Biology subjects

Trevisan, M.

Publications and source records attributed to Trevisan, M..

13 recordsLinked to original sources

bioRxiv2026

Extensive and heterogeneous viral circular RNA production during Zika virus infection

Circular RNAs (circRNAs) are covalently closed RNA molecules with regulatory functions. Although virus-derived circRNAs (vcircRNAs) are well characterized in DNA viruses, their occurrence in RNA viruses remains poorly understood. Recent reports in coronaviruses and hepatitis C virus suggest that vcircRNA production extends beyond nuclear-replicating viruses. Here, we show that Zika virus (ZIKV), a vector-borne orthoflavivirus, produces vcircRNAs during infection of neural stem cells. Using a custom computational pipeline optimized for viral back-splice junction detection, we identified at 72 hours post infection a core set of 113 putative vcircRNAs shared across three biological replicates and distributed throughout the viral genome. Eight candidates spanning different genomic regions and abundance levels were experimentally validated by rolling-circle reverse transcription and Nanopore sequencing. These findings provide the first evidence of vcircRNA production in an orthoflavivirus, suggesting that circular RNA biogenesis may represent a previously underappreciated feature of RNA virus biology.

microbiology↗

bioRxiv2026

Diverse signaling proteins recruit RCC1-Like Domain proteins to the plasma membrane through a common structural framework.

Plants translate diverse environmental cues into spatially regulated growth responses through intracellular signaling mechanisms that remain incompletely understood. Here, we identify the BREVIS RADIX (BRX) domain of RCC1-LIKE DOMAIN (RLD) proteins as a versatile interaction module that recognizes multiple signaling proteins in Arabidopsis. We identified members of the PHYTOCHROME KINASE SUBSTRATE (PKS) and BIG GRAIN (BG) families as novel RLD interactors families, in addition to the previously characterized LAZY1-LIKE (LZY) proteins and BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL). Structural, biochemical, and cell-based analyses demonstrate that these diverse partners, despite having divergent interaction sequences, bind a common surface on the RLD BRX domain to recruit RLD to the plasma membrane. This interaction relies on a shared {beta}-strand-based recognition mode, in which distinct peptide conformations accommodate binding to the same BRX-domain surface. Furthermore, we show that RLD2 and RLD3 contribute to hypocotyl phototropism, and that disrupting the conserved PKS interaction motif abolishes PKS4 function in this response. Together, our findings identify the RLD BRX domain as a molecular platform for diverse protein interactions and establish a PKS-RLD module that operates in phototropism. Furthermore, these findings strongly suggest that RLD recruitment to the plasma membrane via PKS underlies phototropic signal transduction.

plant biology↗

bioRxiv2026

Selective Disruption of Mutant TP63 Alleles Restores Corneal Epithelial proliferation in EEC Syndrome

Ectrodactyly-Ectodermal Dysplasia-Cleft Lip/Palate (EEC) syndrome is a rare disorder caused by dominant-negative mutations in the TP63 gene, frequently leading to limbal stem cell deficiency (LSCD) and progressive corneal degeneration. Current therapeutic strategies are limited, primarily due to impaired epithelial renewal and poor proliferative capacity of patient-derived cells. We have recently shown that decreasing the expression of the mutated allele by means of siRNA-mediated silencing can restore epithelial cell proliferation. However, the clinical utility of this approach is hindered by the presence of different TP63 mutations causing EEC syndrome, and the need for continuous siRNA administration to achieve sustained gene silencing. To address these challenges, we employed a CRISPR/Cas9-based genome editing strategy to disrupt mutant TP63 alleles in human induced pluripotent stem cells (hiPSCs) derived from EEC patients carrying R279H and R304Q mutations. Targeted editing of exon 6 induced frameshift mutations that activated nonsense-mediated mRNA decay, leading to a significant reduction in mutant transcript levels. Edited hiPSC-derived corneal epithelial cells exhibited improved cell proliferation compared to unedited isogenic controls. These findings demonstrate the feasibility and therapeutic potential of allele-specific genome editing to correct TP63-associated epithelial defects in EEC syndrome paving the way toward future regenerative therapies for TP63-related corneal diseases.

genetics↗

bioRxiv2025

Towards an armed oncolytic virus approach to glioblastoma treatment.

Glioblastoma (GBM) is among the most aggressive and lethal human tumors. The current standard of care--surgical resection followed by chemotherapy--offers limited efficacy, as recurrence remains frequent and severe, underscoring the urgent need for novel therapeutic strategies. Photodynamic therapy (PDT) and oncolytic virotherapy have emerged as promising alternatives. PDT utilizes light-sensitive molecules to generate reactive oxygen species (ROS), selectively inducing tumor cell death, while oncolytic virotherapy employs viruses to lyse tumor cells and activate anti-tumor immune responses. Notably, Talimogene laherparepvec (T-VEC), an HSV-1-based oncolytic virus (oHSV1), is already approved for treating unresectable melanoma. To explore a combinatorial approach for GBM, we engineered highly neuroattenuated oHSV1 variants with a genetic background similar to T-VEC, expressing KillerRed (KR)--a photosensitizing protein--alone or in combination with immunotherapeutic factors. Our results demonstrate potent cytolytic effects of these recombinant viruses in multiple murine and human GBM cell lines, as well as in primary tumor cells. In a syngeneic C57BL/6J mouse model, oHSV1 administration alone or carried by monocytes induced extensive tumor necrosis, accompanied by infiltration of CD3+ immune cells.

cancer biology↗

bioRxiv2023

Pectin methylesterification modulates cell wall properties to promote neighbour proximity-induced hypocotyl growth

Plants growing with neighbours compete for light and consequently increase growth of their vegetative organs to enhance access to sunlight. This response, called shade avoidance syndrome (SAS), involves photoreceptors such as phytochromes as well as phytochrome interacting factors (PIFs), which regulate the expression of growth-mediating genes. Numerous cell wall-related genes belong to the putative targets of PIFs, and the importance of cell wall modifications for enabling growth was extensively shown in developmental models such as dark-grown hypocotyl. However, the role of the cell wall in the growth of de-etiolated seedlings regulated by shade cues remains poorly established. Through analyses of mechanical and biochemical properties of the cell wall coupled with transcriptomic analysis of cell wall-related genes, we show the importance of cell wall modifications in neighbour proximity-induced elongation. Further analysis using loss-of-function mutants impaired in the synthesis and remodeling of the main cell wall polymers corroborated this. We focused on the cgr2cgr3 double mutant that is defective in homogalacturonan (HG) methyltransferase activity required for methylesterification of HG-type pectins. By following hypocotyl growth kinetically and spatially and analyzing the mechanical and biochemical properties of cell walls, we found that methylesterification of HG-type pectins was required to enable global cell wall modifications. Moreover, HG-class pectin modification was needed for plant competition-induced hypocotyl growth. Collectively our work suggests that in the hypocotyl PIFs orchestrate changes in the expression of numerous cell wall genes to enable neighbour proximity-induced growth. One sentence summaryThe degree of methylesterification of pectins modulates global changes in the cell wall and its mechanical properties that contribute to the neighbour proximity-induced hypocotyl growth in Arabidopsis

plant biology↗

bioRxiv2023

USP8 inhibition promotes Parkin-independent mitophagy in the Drosophila brain and in human neurons

Stress-induced mitophagy, a tightly regulated process that targets dysfunctional mitochondria for autophagy-dependent degradation, mainly relays on two proteins, PINK1 and Parkin, which genes are mutated in some forms of familiar Parkinsons Disease (PD). Upon mitochondrial damage, the protein kinase PINK1 accumulates on the organelle surface where it controls the recruitment of the E3-ubiquitin ligase Parkin. On mitochondria, Parkin ubiquitinates a subset of mitochondrial resident proteins located on the outer mitochondrial membrane, leading to the recruitment of downstream cytosolic autophagic adaptors, and subsequent autophagosome formation. Importantly, PINK1/Parkin-independent mitophagy pathways also exist that can be counteracted by specific deubiquitinating enzymes (DUBs). Downregulation of these specific DUBs can presumably enhances basal mitophagy, and be beneficial in models in which accumulation of defective mitochondria is implicated. Among these DUBs, USP8 is an interesting target because of its role in the endosomal pathway and autophagy, and its beneficial effects, when inhibited, in models of neurodegeneration. Based on this, we evaluated autophagy and mitophagy levels when USP8 activity is altered. We used genetic approaches in D. melanogaster to measure autophagy and mitophagy in vivo, and complementary in vitro approaches to investigate the molecular pathway that regulates mitophagy via USP8. We found an inverse correlation between basal mitophagy and USP8 levels, in that inhibition of USP8 correlates with increased Parkin-independent mitophagy. These results suggest the existence of a yet uncharacterized mitophagic pathway that is inhibited by USP8.

cell biology↗

bioRxiv2022

Abscisic Acid modulates neighbor proximity-induced leaf hyponasty in Arabidopsis

Leaves of shade avoiding plants like Arabidopsis thaliana change their growth pattern and position in response to a low red to far-red ratio (LRFR) that is encountered in dense plant communities. In LRFR, transcription factors of the phytochrome interacting family (PIFs) are de-repressed. PIFs induce auxin production, which is required to promote leaf hyponasty thereby favoring access to unfiltered sunlight. Abscisic acid (ABA) has also been implicated in the control of leaf hyponasty. In addition, gene expression patterns suggest that LRFR regulates the ABA response. Here we show that, in leaves, LRFR leads to a rapid increase in ABA levels. Changes in ABA levels depend on PIFs, which regulate the expression of genes encoding isoforms of the enzyme catalyzing a rate-limiting step in ABA biosynthesis. Interestingly, ABA biosynthesis and signaling mutants have more erect leaves in white light but respond less to LRFR. Consistent with this, ABA application decreases the leaf angle in white light but this response is inhibited in LRFR. Tissue-specific interference with ABA signaling indicates that an ABA response is required in different cell types for LRFR-induced hyponasty. Collectively, our data indicate LRFR triggers rapid PIF-mediated ABA production. ABA plays a different role in controlling hyponasty in white light compared to LRFR. Moreover, ABA exerts its activity in multiple cell types to control leaf position. One sentence summaryAbscisic acid biosynthesis and signaling are required to promote leaf hyponasty in response to a drop in the red to far-red ratio.

plant biology↗

bioRxiv2021

Shade suppresses wound-induced leaf repositioning through a mechanism involving PHYTOCHROME KINASE SUBSTRATE (PKS) genes

Shaded plants challenged with herbivores or pathogens prioritize growth over defense. However, most experiments have focused on the effect of shading light cues on defense responses. To investigate the potential interaction between shade-avoidance and wounding-induced Jasmonate (JA)-mediated signaling on leaf growth and movement, we used repetitive mechanical wounding of leaf blades to mimic herbivore attacks. Phenotyping experiments with combined treatments on Arabidopsis thaliana rosettes revealed that shade strongly inhibits the wound effect on leaf elevation. By contrast, petiole length is reduced by wounding both in the sun and in the shade. Thus, the relationship between the shade and wounding/JA pathways varies depending on the physiological response, implying that leaf growth and movement can be uncoupled. Using RNA-sequencing, we identified genes with expression patterns matching the hyponastic response (opposite regulation by both stimuli, interaction between treatments with shade dominating the wound signal). Among them were genes from the PKS (Phytochrome Kinase Substrate) family, which was previously studied for its role in phototropism and leaf positioning. Interestingly, we observed reduced shade suppression of the wounding effect in pks2pks4 double mutants while a PKS4 overexpressing line showed constitutively elevated leaves and was less sensitive to wounding. Our results indicate a trait-specific interrelationship between shade and wounding cues on Arabidopsis leaf growth and positioning. Moreover, we identify PKS genes as integrators of external cues in the control of leaf hyponasty further emphasizing the role of these genes in aerial organ positioning. Author summaryPlants face different types of stressful situations without the ability to relocate to favorable environments. For example, increasing plant density reduces access to sunlight as plants start to shade each other. Foliar shading represents a stress that many plants cope with by changing their morphology. This includes elongation of stem-like structures and repositioning of leaves to favor access to unfiltered sunlight. Plants also defend themselves against various pathogens including herbivores. Defense mechanisms include the production of deterrent chemical and morphological adaptations such as stunted growth and downwards leaf repositioning. Here we studied the morphological response of plants when simultaneously facing shade and herbivore stress. When facing both stresses petiole growth was intermediate between the shade-enhanced and wound-repressed response. In contrast, the shade cue overrides the wounding cue leading to a similar upwards leaf repositioning in the combined treatments or in the response to shade alone. Using gene expression analyses and genetics we identified two members of the Phytochrome Kinase Substrate family as playing a signal integration role when plants simultaneously faced both stresses. This contributes to our understanding of the mechanisms underlying plant morphological adaptations when facing multiple stresses.

plant biology↗

bioRxiv2021

Reduced light access promotes hypocotyl growth via autophagy-mediated recycling

Plant growth ultimately depends on fixed carbon, thus the available light for photosynthesis. Due to canopy light absorption properties, vegetative shade combines reduced light and a low red to far-red ratio (LRFR). In shade-avoiding plants, these two conditions independently promote growth adaptations to enhance light access. However, how these conditions, differing in photosynthetically-available light, similarly promote growth remains unknown. Here, we show that Arabidopsis seedlings adjust metabolism according to light conditions to supply resources for hypocotyl growth enhancement. Transcriptome analyses indicate that reduced light induces starvation responses, suggesting a switch to a catabolic state to promote growth. Accordingly, reduced light promotes autophagy. In contrast, LRFR promotes anabolism including biosynthesis of plasma-membrane sterols downstream of PHYTOCHROME-INTERACTING FACTORs (PIFs) acting in hypocotyls. Furthermore, sterol biosynthesis and autophagy are indispensable for shade-induced hypocotyl growth. We conclude that vegetative shade enhances hypocotyl growth by combining autophagy-mediated recycling and promotion of specific anabolic processes. HIGHLIGHTSO_LIReduced light and LRFR induce catabolism and anabolism, respectively C_LIO_LIReduced light promotes autophagy to enhance hypocotyl growth in vegetative shade C_LIO_LILRFR enhances hypocotyl growth by promoting plasma membrane lipid biosynthesis C_LIO_LIIn LRFR, PIFs promote sterol biosynthesis specifically in the hypocotyl C_LI

plant biology↗

bioRxiv2021

Phototropin-mediated perception of light direction in Arabidopsis leaves regulates blade flattening

One conserved feature among angiosperms is the development of flat thin leaves. This developmental pattern optimizes light capture and gas exchange for photosynthesis. The blue light receptors phototropins are required for leaf flattening, with the null phot1phot2 mutant showing downwards curled leaves in Arabidopsis. However, key aspects of their function in leaf development remain unknown. Here, we performed a detailed spatiotemporal characterization of phototropin function in Arabidopsis leaves. We found that phototropins perceive light direction in the leaf blade, and similar to their role in hypocotyls they control the spatial pattern of auxin signaling possibly modulating auxin transport, to ultimately regulate cell expansion. Phototropin signaling components in the leaf partially differ from hypocotyls. Moreover, the light response on the upper (adaxial) and lower (abaxial) sides of the leaf blade suggest a partially distinct requirement of phototropin signaling components on each side. In particular, NON PHOTOTROPIC HYPOCOTYL 3 (NPH3) showed an adaxial-specific function. In addition, we show a prominent role of PHYTOCHROME KINASE SUBSTRATE 3 (PKS3) in leaf flattening. Among the auxin transporters tested, PINs and AUX/LAX influence the response most prominently. Overall, our results show that directional blue light perception by the phototropins is a key aspect of leaf development, integrating endogenous and exogenous signals. One sentence summaryPhototropins perceive light direction in the leaf and control the auxin signaling pattern to regulate blade flattening.

plant biology↗

bioRxiv2021

The hidden effects of agrochemicals on plant metabolism and root-associated microorganisms

Agrochemicals are commonly used in agriculture to protect crops and ensure yields. Several of them are mobile within the plant and, being perceived as xenobiotics regardless of their protective/curative roles, they induce a reprogramming of secondary metabolism linked to the detoxification processes even in the absence of phenotype symptoms. Moreover, it is well documented that plants, thanks to the root exudation of different metabolites, are able to shape the microbial population at the rhizosphere and to significantly affect the processes occurring therein. Here we show that plant metabolic response to foliarly-applied pesticides is much broader than what previously thought and includes diverse and compound-specific hidden processes. Among others, stress-related metabolism and phytohormones profile underwent a considerable reorganization. Moreover, a distinctive microbial rearrangement of the rhizosphere was recorded following foliar application of pesticides. Such effects have unavoidably energetic and metabolic costs for the plant paving the way to both positive and negative aspects. The understanding of these effects is crucial for an increasingly sustainable use of pesticides in agriculture. HighlightThe foliar application of pesticides induces a broad metabolic reprogramming in plant and shapes the microbial population of the rhizosphere.

plant biology↗

bioRxiv2020

Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazol

BackgroundThiabendazole (TBZ), is a benzimidazole fungicide and anthelminthic whose high persistence and toxicity pose a serious environmental threat. In our quest for environmental mitigation we previously isolated the first TBZ-degrading bacterial consortium and provided preliminary evidence for its composition and the degrading role of a Sphingomonas. Here, we employed a multi-omic approach combined with DNA-stable isotope probing (SIP) to determine the genetic make-up of the key consortium members, to disentangle nutritional and metabolic interdependencies, to identify the transformation pathway of TBZ and to understand the genetic network driving its transformation. ResultsTime-series SIP in combination with amplicon sequencing analysis verified the key role of Sphingomonas in TBZ degradation by assimilating over 80% of the 13C-labelled phenyl moiety of TBZ. Non-target mass spectroscopy (MS) analysis showed the accumulation of thiazole-4-carboxamidine as a single dead-end transformation product and no phenyl-containing derivative, in line with the phenyl moiety assimilation in the SIP analysis. Time series metagenomic analysis of the consortium supplemented with TBZ or succinate led to the assembly of 18 metagenome-assembled genomes (MAGs) with >80% completeness, six (Sphingomonas 3X21F,{gamma} -Proteobacterium 34A, Bradyrhizobiaceae 9B and Hydrogenophaga 19A, 13A, and 23F) being dominant. Meta-transcriptomic and -proteomic analysis suggested that Sphingomonas mobilize a carbazole dioxygenase (car) operon during the initial cleavage of TBZ to thiazole-4-carboxamidine and catechol, the latter is further transformed by enzymes encoded in a catechol ortho-cleavage (cat) operon; both operons being up-regulated during TBZ degradation. Computational docking analysis of the terminal oxygenase component of car, CarAa, showed high affinity to TBZ, comparable to carbazole, reinforcing its high potency for TBZ transformation. These results suggest no interactions between consortium members in TBZ transformation, performed solely by Sphingomonas. In contrast, gene expression network analysis revealed strong interactions between Sphingomonas MAG 3X12F and Hydrogenophaga MAG 23F, with Hydrogenophaga activating its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway along TBZ degradation. ConclusionsOur findings suggest interactions between consortium members which align with the "black queen hypothesis": Sphingomonas detoxifies TBZ, releasing consortium members by a toxicant; in return for this, Hydrogenophaga 23F provides cobalamin to the auxotrophic Sphingomonas.

systems biology↗

bioRxiv2018

PIF transcription factors link a neighbor threat cue to accelerated reproduction in Arabidopsis

Changes in light quality indicative of competition for this essential resource influence plant growth and developmental transitions. Little is known about neighbor proximity-induced acceleration of reproduction. phytochrome B (phyB) senses light cues from plant competitors ultimately leading to the expression of the floral inducers FLOWERING LOCUS (FT) and TWIN SISTER of FT (TSF). Here we show that three PHYTOCHROME INTERACTING FACTOR (PIF) transcriptional regulators act directly downstream of phyB to promote expression of FT and TSF. Neighbor proximity enhances PIF accumulation towards the end of the day coinciding with enhanced floral inducer expression. We present evidence for direct PIF-mediated TSF expression. The relevance of our findings is illustrated by the prior identification of FT, TSF and PIF4 as loci underlying flowering time regulation in nature.\n\nOne Sentence SummaryPIF transcription factors mediate reproductive transition in response to neighbor proximity light cues in Arabidopsis.

plant biology↗