Biology subjects

Fontana, C.

Publications and source records attributed to Fontana, C..

5 recordsLinked to original sources

bioRxiv2026

Drosophila melanogaster as a platform for the functional expression of engineered PET-degrading enzymes

Insects offer promising opportunities for organic waste bioconversion; however, they cannot efficiently degrade synthetic polymers such as polyethylene terephthalate (PET). Here, we generated transgenic Drosophila melanogaster lines to express in vitro-evolved variants of two PET-degrading enzymes with distinct biochemical properties: an engineered Ideonella sakaiensis PETase variant (TS-{Delta}IsPET) and a leaf-branch compost cutinase variant (TA-{Delta}LCC). Both enzymes, fused to a Drosophila gut-derived secretory signal, were produced and secreted by both Drosophila cultured S2R+ cells and transgenic larvae. Both enzymes were glycosylated upon secretion, a post-translational modification that did not abolish their catalytic activity. Notably, TA-{Delta}LCC displayed [~]6-fold higher esterase activity than TS-{Delta}IsPET in larval extracts and TA-{Delta}LCC-containing extracts depolymerised PET nanoparticles in vitro under enzyme-favourable conditions. Transgenic flies showed normal development, fertility and survival. Morphological and biochemical analysis confirmed that TA-{Delta}LCC expression did not alter midgut structure and function. Together, these results establish Drosophila melanogaster as a model for functional expression and comparative evaluation of engineered PET-degrading enzymes and identify TA-{Delta}LCC as a promising candidate for exploitation in insect species relevant to plastic contaminated waste bioconversion. HighlightsO_LITransgenic D. melanogaster enables in vivo study of engineered PET enzymes C_LIO_LIEngineered TS-{Delta}IsPET and TA-{Delta}LCC are functional in larval extracts C_LIO_LITA-{Delta}LCC was selected for PET nanoparticle assays due to higher pNPA activity C_LIO_LID. melanogaster model enables comparative evaluation of PET-degrading enzymes C_LI

biochemistry↗

bioRxiv2026

Universal 3D Motif dynamics in RNA: The A-minor Switch

A-minor motifs consist of adenosines docking into adjacent RNA minor grooves, are the most prevalent 3D interaction stabilizing RNA structures, and widely considered as being static. NMR spectroscopy reveals a secondary structure equilibrium of these motifs between engaged and disengaged states, which we term the A-minor switch. A switch in E.coli ribosome helix 44 consists of a sparsely populated, transient single-nucleotide register shift that sequesters adenosines from their 3D structural A-minor contacts. Mutational trapping of the NMR-defined, A-minor-engaged ground and-disengaged excited state, combined with cryo-electron microscopy, visualizes this dynamic switch mechanism. Additionally, A-minor switches were identified using secondary structure ensemble analysis and mutational trapping was found to impair bacterial growth, directly linking RNA dynamics and function. Because A-minor motifs are widespread in structured RNAs, these findings establish A-minor switches as a general regulatory layer between secondary structure dynamics and tertiary contacts, exposing a new therapeutic target class.

biophysics↗

bioRxiv2024

Building a model of sepsis: data integration unravels pathogenic mechanisms in severe P. aeruginosa infections.

Understanding host-pathogen interactions is crucial for explaining the variability in sepsis outcomes, with Pseudomonas aeruginosa (PA) remaining a significant public health concern. In this work, we explored PA-human host interaction mechanisms through a data integration workflow, focusing on protein-protein and metabolite-protein interactions, along with pathway modulation in affected organs during severe infections. A scoping literature review enabled us to construct a domain-based infection network encompassing pathogenesis concepts, molecular interactions, and host response signatures, providing a wide view of the relevant mechanisms involved in severe bacterial infections. Our analysis yielded a literature-based comprehensive description of PA infection mechanisms and an annotated dataset of 189 PA-human interactions involving 152 proteins/molecules (109 human proteins, 3 human molecules, 34 PA proteins, and 5 PA molecules). This dataset was complemented with gene expression analysis from in vivo PA-infected lung samples. The results indicated a notable overexpression of proinflammatory pathways and PA-mediated modulation of host lung responses. Our comprehensive molecular network of PA infection represents a valuable tool for the understanding of severe bacterial infections and offers potential applications in predicting clinical phenotypes. Through this approach combining omics data, clinical information, and pathogen characteristics, we have provided a foundation for future research in host-pathogen interactions and the mechanistic grounds to build dynamic computational models for clinical phenotype predictions.

systems biology↗

bioRxiv2024

Cyanobacteria form a procarboxysome-like structure in response to high CO2

Fixing 25% of CO2 globally, cyanobacteria are integral to climate change efforts. The cyanobacterial CO2 concentrating mechanism (CCM) features the carboxysome, a bacterial microcompartment which houses their CO2 fixing machinery. The proteinaceous shell of the carboxysome restricts diffusion of CO2, both inward and outward. While necessary for CCM function in air (0.04% CO2), when grown in high CO2 levels (3% CO2) representative of early earth, the shell would harmfully limit CO2 fixation. To understand how carboxysomes change form and function in response to increased CO2 conditions, we used a Grx1-roGFP2 redox sensor and single cell timelapse fluorescence microscopy to track subcellular redox states of Synechococcus sp. PCC 7002 grown in air or 3% CO2. Comparing different levels of compartmentalization, we targeted the cytosol, a shell-less carboxysomal assembly intermediate called the procarboxysome, and the carboxysome. The carboxysome redox state was dynamic and, under 3% CO2, procarboxysome-like structures formed and mirrored cytosolic redox states, indicating that a more permeable shell architecture may be favorable when [CO2] is high. This work represents a step in understanding how cyanobacteria respond to changing CO2 concentrations and the selective forces driving carboxysome evolution.

biochemistry↗

bioRxiv2022

Ontogeny of learning and visual discrimination in zebrafish

With the exception of humans, early cognitive development has been thoroughly investigated only in precocial species, well developed at birth and with a broad behavioural and cognitive repertoire. We investigated another highly altricial species, the zebrafish, Danio rerio, whose embryonic development is very rapid: 72 hours. The nervous system of hatchlings is poorly developed, and their cognitive capacities are largely unknown. Larvae trained at 8 days post-fertilisation rapidly learned to associate a visual pattern with a food reward, showing significant performance at 10 days post-fertilisation. We exploited this capacity to study hatchlings discrimination learning capacities. Larval zebrafish rapidly and accurately learned colour and shape discriminations. They also discriminated a figure from its mirror image and from its 90{degrees}-rotated version, although with lower performance. Our study revealed impressive similarities in learning and visual discrimination capacities between newborn and adult zebrafish despite their enormous differences in brain size and degree of development.

animal behavior and cognition↗