Biology subjects

Baum, B.

Publications and source records attributed to Baum, B..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

The antigenic landscape of N1 neuraminidase in human influenza A virus strains isolated between 2009 and 2020

The clinical burden caused by influenza can be mitigated by the prophylactic use of seasonal influenza vaccines. Their immunogen composition is revised biannually to optimally match the antigenic drift of the hemagglutinin of circulating influenza virus strains. Antibodies directed against the influenza neuraminidase also correlate with protection against influenza, yet the antigenic evolution of influenza neuraminidase remains underexplored. To evaluate the antigenic diversity of N1 neuraminidase, we generated a panel of immune sera directed against 17 N1 neuraminidases derived from human H1N1 strains that were isolated between 2009 and 2020 and determined its neuraminidase inhibition titers against a panel of 15 HxN1 viruses. The resulting neuraminidase inhibition pattern revealed two antigenic groups that circulated in this period. A machine learning method identified K432E and I321V as key determinants of N1 neuraminidase antigenicity.

immunology↗

bioRxiv2024

Stability vs flexibility: reshaping monolayer and bilayer archaeal membranes in silico

Cellular membranes differ across the tree of life. In most bacteria and eukaryotes, single-headed lipids self-assemble into flexible bilayer membranes. By contrast, thermophilic archaea tend to possess bilayer lipids together with double-headed, monolayer spanning bolalipids, which are thought to enable cells to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we explore the trade-offs at play when forming membranes. We find that flexible bolalipids form membranes that resemble bilayer membranes because they are able to assume a U-shaped conformation. Conversely, rigid bolalipids, which resemble the bolalipids with cyclic groups found in thermophilic archaea, take on a straight conformation and form membranes that are stiff and prone to pore formation when they undergo changes in shape. Strikingly, however, the inclusion of small amounts of bilayer lipids in a bolalipid membrane is enough to achieve fluid bolalipid membranes that are both stable and flexible - resolving this trade-off. Our study suggests a mechanism by which archaea can tune the material properties of their membranes as and when required to enable them to survive in harsh environments and to undergo essential membrane remodelling events like cell division.

biophysics↗

bioRxiv2024

Evolutionarily conserved principles of ESCRT-III-mediated membrane remodelling revealed by a two-subunit Asgard archaeal system

ESCRT-III proteins assemble into composite polymers that undergo stepwise changes in composition and structure to deform membranes across the tree of life. Here, using a phylogenetic analysis we demonstrate that the two ESCRT-III proteins present in our closest archaeal relatives are evolutionarily related to B-type and A-type eukaryotic paralogues, which initiate and execute membrane remodelling, respectively. This deep homology is reflected in ESCRT-III structure and function as demonstrated by the fact that ESCRT-IIIB assembles into parallel arrays on planar membranes to initiate membrane deformation, and is required to recruit ESCRT-IIIA to generate composite polymers. ESCRT-IIIA homopolymers can then remodel membranes into tubes, as a likely prelude to scission. Taken together, this analysis reveals a set of conserved principles governing ESCRT-III-dependent membrane remodelling that first emerged with the evolution of a two-component ESCRT-III system in the Asgard archaea, and which continue to underlie complex multi-component, ESCRT-III-dependent membrane remodelling in eukaryotes.

evolutionary biology↗

bioRxiv2023

The intracellular lifestyle of an archaeal symbiont

DPANN Archaea are a diverse group of organisms typically characterised by small cells and reduced genomes. To date, all cultivated DPANN Archaea are ectosymbionts that require direct cell contact with an archaeal host species for proliferation. However, the dynamics of DPANN - host interactions and the impacts of these interactions on the host species are poorly understood. Here, we show that one DPANN archaeon (Candidatus Nanohaloarchaeum antarcticus) engages in parasitic interactions with its host (Halorubrum lacusprofundi) that result in host cell lysis. Our data also suggest that these interactions involve invasion of the host cell by the nanohaloarchaeon. This is the first reported instance of such a predatory-like lifestyle amongst Archaea and indicates that some DPANN Archaea may interact with host populations in a manner similar to viruses.

microbiology↗

bioRxiv2023

Oncogenic Ras deregulates cell-substrate interactions during mitotic rounding and respreading to alter cell division orientation

Oncogenic Ras has been shown to change the way cancer cells divide by increasing the forces generated during mitotic rounding. In this way, RasV12 enables cancer cells to divide across a wider range of mechanical environments than normal cells. Here, we identify a further role for oncogenic Ras-ERK signalling in division by showing that RasV12 expression alters the shape, division orientation and respreading dynamics of cells as they exit mitosis, in a manner that depends on MEK and ERK. Many of these effects appear to result from the impact of RasV12 signalling on actomyosin contractility, since RasV12 induces the severing of retraction fibres that normally guide spindle positioning and provide a memory of the interphase cell shape. In support of this idea, the RasV12 phenotype is reversed by inhibition of actomyosin contractility, and can be mimicked by the loss of cell-substrate adhesion during mitosis. Thus, the induction of oncogenic Ras-ERK signalling leads to rapid changes in division orientation that, along with the effects of RasV12 on cell growth and cell cycle progression, are likely to disrupt epithelial tissue organisation and contribute to cancer dissemination.

cell biology↗

bioRxiv2023

SCAR and the Arp2/3 complex polarise the actomyosin cortex and plasma membrane organization in asymmetrically dividing neuroblasts

While the Formin-nucleated actomyosin cortex has been shown to drive the changes in cell shape that accompany cell division in both symmetric and asymmetric cell divisions, it is not clear whether or not Arp2/3-nucleated branched actin filament networks also play a role. In order to look for mitotic roles of the Arp2/3 complex, here we use Drosophila neural stem cells as a model system. These cells are unusual in that they divide asymmetrically to produce a large and small daughter cell with different fates. Our analysis identifies a pool of Arp2/3-dependent actin-based membrane protrusions that form at the apical cortex of these cells as they enter mitosis. Strikingly, at metaphase, these protrusions co-localise with components of the SCAR complex. By perturbing Arp2/3 complex activity we show that this apical pool of actin likely functions to limit the accumulation of apical Myosin in metaphase. Following the onset of anaphase, the loss of these SCAR and Arp2/3 dependent structures then leads to a delay in the clearance of apical Myosin and to cortical instability at cytokinesis. These data point to a role for a polarised branched actin filament network in fine tuning the apical actomyosin cortex to enable the precise control of cell shape during asymmetric cell division.

cell biology↗

bioRxiv2022

Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments

ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks. Author summaryESCRT-III proteins have the unique ability to cut membrane necks from within, which is needed for a vast number of cell remodelling events including the release of cargo-containing vesicles. ESCRT-III proteins exist in different forms, which can assemble into spiral and helical homopolymers of different curvatures, and they have been suggested to polymerize and depolymerize with each other in a staged manner to deform and cut membranes. We developed a computer model to explore the physical mechanisms behind vesicle budding driven by the staged assembly and disassembly of multiple elastic filaments. We identified rules that determine the outcomes of membrane remodelling, which depend on the relative physical features of the distinct filaments, the dynamics of their disassembly, and on the presence of cargo; thereby providing experimentally testable predictions. Our study provides new physical insights into the ESCRT-III-mediated vesicle budding process, at a single subunit level, and identifies the general design principles of nanomachines built from shapeshifting copolymers, which might also be realized in synthetic systems.

biophysics↗

bioRxiv2022

The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division

ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems sequential changes in the composition of ESCRT-III polymers induced by the AAA ATPase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organised and remodelled in space and time in cells. Here, taking advantage of the relative simplicity of the ESCRT-III-dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relative of eukaryotes, we use super-resolution microscopy and computational modelling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III-dependent membrane remodelling.

cell biology↗

bioRxiv2022

Mechanochemical rules for membrane-reshaping composite filaments

The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how ESCRT-III polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein-membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodelling and show this mechanism is efficient because sequential polymer assembly lowers the energetic barrier for membrane deformation.

biophysics↗

bioRxiv2022

Spindle reorientation in response to mechanical stress is an emergent property of the spindle positioning mechanisms

Proper orientation of the mitotic spindle plays a crucial role in embryos, during tissue development, and in adults, where it functions to dissipate mechanical stress to maintain tissue integrity and homeostasis. While mitotic spindles have been shown to reorient in response to external mechanical stresses, the subcellular cues that mediate spindle reorientation remain unclear. Here, we have used a combination of optogenetics and computational modelling to better understand how mitotic spindles respond to inhomogeneous tension within the actomyosin cortex. Strikingly, we find that the optogenetic activation of RhoA only influences spindle orientation when it is induced at both poles of the cell. Under these conditions, the sudden local increase in cortical tension induced by RhoA activation reduces pulling forces exerted by cortical regulators on astral microtubules. This leads to a perturbation of the torque balance exerted on the spindle, which causes it to rotate. Thus, spindle rotation in response to mechanical stress is an emergent phenomenon arising from the interaction between the spindle positioning machinery and the cell cortex.

cell biology↗

bioRxiv2022

Tension at intercellular junctions is necessary for accurate orientation of cell division in the epithelium plane

The direction in which a cell divides is set by the orientation of its mitotic spindle and is important for determining cell fate, controlling tissue shape and maintaining tissue architecture. Division perpendicular to the plane of the substrate can promote tissue stratification during development or wound healing, but also metastasis when orientation is aberrant. Much is known about the molecular mechanisms involved in setting the spindle orientation. However, less is known about the contribution of mechanical factors, such as tissue tension, in ensuring spindle orientation in the plane of the epithelium, despite epithelia being continuously subjected to mechanical stresses. Here, we used suspended epithelial monolayers devoid of extracellular matrix and subjected to varying levels of tissue tension to study the orientation of division relative to the tissue plane. We found that decreasing tissue tension by compressing the monolayers or by inhibiting myosin contractility leads to a higher frequency of out-of-plane divisions. Reciprocally, accurate in-plane division can be restored by increasing tissue tension by increasing cell contractility or by tissue stretching. By considering the full three-dimensional geometry of the epithelium, we show that spindles are sensitive to tissue tension, independently of cell shape, through its impact on the tension at subcellular surfaces. Overall, our data suggest that accurate spindle orientation in the plane of the epithelium necessitates the presence of a sufficiently large tension at intercellular junctions. Significance statementIn growing epithelia, divisions are typically oriented in the plane of the tissue to drive expansion. In some organs, divisions are then re-oriented so that they occur perpendicular to the epithelium plane to drive tissue stratification and cell differentiation. When uncontrolled, this switch in orientation can lead to defects in tissue organisation and, in cancer, likely contribute to metastasis. While much is known about the molecular mechanisms controlling mitotic spindle orientation, less is known about the role of mechanical factors. Here we use mechanical and chemical perturbations to show that mechanics plays a role in controlling the plane of division. Overall, our data suggest that the orientation of spindles in the epithelium plane requires sufficient tension across intercellular junctions.

biophysics↗

bioRxiv2021

Characterisation of the Ubiquitin-ESCRT pathway in Asgard archaea sheds new light on origins of membrane trafficking in eukaryotes

The ESCRT machinery performs a critical role in membrane remodelling events in all eukaryotic cells, including in membrane trafficking, membrane repair, cytokinetic abscission, in viral egress, and in the generation of extracellular vesicles. While the machinery is complex in modern day eukaryotes, where it comprises dozens of proteins, the system has simpler and more ancient origins. Indeed, homologues of ESCRT-III and the Vps4 ATPase, the proteins that execute the final membrane scission reaction, play analogous roles in cytokinesis and potentially in extracellular vesicle formation in TACK archaea where ESCRT-I and II homologues seem to be absent. Here, we explore the phylogeny, structure, and biochemistry of homologues of the ESCRT machinery and the associated ubiquitylation system found in genome assemblies of the recently discovered Asgard archaea. In these closest living prokaryotic relatives of eukaryotes, we provide evidence for the ESCRT-I and II sub-complexes being involved in the ubiquitin-directed recruitment of ESCRT-III,_as it is in eukaryotes. This analysis suggests a pre-eukaryotic origin for the Ub-coupled ESCRT system and a likely path of ESCRT evolution via a series of gene duplication and diversification events.

cell biology↗

bioRxiv2021

Physical mechanisms of ESCRT-III-driven cell division in archaea

Living systems propagate by undergoing rounds of cell growth and division. Cell division is at heart a physical process that requires mechanical forces, usually exerted by protein assemblies. Here we developed the first physical model for the division of archaeal cells, which despite their structural simplicity share machinery and evolutionary origins with eukaryotes. We show how active geometry changes of elastic ESCRT-III filaments, coupled to filament disassembly, are sufficient to efficiently split the cell. We explore how the non-equilibrium processes that govern the filament behaviour impact the resulting cell division. We show how a quantitative comparison between our simulations and dynamic data for ESCRTIII-mediated division in Sulfolobus acidocaldarius, the closest archaeal relative to eukaryotic cells that can currently be cultured in the lab, and reveal the most likely physical mechanism behind its division.

biophysics↗

bioRxiv2021

Oncogenic RAS instructs morphological transformation of human epithelia via differential tissue mechanics.

The RAS proto-oncogene is a critical regulator of cell state, morphology and mechanics, and plays a key role in cancer progression. Here, by using a human epithelial model in vitro, we ask how morpho-mechanical changes driven by oncogenic RAS activation at the level of individual cells are collectively integrated to drive changes in tissue behaviour. We found that the uniform oncogenic expression of HRAS.V12 in confined epithelial monolayers causes reproducible changes in the structure and organization of the tissue, which acquires a transitory bilayered morphology. RAS-driven bilayering associates with reproducible layer-specific differences in cell-cell contractility and cell-matrix forces. These drive the initially flat tissues to form three-dimensional structures mimicking some of the behaviours seen in human cancers. Our findings establish a physical mechanism of cellular collectives through which uniform expression of RAS can be interpreted differently in different places of the same tissue to regulate its physiological and pathological morphology.

cancer biology↗

bioRxiv2020

Asymmetric nuclear division of neural stem cells contributes to the formation of sibling nuclei with different identities

Cellular diversity in multicellular organisms is often generated via asymmetric divisions. In the fly, for example, neural stem cells divide asymmetrically to generate a large self-renewing stem cell and a smaller sibling that differentiates. Efforts to understand how these different cell fates are generated have focused on the asymmetric segregation of cortically-localised transcription factors at division, which preferentially enter single daughter cell nuclei to change their fate. However, we find that the nuclear compartment in these cells remains intact throughout mitosis and is asymmetrically inherited, giving rise to sibling nuclei that differ profoundly in size, envelope composition and fate markers. These data reveal the importance of considering nuclear remodelling during stem cell divisions, and show how daughter cell fates depend on the coordination of the asymmetric inheritance of cortical fate markers with asymmetric nuclear division.

cell biology↗

bioRxiv2020

Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodelling superfamily

Membrane remodelling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, CdvB in TACK archaea and ESCRT-III in eukaryotes. Here, we show that these protein families are homologous and share a common evolutionary origin. Using cryo-electron microscopy we present structures for Vipp1 rings over a range of symmetries. Each ring is built from rungs that stack and spontaneously self-organise to form domes. Rungs are assembled from a polymer that is strikingly similar in structure to ESCRT-III. A tilt between rungs generates the dome-shaped curvature with constricted open ends and an inner membrane-binding lumen. Overall, our results reveal conserved mechanistic principles that underlie Vipp1, PspA and ESCRT-III dependent membrane remodelling across all domains of life. One sentence summaryEvolutionary and structural analyses of Vipp1/IM30 rings reveal ESCRT-III-like polymers that remodel membranes in bacteria.

microbiology↗

bioRxiv2020

Designing membrane-reshaping nanostructures through artificial evolution

In this paper we combine the rules of natural evolution with molecular dynamics simulations to design a nanostructure with a desired function. We apply this scheme to the case of a ligand-covered nanoparticle and evolve ligand patterns that promote efficient cell uptake. Surprisingly, we find that in the regime of low ligand number the fittest structures are characterised by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. This demonstrates the efficacy of artificial evolution to identify non-intuitive design rules and reveals a new principle of design that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry.

biophysics↗

bioRxiv2020

Live cell imaging of the hyperthermophilic archaeon Sulfolobus acidocaldarius identifies complementary roles for two ESCRTIII homologues in ensuring a robust and symmetric cell division

Live-cell imaging has revolutionized our understanding of dynamic cellular processes in bacteria and eukaryotes. While similar techniques have recently been applied to the study of halophilic archaea, our ability to explore the cell biology of thermophilic archaea is limited, due to the technical challenges of imaging at high temperatures. Here, we report the construction of the Sulfoscope, a heated chamber that enables live-cell imaging on an inverted fluorescent microscope. Using this system combined with thermostable fluorescent probes, we were able to image Sulfolobus cells as they divide, revealing a tight coupling between changes in DNA compaction, segregation and cytokinesis. By imaging deletion mutants, we observe important differences in the function of the two ESCRTIII proteins recently implicated in cytokinesis. The loss of CdvB1 compromises cell division, causing occasional division failures and fusion of the two daughter cells, whereas the deletion of cdvB2 leads to a profound loss of division symmetry, generating daughter cells that vary widely in size and eventually generating ghost cells. These data indicate that DNA separation and cytokinesis are coordinated in Sulfolobus, as is the case in eukaryotes, and that two contractile ESCRTIII polymers perform distinct roles to ensure that Sulfolobus cells undergo a robust and symmetrical division. Taken together, the Sulfoscope has shown to provide a controlled high temperature environment, in which cell biology of Sulfolobus can be studied in unprecedent details.

microbiology↗