Biology subjects

Balor, S.

Publications and source records attributed to Balor, S..

10 recordsLinked to original sources

bioRxiv2026

Layered helical order reveals assembly states in podosome actin networks

How stochastic molecular events are converted into ordered cellular machines that perform mechanical work remains a central question in biology. Cryo-electron tomography enables visualization of macromolecular assemblies inside cells at molecular resolution, but static tomograms are generally interpreted as structural snapshots, with limited access to assembly state and temporal progression. Here, we show that cellular tomograms retain interpretable information about the assembly of a force-generating actin network. Using human macrophage podosomes as a physiologically relevant system, we combine spatial mapping of actin filaments (F-actin) and Arp2/3-mediated branch junctions, orientation analysis of deep-learning-based filament segmentations and Markov-chain modeling to infer actin-network assembly in situ. We identify favored membrane-directed actin polymerization and Arp2/3-mediated branching, establishing a local growth axis for podosome network organization. At the network scale, podosomes display layered helical order: filament-orientation classes recur at intervals of approximately 33 nm along the membrane-normal axis, forming a three-class cycle that returns to an approximately equivalent non-polar orientation. Markov modeling identifies preferred mother-to-daughter filament-orientation transitions and yields a stationary composition of branch-orientation states that closely matches that observed in structurally more advanced network regions. Together, these results link local actin nucleation, network-scale architecture and structural assembly state in a native cellular machine. Our study advances cryo-electron tomography from structural description toward temporal inference and 4D in situ structural biology.

cell biology↗

bioRxiv2025

Pera virus mimics bacteria to infect Pedopumella sp. a freshwater heterotrophic Chrysophyceae

Heterotrophic Chrysophyceae play a key role in the functioning of many aquatic food webs as primary predators of prokaryotes, but their top-down regulatory factors are poorly understood. To date, no virus isolates from heterotrophic Chrysophyceae have been described in the literature. Here we describe Pera virus, a giant virus infecting the heterotrophic Chrysophyceae Pedospumella sp.. Pera virus have an icosahedral capsid-vesicle morphology, a feature unprecedented in viruses. We hypothesize that this vesicle mimics the shape of bacteria so that the virus is recognized as such by its bacteriophage protist host. This constitutes a morphological evolution of viruses that promotes infection of their heterotrophic host. The capside measures 414 nm in diameter. The vesicle has a variable diameter ranging from 231 to 587 nm. The virion as a whole can reach 1008 nm in length. We searched for this new type of virus under environmental conditions during time series studies in hyper-eutrophic freshwater lakes. Surprisingly, we report the existence of Pera virus-like particles (PVLs) of various shapes and size that can reach 5 {micro}m illustrating the hidden diversity of this undescribed virus types. The dynamics of PVLs, which can reach 2.4 x 105 PVL.mL-1, are closely associated with those of unicellular heterotrophic eukaryotes, acting as major regulatory agents of protozoan bacterivory in freshwater. This pair provides a new model for understanding the evolution of giant viruses and their ecological role.

ecology↗

bioRxiv2025

The phosphoinositide PI5P impairs mitochondrial function through endosome-mitochondria proximity

Alterations of mitochondrial structure and bioenergetic dysfunction are hallmarks of metabolic stress and in the progression of heart failure (HF). However, the impact of lipid signalling, particularly the dynamics of phosphoinositides is not fully characterized. Here, we investigate the effect of phosphatidylinositol 5-phosphate (PI5P) on mitochondrial structure and function in cardiomyocytes. We show that exogenous PI5P induces mitochondrial fragmentation, loss of mitochondrial membrane potential, increased ROS production, and impaired mitochondrial respiration. Using a PI5P biosensor, we identify a significant mitochondrial PI5P pool, whose abundance increases upon metabolic stress induced by 2-deoxy-D-glucose exposure, most likely in a PIKfyve-dependent manner. Furthermore, we demonstrate that PIKfyve-positive endolysosomes localize in close proximity to mitochondria in an actin-dependent manner, suggesting a spatial and functional coupling between these two organelles. Overall, our findings reveal a novel mechanism by which PI5P contributes to mitochondrial dysfunction during metabolic stress, potentially linking endolysosomal signalling to mitochondrial metabolism and cardiomyocyte bioenergetic status.

cell biology↗

bioRxiv2025

Structural Basis of Lipopolysaccharide Assembly by the Outer Membrane Translocon Holo-Complex

Lipopolysaccharide (LPS) assembly at the surfaces-exposed leaflet of the bacterial outer membrane (OM) is mediated by the OM LPS translocon. An essential transmembrane {beta}-barrel protein, LptD, and a cognate lipoprotein, LptE, translocate LPS selectively into the OM external leaflet via a poorly understood mechanism. Here, we characterize two additional translocon subunits, the lipoproteins LptM and LptY (formerly YedD). We use single-particle cryo-EM analysis, functional assays and molecular dynamics simulations to visualize the roles of LptM and LptY at the translocon holo-complex LptDEMY, uncovering their impact on LptD conformational dynamics. Whereas LptY binds and stabilizes the periplasmic LptD {beta}-taco domain that functions as LPS receptor, LptM intercalates the lateral gate of the {beta}-barrel domain, promoting its opening and access by LPS. Remarkably, we demonstrate a conformational switch of the LptD {beta}-taco/{beta}-barrel interface alternating between contracted and extended states. The LptD {beta}-strand 1, which defines the mobile side of the lateral gate, binds LPS and performs a stroke movement toward the external leaflet during the contracted-to-extended state transition. Our findings establish a detailed mechanistic framework explaining the selective transport of LPS to the membrane external leaflet.

microbiology↗

bioRxiv2024

Integrative in vivo analysis of the ethanolamine utilization bacterial microcompartment in Escherichia coli.

Bacterial microcompartments (BMCs) are self-assembling protein megacomplexes that encapsulate metabolic pathways. Although approximately 20% of sequenced bacterial genomes contain operons encoding putative BMCs, few have been thoroughly characterized, nor any in the most studied Escherichia coli strains. We used an interdisciplinary approach to gain deep molecular and functional insights into the ethanolamine utilization (Eut) BMC system encoded by the eut operon in E. coli K-12. The eut genotype was linked with the ethanolamine utilization phenotype using deletion and overexpression mutants. The subcellular dynamics and morphology of the E. coli Eut BMC were characterized in cellula by fluorescence microscopy and electron (cryo)microscopy. The minimal proteome reorganization required for ethanolamine utilization and the in vivo stochiometric composition of the Eut BMC were determined by quantitative proteomics. Finally, the first flux map connecting the Eut BMC with central metabolism in cellula was obtained by genome scale modelling and 13C-fluxomics. Our results reveal that, contrary to previous suggestions, ethanolamine serves both as a nitrogen and a carbon source in E. coli K-12, while also contributing significant metabolic overflow. Overall, this study provides a quantitative molecular and functional understanding of the BMCs involved in ethanolamine assimilation by E. coli. ImportanceThe properties of BMCs make them an ideal tool to build orthogonal network structures with minimal interactions with native metabolic and regulatory networks. However, this requires an understanding of how BMCs work natively. In this study, we combined genetic manipulation, multi-omics, modelling and microscopy to address this issue for Eut BMCs. We show that the Eut BMC in E. coli turns ethanolamine into usable carbon and nitrogen substrates to sustain growth. These results improve our understanding of compartmentalization in a widely used bacterial chassis.

microbiology↗

bioRxiv2023

Conformational diversity in class C GPCR positive allosteric modulation

The metabotropic glutamate receptors (mGlus) are class C G protein coupled receptors (GPCR) that form obligate dimers activated by the major excitatory neurotransmitter L-glutamate1,2. The architecture of mGlu receptor comprises an extracellular Venus-Fly Trap domain (VFT) connected to a transmembrane domain (7TM) through a Cysteine-Rich Domain (CRD). The binding of L-glutamate in the VFTs and subsequent conformational change results in the signal being transmitted to the 7TM inducing G-protein binding and activation 3-6. The mGlu receptors signal transduction can be allosterically potentiated by positive allosteric modulators (PAMs) binding to the 7TMs, which are of therapeutic interest in various neurological disorders7-9. Here, we report the cryoEM structures of metabotropic glutamate receptor 5 (mGlu5) purified with three chemically and pharmacologically distinct PAMs. We find that PAMs modulate the receptor equilibrium through their different binding modes, revealing how their interactions in the 7TMs impact the mGlu5 receptor conformational landscape and function. In addition, we identified a PAM-free but agonist-bound intermediate state that is stabilised by interactions mediated by intracellular loop 2. The activation of mGlu5 receptor is a multi-step sequential process in which the binding of the PAMs in the 7TM modulates the equilibrium towards the active state.

biochemistry↗

bioRxiv2022

Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements

Bacterial microcompartments (BMC) are complex macromolecular assemblies that participate to varied chemical processes in about one fourth of bacterial species. BMC-encapsulated enzymatic activities are segregated from other cell contents by means of semipermeable shells, justifying why BMC are viewed as prototype nano-reactors for biotechnological applications. Herein, we undertook a comparative study of trends of self-assembly of BMC hexamers (BMC-H), the most abundant shell constituents. Published and new microscopy data show that some BMC-H, like {beta}-carboxysomal CcmK, tend to assemble flat whereas other BMC-H often build curved-implying objects. Inspection of available crystal structures presenting BMC-H in tiled arrangements permitted to identify two major assembly modes with a striking connection with experimental trends. All-atom molecular dynamics (MD) supported that BMC-H bending is triggered robustly only from the disposition adopted by BMC-H that form curved objects experimentally, conducting to almost identical arrangements to those found in structures of recomposed BMC shells. Simulations on ensembles of planar-behaving hexamers, which were previously reconfigured to comply with such disposition, confirmed that bending is defined by assembly details, rather than by BMC-H identity. Finally, although no common atomic determinants could be identified as responsible of BMC-H spontaneous curvature, an inter-hexamer ionic pair was pinpointed as contributor to hold a subset of BMC-H in low bending dispositions. These results are expected to improve our understanding of the variable mechanisms of biogenesis characterized for BMC, and of possible strategies to regulate BMC size and shape.

biochemistry↗

bioRxiv2022

Plasma cell maintenance and antibody secretion are under the control of Sec22b-mediated regulation of organelle dynamics

Despite the essential role of plasma cells in health and disease, the cellular mechanisms controlling their survival and secretory capacity are still poorly understood. Here, we identified the SNARE Sec22b as a unique and critical regulator of plasma cell maintenance and function. In absence of Sec22b, plasma cells were barely detectable and serum antibody titres were dramatically reduced. Accordingly, Sec22b deficient mice fail to mount a protective immune response. At the mechanistic level, we demonstrated that Sec22b is indispensable for efficient antibody secretion but also for plasma cell fitness through the regulation of the morphology of the endoplasmic reticulum and mitochondria. Altogether, our results unveil a critical role for Sec22b-mediated regulation of plasma cell biology through the control of organelle dynamics.

immunology↗

bioRxiv2021

Elasticity of dense actin networks produces nanonewton protrusive forces

Actin filaments assemble into force-generating systems involved in diverse cellular functions, including cell motility, adhesion, contractility and division. It remains unclear how networks of actin filaments, which individually generate piconewton forces, can produce forces reaching tens of nanonewtons. Here we use in situ cryo-electron tomography to unveil how the nanoscale architecture of macrophage podosomes enables basal membrane protrusion. We show that the sum of the actin polymerization forces at the membrane is not sufficient to explain podosome protrusive forces. Quantitative analysis of podosome organization demonstrates that the core is composed of a dense network of bent actin filaments storing elastic energy. Theoretical modelling of the network as a spring-loaded elastic material reveals that it exerts forces of up to tens of nanonewtons, similar to those evaluated experimentally. Thus, taking into account not only the interface with the membrane but also the bulk of the network, is crucial to understand force generation by actin machineries. Our integrative approach sheds light on the elastic behavior of dense actin networks and opens new avenues to understand force production inside cells.

biophysics↗

bioRxiv2018

Real-time visualization and quantification of human Cytomegalovirus replication in living cells using the ANCHOR DNA labeling technology.

Human cytomegalovirus (HCMV) induces latent life-long infections in all human populations. Depending on geographic area and socio-economic conditions between 30 to nearly 100% of individuals are affected. The biology of this virus is difficult to explore due to its extreme sophistication and the lack of pertinent animal model. Here we present the first application of the ANCHOR DNA labeling system to a herpes virus, allowing real time imaging and direct monitoring of HCMV infection and replication in human living cells. The ANCHOR system is composed of a protein (OR) which specifically binds to a short, non-repetitive DNA target sequence (ANCH) and spreads onto neighboring sequences due to protein oligomerization. If OR protein is fused to GFP, this accumulation results in a site specific fluorescent focus. We have created a recombinant ANCHOR-HCMV harboring an ANCH target sequence and the gene encoding the cognate OR-GFP fusion protein. Infection of permissive cells with ANCHOR-HCMV enables visualization of the nearly complete viral cycle until cell fragmentation and death. Quantitative analysis of infection kinetics and of viral DNA replication revealed cell-type specific behavior of HCMV and sensitivity to inhibitors. Our results show that the ANCHOR technology is a very efficient tool for the study of complex DNA viruses and new highly promising biotechnology applications.\n\nIMPORTANCEThe ANCHOR technology is to date the most powerful tool to follow and quantify the replication of HCMV in living cells and to gain new insights into its biology. This technology is applicable to virtually any DNA virus or virus presenting a dsDNA phase, paving the way to infection imaging in various cell lines or even in animal models and opening fascinating fundamental and applied prospects. Associated to high content automated microscopy, this technology permitted rapid, robust and precise determination of Ganciclovir IC50 and IC90 on HCMV replication, with minimal hands-on investment. To search for new antiviral activities, the experiment is easy to up-grade towards efficient and cost-effective screening of large chemical libraries. The simple infection of permissive cells with ANCHOR-viruses in the presence of a compound of interest may even provide a first estimation about the stage of the viral cycle this molecule is acting upon.

microbiology↗