Biology subjects

Fenel, D.

Publications and source records attributed to Fenel, D..

17 recordsLinked to original sources

bioRxiv2026

Thylakoid plasticity primes photoprotection in diatoms

For many millions of years, diatoms have been major primary producers in marine ecosystems, supporting food webs and contributing to carbon sequestration through the export of photosynthetically fixed carbon to the deep ocean, mitigating atmospheric carbon dioxide levels and global climate. A key factor in their ecological success is their ability to rapidly adapt to fluctuating light, balancing efficient light harvesting under dim conditions with energy dissipation under excess light. However, the mechanisms behind this regulation have not been fully elucidated. This study shows that several processes contribute to dissipating excess excitation energy in diatoms exposed to light stress: (i) the detachment of the oxygen-evolving complex proteins from the PSII core, leading to energy dissipation via charge recombination, (ii) Non-Photochemical Quenching (NPQ) in the antenna, i.e., thermal dissipation of excited states and (iii) excitation energy transfer from PSII to PSI via energy spillover. The latter process is observed in parallel with high light-induced topological changes of the thylakoids that may favor transient interactions between the photosystems. Along with the accumulation of light-stress-protecting carotenoids on longer time-scales, this ensemble of photoprotective mechanisms provides a dynamic and flexible response to the light challenges expected in coastal marine habitats.

biochemistry↗

bioRxiv2026

Effects of polystyrene and polylactide nanoparticles on macrophages under a repeated exposure mode

Micro and nanoplastics are pollutants which concentration in different biotopes increases continuously over time, which poses the question of their potential effects on health. In animals, these micro and nanoplastics are recognized as particulate materials and thus handled by macrophages, which are therefore a key cell type to study. Most studies have used an experimental scheme in which the cells are exposed to a single dose of plastics, with a readout made immediately after exposure. However, this classical experimental scheme does not take into account the impact of biopersistence, nor the potential cellular adaptation that may take place when cells are exposed repeatedly to a low dose of plastics. We thus used a repeated exposure scheme, in order to better take into account these phenomena. Within this frame, we compared the macrophages responses to a persistent nanoplastic, i.e. polystyrene nanoparticles and to a biodegradable nanoplastic, i.e. polylactide, by a combination of proteomic and targeted experiments. Our results show that under this repeated exposure scheme, the proteome changes were of a lesser (for PS) or similar (for PLA) extent than under the acute exposure mode, indicating cell adaptation. However, PLA particles induced mitochondrial dysfunction and depression of response to bacterial molecules perceived as danger signals, such as lipopolysaccharide. Polystyrene nanoparticles also induced a slight alteration of the immune functions of macrophages. This indicates harmful effects even in the repeated exposure scheme.

pharmacology and toxicology↗

bioRxiv2025

Effects of manganese dioxide on macrophages under different exposure schemes

Manganese dioxide is a material that is more and more used in its particular form, for many industrial applications such as chemical catalysis or for batteries. Thus, workers can be exposed to this particulate chemical. It is known that overexposure to manganese leads to a brain disease called manganism. However, manganese is also known to impact the pulmonary function, which is important as pulmonary exposure is of prime importance for workers. We thus investigated the effects of manganese dioxide on macrophages, i.e. the scavenger cells that take particulates in charge in our bodies. To this purpose, we used a combination of proteomic and targeted approaches, in order to obtain a wide view of the cellular responses to manganese dioxide. We also used a repeated exposure mode, in order to better mimic occupational exposure. Our results point out the fact that manganese oxide nanoparticles are rather toxic for macrophages and induce mitochondrial dysfunction, oxidative stress and a pro-inflammatory response. Environmental significanceManganese dioxide is more and more used in batteries, so that workers in batteries factories are exposed to this metallic oxide. As always for particulate materials, macrophages are the first line of defense of the organism. We thus investigated the effects of manganese dioxide on macrophages, using a repeated exposure scheme to mimic occupational exposure, and the effects were documented by a combination of proteomic and targeted approaches. The functional effects include mitochondrial dysfunction, oxidative stress and inflammation.

pharmacology and toxicology↗

bioRxiv2025

The devil lies in the details: small structural and chemical changes in iron oxide pigments largely alter the biological outcomes in macrophages

Because of their technical qualities, such as resistance to fading and to high temperatures, mineral pigments are still widely used nowadays. Among the diversity of mineral pigments, iron oxide pigments represent a widely-used class, because of their technical qualities, diversity of shades (from yellow to red to brown to black) and low toxicity compared to heavy metals-based pigments. However, a low toxicity does not mean the absence of adverse effects. We thus investigated the effects on macrophages of two different subtypes of Pigment Red 101, i.e. hematite, produced by two different processes, namely a wet precipitation process and a calcination process. Macrophages were chosen as a target cell type because they represent the main scavenger cell type that is in charge of handling particulate materials in the body. During this comparison, we realized that the calcined pigment was contaminated from the start by bacterial endotoxins, which induced intense inflammatory responses and biased the comparison. After depyrogenation, the calcined pigment proved to dissolve to a higher extent in macrophages, but to show less important adverse effects (e.g. alteration of the mitochondrial transmembrane potential, oxidative stress and inflammatory responses) than the precipitated pigment in a recovery exposure mode, allowing to investigate delayed effects of the pigments. Thus, despite their identical pigment number, pigments differing in their structure and in their synthesis induce different responses from living cells, even if administrated in equivalent amount. This should be taken into account for some applications, such as tattooing. Moreover, endotoxin contamination should also be checked to increase workers and users safety

pharmacology and toxicology↗

bioRxiv2025

Beyond the ink: cellular and molecular effects of iron-based pigments on macrophages

As ochre, iron oxide is among the most ancient pigments used by mankind for different purposes, including tattooing as demonstrated on tattoed mummies. Iron oxides are still used in tattooing nowadays and especially in dermopigmentation, an area of medical tattoing aiming at restoring the color of skin. This ancient use of iron oxide does not mean that it has no effect on cells, and especially on macrophages, the cells that maintain pigments particles on site in tattoos. We thus investigated in vitro the delayed/sustained effects of iron oxide pigments on macrophages, i.e. the effects occurring a few days after the exposure to pigments, on pigments-loaded macrophages but in a pigment-free medium, mimicking the status of tattooed skin after all the pigment particles have been captured. By combining proteomic and targeted approaches, we determined that red iron oxide (but not black iron oxide) induces perturbations in mitochondria, altering the mitochondrial transmembrane potential. Red iron oxide also induces oxidative stress and the secretion of pro-inflammatory cytokines such as interleukin 6 and tumor necrosis factor. Thus, red iron oxide induces adverse effects on macrophages that may persist over time, owing to its low intracellular dissolution.

immunology↗

bioRxiv2025

Lipid nanoemulsion incorporating DOTAP reverse micelles as clinically translatable carriers of ALDH inhibitors for lung cancer therapy

Lung cancer remains the most prevalent malignancy worldwide and the leading cause of cancer-related deaths. In this study, we designed and optimized a lipid nanosystem incorporating the cationic lipid DOTAP by utilizing reverse micelle structures to enhance pulmonary tropism. Fluorescence quenching assays confirmed the incorporation of reverse micelles into the oily core, thus validating the structural integrity of the system. This nanosystem was tailored for the encapsulation of ABD0171, a potent inhibitor of ALDH1A3, an enzyme strongly associated with chemoresistance in lung cancer. Physicochemical characterization revealed robust colloidal properties with a particle diameter of 60 nm, a surface charge of +45 mV, and a drug encapsulation yield of 99%. In vitro, formulations with/without DOTAP demonstrated high efficacy against epithelial-like H358 cells derived from human bronchioalveolar carcinoma, with IC50 values < 5 {micro}M. Chicken ChorioAllantoic Membrane (CAM) evaluations demonstrated good tolerability of the DOTAP-containing formulation and significant H358 tumor reduction by 28% compared with the untreated control, while maintaining a favorable safety profile. By combining industrially feasible methods with FDA-approved components, this study demonstrated the potential of DOTAP-containing lipid nanosystems as scalable platforms for the delivery of ALDH inhibitors for lung cancer treatment. These findings provide a pathway for future applications in cancer therapy, bridging the gap between nanosystem innovation and clinical translation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/659868v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@dbc8org.highwire.dtl.DTLVardef@5d5187org.highwire.dtl.DTLVardef@9391f3org.highwire.dtl.DTLVardef@52fd54_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

bioengineering↗

bioRxiv2025

Functional and phylogenomic approaches reveal novel types of M42 peptidases with contrasted enzymatic properties in Archaea

M42 peptidases are half-megadalton aminopeptidases characterized by a tetrahedral architecture (TET) ubiquitous across all domains of life. Despite their widespread occurrence, their evolutionary history and functional diversity remain largely unexplored. Here we show an unsuspected and largely untapped wealth of archaeal TET peptidases, exhibiting remarkable functional heterogeneity, as illustrated by the characterization of six novel enzymes. Using structural biology, phylogeny, and enzymatic studies, we establish robust criteria for high-throughput identification of TET peptidases and perform the first systematic study of their genomic distribution and functional diversity across the archaeal kingdom. We propose an 11-group classification for these enzymes and identify one group as the ancestral lineage that first emerged in Archaea. By coupling taxonomic distribution patterns with functional insights, we highlight the presence of multiple TET enzymes with selective activities in heterotrophic and mixotrophic organisms, suggesting a role for TET peptidases in the degradation of environmental peptides. Overall, this work illuminates the underexplored diversity of TET enzymes, uncovering a complex evolutionary history linked to their potential biological function.

molecular biology↗

bioRxiv2024

The plastid-encoded RNA polymerase structures a logistic chain for light-induced photosynthesis

The chloroplast is the semi-autonomous organelle of eukaryotes that performs photosynthesis. In higher plants, chloroplast biogenesis depends on a tight transcriptional coordination of both nuclear- and-plastid photosynthesis-associated genes. The plastid-encoded RNA-polymerase (PEP) is composed of a plastid-encoded catalytic core, similar to multi-subunit RNA polymerases, bound to fifteen nuclear-encoded PEP-associated proteins (PAPs). The binding of all the PAPs to the catalytic core is essential for plastid transcription of photosynthesis-associated genes. Our cryo-electron microscopy structure of the native 21-subunit PEP from Sinapis alba reveals the distinctive patterning of PAP interactions, which evolved upon the ancestral cyanobacterial catalytic core acting as a scaffold. Using PAP8 in planta as bait for affinity purification and proximity labeling, we provide the protein landscapes surrounding the PEP and other PAP8-interacting complexes at the transition from skotomorphogenesis to photomorphogenesis. The data highlight multiple functional couplings in which plastid transcription is at the beginning of a spatial logistic chain, extending from transcription to the assembly of the photosynthetic apparatus into the thylakoids. In addition, dark-specific interactions between photoreceptors and PAP8 establish a physical link between an integrated light signaling and plastid functions.

plant biology↗

bioRxiv2022

Structure of the human heparan sulfate polymerase complex EXT1-EXT2

Heparan sulfates are complex polysaccharides that mediate the interaction with a broad range of protein ligands at the cell surface. A key step in heparan sulfate biosynthesis is catalyzed by the bi-functional glycosyltransferases EXT1 and EXT2, which generate the glycan backbone consisting of repeating N-acetylglucosamine and glucuronic acid units. The molecular mechanism of heparan sulfate chain polymerization remains, however, unknown. Here, we present the cryo-electron microscopy structure of human EXT1-EXT2, which reveals the formation of a tightly packed hetero-dimeric complex harboring four glycosyltransferase domains with their catalytic sites facing in opposite directions. Along with in vitro activity assays using fluorescently labeled and chemically defined substrates, these findings provide a molecular insight into donor substrate recognition and demonstrate that the glycosyltransferase reactions are highly specific. A combination of in vitro and in cellulo mutational studies was used to dissect the functional role of the four catalytic sites. While EXT1 is able to catalyze both glycosyltransferase reactions, EXT2 harbors only N-acetylglucosamine transferase activity. Our results provide mechanistic insight into heparan sulfate chain elongation as a non processive process and lay the cornerstone for future studies on EXT1-EXT2 function in health and disease.

molecular biology↗

bioRxiv2022

Three-dimensional envelope and subunit interactions of the plastid-encoded RNA polymerase from Sinapis alba

RNA polymerases (RNAPs) involved in gene transcription are found in all living organisms with degrees of complexity ranging from single polypeptide chains to multimeric enzymes. In the chloroplasts, the nuclear-encoded RNA polymerase and the plastid-encoded RNA polymerase (PEP) are both involved in the selective transcription of the plastid genome. The PEP is a prokaryotic-type multimeric RNAP found in different states depending on light stimuli and cell identity. One of its active states requires the assembly of nuclear-encoded PEP-Associated Proteins (PAPs) on the catalytic core, producing a complex of more than 900 kDa regarded as essential for chloroplast biogenesis. A purification procedure compatible with structural analysis was used to enrich the native PEP from Sinapis alba chloroplasts. Mass spectrometry (MS)-based proteomic analysis identified the core components, the PAPs and additional members, and coupled to cross-linking (XL-MS) provided initial structural information about the relative position of PEP subunits. Sequence alignments of the catalytic core subunits across various chloroplasts of the green lineage and prokaryotes combined with structural data show that the overall shape of the catalytic core and the residues essential for the catalytic activity are conserved. However, variations are observed at the surface of the core, some of them corresponding to PAP binding sites as suggested by XL-MS experiments. Using negative stain electron microscopy, the PEP 3D envelope was calculated. 3D classification shows that the protrusions which we attribute to the PAPs are firmly associated with the catalytic core. Overall, the shape of the S. alba PEP envelope is different from that of RNAPs.

biochemistry↗

bioRxiv2021

De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.

molecular biology↗

bioRxiv2021

Structural Basis for the Inhibition of IAPP Fibril Formation by the Hsp60 Co-Chaperonin Prefoldin

Chaperones, as modulators of protein conformational states, are key cellular actors to prevent the accumulation of fibrillar aggregates. Here, we integrated kinetic investigations with structural studies to elucidate how the ubiquitous co-chaperonin prefoldin (PFD) inhibits diabetes associated islet amyloid polypeptide (IAPP) fibril formation. We demonstrated that both human and archaeal PFD interfere similarly with the IAPP fibril elongation and secondary nucleation pathways. Using archaeal prefoldin model, we combined NMR spectroscopy with EM to establish that the inhibition of fibril formation is mediated by the binding of prefoldins coiled-coil helices to the flexible IAPP N-terminal segment accessible on the fibril surface and fibril ends. AFM demonstrates that binding of prefoldin to IAPP leads to the formation of lower amounts of aggregates, composed of shorter fibrils, clustered together. Linking structural models with observed fibrillation inhibition processes opens new perspectives for understanding the interference between natural chaperones and formation of disease-associated amyloids.

biophysics↗

bioRxiv2021

The archaeal division protein CdvB1 assembles into polymers that are depolymerized by CdvC

The Cdv proteins constitute the cell-division system of the Crenarchaea, in a protein machinery that is closely related to the ESCRT system of eukaryotes. The CdvB paralog CdvB1 is believed to play a major role in the constricting ring that is the central actor in cell division in the crenarchaea. Here, we present an in vitro study of purified CdvB1 from the crenarchaeon M. sedula with a combination of TEM imaging and biochemical assays. We show that CdvB1 self-assembles into filamentous polymers that are depolymerized by the action of the Vps4-homolog ATPase CdvC. Using liposome flotation assays, we show that CdvB1 binds to negatively charged lipid membranes and can be detached from the membrane by the action of CdvC. Interestingly, we find that the polymerization and the membrane binding are mutually exclusive properties of the protein. Our findings provide novel insight into one of the main components of the archaeal cell division machinery.

biochemistry↗

bioRxiv2021

Elicitation of potent SARS-CoV-2 neutralizing antibody responses through immunization using a versatile adenovirus-inspired multimerization platform

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown that vaccine preparedness is critical to anticipate a fast response to emergent pathogens with high infectivity. To rapidly reach herd immunity, an affordable, easy to store and versatile vaccine platform is thus desirable. We previously designed a non-infectious adenovirus-inspired nanoparticle (ADDomer), and in the present work, we efficiently decorated this original vaccine platform with glycosylated receptor binding domain (RBD) of SARS-CoV-2. Cryo-Electron Microscopy structure revealed that up to 60 copies of this antigenic domain were bound on a single ADDomer particle with the symmetrical arrangements of a dodecahedron. Mouse immunization with the RBD decorated particles showed as early as the first immunization a significant anti-coronavirus humoral response, which was boosted after a second immunization. Neutralization assays with spike pseudo-typed-virus demonstrated the elicitation of strong neutralization titers. Remarkably, the existence of pre-existing immunity against adenoviral-derived particles enhanced the humoral response against SARS-CoV-2. This plug and play vaccine platform revisits the way of using adenovirus to combat emergent pathogens while potentially taking advantage of the adenovirus pre-immunity.

microbiology↗

bioRxiv2021

Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects Macaques from infection

The SARS-CoV-2 pandemic causes an ongoing global health crisis, which requires efficient and safe vaccination programs. Here, we present synthetic SARS-CoV2 S glycoprotein-coated liposomes that resemble in size and surface structure virus-like particles. Soluble S glycoprotein trimers were stabilized by formaldehyde cross-linking and coated onto lipid vesicles (S-VLP). Immunization of cynomolgus macaques with S-VLPs induced high antibody titers and TH1 CD4+ biased T cell responses. Although antibody responses were initially dominated by RBD specificity, the third immunization boosted non-RBD antibody titers. Antibodies showed potent neutralization against the vaccine strain and the Alpha variant after two immunizations and robust neutralization of Beta and Gamma strains. Challenge of animals with SARS-CoV-2 protected all vaccinated animals by sterilizing immunity. Thus, the S-VLP approach is an efficient and safe vaccine candidate based on a proven classical approach for further development and clinical testing.

immunology↗

bioRxiv2021

Immediate and sustained effects of cobalt-containing pigments on macrophages

Pigments are among the oldest nanoparticulate products known to mankind, and their use in tattoos is also very old. Nowadays, 25% of American people aged 18 to 50 are tattooed, which poses the question of the delayed effects of tattoos. In this article, we investigated three cobalt (Pigment Violet 14 (purple color)) or cobalt alloy pigments (Pigment Blue 28 (blue color), Pigment Green 14 (green color)), and one zinc pigment (Pigment White 4 (white color)) which constitute a wide range of colors found in tattoos. These pigments contain microparticles and a significant proportion of submicroparticles or nanoparticles (in either aggregate or free form). Because of the key role of macrophages in the scavenging of particulate materials, we tested the effects of cobalt- and zinc-based pigments on the J774A.1 macrophage cell line. In order to detect delayed effects, we compared two exposure schemes: acute exposure for 24 hours and an exposure for 24 hours followed by a 3-day post-exposure recovery period. The conjunction of these two schemes allowed for the investigation of the delayed or sustained effects of pigments. All pigments induced functional effects on macrophages, most of which were pigment-dependent. For example, Pigment Green 19, Pigment Blue 28, and Pigment White 4 showed a delayed alteration of the phagocytic capacity of cells. Moreover, all the pigments tested induced a slight but significant increase in tumor necrosis factor secretion. This effect, however, was transitory. Conversely, only Pigment Blue 28 induced both a short and sustained increase in interleukin 6 secretion. Results showed that in response to bacterial stimuli (LPS), the secretion of tumor necrosis factor and interleukin 6 declined after exposure to pigments followed by a recovery period. For chemoattractant cytokines (MCP-1 or MIP-1), delayed effects were observed with a secretion decreased in presence of Pigment Blue 28 and Pigment violet 14, both with or without LPS stimuli. The pigments also induced persisting changes in some important macrophage membrane markers such as CD11b, an integrin contributing to cell adhesion and immunological tolerance. In conclusion, the pigments induced functional disorders in macrophages, which, in some cases, persist long after exposure, even at non-toxic doses. Contribution to the field statementUnlike dyes, which are water-soluble, pigments are water-insoluble and thus viewed as inert coloring substances. However, historical pigments such as lead white or vermilion (mercuric sulfide) have been shown to be toxic, suggesting that pigments inertness may not be complete under biological conditions. Pigments being particulate (nano) materials, they are taken up by professional scavenger cells such as macrophages once they have penetrated into the body. One epitome of this situation is represented by tattooing: the pigments injected with the ink are taken up by dermal macrophages, which life cycle ensures the localized persistence of tattoos over time. Using an in vitro macrophage culture system adapted to study delayed effects, we have investigated the effects of a series of cobalt- and zinc-containing pigments on macrophages. First of all, the toxicity of the pigments correlated well with their solubility in acidic media, i.e. conditions prevailing in the phagolysosomes. Even when used at non-toxic doses, the cobalt and zinc pigments showed immediate and/or delayed effects on macrophage functions such as phagocytosis, adhesion, tissue repair or response to bacterial stimuli. Overall, these results show that some pigments may not be as inert as previously thought, and describe a system to investigate these effects.

immunology↗

bioRxiv2020

DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist

The efficient spread of SARS-CoV-2 resulted in a pandemic that is unique in modern history. Despite early identification of ACE2 as the receptor for viral spike protein, much remains to be understood about the molecular events behind viral dissemination. We evaluated the contribution of C-type lectin receptors (CLRS) of antigen-presenting cells, widely present in air mucosa and lung tissue. DC-SIGN, L-SIGN, Langerin and MGL bind to diverse glycans of the spike using multiple interaction areas. Using pseudovirus and cells derived from monocytes or T-lymphocytes, we demonstrate that while virus capture by the CLRs examined does not allow direct cell infection, DC/L-SIGN, among these receptors, promote virus transfer to permissive ACE2+ cells. A glycomimetic compound designed against DC-SIGN, enable inhibition of this process. Thus, we described a mechanism potentiating viral capture and spreading of infection. Early involvement of APCs opens new avenues for understanding and treating the imbalanced innate immune response observed in COVID-19 pathogenesis

immunology↗