Hugo Wioland

Fluid flows created by swimming bacteria drive self-organization in confined suspensions

Significance The collective dynamics of swimming microorganisms exhibits a complex interplay with the surrounding fluid: the motile cells stir the fluid, which in turn can reorient and advect them. This feedback loop can result in long-range interactions between the cells, an effect whose significance remains controversial. We present a computational model that takes into account these cell–fluid interactions and cell–cell forces and that predicts counterintuitive cellular order driven by long-range flows. This prediction is confirmed with experimental studies that track the orientation of cells in a confined, dense bacterial suspension. Concentrated suspensions of swimming microorganisms and other forms of active matter are known to display complex, self-organized spatiotemporal patterns on scales that are large compared with those of the individual motile units. Despite intensive experimental and theoretical study, it has remained unclear the extent to which the hydrodynamic flows generated by swimming cells, rather than purely steric interactions between them, drive the self-organization. Here we use the recent discovery of a spiral-vortex state in confined suspensions of Bacillus subtilis to study this issue in detail. Those experiments showed that if the radius of confinement in a thin cylindrical chamber is below a critical value, the suspension will spontaneously form a steady single-vortex state encircled by a counter-rotating cell boundary layer, with spiral cell orientation within the vortex. Left unclear, however, was the flagellar orientation, and hence the cell swimming direction, within the spiral vortex. Here, using a fast simulation method that captures oriented cell–cell and cell–fluid interactions in a minimal model of discrete particle systems, we predict the striking, counterintuitive result that in the presence of collectively generated fluid motion, the cells within the spiral vortex actually swim upstream against those flows. This prediction is then confirmed by the experiments reported here, which include measurements of flagella bundle orientation and cell tracking in the self-organized state. These results highlight the complex interplay between cell orientation and hydrodynamic flows in concentrated suspensions of microorganisms.

Confinement stabilizes a bacterial suspension into a spiral vortex.

Confining surfaces play crucial roles in dynamics, transport, and order in many physical systems, but their effects on active matter, a broad class of dynamically self-organizing systems, are poorly understood. We investigate here the influence of global confinement and surface curvature on collective motion by studying the flow and orientational order within small droplets of a dense bacterial suspension. The competition between radial confinement, self-propulsion, steric interactions, and hydrodynamics robustly induces an intriguing steady single-vortex state, in which cells align in inward spiraling patterns accompanied by a thin counterrotating boundary layer. A minimal continuum model is shown to be in good agreement with these observations.

Oxidation of F-actin controls the terminal steps of cytokinesis

Cytokinetic abscission, the terminal step of cell division, crucially depends on the local constriction of ESCRT-III helices after cytoskeleton disassembly. While the microtubules of the intercellular bridge are cut by the ESCRT-associated enzyme Spastin, the mechanism that clears F-actin at the abscission site is unknown. Here we show that oxidation-mediated depolymerization of actin by the redox enzyme MICAL1 is key for ESCRT-III recruitment and successful abscission. MICAL1 is recruited to the abscission site by the Rab35 GTPase through a direct interaction with a flat three-helix domain found in MICAL1 C terminus. Mechanistically, in vitro assays on single actin filaments demonstrate that MICAL1 is activated by Rab35. Moreover, in our experimental conditions, MICAL1 does not act as a severing enzyme, as initially thought, but instead induces F-actin depolymerization from both ends. Our work reveals an unexpected role for oxidoreduction in triggering local actin depolymerization to control a fundamental step of cell division.

Ferromagnetic and antiferromagnetic order in bacterial vortex lattices

Despite their inherent non-equilibrium nature1, living systems can self-organize in highly ordered collective states2,3 that share striking similarities with the thermodynamic equilibrium phases4,5 of conventional condensed matter and fluid systems. Examples range from the liquid-crystal-like arrangements of bacterial colonies6,7, microbial suspensions8,9 and tissues10 to the coherent macro-scale dynamics in schools of fish11 and flocks of birds12. Yet, the generic mathematical principles that govern the emergence of structure in such artificial13 and biological6–9,14 systems are elusive. It is not clear when, or even whether, well-established theoretical concepts describing universal thermostatistics of equilibrium systems can capture and classify ordered states of living matter. Here, we connect these two previously disparate regimes: Through microfluidic experiments and mathematical modelling, we demonstrate that lattices of hydrodynamically coupled bacterial vortices can spontaneously organize into distinct phases of ferro- and antiferromagnetic order. The preferred phase can be controlled by tuning the vortex coupling through changes of the inter-cavity gap widths. The emergence of opposing order regimes is tightly linked to the existence of geometry-induced edge currents15,16, reminiscent of those in quantum systems17–19. Our experimental observations can be rationalized in terms of a generic lattice field theory, suggesting that bacterial spin networks belong to the same universality class as a wide range of equilibrium systems.

ADF/Cofilin Accelerates Actin Dynamics by Severing Filaments and Promoting Their Depolymerization at Both Ends

Summary Actin-depolymerizing factor (ADF)/cofilins contribute to cytoskeletal dynamics by promoting rapid actin filament disassembly. In the classical view, ADF/cofilin sever filaments, and capping proteins block filament barbed ends whereas pointed ends depolymerize, at a rate that is still debated. Here, by monitoring the activity of the three mammalian ADF/cofilin isoforms on individual skeletal muscle and cytoplasmic actin filaments, we directly quantify the reactions underpinning filament severing and depolymerization from both ends. We find that, in the absence of monomeric actin, soluble ADF/cofilin can associate with bare filament barbed ends to accelerate their depolymerization. Compared to bare filaments, ADF/cofilin-saturated filaments depolymerize faster from their pointed ends and slower from their barbed ends, resulting in similar depolymerization rates at both ends. This effect is isoform specific because depolymerization is faster for ADF- than for cofilin-saturated filaments. We also show that, unexpectedly, ADF/cofilin-saturated filaments qualitatively differ from bare filaments: their barbed ends are very difficult to cap or elongate, and consequently undergo depolymerization even in the presence of capping protein and actin monomers. Such depolymerizing ADF/cofilin-decorated barbed ends are produced during 17% of severing events. They are also the dominant fate of filament barbed ends in the presence of capping protein, because capping allows growing ADF/cofilin domains to reach the barbed ends, thereby promoting their uncapping and subsequent depolymerization. Our experiments thus reveal how ADF/cofilin, together with capping protein, control the dynamics of actin filament barbed and pointed ends. Strikingly, our results propose that significant barbed-end depolymerization may take place in cells.

Modulation of formin processivity by profilin and mechanical tension

Formins are major regulators of actin networks. They enhance actin filament dynamics by remaining processively bound to filament barbed ends. How biochemical and mechanical factors affect formin processivity are open questions. Monitoring individual actin filaments in a microfluidic flow, we report that formins mDia1 and mDia2 dissociate faster under higher ionic strength and when actin concentration is increased. Profilin, known to increase the elongation rate of formin-associated filaments, surprisingly decreases the formin dissociation rate, by bringing formin FH1 domains in transient contact with the barbed end. In contrast, piconewton tensile forces applied to actin filaments accelerate formin dissociation by orders of magnitude, largely overcoming profilin-mediated stabilization. We developed a model of formin conformations showing that our data indicates the existence of two different dissociation pathways, with force favoring one over the other. How cells limit formin dissociation under tension is now a key question for future studies.

Torsional stress generated by ADF/cofilin on cross-linked actin filaments boosts their severing

Proteins of the Actin Depolymerizing Factor (ADF)/cofilin family are the central regulators of actin filament disassembly. A key function of ADF/cofilin is to sever actin filaments. However, how it does so in a physiological context, where filaments are interconnected and under mechanical stress, remains unclear. Here, we monitor and quantify the action of ADF/cofilin in different mechanical situations by using single molecule, single filament, and filament network techniques, coupled to microfluidics. We find that local curvature favors severing, while tension surprisingly has no effect on either cofilin binding or severing. Remarkably, we observe that filament segments that are held between two anchoring points, thereby constraining their twist, experience a mechanical torque upon cofilin binding. We find that this ADF/cofilin-induced torque does not hinder ADF/cofilin binding, but dramatically enhances severing. A simple model, which faithfully recapitulates our experimental observations, indicates that the ADF/cofilin-induced torque increases the severing rate constant 100-fold. A consequence of this mechanism, which we verify experimentally, is that cross-linked filament networks are severed by cofilin far more efficiently than non-connected filaments. We propose that this mechano-chemical mechanism is critical to boost ADF/cofilin’s ability to sever highly connected filament networks in cells.

Quantitative variations of ADF/cofilin's multiple actions on actin filaments with pH

Actin Depolymerizing Factor (ADF)/cofilin is the main protein family promoting the disassembly of actin filaments, which is essential for numerous cellular functions. ADF/cofilin proteins disassemble actin filaments through different reactions, as they bind to their sides, sever them, and promote the depolymerization of the resulting ADF/cofilin-saturated filaments. Moreover, the efficiency of ADF/cofilin is known to be very sensitive to pH. ADF/cofilin thus illustrates two challenges in actin biochemistry: separating the different regulatory actions of a single protein, and characterizing them as a function of specific biochemical conditions. Here, we investigate the different reactions of ADF/cofilin on actin filaments, over four different values of pH ranging from pH 6.6 to pH 7.8, using single filament microfluidics techniques. We show that lowering pH reduces the effective filament severing rate by increasing the rate at which filaments become saturated by ADF/cofilin, thereby reducing the number of ADF/cofilin domain boundaries, where severing can occur. The severing rate per domain boundary, however, remains unchanged at different pH values. The ADF/cofilin-decorated filaments (refered to as “cofilactin” filaments) depolymerize from both ends. We show here that, at physiological pH (pH 7.0 to 7.4), the pointed end depolymerization of cofilactin filaments is barely faster than that of bare filaments. In contrast, cofilactin barbed ends undergo an “unstoppable” depolymerization (depolymerizing for minutes despite the presence of free actin monomers and capping protein in solution), throughout our range of pH. We thus show that, at physiological pH, the main contribution of ADF/cofilin to filament depolymerization is at the barbed end. A number of key cellular processes rely on the proper assembly and disassembly of actin filament networks 1. The central regulator of actin disassembly is the ADF/cofilin protein family 2, 3, which comprises three isoforms in mammals: cofilin-1 (cof1, found in nearly all cell types), cofilin-2 (cof2, found primarily in muscles) and Actin Depolymerization Factor (ADF, found mostly in neurons and epithelial cells). We refer to them collectively as “ADF/cofilin”. Over the years, the combined efforts of several labs have led to the following understanding of actin filament disassembly by ADF/cofilin. Molecules of ADF/cofilin bind stoechiometrically 4, 5 to the sides of actin filaments, with a strong preference for ADP-actin subunits 6–10. Though ADF/cofilin molecules do not contact each other 11, they bind in a cooperative manner, leading to the formation of ADF/cofilin domains on the filaments 5, 7, 9, 12, 13. Compared to bare F-actin, the filament portions decorated by ADF/cofilin (refered to as “cofilactin”) are more flexible 14, 15 and exhibit a shorter right-handed helical pitch, with a different subunit conformation 11, 16–19. Thermal fluctuations are then enough to sever actin filaments at (or near) domain boundaries8, 9, 13, 20, 21. Cofilactin filaments do not sever, but depolymerize from both ends 13 thereby renewing the actin monomer pool. ADF/cofilin thus disassembles actin filaments through the combination of different actions. As such, it vividly illustrates a current challenge in actin biochemistry: identifying and quantifying the multiple reactions involving a single protein. This is a very difficult task for bulk solution assays, where a large number of reactions take place simultaneously, and single-filament techniques have played a key role in deciphering ADF/cofilin’s actions 9, 13, 20, 22–24. In particular, the microfluidics-based method that we have developed over the past years, is a powerful tool for such investigations 25. It has recently allowed us to quantify the kinetics of the aforementioned reactions, and to discover that ADF/cofilin-saturated filament (cofilactin) barbed ends can hardly stop depolymerizing, even when ATP-G-actin and capping protein are present in solution 13. In addition, ADF/cofilin is very sensitive to pH 4, 5, 26–29. In cells, pH can be a key regulatory factor 30. It can vary between compartments, between cell types, and be specifically modulated. We can consider that a typical cytoplasmic pH would be comprised between 7.0 and 7.4. Recently, we have quantified the different reactions involving ADF/cofilin at pH 7.8 13, leaving open the question of how these reaction rates are indivdually affected by pH variations. For instance, it has been reported that ADF/cofilin is a more potent filament disassembler at higher pH values 4, 5, 26–29 but the actual impact of pH on the rate constants of individual reactions has yet to be characterized. Moreover, whether the unstoppable barbed end depolymerization that we have recently discovered for ADF/cofilin-saturated filaments at pH 7.8 13 remains significant at lower, more physiological pH values is an open question. Here, we investigate how the different contributions of ADF/cofilin (using unlabeled ADF, unlabeled cof1 and eGFP-cof1) to actin filament disassembly depend on pH, which we varied from 6.6 to 7.8. We first present the methods which we have used to do so, based on the observation of individual filaments, using microfluidics (Fig. 1). We measured cofilin’s abitility to decorate actin filament by binding to its sides (Fig. 2), and the rate at which individual cofilin domains severed actin filaments (Fig. 3). We next quantified the kinetic parameters of filament ends, for bare and ADF/cofilin-saturated (cofilactin) filaments (Fig. 4), and we specifically quantified the extent to which the barbed ends of cofilactin filaments are in a state which can hardly stop depolymerizing (Fig. 5). We finally summarize our results (Fig. 6).

Mechanical Regulation of Actin Filament Disassembly by ADF/Cofilin

thermal agitation. Despite the decades of studies, however, the essential mechanisms of directional motion remain unclear. For example, we do not understand how the structural change of motors, and the asymmetric structures of the motor-filament interface contribute to directional motion. A limitation is that neither motors nor cytoskeletal filaments can be rationally re-designed, making it difficult to address these key questions. To overcome this limitation, we took bottom-up approaches where new molecular motors and tracks are designed and created based on protein and DNA building blocks. Through the process of creation, we will understand the essential factors for a molecular motor to move forward. Here we constructed a new hybrid motor from dynein and a DNA-binding protein. We chose DNA as a track instead of cytoskeletal filaments because DNA have a lot of advantages: it is stable, synthesizable, and can be self-organized into higher order structures. In in vitro motility assays, the new hybrid motors successfully translocated 10-helix DNA nanotubes at an average velocity of 8 nm s . Furthermore, the multiple molecules of hybrid motors transported single DNA origami cargoes along immobilized DNA nanotubes. Control experiments showed that the hybrid motors recognize the specific DNA sequence that is periodically incorporated along the long axis of the DNA nanotube. Our strategy opens the way to systematic studies on the mechanisms of motors, and to nanotechnological applications using the powerful DNA-based molecular toolbox.

Using in vivo Optical Sectioning to Investigate Mechanical Aspects of Volvox Development

Volvox is a genus of swimming algae consisting of a spherical single sheet of cells. At the end of cell division, embryos form a sphere with their flagella pointing the wrong way (to the inside) and must complete their development by turning themselves inside out. Although this phenomenon was observed hundreds of years ago and has been the subject of extensive study, no quantification of the mechanics has been performed. The simple geometry and connectivity of the cells makes these organisms a tractable example for studying morphogenic processes, while their development still shares features with more complicated mechanisms of gastrulation in animals. Previous study of embryo shapes during inversion required chemical fixation, so that individuals could not be followed through all stages and dynamics were lost. An open-source selective plane illumination microscope (SPIM) [1], has enabled accurate recording of the shapes of embryos as they progress through their inversion process. Unprecedented views of the progress of cell division and the growth of mature spheroids are also within reach. With this dynamic, three-dimensional data, new analysis of embryo and tissue mechanics become possible.[1] Pitrone P. G., Schindelin J., Stuyvenberg L., Preibisch S., Weber M.; Eliceiri K. W., Huisken J., Tomancak P. OpenSPIM: an open access light sheet microscopy platform Nature Methods 10, 598-599 (2013).