Biology subjects

Zimmerberg, J.

Publications and source records attributed to Zimmerberg, J..

11 recordsLinked to original sources

bioRxiv2026

The Influenza Hemagglutinin Cytoplasmic Tail Domain Interacts with Phosphatidylinositol 4,5-bisphosphate

During the influenza viral life cycle, the viral glycoprotein hemagglutinin (HA) mediates binding, entry, and fusion. Densely packed clusters of HA trimers at the plasma membrane are required to produce infectious virions; however, the mechanism of HA clustering is still unknown. We have shown previously that HA co-clusters with and modulates phosphatidylinositol 4,5-bisphosphate (PIP2) in host cell plasma membranes (PM). Here, we further characterize the relationship between HA and PIP2 using molecular dynamics simulations (MD) and fluorescence photoactivation localization microscopy (FPALM) to elucidate a mechanism of HA-PIP2 interaction. We found that the interaction occurs largely between the PIP2 head group and the cytoplasmic tail domain (CTD) of HA. Mutations of the CTD were made to alter charge (HARE, HARREQ), palmitoylation sites (HAMAY), or a combination thereof (HAREMAY, RREQMAY). MD showed that HARREQ and RREQMAY had the strongest effect on HA-PIP2 interactions through a depletion in the radial distribution function of PIP2 around HA at distances [≤]2.5 nm. FPALM revealed that HA cluster density at the PM was significantly reduced by CTD mutations, with the largest reduction occurring in mutants where the CTD charge and acylation were both altered (HAREMAY). HAREMAY clusters were also found to have larger circularities and perimeters, implying a structural change to the clusters. Mutations in the HA transmembrane domain also caused modest changes to the cluster properties of HA and its co-clustering with PIP2. FPALM showed PIP2 co-clustering with HA was also affected by HA mutations with more free PIP2 localized under HAREMAY clusters. A chemical model of simultaneous HA-PIP2 and PH-PIP2 binding enables interpretation of HA-PIP2 interactions and reveals quantitative differences between PIP2 binding by HA CTD mutants. We conclude that the mechanism of HA-PIP2 interaction consists of at least electrostatic and hydrophobic components. Our insights into the mechanism of HA-PIP2 interaction, and the prevalence of putative PIP2-interacting domains in a number of viral spike proteins suggest it may be fruitful to identify methods of disrupting interactions between phosphoinositides and viral proteins.

biophysics↗

bioRxiv2024

The invasion pore induced by Toxoplasma gondii

Obligate intracellular parasites invade host cells to survive. Following host cell contact, the apicomplexan Toxoplasma gondii injects proteins required for invasion into the host cell. Here, electrophysiological recordings of host cells acquired at sub- 200 ms resolution allowed detection and analysis of a transient increase in host membrane conductance following exposure to Toxoplasma gondii. Transients always preceded invasion but parasites depleted of the moving junction protein RON2 generated transients without invading, ruling out a direct structural role for RON2 in generating the conductance pathway or restricting the diffusion of its components. Time-series analysis developed for transients and applied to the entire transient dataset (910,000 data points) revealed multiple quantal conductance changes in the parasite-induced transient, consistent with a rapid insertion, then slower removal, blocking, or inactivation of pore-like conductance steps. Quantal steps for RH had a principal mode with Gaussian mean of 0.26 nS, similar in step size to the apicomplexan protein translocon EXP2. Without RON2 the quantal mean was significantly different (0.19 nS). Because no invasion occurs without poration, the term invasion pore is proposed.

biophysics↗

bioRxiv2024

Perforation of the host cell plasma membrane during Toxoplasma gondii invasion requires rhoptry exocytosis

Toxoplasma gondii is an obligate intracellular parasite, and the delivery of effector proteins from the parasite into the host cell during invasion is critical for invasion itself and for parasite virulence. The effector proteins are released from specialized apical secretory organelles known as rhoptries. While much has been learned recently about the structure and composition of the rhoptry exocytic machinery and the function of individual rhoptry effector proteins that are exocytosed, virtually nothing is known about how the released proteins are translocated across the host cell plasma membrane. Previous electrophysiology experiments reported an unanticipated observation that invasion by T. gondii is preceded by a transient increase in host cell plasma membrane conductance. Here, we confirm this electrophysiological observation and propose that the conductance transient represents a parasite-induced perforation in the host cell plasma membrane through which rhoptry proteins are delivered. As a first step towards testing this hypothesis, and to provide higher throughput than patch clamp electrophysiology, we developed an alternative assay to detect the perforation. This assay utilizes high-speed, multi-wavelength fluorescence imaging to enable simultaneous visualization of host cell perforation and parasite invasion. Using this assay, we interrogated a panel of mutant parasites conditionally depleted of key invasion-related proteins. Parasites lacking signaling proteins involved in triggering rhoptry secretion (e.g., CLAMP) or components of the rhoptry exocytic machinery (e.g., Nd9, RASP2) are defective in their ability to induce the perforation. These data are consistent with a model in which the perforating agents that disrupt host cell membrane integrity during invasion - and may thereby provide the conduit for delivery of rhoptry effector proteins - are stored within the rhoptries themselves and released upon contact with the host cell.

microbiology↗

bioRxiv2024

Defining the EM-signature of successful cell-transfection

In this report, we describe the architecture of Lipofectamine 2000 and 3000 transfection- reagents, as they appear inside of transfected cells, using classical transmission electron microscopy (EM). We also demonstrate that they provoke consistent structural changes after they have entered cells, changes that not only provide new insights into the mechanism of action of these particular transfection-reagents, but also provide a convenient and robust method for identifying by EM which cells in any culture have been successfully transfected. This also provides clues to the mechanism(s) of their toxic effects, when they are applied in excess. We demonstrate that after being bulk-endocytosed by cells, the cationic spheroids of Lipofectamine remain intact throughout the entire time of culturing, but escape from their endosomes and penetrate directly into the cytoplasm of the cell. In so doing, they provoke a stereotypical recruitment and rearrangement of endoplasmic reticulum (ER), and they ultimately end up escaping into the cytoplasm and forming unique inclusion-bodies. Once free in the cytoplasm, they also invariably develop dense and uniform coatings of cytoplasmic ribosomes on their surfaces, and finally, they become surrounded by annulate lamellae of the ER. In the end, these annulate-lamellar enclosures become the ultrastructural signatures of these inclusion-bodies, and serve to positively and definitively identify all cells that have been effectively transfected. Importantly, these new EM-observations define several new and unique properties of these classical Lipofectamines, and allow them to be discriminated from other lipoidal or particulate transfection-reagents, which we find do not physically break out of endosomes or end up in inclusion bodies, and in fact, provoke absolutely none of these signature cytoplasmic reactions.

cell biology↗

bioRxiv2022

Endothelial cells release microvesicles that harbor multivesicular bodies and secrete exosomes

Extracellular vesicles (EVs) released by resting endothelial cells support vascular homeostasis. To better understand endothelial cell EV biogenesis, we examined cultured human umbilical vein endothelial cells (HUVECs) prepared by rapid freezing, freeze-substitution, and serial thin section electron microscopy. Thin sections of HUVECs revealed clusters of membrane protrusions on the otherwise smooth cell surface. The protrusions contained membrane-bound organelles, including multivesicular bodies (MVBs), and appeared to be on the verge of pinching off to form microvesicles. Beyond cell peripheries, membrane-bound vesicles with internal MVBs were observed, and serial sections confirmed that they were not connected to cells. These observations are consistent with the notion that these multi-compartmented microvesicles (MCMVs) pinch-off from protrusions. Remarkably, omega figures formed by fusion of MVBs with the MCMV limiting membrane were directly observed, apparently caught in the act of releasing exosomes from the MCMV. In summary, MCMVs are a novel form of EV that bud from membrane protrusions on the HUVEC surface, contain MVBs and release exosomes. These observations suggest that exosomes can be harbored within and released from transiting microvesicles after departure from the parent cell, constituting a new site of exosome biogenesis occurring from endothelial and potentially additional cell types.

cell biology↗

bioRxiv2022

The Delta variant SARS-CoV-2 spike protein uniquely promotes aggregation of pseudotyped viral particles

Individuals infected with the SARS-CoV-2 Delta variant, lineage B.1.617.2, exhibit faster initial infection with a higher viral load than prior variants, and pseudotyped particles bearing the SARS-CoV-2 Delta variant spike protein induce a faster initial infection rate of target cells compared to those bearing other SARS-CoV-2 variant spikes. Here, we show that pseudotyped particles bearing the Delta variant spike form unique aggregates, as evidenced by negative stain and cryogenic electron microscopy (EM), flow cytometry, and nanoparticle tracking analysis. Viral particles pseudotyped with other SARS-CoV-2 spike variants do not show aggregation by any of these criteria. The contribution to infection kinetics of the Delta spikes unique property to aggregate is discussed with respect to recent evidence for collective infection by other viruses. Irrespective of this intriguing possibility, spike-dependent aggregation is a new functional parameter of spike-expressing viral particles to evaluate in future spike protein variants.

microbiology↗

bioRxiv2022

PIEZO1-dependent erythrocyte dehydration as the mechanism for selection of an allele protecting from severe malaria.

PIEZO1 is a cation specific mechanoreceptor channel implicated in red blood cell (RBC) volume homeostasis. Several PIEZO1 gain of function (GoF) variants demonstrate delayed channel inactivation and can cause hereditary xerocytosis (HX), a disease characterized by hemolytic anemia, RBC dehydration, and shape distortion. The milder PIEZO1E756del GoF variant, prevalent in populations of African descent, protects carriers from severe malaria caused by Plasmodium falciparum and ameliorate disease in a rodent malaria model. To explore the mechanism of this malaria protection, P. falciparum infection of human PIEZO1E756del RBC was analyzed in shear-stressed and static cultures with and without Yoda1, a PIEZO1 agonist. RBC dehydration was a common pathophysiological factor affecting parasite replication in both culture conditions. PIEZO1 channel opening by either Yoda1 or shear stress produced dehydration-dependent cell hemolysis, inhibiting P. falciparum infection. Since the physiological activator of PIEZO1 in circulating RBC is shear stress, we propose that shear stress-induced dehydration, disproportionally affecting RBC of GoF PIEZO1 E756del carriers, makes erythrocytes less habitable for P. falciparum to the point of hemolysis, and thus ameliorates malaria in GoF PIEZO1E756del carriers. More generally, RBC dehydration processes may be a pathway for protection from the severe form of malaria common to several hematological disorders, including sickle cell trait. Key pointsO_LIPIEZO1E756del activation in African American donor RBC provokes dehydration-dependent cell hemolysis, impairing P. falciparum replication. C_LIO_LIRBC dehydration could be a malaria ameliorating factor in several known RBC hematological disorders, including sickle cell trait. C_LI

biophysics↗

bioRxiv2021

A high throughput screening assay for inhibitors of SARS-CoV-2 pseudotyped particle entry

Effective small molecule therapies to combat the SARS-CoV-2 infection are still lacking as the COVID-19 pandemic continues globally. High throughput screening assays are needed for lead discovery and optimization of small molecule SARS-CoV-2 inhibitors. In this work, we have applied viral pseudotyping to establish a cell-based SARS-CoV-2 entry assay. Here, the pseudotyped particles (PP) contain SARS-CoV-2 spike in a membrane enveloping both the murine leukemia virus (MLV) gag-pol polyprotein and luciferase reporter RNA. Upon addition of PP to HEK293-ACE2 cells, the SARS-CoV-2 spike protein binds to the ACE2 receptor on the cell surface, resulting in priming by host proteases to trigger endocytosis of these particles, and membrane fusion between the particle envelope and the cell membrane. The internalized luciferase reporter gene is then expressed in cells, resulting in a luminescent readout as a surrogate for spike-mediated entry into cells. This SARS-CoV-2 PP entry assay can be executed in a biosafety level 2 containment lab for high throughput screening. From a collection of 5,158 approved drugs and drug candidates, our screening efforts identified 7 active compounds that inhibited the SARS-CoV-2-S PP entry. Of these seven, six compounds were active against live replicating SARS-CoV-2 virus in a cytopathic effect assay. Our results demonstrated the utility of this assay in the discovery and development of SARS-CoV-2 entry inhibitors as well as the mechanistic study of anti-SARS-CoV-2 compounds. Additionally, particles pseudotyped with spike proteins from SARS-CoV-2 B.1.1.7 and B.1.351 variants were prepared and used to evaluate the therapeutic effects of viral entry inhibitors.

pharmacology and toxicology↗

bioRxiv2021

Condensation of the influenza viral fusion peptide alters membrane structure and water permeability

To infect, enveloped viruses employ spike protein, spearheaded by its amphipathic fusion peptide (FP), that upon activation extends out from the viral surface to embed into the target cellular membrane. Here we report that synthesized influenza virus FP are membrane active, generating pores in giant unilamellar vesicles (GUV), and thus potentially explain both influenza virus hemolytic activity and the liposome poration seen in cryo-electron tomography. Experimentally, FP were heterogeneously distributed on the GUV at the time of poration. Consistent with this heterogeneous distribution, molecular dynamics (MD) simulations of asymmetric bilayers with different numbers of FP in one leaflet show FP aggregation. At the center of FP aggregates, a profound change in the membrane structure results in thinning, higher water permeability, and curvature. Ultimately, a hybrid bilayer nanodomain can form with one lipidic leaflet and one peptidic leaflet. Membrane elastic theory predicts a reduced barrier to water pore formation when even a dimer of FP thins the membrane as above, and the FP of that dimer tilts, to continue the leaflet bending initiated by the hydrophobic mismatch between the FP dimer and the surrounding lipid.

biophysics↗

bioRxiv2020

Ultra-fast electroporation of giant unilamellar vesicles -- Experimental validation of a molecular model

Delivery of molecules to cells via electropermeabilization (electroporation) is a common procedure in laboratories and clinics. However, despite a long history of theoretical effort, electroporation protocols are still based on trial and error because the biomolecular structures and mechanisms underlying this phenomenon have not been established. Electroporation models, developed to explain observations of electrical breakdown of lipid membranes, describe the electric field-driven formation of pores in lipid bilayers. These transient pore models are consistent with molecular dynamics simulations, where field-stabilized lipid pores form within a few nanoseconds and collapse within tens of nanoseconds after the field is removed. Here we experimentally validate this nanoscale restructuring of bio-membranes by measuring the kinetics of transport of the impermeant fluorescent dye calcein into lipid vesicles exposed to ultrashort electric fields (6 ns and 2 ns), and by comparing these results to molecular simulations. Molecular transport after vesicle permeabilization induced by multiple pulses is additive for interpulse intervals as short as 50 ns, while the additive property of transport is no longer observed when the interval is reduced to 0 ns, consistent with the lifetimes of lipid electropores in molecular simulations. These results show that lipid vesicle responses to pulsed electric fields are significantly different from those of living cells where, for similar pulse properties, the uptake of fluorescent dye continues for several minutes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/890137v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1397967org.highwire.dtl.DTLVardef@516b42org.highwire.dtl.DTLVardef@158c373org.highwire.dtl.DTLVardef@87c318_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2019

Contacting domains that segregate lipid from solute transporters in malaria parasites

While membrane contact sites (MCS) between intracellular organelles are abundant1, and cell-cell junctions are classically defined2, very little is known about the contacts between membranes that delimit extracellular junctions within cells, such as those of chloroplasts and intracellular parasites. The malaria parasite replicates within a unique organelle, the parasitophorous vacuole (PV) but the mechanism(s) are obscure by which the limiting membrane of the PV, the parasitophorous vacuolar membrane (PVM), collaborates with the parasite plasma membrane (PPM) to support the transport of proteins, lipids, nutrients, and metabolites between the cytoplasm of the parasite and the cytoplasm of the host erythrocyte (RBC). Here, we demonstrate the existence of multiple micrometer-sized regions of especially close apposition between the PVM and the PPM. To determine if these contact sites are involved in any sort of transport, we localized the PVM nutrient-permeable and protein export channel EXP2, as well as the PPM lipid transporter PfNCR1. We found that EXP2 is excluded from, but PfNCR1 is included within these regions of close apposition. Thus, these two different transport systems handling hydrophilic and hydrophobic substances, respectively, assume complementary and exclusive distributions. This new structural and molecular data assigns a functional significance to a macroscopic membrane domain.

microbiology↗