What is motion? Recent advances in the study of molecular movement patterns of the peptidoglycan synthesis machines

How proteins move through space and time is a fundamental question in biology. While great strides have been made towards a mechanistic understanding of protein movement, many questions remain. We discuss the biological implications of motion in the context of the peptidoglycan (PG) synthesis machines. We review systems in several bacteria, including Escherichia coli , Bacillus subtilis , and Streptococcus pneumoniae , and present a comprehensive view of our current knowledge regarding movement dynamics. Discrepancies are also addressed since “one size does not fit all”. For bacteria to divide, new PG is synthesized and incorporated into the growing cell wall by complex multi-protein nanomachines consisting of PG synthases (transglycosylases [TG] and/or transpeptidases [TP]) as well as a variety of regulators and cytoskeletal factors. Advances in imaging capabilities and labeling methods have revealed that these machines are not static but rather circumferentially transit the cell via directed motion perpendicular to the long axis of model rod-shaped bacteria such as E. coli and B. subtilis . The enzymatic activity of the TG:TPs drives motion in some species, while motion is mediated by FtsZ treadmilling in others. In addition, both directed and diffusive motion of the PG synthases has been observed using single particle tracking technology. Here, we examine the biological role of diffusion regarding transit. Lastly, findings regarding the monofunctional transglycosylases (RodA and FtsW) as well as the Class A PG synthases are discussed. This minireview serves to showcase recent advances, broach mechanistic unknowns, and stimulate future areas of study.

Systematic analysis of C. elegans embryo behavior reveals a stereotyped developmental progression and a rhythmic pattern of behavioral quiescence

Systematic analysis of rich behavioral recordings is being used to uncover how circuits encode complex behaviors. Here we apply the approach to embryos. What are the first embryonic behaviors and how do they evolve as early neurodevelopment ensues? To address these questions, we present a systematic description of behavioral maturation for Caenorhabditis elegans embryos. Posture libraries were derived from a genetically encoded motion capture suit imaged with light-sheet microscopy and annotated using custom semi-automated tracking software (Multiple Hypothesis Hypergraph Tracking; MHHT). Analysis of cell trajectories, postures, and behavioral motifs revealed a stereotyped developmental progression. Early movement is dominated by flipping between dorsal and ventral coiling, which gradually slows into a period of reduced motility. Late-stage embryos exhibit sinusoidal waves of dorsoventral bends, prolonged bouts of directed motion, and a rhythmic pattern of pausing, which we designate slow wave twitch (SWT). Synaptic transmission is required for late-stage motion but not for early flipping or the intervening inactive phase. A high-throughput behavioral assay and calcium imaging revealed that SWT is elicited by the rhythmic activity of a quiescence-promoting neuron (RIS). Similar periodic quiescent states are seen prenatally in divergent animals and may play an important role in promoting normal developmental outcomes.

Morphological fluctuations of individual mitochondria in living cells

Uncovering the link between mitochondrial morphology, dynamics, positioning and function is challenging. Mitochondria are very flexible organelles that are subject to tension and compression within cells. Recent findings highlighted the importance of these mechanical aspects in the regulation of mitochondria dynamics, arising the question on which are the processes and mechanisms involved in their shape remodeling. In this work we explored in detail the morphological changes and spatio- temporal fluctuations of these organelles in living Xenopus laevis melanophores, a well- characterized cellular model. We developed an automatic method for the classification of mitochondria shapes based on the analysis of the curvature of the contour shape from confocal microscopy images. A persistence length of 2.1 μm was measured, quantifying, for the first time, the bending plasticity of mitochondria in their cellular environment. The shape evolution at the single organelle level was followed during a few minutes revealing that mitochondria can bend and unbend in the seconds timescale. Furthermore, the inspection of confocal movies simultaneously registering fluorescent mitochondria and microtubules suggests that the cytoskeleton network architecture and dynamics play a significant role in mitochondria shape remodeling and fluctuations. For instance changes from sinuous to elongated organelles related to transitions from confined behavior to fast directed motion along microtubule tracks were observed.

Interactions in Active Colloids

The past two decades have seen a remarkable progress in the development of synthetic colloidal agents which are capable of creating directed motion in an unbiased environment at the microscale. These self-propelling particles are often praised for their enormous potential to self-organize into dynamic nonequilibrium structures such as living clusters, synchronized superrotor structures or self-propelling molecules featuring a complexity which is rarely found outside of the living world. However, the precise mechanisms underlying the formation and dynamics of many of these structures are still barely understood, which is likely to hinge on the gaps in our understanding of how active colloids interact. In particular, besides showing comparatively short-ranged interactions which are well known from passive colloids (Van der Waals, electrostatic etc.), active colloids show novel hydrodynamic interactions as well as phoretic and substrate-mediated “osmotic” cross-interactions which hinge on the action of the phoretic field gradients which are induced by the colloids on other colloids in the system. The present article discusses the complexity and the intriguing properties of these interactions which in general are long-ranged, non-instantaneous, nonpairwise and non-reciprocal and which may serve as key ingredients for the design of future nonequilibrium colloidal materials. Besides providing a brief overview on the state of the art of our understanding of these interactions a key aim of this review is to emphasize open key questions and corresponding open challenges.

Chemophoresis Engine: Universal Principle of ATPase-driven Cargo Transport

Cell polarity regulates the orientation of the cytoskeleton members that directs intracellular transport for cargo-like organelles, using chemical gradients sustained by ATP or GTP hydrolysis. However, how cargo transports are directly mediated by chemical gradients remains unknown. We previously proposed a physical mechanism that enables directed movement of cargos, referred to as chemophoresis. According to the mechanism, a cargo with reaction sites is subjected to a chemophoresis force in the direction of the increased concentration. Based on this, we introduce an extended model, the chemophoresis engine, as a general mechanism of cargo motion, which transforms chemical free energy into directed motion through the catalytic ATP hydrolysis. We applied the engine to plasmid motion in a parABS system to demonstrate the the self-organization system for directed plasmid movement and pattern dynamics of ParA-ATP concentration, thereby explaining plasmid equi-positioning and pole-to-pole oscillation observed in bacterial cells and in vitro experiments. We mathematically show the existence and stability of the plasmid-surfing pattern, which allows the cargo-directed motion through the symmetry-breaking transition of the ParA- ATP spatiotemporal pattern. Finally, based on its generality, we discuss the chemophoresis engine as a universal principle of hydrolysis-driven intracellular transport.

Phoretic self-propulsion of helical active particles

Chemically active colloids self-propel by catalysing the decomposition of molecular ‘fuel’ available in the surrounding solution. If the various molecular species involved in the reaction have distinct interactions with the colloid surface, and if the colloid has some intrinsic asymmetry in its surface chemistry or geometry, there will be phoretic flows in an interfacial layer surrounding the particle, leading to directed motion. Most studies of chemically active colloids have focused on spherical, axisymmetric ‘Janus’ particles, which (in the bulk, and in absence of fluctuations) simply move in a straight line. For particles with a complex (non-spherical and non-axisymmetric) geometry, the dynamics can be much richer. Here, we consider chemically active helices. Via numerical calculations and slender body theory, we study how the translational and rotational velocities of the particle depend on geometry and the distribution of catalytic activity over the particle surface. We confirm the recent finding of Katsamba et al. (J. Fluid Mech., vol. 898, 2020, p. A24) that both tangential and circumferential concentration gradients contribute to the particle velocity. The relative importance of these contributions has a strong impact on the motion of the particle. We show that, by a judicious choice of the particle design parameters, one can suppress components of angular velocity that are perpendicular to the screw axis, or even select for purely ‘sideways’ translation of the helix.

Study of the Leidenfrost Effect on Heterogeneous Surfaces of Complex Structure

This work is devoted to a research of water droplets that are put in-between two parallel metal strings the distance between which is comparable to linear size of the droplet. Strings are heated by Joule heating to temperatures that exceed critical temperatures of nucleate and film boiling. Different configurations of strings’ side surface have been tested: smooth and with winding made of the same material (intermittent and uninterrupted). Experiments have shown that droplets on these types of surface do not boil away quickly or fall down. Instead they displayed behavior that can be described as floating, either stable or with directed motion, depending on surface structure or relief. Multiple experiments have shown that it is quite similar to Leidenfrost effect demonstrated on a flat overheated surface by liquids.

The control effort to steer self-propelled microswimmers depends on their morphology: comparing symmetric spherical versus asymmetric L -shaped particles

Active goal-directed motion requires real-time adjustment of control signals depending on the system’s status, also known as control. The amount of information that needs to be processed depends on the desired motion and control, and on the system’s morphology. The morphology of the system may directly effectuate or support the desired motion. This morphology-based reduction to the neuronal ‘control effort’ can be quantified by a novel information-entropy-based approach. Here, we apply this novel measure of ‘control effort’ to active microswimmers of different morphology. Their motion is a combination of directed deterministic and stochastic motion. In spherical microswimmers, the active propulsion leads to linear velocities. Active propulsion of asymmetric L -shaped particles leads to circular or—on tilted substrates—directed motion. Thus, the difference in shape, i.e. the morphology of the particles, directly influence the motion. Here, we quantify how this morphology can be exploited by control schemes for the purpose of steering the particles towards targets. Using computer simulations, we found in both cases a significantly lower control effort for L -shaped particles. However, certain movements can only be achieved by spherical particles. This demonstrates that a suitably designed microswimmer’s morphology might be exploited to perform specific tasks.