapid increase for smaller radii. Landscape homogeneity, terrain ruggedness and human impact increased the risk of leaving, with stronger effects at small scales. Contrary to other predictors, agricultural cover exerted a strong effect on risk of leaving over large spatial scales, especially when it was abundant. C_LIO_LIAcross Europe, a buffer radius of [~]8 km is likely sufficient around high-risk infection zones in most areas (considering an infectious period of 14 days and a risk threshold of 5%); however, in certain areas, a radius of up to 20 km may be needed to effectively limit wild boar movement. C_LIO_LISynthesis and applications: Our results highlight the need for adaptive, context-specific restricted zones. Buffers of 8 km around ASF-affected areas can limit the risk of infected wild boar dispersal, but they may be reduced to 5 km in highly heterogeneous landscapes or high-human impacted areas. Larger buffers may be required in agricultural landscapes. We provide spatially explicit outputs (optimal buffer sizes) that can directly inform policy and wildlife disease response strategies. The approach can be adapted to any other infectious disease. C_LI

ecology↗

bioRxiv2025

Contrasting evolutionary forces of specialization and admixture underlie the genomic and phenotypic diversity of Yarrowia lipolytica

Microbial diversity emerges from evolutionary processes that shape genomic and phenotypic traits in response to complex environmental pressures. Deciphering these dynamics is key to understanding microbial ecology and advancing biotechnological applications. Here, we use the yeast Yarrowia lipolytica to study genomic signatures of adaptation across a broad range of environments and to illustrate how population-level data can inform targeted bioprospecting for industrial traits. Whole-genome and phenotypic analyses of 126 isolates from natural and anthropogenic environments reveal a complex population structure in this species, shaped by both niche specialization and admixture events. Structured lineages exhibit ecological filtering, reduced genetic diversity, and distinct gene content, consistent with adaptation to substrates like dairy, hydrocarbons, or industrial substrates. In contrast, admixed populations display greater genetic diversity and broader phenotypic capacity, including enhanced stress tolerance and metabolic flexibility. Genome plasticity, reflected in pangenome and CNV variation, aligns with ecological origin, while trait assays link phenotypic divergence to underlying genetic variation. For instance, better growth performance on acetate, an ecological and industrially relevant trait, is associated with hydrocarbon-adapted strains and likely linked to variation in regulatory regions of acetate metabolism genes. Together, our results reflect how divergent evolutionary trajectories--ranging from ecological specialization to genomic plasticity through admixture-- underpin the species ecological success and provide a framework for harnessing its natural diversity in microbial bioprospecting.

evolutionary biology↗

bioRxiv2025

A look at the ground: time lapse camera trapping to determine the composition and abundance of small sized wildlife communities

Micromammals are critical species in the context of ecosystem functioning, assuming a significant role as prey species and environmental engineers. Nevertheless, they present a challenge when developing monitoring programs. As a proof of concept, a time-lapse based camera-trapping non-invasive protocol was tested with the application of the Space to Event Model (STE) was determined. The objective of this study was to estimate the density of micromammals in Donana National Park (DNP, Southwest Spain) by comparing estimates against independent ones obtained from capture-mark-recapture (CRM) methodology with a standardized protocol using Sherman traps. The micromammal species richness in the area exhibited a strong correlation with the capture methodology employed. Regarding the estimation of abundance, the densities of micromammals determined by STE were found to be within the range of the estimations of minimum population size determined by CRM. The STE, which was found to be promising, also allowed the determination of the abundance of other small-sized terrestrial wildlife, such as reptiles. Our findings indicate its potential for camera trap multi-species monitoring. In terms of practicability, field and data processing efforts for STE are both viable and will continue to improve as new automatic identification tools are incorporated. It is imperative that the STE protocols are examined in a series of study areas exhibiting varying micromammal densities and species compositions, in addition to other small-sized terrestrial wildlife.

ecology↗

bioRxiv2025

Hidden in Plain Sight: A Novel Symbiotic Haplosclerid Sponge Species Revealed by its Mitochondrial Genome

An unusual third mitochondrial genome was discovered in the genomic data from the symbiotic association between two sponges, Haliclona plakophila (Haplosclerida, Demospongiae) and Plakortis symbiotica (Homoscleromorpha). This mitogenome exhibited an unusually high GC content, lacked the cox2 gene, and could not be reliably positioned among animals based on phylogenetic analysis of the sequence data. Nevertheless, conserved gene clusters and the presence of atp9 indicated that this species is a sponge, while phylogenetic analysis using 18S and 28S places it in the order Haplosclerida of Demospongiae. Since no tissue of the cryptic sponge was found in the investigated association, its relationship with other sponges remained unclear. Therefore, we sampled 10 additional samples assumed to be H. plakophila - P. symbiotica associations in the field to search for the mysterious third sponge. PCR analysis revealed that one of the collected samples contained the novel sponge, but not H. plakophila. A follow-up morphological investigation revealed that this sponge, Haplosclerida sp. nov., while superficially indistinguishable from H. plakophila, differs in skeletal organization and spicule composition. Here, we report the unusual mitochondrial genome of the new species, along with a phylogenetic analysis using 18S and 28S sequences, and demonstrate that Haplosclerida sp. nov. belongs to a new clade of Haplosclerida. We also report the mitogenome of Xestospongia deweerdtae, another haplosclerid species described in association with multiple Plakortis species, including P. symbiotica. Our results support multiple origins of Haplosclerida-Plakortis symbiosis and open new avenues for its investigation.

evolutionary biology↗

bioRxiv2024

Pervasive mitochondrial tRNA gene loss in the clade B of haplosclerid sponges (Porifera, Demospongiae).

AbstractMitochondrial tRNA gene loss and cytosolic tRNA import to mitochondria are two common phenomena in mitochondrial biology, but their importance is often under-appreciated in animals. This is because most bilaterally symmetrical animals (Bilateria) encode a complete set of tRNAs needed for mitochondrial translation. By contrast, studies of mitochondrial genomes in non-bilaterian animals have shown a reduced tRNA gene content in several lineages, necessitating tRNA import. Interestingly, in most of these lineages tRNA gene content appears to be set early in the evolution of the group and conserved thereafter. Here we demonstrate that Clade B of Haplosclerid Sponges (CBHS) represent an exception to this pattern. We determined mt-genome sequences for eight species from this group and analyzed them with six that had been previously available. In addition, we determined mt-genome sequences for two species of haploslerid sponges outside the CBHS and used them with eight previously available sequences as outgroups. We found that tRNA gene content varied widely among CBHS species: from three in an undescribed Haliclona species (Haliclona sp. TLT785) to 25 in Xestospongia muta and X. testudinaria. Furthermore, we found that all CBHS species outside the genus Xestospongia lacked atp9, while some also lacked atp8. Analysis of nuclear sequences from Niphates digitalis revealed that both atp8 and atp9 had transferred to the nuclear genome, while the absence of mt-tRNA genes represented their genuine loss. Overall, CBHS can be a useful animal system to study mt-tRNA genes loss, mitochondrial import of cytosolic tRNA, and the impact of both of these processes on mitochondrial evolution. Significance statementIt is generally believed that the gene content is stable in animal mitochondrial (mt) DNA. Indeed, mtDNA in most bilaterally symmetrical animals encompasses a conserved set of 37 genes coding for 13 proteins, two rRNAs and 22 tRNAs. By contrast, mtDNA in non-bilaterian animals shows more variation in mt gene content, in particular in the number of tRNA genes. However, most of this variation occurs between major non-bilaterian lineages. Here we demonstrate that a group of demosponges called Clade B of Haplosclerid Sponges (CBHS) represents a fascinating exception to this pattern, with species experiencing recurrent losses of up to 22 mt-tRNA genes. We argue that this group constitutes a promising system to investigate the effects of tRNA gene loss on evolution of mt-genomes as well as mitochondrial tRNA import machinery.

evolutionary biology↗

bioRxiv2023

Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations

BackgroundConnecting the composition and function of industrial microbiomes is a major aspiration in microbial biotechnology. Here, we address this question in wine fermentation, a model system where the diversity and functioning of fermenting yeast species is determinant of the flavor and quality of the resulting wines. ResultsFirst, we surveyed yeast communities associated with grape musts collected across wine appellations, revealing the importance of environmental (i.e., biogeography) and anthropic factors (i.e., farming system) in shaping community composition and structure. Then, we assayed the fermenting yeast communities in synthetic grape must under common winemaking conditions. The dominating yeast species defines the fermentation performance and metabolite profile of the resulting wines, and it is determined by the initial fungal community composition rather than the imposed fermentation conditions. Yeast dominance also had a more pronounced impact on wine meta-transcriptome than fermentation conditions. We unveiled yeast-specific transcriptomic profiles, leveraging different molecular functioning strategies in wine fermentation environments. We further studied the orthologs responsible for metabolite production, revealing modules associated with the dominance of specific yeast species. This emphasizes the unique contributions of yeast species to wine flavor, here summarized in an array of orthologs that defines the individual contribution of yeast species to wine ecosystem functioning. ConclusionsOur study bridges the gap between yeast community composition and wine metabolite production, providing insights to harness diverse yeast functionalities with the final aim to producing tailored high-quality wines.

microbiology↗

bioRxiv2023

DNA nanopores as artificial membrane channels for origami based bioelectronics

Biological membrane channels mediate information exchange between cells and facilitate molecular recognition1-4. While tuning the shape and function of membrane channels for precision molecular sensing via de-novo routes is complex, an even more significant challenge is interfacing membrane channels with electronic devices for signal readout5-8. This challenge at the biotic-abiotic interface results in low efficiency of information transfer - one of the major barriers to the continued development of high-performance bioelectronic devices9. To this end, we integrate membrane spanning DNA nanopores with bioprotonic contacts to create programmable, modular, and efficient artificial ion-channel interfaces that resolve the iono-electronic disparity between the biotic environment and electronics. Through simulations and experiments, we show that cholesterol modified DNA nanopores spontaneously and with remarkable affinity span the lipid bilayer formed over the planar bio-protonic electrode surface and mediate proton transport across the bilayer. Using the ability to easily modify DNA nanostructures, we illustrate that this bioelectronic device can be programmed for electronic recognition of biomolecular signals such as presence of Streptavidin, without disrupting the native environment of the biomolecule. We anticipate this robust biotic-abiotic interface will allow facile electronic measurement of inter-cellular ionic communication and also open the door for active control of cell behavior through externally controlled selective gating of the channels.

bioengineering↗

bioRxiv2022

Multilocus typing of Lachancea thermotolerans for wine fermentation monitoring

Climate change is causing a lack of acidity during winemaking and oenologists use several solutions to cope with such a problem. Lachancea thermotolerans, which has the potential to tolerate the harsh physicochemical conditions of wine, has emerged as a promising alternative for pH management during winemaking and, currently, it is the most valuable yeast used for acidity control in wine. In this work an amenable method for L. thermotolerans genotyping based on a multiplexed microsatellite amplification in 6 different loci was developed. This specific and sensitive method was used to distinguish between 103 collection strains obtained from different geographical and isolation sources, and then challenged against a 429 L. thermotolerans isolates from several wineries and harvests. The procedure was also tested for fermentation monitoring and strain implantation. The procedure was conceived to simplify the methodology available for L. thermotolerans genotyping, making it easy for applying in wine-related laboratories. This method can be applied to distinguish between L. thermotolerans strains in selection programs and to follow implantation of inoculated strains during winemaking with optimal results.

microbiology↗

bioRxiv2021

Cholesteryl Hemiazelate Induces Lysosome Dysfunction and Exocytosis in Macrophages

OBJECTIVEA key event in atherogenesis is the formation of lipid-loaded macrophages, lipidotic cells, which exhibit irreversible accumulation of undigested modified low-density lipoproteins in lysosomes. This event culminates with the loss of cell homeostasis, inflammation and cell death. In this study we propose to identify the chemical etiological factors and understanding the molecular and cellular mechanisms responsible for the impairment of lysosome function in macrophages. APPROACH AND RESULTSUsing shotgun lipidomics we have discovered that a family of oxidized lipids (cholesteryl hemiesters, ChE), end products of oxidation of polyunsaturated cholesteryl esters, occurs at higher concentrations in the plasma of two cohorts of cardiovascular disease patients than in the plasma of a control cohort. Macrophages exposed to the most prevalent ChE, cholesteryl hemiazelate (ChA) exhibit lysosome enlargement, peripheral lysosomal positioning, lysosome dysfunction and lipidosis which are irreversible. The transcriptomic profile of macrophages exposed to ChA indicates that the lysosome pathway is deeply affected and is well correlated with lysosome phenotypic and functional changes. Interestingly, the dysfunctional peripheral lysosomes are more prone to fuse with the plasma membrane, secreting their undigested luminal content into the extracellular milieu with potential consequences to the pathology. CONCLUSIONWe identify ChA not only as one of the molecules involved in the etiology of irreversible lysosome dysfunction culminating with lipidosis but also as a promoter of exocytosis of the dysfunctional lysosomes. The latter event is a new mechanism that may be important in the pathogenesis of atherosclerosis.

cell biology↗

bioRxiv2019

Ethylene-mediated nitric oxide depletion pre-adapts plants to hypoxia stress

Timely perception of adverse environmental changes is critical for survival. Dynamic changes in gases are important cues for plants to sense environmental perturbations, such as submergence. In Arabidopsis thaliana, changes in oxygen and nitric oxide (NO) control the stability of ERFVII transcription factors. ERFVII proteolysis is regulated by the N-degron pathway and mediates adaptation to flooding-induced hypoxia. However, how plants detect and transduce early submergence signals remains elusive. Here we show that plants can rapidly detect submergence through passive ethylene entrapment and use this signal to pre-adapt to impending hypoxia. Ethylene can enhance ERFVII stability prior to hypoxia by increasing the NO-scavenger PHYTOGLOBIN1. This ethylene-mediated NO depletion and consequent ERFVII accumulation pre-adapts plants to survive subsequent hypoxia. Our results reveal the biological link between three gaseous signals for the regulation of flooding survival and identifies novel regulatory targets for early stress perception that could be pivotal for developing flood-tolerant crops.

plant biology↗