Biology subjects

Fontana, A.

Publications and source records attributed to Fontana, A..

9 recordsLinked to original sources

bioRxiv2025

The first photosynthetic mutant in diatoms targets the subunit γ of plastidial ATP synthase and reveals a key role of thylakoid electrochemical proton gradient in photosynthesis regulation and heterotrophic metabolism.

Diatoms are major phytoplanktonic algae with secondary endosymbiotic plastids that differ in cellular and regulatory traits from those of the green lineage. Here we exploited the heterotrophic growth ability of Cyclotella cryptica to create the first diatom photosynthetic mutant by CRISPR-Cas inactivation of the nucleus-encoded ATP synthase subunit {gamma}. These mutants showed impaired phototrophic capacity and altered thylakoids morphology. In absence of {gamma}-ATP, protons that accumulate in the thylakoid lumen slow down the cytochrome b6f complex, thus keeping the electron carriers downhill oxidized. These results, reversible when the proton gradient is suppressed, demonstrate the existence of a photosynthetic control in diatoms. At variance with the wild type, {gamma} ATP synthase mutants cannot grow heterotrophically in darkness nor in the light when photosystem II is inhibited. This requirement of heterotrophic growth on photosynthetic electron transfer or on the presence of plastidial ATP synthase suggests that the proton motive force (pmf) is a central integrator of the metabolic interaction between photosynthesis and heterotrophy. Our results establish C. crytica as a robust model for analysis of photosynthetic function, regulation and metabolic integration in organisms with secondary plastids. TeaserMutagenesis in the facultative autotroph diatom Cyclotella cryptica enables exploration of essential plastid functions in diatoms

plant biology↗

bioRxiv2025

Genome based analysis of Antibacterial Biosynthetic Clusters in Lactiplantibacillus plantarum C6 and Exploration of their Natural Small Molecules as anti-biofilm in Methicillin-Resistant Staphylococcus aureus

This study presents the complete genome characterization of Lactiplantibacillus plantarum C6, a strain isolated from Indian dairy cheese, using Illumina NovaSeq sequencing. The assembled genome (3.22 Mb, 44.5% GC) comprised 3,076 coding sequences, 59 tRNAs, 10 rRNAs, and 2 CRISPR arrays. Phylogenomic and ANI analyses confirmed its identity within the L. plantarum clade (>99% similarity with NMGL2 and DMDL 9010). Functional annotation revealed genes enriched in carbohydrate metabolism (10.7%), stress response, and host-adaptation pathways, supporting its probiotic potential. Bacteriocin biosynthetic gene clusters were identified, including those encoding PlnE, PlnF, PlnJ, PlnK, and PlnN, indicating the strains ability to produce class II plantaricins. A RiPP cluster encoding a cyclic uberolysin-like peptide was also detected, with structural similarity to known lanthipeptides such as Streptococcin A, Nisin Q, and Lacticin 3147 (Tanimoto scores 0.93-1.0), suggesting antimicrobial relevance. CAZy analysis revealed 102 carbohydrate-active enzymes (GHs, GTs), highlighting metabolic flexibility. To evaluate the antibiofilm potential of L. plantarum-derived metabolites, 15 small molecules from cell-free supernatants (CFS) were selected through literature mining and subjected to molecular docking against the MRSA biofilm-associated enzyme poly-{beta}-1,6-N-acetyl-D-glucosamine synthase (encoded by icaA). 2,4-Di-tert-butylphenol (-7.2 kcal/mol) and Indole-3-lactic acid (-7.1 kcal/mol) showed the strongest binding, followed by Cyclo (L-propyl-L-valine) (-6.8 kcal/mol) and DL-4-Hydroxyphenyllactic acid (-6.4 kcal/mol), indicating promising inhibition of MRSA biofilm synthesis. Organic acids like acetic and lactic acid showed weaker interactions but may contribute synergistically through acidification. Overall, L. plantarum C6 combines robust probiotic features, genomic safety, and antimicrobial potential, supported by bacteriocin gene clusters and effective antibiofilm metabolites, highlighting its application in functional foods and novel antimicrobial development.

genomics↗

bioRxiv2025

Physical principles of phase-separation action on chromatin looping associated to pathogenic gene activation

Phase-separation of chimeric proteins resulting from genetic mutations has been shown to trigger aberrant chromatin looping, contributing to disease development, including cancer. However, the physical mechanisms regulating these processes are not yet fully understood. In this study, we employ polymer physics models of chromatin and numerical simulations to investigate the relationship between phase-separation of proteins and chromatin structure. We demonstrate that a simple model, including only protein-protein and protein-chromatin interactions, effectively explains the aberrant looping observed around oncogenes, such as PBX3, in cells expressing the NUP98-HOXA9 chimeric protein, which is associated with leukemia. In this scenario, looping occurs through a switch-like mechanism controlled by the concentration of the chimera and its affinity with chromatin. Moreover, when incorporating the presence of extruding factors in a more complex model, similar results are observed, indicating a mild dependence of this looping mechanism on loop-extrusion activity. Finally, leveraging our numerical simulations, we propose potential strategies to inhibit the formation of enhancer-gene loops by directly targeting the chimeric protein with interfering molecules.

biophysics↗

bioRxiv2025

Ecology and demographic structure of an extinct ibex population in Upper Palaeolithic Italian Alps

Alpine Upper Palaeolithic contexts exhibit specialised subsistence strategies, heavily dependent on Capra ibex. Among them, the rock shelter Riparo Dalmeri stands out, with C. Ibex dominating faunal remains across all occupation phases, spanning the Pleistocene/Holocene transition. This evidence positions Riparo Dalmeri as a key site for exploring the interdependence between human groups and C. ibex during one of the most critical climatic and cultural shifts in human evolution. Here, we present the first multidisciplinary study on Late Palaeolithic C. ibex teeth from Riparo Dalmeri, integrating direct radiocarbon dating, isotope (87Sr/86Sr, {delta}13C, {delta}18O), proteomic, and aDNA analyses. We generated the earliest aDNA sequences for C. ibex and contextual evidence on mobility, seasonality, and sex ratios. We found that most C. ibex were local to the area despite consistent human presence. They reveal significant dietary differences between sexes as well as increased seasonality at the Pleistocene-Holocene transition. Our results identify Riparo Dalmeri as an extinct branch of the ibex mtDNA phylogeny, offering unprecedented insights into ibex ecology and evolution that resonate with present-day issues on the conservation of this species in the face of climate change.

ecology↗

bioRxiv2025

Maturase K forms a plastidial splicing complex with a neofunctionalized branching enzyme

Chloroplast group IIA introns derive from bacterial ribozymes. Their splicing likely requires Maturase K (MatK), which has been largely inaccessible to functional analyses being itself a chloroplast intron-encoded protein. Here we show that MatK physically interacts with a conserved, essential plastid-localized homolog of starch-branching enzymes (BEs), dubbed MATURASE K INTERACTING PROTEIN1 (MKIP1). We demonstrate that MKIP1 proteins have lost BE activity and acquired an insertion enabling direct interaction with the N-terminal region of MatK. Arabidopsis MKIP1 specifically co-precipitates all known intron targets of MatK. Induced MKIP1 silencing results in pale newly emerging leaves, in which the splicing of these intron targets is strongly reduced. Our data suggest that MKIP1 functionally diverged from canonical BEs to facilitate splicing in conjunction with MatK. We propose that the N-terminus of MatK, in turn, has evolved from an RNA-binding domain into a platform for protein interaction, helping its transition towards a general splicing factor.

plant biology↗

bioRxiv2024

Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations

Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2Mb wide genomic region encompassing the human LTN1 gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in-silico the ensemble of single-molecule LTN1 3D structures, which we benchmark against recent in-situ Hi-C 2.0 data. The model-derived single molecules are then used to predict structural folding features at the single-cell level, providing testable predictions for super-resolution microscopy experiments.

molecular biology↗

bioRxiv2023

Proteomic Analysis Reveals the Molecular Pathways Responsible for Solar UV-B Acclimation in High-altitude Malbec Berries

Grapevine cultivation at high altitudes provides a viable option for producing premium quality wines in the context of climate change. This is primarily attributed to cooler temperatures, wider thermal amplitudes, and increased UV-B radiation. Although high UV-B levels can cause oxidative-stress, grape berries acclimate by generating UV-blocking anthocyanins and antioxidant compounds accumulated in the berry skins, thereby enhancing the organoleptic qualities and aging capacity of wine. This UV-B exclusion study examines how Malbec berries respond to solar UV-B at a high-altitude vineyard in Mendoza, Argentina (1350 m a.s.l.). The results showed that high solar UV-B acts both as a photomorphogenic signal and a stressor. The proteomic changes of berries exposed to +UV-B conditions indicate a decrease of photosynthesis and oxidative phosphorylation, coupled with an increase of glycolysis and tricarboxylic acid cycle as compensatory respiration pathways. Furthermore, numerous chaperones and proteins associated with the antioxidant system exhibited increased abundance to maintain cellular homeostasis. Lastly, veraison-stage berries exposed to +UV-B displayed an activation of the UVR8 signaling cascade and the phenylpropanoid pathway, resulting in higher concentration of phenolic compounds and more oxidation-resistant types of anthocyanins. This is the first report of field-grown grape berry proteomic modulation in response to solar UV-B, and it may have significant implications for the cultivation of high-quality wine grapes in both current and future climate scenarios. Significance

plant biology↗

bioRxiv2023

Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells

SARS-CoV-2 is able to re-structure chromatin organization and alters the epigenomic landscape of the host genome, though the mechanisms that produce such changes are still poorly understood. Here, we investigate with polymer physics chromatin re-organization of the host genome, in space and time upon SARS-CoV-2 viral infection. We show that re-structuring of A/B compartments is well explained by a re-modulation of intra-compartment homotypic affinities, which leads to the weakening of A-A interactions and enhances A-B mixing. At TAD level, re-arrangements are physically described by a general reduction of the loop extrusion activity coupled with an alteration of chromatin phase-separation properties, resulting in more intermingling between different TADs and spread in space of TADs themselves. In addition, the architecture of loci relevant to the antiviral interferon (IFN) response, such as DDX58 or IFIT, results more variable within the 3D single-molecule population of the infected model, suggesting that viral infection leads to a loss of chromatin structural specificity. Analysis of time trajectories of pairwise gene-enhancer and higher-order contacts reveals that such variability derives from a more fluctuating dynamics in infected case, suggesting that SARS-CoV-2 alters gene regulation by impacting the stability of the contact network in time. Overall, our study provides the first polymer-physics based 4D reconstruction of SARS-CoV-2 infected genome with mechanistic insights on the consequent gene mis-regulation.

biophysics↗

bioRxiv2023

Cystine/glutamate antiporter system Xc- deficiency impairs insulin secretion.

System Xc-, encoded by Slc7a11, is an antiporter that exports glutamate and imports cystine. Cystine is used for protein synthesis and incorporation in thiol peptides such as glutathione, which function as cofactors for reactive oxygen species scavenging enzymes. Glutamate export by astrocytes through system Xc- has been implicated in excitotoxicity, a form of neurotoxicity that has been postulated to also occur in insulin-producing beta-cells in the pancreatic islets. This study describes the implications of Slc7a11 deficiency on glucose metabolism in both constitutive and myeloid cells-specific knockout mice. Constitutive Slc7a11 deficiency leads to drastically lowered glutathione levels in the pancreatic islets and immune cells in addition to diminished insulin secretion both in vitro and in vivo. Macrophage-specific deletion did not have a significant impact on metabolism or islet function. These findings suggest that system Xc- is required for glutathione maintenance and insulin production in beta-cells, but is dispensable for islet macrophage function.

molecular biology↗