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Physical Mechanisms of ESCRT-III-Driven Cell Division in Archaea

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Physical Mechanisms of ESCRT-III-Driven Cell Division in Archaea bioRxiv preprint doi: https://doi.org/10.1101/2021.03.23.436559; this version posted March 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Physical mechanisms of ESCRT-III-driven cell division in archaea L. Harker-Kirschneck1, 2, 3 **, A. E. Hafner1, 2, 3 **, T. Yao1,2, A. Pulschen3, 4, F. Hurtig4, C. Vanhille-Campos1, 2, 3, D. Hryniuk1,2, S. Culley2,3, R. Henriques2, 3, B. Baum2, 3, 4, A. Sariˇ c´1, 2, 3* Abstract 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. 1Department of Physics & Astronomy, UCL, London, United Kingdom 2Institute for the Physics of Living Systems, UCL, London, United Kingdom 3MRC Laboratory for Molecular Cell Biology, UCL, London, United Kingdom 4MRC Laboratory Molecular Biology, Cambridge, United Kingdom **Contributed equally; *Correspondence: [email protected] Cell division is one of the most fundamental requirements ESCRT-III proteins polymerise into at least two distinct fila- for the existence of life on Earth. During division the mate- mentous rings which likely form a copolymer that is adsorbed rial from a single cell is divided into two separate daughter on the cytoplasmic side of the cell membrane. The first fil- cells. This is an inherently physical process. Living cells amenteous ring (called CdvB) serves as a template for the have evolved multiple ways to apply mechanical forces for assembly of a contractile ring (made of CdvB1 and CdvB2 this purpose. In general, the process involves proteins that proteins), see Figure 1. Recently it has been shown that the assemble into long polymeric filaments at the cytoplasmic contractile ring is only free to exert forces to reshape the mem- side of the cell membrane. The filaments then undergo a se- brane once the template CdvB ring has been removed [6]. As ries of energy-driven changes in their form and organisation the membrane constricts, the contractile CdvB1/2 ESCRT-III to deform the associated membrane and/or guide cell wall filament disassembles. assembly. The physics of such non-equilibrium protein self- In our model we investigate different energy-driven pro- assembly processes that produce the mechanical work needed tocols that can lead to the contraction and disassembly of an to reshape and cut soft surfaces is largely underexplored. ESCRT-III ring in contact with a deformable cell. We quantify Although the mechanisms of division differ across the the rates, reliability, and symmetry of the resulting cell divi- tree of life, recent data support the idea that eukaryotic cells sion processes. We then quantitatively compare the dynamics likely arose from the symbiosis of an archaeal cell and an of cell division collected in simulations with that observed via alphaproteobacterial cell, where the archaeal host gave rise live imaging of the archeon Sulfolobus acidocaldarius, the to the eukaryotic cell body and the proteobacteria went on closest archaeal relative to eukaryotic cells that can be easily to become the mitochondria [1, 2, 3]. Because of this, many cultured in a laboratory. This comparison identifies a physical physical processes that control eukaryotic cell division likely mechanism that matches all the available experimental data originate in archaea. In particular, ESCRT-III filaments, which remarkably well. drive cell division in a subgroup of archaea called TACK Our study advances the understanding of the physical archaea, also catalyze the final step of cell division in many mechanisms governing cell division across evolution. In a eukaryotes [4, 5]. broader sense, our simulations show how the different proto- Here we develop the first physical model to study the cols that underpin the behaviour of a simple non-equilibrium archaeal cell division by ESCRT-III filaments. In archaea, nanomachine contribute to its function. Our results can hence bioRxiv preprint doi: https://doi.org/10.1101/2021.03.23.436559; this version posted March 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Physical mechanisms of ESCRT-III-driven cell division in archaea — 2/10 Figure 1. Computational model. a) Division of an archaeon S. acidocaldarius. The cell membrane is indicated with a dashed line, the template filament (CdvB) is fluorescently labelled in magenta, while the constricting ESCRT-III filament (CdvB1/2) is labeled in green. b) The initial ESCRT-III filament state (CdvB+CdvB1/2) is modelled as a single helical filament with a target radius equal to the cell radius Rcell. The filament is attached to the inside of the fluid vesicle that represents the archaeal cell. To constrict, upon CdvB degradation, the ESCRT-III filament (CdvB1/2) reduces its target radius to Rtarget, which results in a new target state of a tighter helix. The filament model itself consists of triplet subunits that are connected to each other via 9 bonds whose lengths control the filament curvature (see inset and SI). c) An example of a cell division simulation: the target radius of the filament is instantaneously decreased to 5% of the original cell radius. The filament is then disassembled from both ends 2 with a rate 10 × vdis = 6:7=t (t is the MD unit of time). The filament first forms a superhelix which consists of multiple short helices of alternating chiralities (shown in the dashed box). As the superhelix contracts and disassembles, it pulls the membrane into a tight neck, which spontaneously breaks (Movie S1). be of help in designing protocols for synthetic nanomachinery, brane via volume exclusion. The system is evolved using in particular in the context of building synthetic cells [7, 8, 9]. molecular dynamics simulation with a Langevin thermostat (see Methods and Supplementary Information Section 1 for more details). Results The removal of the template CdvB filament and subse- A minimal model of cell division quential constriction of the ESCRT-III filament (CdvB1/2) are In our model, the ESCRT-III filament (CdvB1/2) bound to modelled by shortening the equilibrium lengths of the bonds the template (CdvB) is described as an elastic helical polymer between the filament’s subunits, which increases the filament made of two full turns whose radius of curvature matches the curvature, from a large radius of curvature Rcell to a small radius R . Figure 1b shows the filament in its initial and radius of the cell, Rcell (Figure 1b). The polymer is modelled target via three beaded monomers that are connected by harmonic target geometrical states. This change in target filament radius springs to each other (inset in Figure 1b). The equilibrium is expected to transform the filament from a wide ring into lengths of the springs determine the curvature of the polymer a tight helix and would drag the membrane with it. To test [10]. The archaeal cell is described as a vesicle made of a this idea, we instantaneously changed the target radius of the coarse-grained, one-particle-thick membrane (developed by filament to 5% of the cell radius and let the system evolve. Yuan et al. [11]), in which a single particle corresponds to Since filament disassembly is needed for scission [6], as soon a cluster of ∼ 10 nm wide lipid molecules. These particles as the new equilibrium bond lengths have been imposed, we interact via an anisotropic pair potential that drives the self- initiated the disassembly process by severing bonds between assembly of fluid membranes with expected physiological filament monomers sequentially from both ends of the helix bending rigidity. The outer side of the filament (coloured in at a specified rate vdis. blue beads in Figure 1b is attracted to the membrane via a Interestingly, rather than adapting the target shape of a generic Lennard-Jones attractive potential, while the inner single tight helix, we find that the filament upon constriction side of the filament (red beads) only interacts with the mem- instantly transforms into a collection of short tight helices of bioRxiv preprint doi: https://doi.org/10.1101/2021.03.23.436559; this version posted March 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Physical mechanisms of ESCRT-III-driven cell division in archaea — 3/10 Figure 2. Reliability of the division. Left panel: The influence of the filament radius reduction, Rtarget=Rcell, and the rate of the filament disassembly, vdis, on the probability of cell division. The colour of each square represents the percentage of successful divisions out of 10 simulations performed with different random seeds. Right panel: The snapshots of the representative simulations.
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