Biology subjects

Leone, S.

Publications and source records attributed to Leone, S..

12 recordsLinked to original sources

bioRxiv2025

Trace metals availability controls terminal electron acceptor utilization in Escherichia coli

Trace metals play an essential role in the metabolism of all living organisms and many metal-containing enzymes contribute to key physiological and ecological processes such as aerobic and anaerobic respiration, photosynthesis, carbon and nitrogen fixation. Despite this, trace metals potential to control microbial functional diversity and metabolic shifts is unknown. Here we demonstrate that the availability of trace metals controls electron acceptors utilization in Escherichia coli. Physiological and proteomic data show that trace metals depleted cultures have significantly reduced growth, start fermentation and increase energy expenditure for metal homeostasis even when more energetically favourable electron acceptors are present. Overall these results suggest how evolutionary and competitive pressures arising from changes in biological trace metals availability in deep time have contributed to shaping evolution and competition.

microbiology↗

bioRxiv2024

SeqLengthPlot: An easy-to-use Python-based Tool for Visualizing and Retrieving Sequence Lengths from fasta files with a Tunable Splitting Point

MotivationAccurate sequence length profiling is essential in bioinformatics, particularly in genomics and proteomics. Existing tools like SeqKit and the Trinity toolkit, among others provide basic sequence statistics but often fall short in offering comprehensive analytics and plotting options. For instance, SeqKit is a very complete and fast tool for sequence analyses, that delivers useful metrics (e.g., number of sequences, average, minimum, maximum length), and can returns the range of sequence shorter or longer (one side, not both at once) on a given lengths. Similarly, Trinitys utility pearl-based scripts provide detailed contig length distributions (e.g., N50, median, and average lengths) but do not encompass the total number of sequences nor offer graphical representations of data. ResultsGiven that key sequence analysis tasks are distributed among separate tools, we introduce SeqLengthPlot: an easy-to-use Python-based script that fills existing gaps in bioinformatics tools on sequence length profiling, crucial. SeqLengthPlot generates comprehensive statistical summaries, filtering and automatic sequences retriving from the input FASTA (nucleotide and proteins) file into two distinct files based on a tunable, user-defined sequence length, as well as the plots or dynamic visualizations of the corresponding sequences. Availability and implementationThe detailed SeqLengthPlot pipeline is available on GitHub at https://github.com/danydguezperez/SeqLengthPlot, released under the GPL-3.0 license. Additional datasets used as sources or compiled as use cases are publicy available through the Mendeley Data repository: DATASET_Ss_SE.1: http://dx.doi.org/10.17632/pmxwfjyyvy.1, DATASET_Ss_SE.2: http://dx.doi.org/10.17632/3rtbr7c9s8.1, DATASET_Ss_SE.3: http://dx.doi.org/10.17632/wn5kbk5ryy.1, DATASET_Ss_SE.4: http://dx.doi.org/10.17632/sh79mdcm2c.1 and DATASET_Ss_SE.5: http://dx.doi.org/10.17632/zmvvff35dx.1.

bioinformatics↗

bioRxiv2024

The proteotranscriptomic characterization of venom in the white seafan Eunicella singularis elucidates the evolution of Octocorallia arsenal

All the members of the phylum Cnidaria are characterized by the production of venom in specialized structures, the nematocysts. Venom of jellyfish (Medusozoa) and sea anemones (Anthozoa) has been investigated since the 1970s, revealing a remarkable molecular diversity. Specifically, sea anemones harbour a rich repertoire of neurotoxic peptides, some of which have been developed in drug leads. However, venoms of the vast majority of Anthozoa species remain uncharacterized, particularly in the class Octocorallia. To fill this gap, we applied a proteo-transcriptomic approach to investigate the venom composition in Eunicella singularis, a gorgonian species common in Mediterranean hard-bottom benthic communities. Our results highlighted the peculiarities of the venom of E. singularis with respect to sea anemones, which is reflected in the presence of several toxins with novel folds, worthy of functional characterization. A comparative genomic survey across the octocoral radiation allowed us to generalize these findings and provided insights into the evolutionary history, molecular diversification patterns and putative adaptive roles of venom toxins. A comparison of whole-body and nematocyst proteomes revealed the presence of different cytolytic toxins inside and outside the nematocysts. Two instances of differential maturation patterns of toxin precursors were also identified, highlighting the intricate regulatory pathways underlying toxin expression.

evolutionary biology↗

bioRxiv2023

Reversal of pathologic changes in fibroblasts from Niemann-Pick type C disease patients by inhibition of bromodomain and extraterminal proteins

Inborn errors of lysosomal function often provoke disorders presenting highly variable onset, diverse visceral, neurologic and psychiatric symptoms and reduced life spans. A prime example is Niemann-Pick type C disease (NPCD). At present, therapeutic options are limited to palliative care and disease-modifying drugs, and there is a need for new treatments. Here, we explored bromodomain and extra-terminal domain (BET) proteins as a new drug target for NPCD using patient-derived skin fibroblasts. Treatment of cells with JQ1, a prototype BET protein inhibitor, enhanced the level of NPC1 protein, diminished lysosomal expansion and cholesterol accumulation, and induced extracellular release of lysosomal components in a dose- and time-dependent manner. The effect of JQ1 on protein levels was largely independent from the patient line tested, but the extent of cholesterol reduction varied in a line-dependent manner. Lastly, JQ1 enhanced and reduced cholesterol accumulation induced by inhibition of NPC1 activity and of histone deacetylases, respectively. Taken together, our results provide further evidence for epigenetic regulation of cellular NPC1 levels and cholesterol homeostasis. Pharmacologic inhibition of bromodomain proteins should be explored as candidate therapeutic approach for NPCD and as a tool to understand basic mechanisms of lysosomal function and lipid metabolism.

cell biology↗

bioRxiv2023

Developmental remodeling repurposes larval neurons for sexual behaviors in adult Drosophila

Most larval neurons in Drosophila are repurposed during metamorphosis for functions in adult life, but their contribution to the neural circuits for sexually dimorphic behaviors is unknown. Here, we identify two interneurons in the nerve cord of adult Drosophila females that control ovipositor extrusion, a courtship rejection behavior performed by mated females. We show that these two neurons are present in the nerve cord of larvae as mature, sexually monomorphic interneurons. During pupal development, they acquire the expression of the sexual differentiation gene, doublesex, undergo doublesex-dependent programmed cell death in males, and are remodeled in females for functions in female mating behavior. Our results demonstrate that the neural circuits for courtship in Drosophila are built in part using neurons that are sexually reprogrammed from former sex-shared activities in larval life.

neuroscience↗

bioRxiv2023

Mapping the gene space at single-cell resolution with gene signal pattern analysis

In single-cell sequencing analysis, several computational methods have been developed to map the cellular state space, but little has been done to map or create embeddings of the gene space. Here, we formulate the gene embedding problem, design tasks with simulated single-cell data to evaluate representations, and establish ten relevant baselines. We then present a graph signal processing approach we call gene signal pattern analysis (GSPA) that learns rich gene representations from single-cell data using a dictionary of diffusion wavelets on the cell-cell graph. GSPA enables characterization of genes based on their patterning on the cellular manifold. It also captures how localized or diffuse the expression of a gene is, for which we present a score called the gene localization score. We motivate and demonstrate the efficacy of GSPA as a framework for a range of biological tasks, such as capturing gene coexpression modules, condition-specific enrichment, and perturbation-specific gene-gene interactions. Then, we showcase the broad utility of gene rep-resentations derived from GSPA, including for cell-cell communication (GSPA-LR), spatial transcriptomics (GSPA-multimodal), and patient response (GSPA-Pt) analysis.

bioinformatics↗

bioRxiv2023

HSP70 binds to specific non-coding RNA and regulates human RNA Polymerase III

Molecular chaperones are critical for protein homeostasis and are implicated in several human pathologies such as neurodegeneration and cancer. While the binding of chaperones to nascent and misfolded proteins has been studied in great detail, the direct interaction between chaperones and RNA has not been systematically investigated. Here we provide the evidence for widespread interaction between chaperones and RNA in human cells. We show that the major chaperone Heat-Shock Protein 70 (HSP70) binds to non-coding RNA transcribed by RNA Polymerase III (Pol III) such as tRNA and 5S rRNA. Global chromatin profiling revealed that HSP70 binds genomic sites of transcription by Pol III. Detailed biochemical analyses showed that HSP70 facilitates transcription of its target non-coding RNA by binding to Pol III. Thus our study uncovers an unexpected role of HSP70-RNA interaction in the biogenesis of a specific class of non-coding RNA with wider implications in neurodegeneration and cancer.

biochemistry↗

bioRxiv2023

Evolution of the ribbon-like organization of the Golgi apparatus in animal cells

The Golgi ribbon is a structural organization formed by linked Golgi stacks that is believed to be exclusive to vertebrate cells. Its functional contribution to cellular processes is unclear, yet its disruption is associated with several human pathologies. In this study we address the evolutionary origin of the Golgi ribbon, describe a potential molecular mechanism for its emergence and identify a cellular process in which it may be involved. We observed the ribbon-like architecture in the cells of several metazoan taxa, suggesting its early appearance during animal evolution before the emergence of vertebrates. Supported by AlphaFold2 modelling, we propose that the evolution of the complex between two Golgi resident proteins, Golgin-45 and GRASP, led to the tethering of Golgi stacks into the ribbon-like configuration. Finally, we find that the ribbon is assembled during the early embryogenesis of deuterostome animals, a strong indication of its role in development. Overall, our study indicates that the Golgi ribbon is functionally relevant beyond vertebrates and calls for further investigations to decipher its elusive functions. O_FIG O_LINKSMALLFIG WIDTH=89 HEIGHT=200 SRC="FIGDIR/small/528797v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@17a404forg.highwire.dtl.DTLVardef@11413b4org.highwire.dtl.DTLVardef@119c036org.highwire.dtl.DTLVardef@19a512f_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

cell biology↗

bioRxiv2022

Neuromuscular embodiment of feedback control elements in Drosophila flight

While insects like Drosophila are flying, aerodynamic instabilities require that they make millisecond-timescale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units--prominent components of the flys steering muscles system--modulate specific elements of the PI controller: the angular displacement (integral, I) and angular velocity (proportional, P), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.

animal behavior and cognition↗

bioRxiv2019

Real-time measurement of E2:ERα transcriptional activity in live-cells.

Kinetic analyses of diverse physiological processes have the potential to unveil new aspects of the molecular regulation of cell biology at temporal levels. 17{beta}-estradiol (E2) regulates diverse physiological effects by binding to the estrogen receptor (ER), which primarily works as a transcription factor. Although many molecular details of the modulation of ER transcriptional activity have been discovered including the impact of receptor plasma membrane localization and its relative E2-evoked signalling, the knowledge of real-time ER transcriptional dynamics in living cells is lacking. Here, we report the generation of MCF-7 and HeLa cells stably expressing a modified luciferase under the control of an E2-sensitive promoter, which activity can be continuously monitored in living cells and show that E2 induces a linear increase in ER transcriptional activity. Ligand-independent (e.g., epidermal growth factor) receptor activation was also detected in a time-dependent manner. Kinetic profiles of ER transcriptional activity measured in the presence of both receptor antagonists and inhibitors of ER plasma membrane localization reveals a biphasic dynamic of receptor behaviour underlying novel aspects of receptor-regulated transcriptional effects. Finally, analysis of the rate of the dose-dependent E2 induction of ER transcriptional activity demonstrates that low doses of E2 induce an effect identical to that determined by high concentrations of E2 as a function of the duration of hormone administration. Overall, we present the characterization of sensitive stable cell lines where to study the kinetic of E2 transcriptional signaling and to identify new aspects of ER function in different physiological or pathophysiological conditions.

physiology↗

bioRxiv2018

In silico screening for ERα downmodulators identifies thioridazine as an anti-proliferative agent in primary, 4OH-tamoxifen-resistant and Y537S ERα-expressing breast cancer cells

PurposeMost breast cancers (BCs) express estrogen receptor (ER) and are treated with the endocrine therapy (ET) drugs 4OH-tamoxifen (Tam) and fulvestrant (i.e., ICI182,780-ICI). Unfortunately, a high fraction of ET-treated women relapses and become resistant to ET. Therefore, additional anti-BC drugs are needed. Recently, we proposed that the identification of novel anti-BC drugs can be achieved using the modulation of the ER intracellular content in BC cells as a pharmacological target. Here, we searched for Food and Drug Administration (FDA)-approved drugs that potentially modify the ER content in BC cells.\n\nMethodsWe screened in silico more than 60,000 compounds to identify FDA-approved drugs with a gene signature similar to that of ICI. We identified mitoxantrone and thioridazine and tested them in primary, Tam-resistant and genome-edited Y537S ER-expressing BC cells.\n\nResultsMitoxantrone and thioridazine induced ER downmodulation and prevented MCF-7 cell proliferation. Interestingly, while mitoxantrone was toxic for normal breast cells, thioridazine showed preferential activity toward BC cells. Thioridazine also reduced the ER content and prevented cell proliferation in primary, Tam-resistant and genome-edited Y537S ER-expressing BC cells.\n\nConclusionsWe suggest that the modulation of the ER intracellular concentration in BC cells can also be robustly exploited in in silico screenings to identify anti-BC drugs and further demonstrate a re-purposing opportunity for thioridazine in primary and metastatic ET-resistant BC treatment.

cancer biology↗

bioRxiv2017

A Functional Drug Re-Purposing Screening Identifies Carfilzomib As A Drug Preventing 17β-Estradiol: ERα Signaling And Cell Proliferation In Breast Cancer Cells

Most cases of breast cancer (BC) are estrogen receptor -positive (ER+) at diagnosis. The presence of ER drives the therapeutic approach for this disease, which often consists of endocrine therapy (ET). 4OH-Tamoxifen and faslodex (i.e., fulvestrant - ICI182,780) are two ETs that render tumor cells insensitive to 17{beta}-estradiol (E2)-dependent proliferative stimuli and prevent BC progression. However, ET has limitations and serious failures in different tissues and organs. Thus, there is an urgent need to identify novel drugs to fight BC in the clinic. Re-positioning of old drugs for new clinical purposes is an attractive alternative for drug discovery. For this analysis, we focused on the modulation of intracellular ER levels in BC cells as target for the screening of about 900 Food and Drug Administration (FDA) approved compounds that would hinder E2:ER signaling and inhibit BC cell proliferation. We found that carfilzomib induces ER degradation and prevents E2 signaling and cell proliferation in two ER+ BC cell lines. Remarkably, the analysis of carfilzomib effects on a cell model system with an acquired resistance to 4OH-tamoxifen revealed that this drug has an antiproliferative effect superior to faslodex in BC cells. Therefore, our results identify carfilzomib as a drug preventing E2:ER signaling and cell proliferation in BC cells and suggest its possible re-position for the treatment of ER+ BC as well as for those diseases that have acquired resistance to 4OH-tamoxifen.

cancer biology↗