Pattern formation on membranes and its role in bacterial cell division

Beyond homogeneity: Assessing the validity of the Michaelis-Menten rate law in spatially heterogeneous environments

The Michaelis-Menten (MM) rate law has been a fundamental tool in describing enzyme-catalyzed reactions for over a century. When substrates and enzymes are homogeneously distributed, the validity of the MM rate law can be easily assessed based on relative concentrations: the substrate is in large excess over the enzyme-substrate complex. However, the applicability of this conventional criterion remains unclear when species exhibit spatial heterogeneity, a prevailing scenario in biological systems. Here, we explore the MM rate law's applicability under spatial heterogeneity by using partial differential equations. In this study, molecules diffuse very slowly, allowing them to locally reach quasi-steady states. We find that the conventional criterion for the validity of the MM rate law cannot be readily extended to heterogeneous environments solely through spatial averages of molecular concentrations. That is, even when the conventional criterion for the spatial averages is satisfied, the MM rate law fails to capture the enzyme catalytic rate under spatial heterogeneity. In contrast, a slightly modified form of the MM rate law, based on the total quasi-steady state approximation (tQSSA), is accurate. Specifically, the tQSSA-based modified form, but not the original MM rate law, accurately predicts the drug clearance via cytochrome P450 enzymes and the ultrasensitive phosphorylation in heterogeneous environments. Our findings shed light on how to simplify spatiotemporal models for enzyme-catalyzed reactions in the right context, ensuring accurate conclusions and avoiding misinterpretations in in silico simulations.

Spatial segregation and aging of metabolic processes underlie phenotypic heterogeneity in mycobacteria

Individual cells within clonal populations of mycobacteria vary in size, growth rate, and antibiotic susceptibility. Heterogeneity is, in part, determined by LamA, a protein found exclusively in mycobacteria. LamA localizes to sites of new cell wall synthesis where it recruits proteins important for polar growth and establishing asymmetry. Here, we report that in addition to this function, LamA interacts with complexes involved in oxidative phosphorylation (OXPHOS) at a subcellular location distinct from cell wall synthesis. Importantly, heterogeneity depends on a unique extension of the mycobacterial ATP synthase, and LamA mediates the coupling between ATP production and cell growth in single cells. Strikingly, as single cells age, concentrations of proteins important for oxidative phosphorylation become less abundant, and older cells rely less on oxidative phosphorylation for growth. Together, our data reveal that central metabolism is spatially organized within a single mycobacterium and varies within a genetically identical population of mycobacteria. Designing therapeutic regimens to account for this heterogeneity may help to treat mycobacterial infections faster and more completely.

The C-terminal domain of MinC, a cell division regulation protein, is sufficient to form a copolymer with MinD

Assembly of cell division protein FtsZ into the Z-ring at the division site is a key step in bacterial cell division. The Min proteins can restrict the Z-ring to the middle of the cell. MinC is the main protein that obstructs Z-ring formation by inhibiting FtsZ assembly. Its N-terminal domain (MinCN ) regulates the localization of the Z-ring by inhibiting FtsZ polymerization, while its C-terminal domain (MinCC ) binds to MinD as well as to FtsZ. Previous studies have shown that MinC and MinD form copolymers in vitro. This copolymer may greatly enhance the binding of MinC to FtsZ, and/or prevent FtsZ filaments from diffusing to the ends of the cell. Here, we investigated the assembly properties of MinCC -MinD of Pseudomonas aeruginosa. We found that MinCC is sufficient to form the copolymers. Although MinCC -MinD assembles into larger bundles, most likely because MinCC is spatially more readily bound to MinD, its copolymerization has similar dynamic properties: the concentration of MinD dominates their copolymerization. The critical concentration of MinD is around 3 μm and when MinD concentration is high enough, a low concentration MinCC could still be copolymerized. We also found that MinCC -MinD can still rapidly bind to FtsZ protofilaments, providing direct evidence that MinCC also interacts directly with FtsZ. However, although the presence of minCC can slightly improve the division defect of minC-knockout strains and shorten the cell length from an average of 12.2 ± 6.7 to 6.6 ± 3.6 μm, it is still insufficient for the normal growth and division of bacteria.

Advancing synthetic biology through cell-free protein synthesis

The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.

Directing Min protein patterns with advective bulk flow

The Min proteins constitute the best-studied model system for pattern formation in cell biology. We theoretically predict and experimentally show that the propagation direction of in vitro Min protein patterns can be controlled by a hydrodynamic flow of the bulk solution. We find downstream propagation of Min wave patterns for low MinE:MinD concentration ratios, upstream propagation for large ratios, but multistability of both propagation directions in between. Whereas downstream propagation can be described by a minimal model that disregards MinE conformational switching, upstream propagation can be reproduced by a reduced switch model, where increased MinD bulk concentrations on the upstream side promote protein attachment. Our study demonstrates that a differential flow, where bulk flow advects protein concentrations in the bulk, but not on the surface, can control surface-pattern propagation. This suggests that flow can be used to probe molecular features and to constrain mathematical models for pattern-forming systems.

Catching a Walker in the Act-DNA Partitioning by ParA Family of Proteins

Partitioning the replicated genetic material is a crucial process in the cell cycle program of any life form. In bacteria, many plasmids utilize cytoskeletal proteins that include ParM and TubZ, the ancestors of the eukaryotic actin and tubulin, respectively, to segregate the plasmids into the daughter cells. Another distinct class of cytoskeletal proteins, known as the Walker A type Cytoskeletal ATPases (WACA), is unique to Bacteria and Archaea. ParA, a WACA family protein, is involved in DNA partitioning and is more widespread. A centromere-like sequence parS, in the DNA is bound by ParB, an adaptor protein with CTPase activity to form the segregation complex. The ParA ATPase, interacts with the segregation complex and partitions the DNA into the daughter cells. Furthermore, the Walker A motif-containing ParA superfamily of proteins is associated with a diverse set of functions ranging from DNA segregation to cell division, cell polarity, chemotaxis cluster assembly, cellulose biosynthesis and carboxysome maintenance. Unifying principles underlying the varied range of cellular roles in which the ParA superfamily of proteins function are outlined. Here, we provide an overview of the recent findings on the structure and function of the ParB adaptor protein and review the current models and mechanisms by which the ParA family of proteins function in the partitioning of the replicated DNA into the newly born daughter cells.

The Xanthomonas RaxH-RaxR Two-Component Regulatory System Is Orthologous to the Zinc-Responsive Pseudomonas ColS-ColR System

Genome sequence comparisons to infer likely gene functions require accurate ortholog assignments. In Pseudomonas spp., the sensor-regulator ColS-ColR two-component regulatory system responds to zinc and other metals to control certain membrane-related functions, including lipid A remodeling. In Xanthomonas spp., three different two-component regulatory systems, RaxH-RaxR, VgrS-VgrR, and DetS-DetR, have been denoted as ColS-ColR in several different genome annotations and publications. To clarify these assignments, we compared the sensor periplasmic domain sequences and found that those from Pseudomonas ColS and Xanthomonas RaxH share a similar size as well as the location of a Glu-X-X-Glu metal ion-binding motif. Furthermore, we determined that three genes adjacent to raxRH are predicted to encode enzymes that remodel the lipid A component of lipopolysaccharide. The modifications catalyzed by lipid A phosphoethanolamine transferase (EptA) and lipid A 1-phosphatase (LpxE) previously were detected in lipid A from multiple Xanthomonas spp. The third gene encodes a predicted lipid A glycosyl transferase (ArnT). Together, these results indicate that the Xanthomonas RaxH-RaxR system is orthologous to the Pseudomonas ColS-ColR system that regulates lipid A remodeling. To avoid future confusion, we recommend that the terms ColS and ColR no longer be applied to Xanthomonas spp., and that the Vgr, Rax, and Det designations be used instead.

Increasing MinD's Membrane Affinity Yields Standing Wave Oscillations and Functional Gradients on Flat Membranes

The formation of large-scale patterns through molecular self-organization is a basic principle of life. Accordingly, the engineering of protein patterns and gradients is of prime relevance for synthetic biology. As a paradigm for such pattern formation, the bacterial MinDE protein system is based on self-organization of the ATPase MinD and ATPase-activating protein MinE on lipid membranes. Min patterns can be tightly regulated by tuning physical or biochemical parameters. Among the biochemically engineerable modules, MinD's membrane targeting sequence, despite being a key regulating element, has received little attention. Here we attempt to engineer patterns by modulating the membrane affinity of MinD. Unlike the traveling waves or stationary patterns commonly observed in vitro on flat supported membranes, standing-wave oscillations emerge upon elongating MinD's membrane targeting sequence via rationally guided mutagenesis. These patterns are capable of forming gradients and thereby spatially target co-reconstituted downstream proteins, highlighting their functional potential in designing new life-like systems.

Dynamics of the Bacillus subtilis Min System

The molecular mechanisms that help to place the division septum in bacteria is of fundamental importance to ensure cell proliferation and maintenance of cell shape and size. The Min protein system, found in many rod-shaped bacteria, is thought to play a major role in division site selection.

Division site selection is a vital process to ensure generation of viable offspring. In many rod-shaped bacteria, a dynamic protein system, termed the Min system, acts as a central regulator of division site placement. The Min system is best studied in Escherichia coli, where it shows a remarkable oscillation from pole to pole with a time-averaged density minimum at midcell. Several components of the Min system are conserved in the Gram-positive model organism Bacillus subtilis. However, in B. subtilis, it is commonly believed that the system forms a stationary bipolar gradient from the cell poles to midcell. Here, we show that the Min system of B. subtilis localizes dynamically to active sites of division, often organized in clusters. We provide physical modeling using measured diffusion constants that describe the observed enrichment of the Min system at the septum. Mathematical modeling suggests that the observed localization pattern of Min proteins corresponds to a dynamic equilibrium state. Our data provide evidence for the importance of ongoing septation for the Min dynamics, consistent with a major role of the Min system in controlling active division sites but not cell pole areas.

Turing Patterning in Stratified Domains

Reaction-diffusion processes across layered media arise in several scientific domains such as pattern-forming E. coli on agar substrates, epidermal-mesenchymal coupling in development, and symmetry-breaking in cell polarization. We develop a modeling framework for bilayer reaction-diffusion systems and relate it to a range of existing models. We derive conditions for diffusion-driven instability of a spatially homogeneous equilibrium analogous to the classical conditions for a Turing instability in the simplest nontrivial setting where one domain has a standard reaction-diffusion system, and the other permits only diffusion. Due to the transverse coupling between these two regions, standard techniques for computing eigenfunctions of the Laplacian cannot be applied, and so we propose an alternative method to compute the dispersion relation directly. We compare instability conditions with full numerical simulations to demonstrate impacts of the geometry and coupling parameters on patterning, and explore various experimentally relevant asymptotic regimes. In the regime where the first domain is suitably thin, we recover a simple modulation of the standard Turing conditions, and find that often the broad impact of the diffusion-only domain is to reduce the ability of the system to form patterns. We also demonstrate complex impacts of this coupling on pattern formation. For instance, we exhibit non-monotonicity of pattern-forming instabilities with respect to geometric and coupling parameters, and highlight an instability from a nontrivial interaction between kinetics in one domain and diffusion in the other. These results are valuable for informing design choices in applications such as synthetic engineering of Turing patterns, but also for understanding the role of stratified media in modulating pattern-forming processes in developmental biology and beyond.

Chemical cloaking

Hiding an object in a chemical gradient requires one to suppress the distortions it would naturally cause on it. To do so, we propose a strategy based on coating the object with a chemical reaction-diffusion network which can act as an active cloaking device. By controlling the concentration of some species in its immediate surrounding, the chemical reactions redirect the gradient as if the object was not there. We also show that a substantial fraction of the energy required to cloak can be extracted from the chemical gradient itself.

Energetic and entropic cost due to overlapping of Turing-Hopf instabilities in the presence of cross diffusion

A systematic introduction to nonequilibrium thermodynamics of dynamical instabilities are considered for an open nonlinear system beyond conventional Turing pattern in presence of cross diffusion. An altered condition of Turing instability in presence of cross diffusion is best reflected through a critical control parameter and wave number containing both the self- and cross-diffusion coefficients. Our main focus is on entropic and energetic cost of Turing-Hopf interplay in stationary pattern formation. Depending on the relative dispositions of Turing-Hopf codimensional instabilities from the reaction-diffusion equation it clarifies two aspects: energy cost of pattern formation, especially how Hopf instability can be utilized to dictate a stationary concentration profile, and the possibility of revealing nonequilibrium phase transition. In the Brusselator model, to understand these phenomena, we have analyzed through the relevant complex Ginzberg-Landau equation using multiscale Krylov-Bogolyubov averaging method. Due to Hopf instability it is observed that the cross-diffusion parameters can be a source of huge change in free-energy and concentration profiles.

Division plane placement in pleomorphic archaea is dynamically coupled to cell shape

One mechanism for achieving accurate placement of the cell division machinery is via Turing patterns, where nonlinear molecular interactions spontaneously produce spatiotemporal concentration gradients. The resulting patterns are dictated by cell shape. For example, the Min system of Escherichia coli shows spatiotemporal oscillation between cell poles, leaving a mid-cell zone for division. The universality of pattern-forming mechanisms in divisome placement is currently unclear. We examined the location of the division plane in two pleomorphic archaea, Haloferax volcanii and Haloarcula japonica, and showed that it correlates with the predictions of Turing patterning. Time-lapse analysis of H. volcanii shows that divisome locations after successive rounds of division are dynamically determined by daughter cell shape. For H. volcanii, we show that the location of DNA does not influence division plane location, ruling out nucleoid occlusion. Triangular cells provide a stringent test for Turing patterning, where there is a bifurcation in division plane orientation. For the two archaea examined, most triangular cells divide as predicted by a Turing mechanism; however, in some cases multiple division planes are observed resulting in cells dividing into three viable progeny. Our results suggest that the division site placement is consistent with a Turing patterning system in these archaea.

Oscillatory Switches of Dorso-Ventral Polarity in Cells Confined between Two Surfaces

To maneuver in a three-dimensional space, migrating cells need to accommodate to multiple surfaces. In particular, phagocytes have to explore their environment in the search for particles to be ingested. To examine how cells decide between competing surfaces, we exposed single cells of Dictyostelium to a defined three-dimensional space by confining them between two planar surfaces: those of a cover glass and of a wedged microcantilever. These cells form propagating waves of filamentous actin and PIP3 on their ventral substrate-attached surface. The dynamics of wave formation in the confined cells was explored using two-focus fluorescence imaging. When waves formed on one substrate, wave formation on the other substrate was efficiently suppressed. The propensity for wave formation switched between the opposing cell surfaces with periods of 2-5 min by one of two modes: 1) a rolling mode involving the slipping of a wave along the nonattached plasma membrane and 2) de novo initiation of waves on the previously blank cell surface. These data provide evidence for a cell-autonomous oscillator that switches dorso-ventral polarity in a cell simultaneously exposed to multiple substrate surfaces.

Cryo-EM structure of the MinCD copolymeric filament from Pseudomonas aeruginosa at 3.1 Å resolution

Positioning of the division site in many bacterial species relies on the MinCDE system, which prevents the cytokinetic Z-ring from assembling anywhere but the mid-cell, through an oscillatory diffusion-reaction mechanism. MinD dimers bind to membranes and, via their partner MinC, inhibit the polymerization of cell division protein FtsZ into the Z-ring. MinC and MinD form polymeric assemblies in solution and on cell membranes. Here, we report the high-resolution cryo-EM structure of the copolymeric filaments of Pseudomonas aeruginosa MinCD. The filaments consist of three protofilaments made of alternating MinC and MinD dimers. The MinCD protofilaments are almost completely straight and assemble as single protofilaments on lipid membranes, which we also visualized by cryo-EM.

Surface reaction-diffusion kinetics on lattice at the microscopic scale

Microscopic models of reaction-diffusion processes on the cell membrane can link local spatiotemporal effects to macroscopic self-organized patterns often observed on the membrane. Simulation schemes based on the microscopic lattice method (MLM) can model these processes at the microscopic scale by tracking individual molecules, represented as hard spheres, on fine lattice voxels. Although MLM is simple to implement and is generally less computationally demanding than off-lattice approaches, its accuracy and consistency in modeling surface reactions have not been fully verified. Using the Spatiocyte scheme, we study the accuracy of MLM in diffusion-influenced surface reactions. We derive the lattice-based bimolecular association rates for two-dimensional (2D) surface-surface reaction and one-dimensional (1D) volume-surface adsorption according to the Smoluchowski-Collins-Kimball model and random walk theory. We match the time-dependent rates on lattice with off-lattice counterparts to obtain the correct expressions for MLM parameters in terms of physical constants. The expressions indicate that the voxel size needs to be at least 0.6% larger than the molecule to accurately simulate surface reactions on triangular lattice. On square lattice, the minimum voxel size should be even larger, at 5%. We also demonstrate the ability of MLM-based schemes such as Spatiocyte to simulate a reaction-diffusion model that involves all dimensions: three-dimensional (3D) diffusion in the cytoplasm, 2D diffusion on the cell membrane, and 1D cytoplasm-membrane adsorption. With the model, we examine the contribution of the 2D reaction pathway to the overall reaction rate at different reactant diffusivity, reactivity, and concentrations.

Design of Sealable Custom-Shaped Cell Mimicries Based on Self-Assembled Monolayers on CYTOP Polymer

In bottom-up synthetic biology, one of the major methodological challenges is to provide reaction spaces that mimic biological systems with regard to topology and surface functionality. Of particular interest are cell- or organelle-shaped membrane compartments, as many protein functions unfold at lipid interfaces. However, shaping artificial cell systems using materials with non-intrusive physicochemical properties, while maintaining flexible lipid interfaces relevant to the reconstituted protein systems, is not straightforward. Herein, we develop micropatterned chambers from CYTOP, a less commonly used polymer with good chemical resistance and a refractive index matching that of water. By forming a self-assembled lipid monolayer on the polymer surface, we dramatically increased the biocompatibility of CYTOP-fabricated systems. The phospholipid interface provides an excellent passivation layer to prevent protein adhesion to the hydrophobic surface, and we succeeded in cell-free protein synthesis inside the chambers. Importantly, the chambers could be sealed after loading by a lipid monolayer, providing a novel platform to study encapsulated systems. We successfully reconstituted pole-to-pole oscillations of the Escherichia coli MinDE system, which responds dramatically to compartment geometry. Furthermore, we present a simplified fabrication of our artificial cell compartments via replica molding, making it a readily accessible technique for standard cleanroom facilities.

Synthetic cell division via membrane-transforming molecular assemblies

Reproduction, i.e. the ability to produce new individuals from a parent organism, is a hallmark of living matter. Even the simplest forms of reproduction require cell division: attempts to create a designer cell therefore should include a synthetic cell division machinery. In this review, we will illustrate how nature solves this task, describing membrane remodelling processes in general and focusing on bacterial cell division in particular. We discuss recent progress made in their in vitro reconstitution, identify open challenges, and suggest how purely synthetic building blocks could provide an additional and attractive route to creating artificial cell division machineries.

Multi-phosphorylation reaction and clustering tune Pom1 gradient mid-cell levels according to cell size

Protein concentration gradients pattern developing organisms and single cells. In Schizosaccharomyces pombe rod-shaped cells, Pom1 kinase forms gradients with maxima at cell poles. Pom1 controls the timing of mitotic entry by inhibiting Cdr2, which forms stable membrane-associated nodes at mid-cell. Pom1 gradients rely on membrane association regulated by a phosphorylation-dephosphorylation cycle and lateral diffusion modulated by clustering. Using quantitative PALM imaging, we find individual Pom1 molecules bind the membrane too transiently to diffuse from pole to mid-cell. Instead, we propose they exchange within longer lived clusters forming the functional gradient unit. An allelic series blocking auto-phosphorylation shows that multi-phosphorylation shapes and buffers the gradient to control mid-cell levels, which represent the critical Cdr2-regulating pool. TIRF imaging of this cortical pool demonstrates more Pom1 overlaps with Cdr2 in short than long cells, consistent with Pom1 inhibition of Cdr2 decreasing with cell growth. Thus, the gradients modulate Pom1 mid-cell levels according to cell size.

All organisms need to know how to arrange different cell types during the development of their organs and tissues. This information is provided by protein concentration patterns, or gradients, that tell cells how to behave based on where they are positioned. The same fundamental principles also work on a smaller scale. For example, although the rod-shaped yeast Schizosaccharomyces pombe is a single-celled organism, it uses protein concentration gradients to control its growth and timing of division.

Before S. pombe cells divide, they need to check that they have reached the right size. Several mechanisms contribute to this information. One of them involves a concentration gradient of a protein known as Pom1, which is found on the cell membrane, with more protein at the cell extremities and less towards the middle. Pom1 serves to block the activity of Cdr2 – an enzyme that localizes to the cell middle and controls cell division. An open question has been whether Pom1 levels at the center drop as the cell grows, coordinating growth and division.

One explanation for how the Pom1 gradient could be regulated is by the removal and addition of phosphate groups. At the cell’s tip, an enzyme removes phosphate groups from Pom1, causing it to bind to the membrane. As Pom1 diffuses along the membrane, it continuously ‘re-phosphorylates’ itself. This promotes Pom1 to gradually detach, restricting it from spreading along the membrane towards the cell middle. Another explanation is that clusters of Pom1, formed at the membrane, help establish a gradient by moving along the membrane at different rates: larger clusters, formed in high concentration areas, move slower than smaller clusters, causing levels of Pom1 to be higher at the tip, and lower towards the middle. Now, Gerganova et al. set out to find which of these two processes contributes more to shaping the Pom1 gradient, and determine where Pom1 acts on Cdr2.

Gerganova et al. used super resolution microscopy to track individual Pom1 molecules inside yeast cells. This revealed two findings. First, that individual Pom1 molecules do not travel all the way from the cell tip to the center, but ‘hop’ between clusters as they move towards the middle. Second, in longer cells levels of Pom1 on the membrane drop at the center, where Pom1 encounters Cdr2. As a result, Cdr2 will come across higher levels of Pom1 in short cells, but low levels of Pom1 in long cells. This allows Pom1 to act as a measure of cell size, preventing short cells from dividing too soon.

The role of clusters in creating gradients is not only relevant for yeast cell division. It could potentially apply to the gradients that organize cells and tissues in different organisms. Future work could examine whether similar principles apply in more complex systems.

Cell-Free Protein Synthesis: Chassis toward the Minimal Cell

The quest for a minimal cell not only sheds light on the fundamental principles of life but also brings great advances in related applied fields such as general biotechnology. Minimal cell projects came from the study of a plausible route to the origin of life. Later on, research extended and also referred to the construction of artificial cells, or even more broadly, as in vitro synthetic biology. The cell-free protein synthesis (CFPS) techniques harness the central cellular activity of transcription/translation in an open environment, providing the framework for multiple cellular processes assembling. Therefore, CFPS systems have become the first choice in the construction of the minimal cell. In this review, we focus on the recent advances in the quantitative analysis of CFPS and on its advantage for addressing the bottom-up assembly of a minimal cell and illustrate the importance of systemic chassis behavior, such as stochasticity under a compartmentalized micro-environment.

Functional Modules of Minimal Cell Division for Synthetic Biology

Cellular reproduction is one of the fundamental hallmarks of life. Therefore, the development of a minimal division machinery capable of proper genome condensation and organization, mid-cell positioning and segregation in space and time, and the final septation process constitute a fundamental challenge for synthetic biology. It is therefore important to be able to engineer such modules for the production of artificial minimal cells. A bottom-up assembly of molecular machines from bulk biochemicals complemented by in vivo experiments as well as computational modelling helps to approach such key cellular processes. Here, minimal functional modules involved in genome segregation and the division machinery and their spatial organization and positioning are reviewed, setting into perspective the design of a minimal cell. Furthermore, the milestones of recent in vitro reconstitution experiments in the context of cell division are discussed and their role in shedding light on fundamental cellular mechanisms that constitute spatiotemporal order is described. Lastly, current challenges in the field of bottom-up synthetic biology as well as possible future developments toward the development of minimal biomimetic systems are discussed.

Lipid Phases and Cell Geometry During the Cell Cycle of Streptococcus pneumoniae

The coexistence of different lipid phases is well-known in vitro, but evidence for their presence and function in cellular membranes remains scarce. Using a combination of fluorescent lipid probes, we observe segregation of domains that suggests the coexistence of liquid and gel phases in the membrane of Streptococcus pneumoniae, where they are localized to minimize bending stress in the ellipsoid geometry defined by the cell wall. Gel phase lipids with high bending rigidity would be spontaneously organized at the equator where curvature is minimal, thus marking the future division site, while liquid phase membrane maps onto the oblong hemispheres. In addition, the membrane-bound cell wall precursor with its particular dynamic acyl chain localizes at the division site where the membrane is highly curved. We propose a complete “chicken-and-egg” model where cell geometry determines the localization of lipid phases that positions the cell division machinery, which in turn alters the localization of lamellar phases by assembling the cell wall with a specific geometry.

Reverse and forward engineering of protein pattern formation

Living systems employ protein pattern formation to regulate important life processes in space and time. Although pattern-forming protein networks have been identified in various prokaryotes and eukaryotes, their systematic experimental characterization is challenging owing to the complex environment of living cells. In turn, cell-free systems are ideally suited for this goal, as they offer defined molecular environments that can be precisely controlled and manipulated. Towards revealing the molecular basis of protein pattern formation, we outline two complementary approaches: the biochemical reverse engineering of reconstituted networks and the de novo design, or forward engineering, of artificial self-organizing systems. We first illustrate the reverse engineering approach by the example of the Escherichia coli Min system, a model system for protein self-organization based on the reversible and energy-dependent interaction of the ATPase MinD and its activating protein MinE with a lipid membrane. By reconstituting MinE mutants impaired in ATPase stimulation, we demonstrate how large-scale Min protein patterns are modulated by MinE activity and concentration. We then provide a perspective on the de novo design of self-organizing protein networks. Tightly integrated reverse and forward engineering approaches will be key to understanding and engineering the intriguing phenomenon of protein pattern formation.This article is part of the theme issue 'Self-organization in cell biology'.

Minimal in vitro systems shed light on cell polarity

Cell polarity - the morphological and functional differentiation of cellular compartments in a directional manner - is required for processes such as orientation of cell division, directed cellular growth and motility. How the interplay of components within the complexity of a cell leads to cell polarity is still heavily debated. In this Review, we focus on one specific aspect of cell polarity: the non-uniform accumulation of proteins on the cell membrane. In cells, this is achieved through reaction-diffusion and/or cytoskeleton-based mechanisms. In reaction-diffusion systems, components are transformed into each other by chemical reactions and are moving through space by diffusion. In cytoskeleton-based processes, cellular components (i.e. proteins) are actively transported by microtubules (MTs) and actin filaments to specific locations in the cell. We examine how minimal systems - in vitro reconstitutions of a particular cellular function with a minimal number of components - are designed, how they contribute to our understanding of cell polarity (i.e. protein accumulation), and how they complement in vivo investigations. We start by discussing the Min protein system from Escherichia coli, which represents a reaction-diffusion system with a well-established minimal system. This is followed by a discussion of MT-based directed transport for cell polarity markers as an example of a cytoskeleton-based mechanism. To conclude, we discuss, as an example, the interplay of reaction-diffusion and cytoskeleton-based mechanisms during polarity establishment in budding yeast.

Bacterial cell division: modeling FtsZ assembly and force generation from single filament experimental data

The bacterial cytoskeletal protein FtsZ binds and hydrolyzes GTP, self-aggregates into dynamic filaments and guides the assembly of the septal ring on the inner side of the membrane at midcell. This ring constricts the cell during division and is present in most bacteria. Despite exhaustive studies undertaken in the last 25 years after its discovery, we do not yet know the mechanism by which this GTP-dependent self-aggregating protein exerts force on the underlying membrane. This paper reviews recent experiments and theoretical models proposed to explain FtsZ filament dynamic assembly and force generation. It highlights how recent observations of single filaments on reconstituted model systems and computational modeling are contributing to develop new multiscale models that stress the importance of previously overlooked elements as monomer internal flexibility, filament twist and flexible anchoring to the cell membrane. These elements contribute to understand the rich behavior of these GTP consuming dynamic filaments on surfaces. The aim of this review is 2-fold: (1) to summarize recent multiscale models and their implications to understand the molecular mechanism of FtsZ assembly and force generation and (2) to update theoreticians with recent experimental results.

Subcellular Organization: A Critical Feature of Bacterial Cell Replication

Spatial organization is a hallmark of all living systems. Even bacteria, the smallest forms of cellular life, display defined shapes and complex internal organization, showcasing a highly structured genome, cytoskeletal filaments, localized scaffolding structures, dynamic spatial patterns, active transport, and occasionally, intracellular organelles. Spatial order is required for faithful and efficient cellular replication and offers a powerful means for the development of unique biological properties. Here, we discuss organizational features of bacterial cells and highlight how bacteria have evolved diverse spatial mechanisms to overcome challenges cells face as self-replicating entities.

Information Thermodynamics of Turing Patterns

We set up a rigorous thermodynamic description of reaction-diffusion systems driven out of equilibrium by time-dependent space-distributed chemostats. Building on the assumption of local equilibrium, nonequilibrium thermodynamic potentials are constructed exploiting the symmetries of the chemical network topology. It is shown that the canonical (resp. semigrand canonical) nonequilibrium free energy works as a Lyapunov function in the relaxation to equilibrium of a closed (resp. open) system, and its variation provides the minimum amount of work needed to manipulate the species concentrations. The theory is used to study analytically the Turing pattern formation in a prototypical reaction-diffusion system, the one-dimensional Brusselator model, and to classify it as a genuine thermodynamic nonequilibrium phase transition.

MinE conformational switching confers robustness on self-organized Min protein patterns

Many fundamental cellular processes are spatially regulated by self-organized protein patterns, which are often based on nucleotide-binding proteins that switch their nucleotide state upon interaction with a second, activating protein. For reliable function, these protein patterns must be robust against parameter changes, although the basis for such robustness is generally elusive. Here we take a combined theoretical and experimental approach to the Escherichia coli Min system, a paradigmatic system for protein self-organization. By mathematical modeling and in vitro reconstitution of mutant proteins, we demonstrate that the robustness of pattern formation is dramatically enhanced by an interlinked functional switching of both proteins, rather than one. Such interlinked functional switching could be a generic means of obtaining robustness in biological pattern-forming systems.

Protein patterning is vital for many fundamental cellular processes. This raises two intriguing questions: Can such intrinsically complex processes be reduced to certain core principles and, if so, what roles do the molecular details play in individual systems? A prototypical example for protein patterning is the bacterial Min system, in which self-organized pole-to-pole oscillations of MinCDE proteins guide the cell division machinery to midcell. These oscillations are based on cycling of the ATPase MinD and its activating protein MinE between the membrane and the cytoplasm. Recent biochemical evidence suggests that MinE undergoes a reversible, MinD-dependent conformational switch from a latent to a reactive state. However, the functional relevance of this switch for the Min network and pattern formation remains unclear. By combining mathematical modeling and in vitro reconstitution of mutant proteins, we dissect the two aspects of MinE’s switch, persistent membrane binding and a change in MinE’s affinity for MinD. Our study shows that the MinD-dependent change in MinE’s binding affinity for MinD is essential for patterns to emerge over a broad and physiological range of protein concentrations. Mechanistically, our results suggest that conformational switching of an ATPase-activating protein can lead to the spatial separation of its distinct functional states and thereby confer robustness on an intracellular protein network with vital roles in bacterial cell division.

The cell division protein MinD from Pseudomonas aeruginosa dominates the assembly of the MinC-MinD copolymers

Cell division of rod-shaped bacteria requires the Z ring, a ring of FtsZ filaments associated with the inner-membrane wall. The MinCDE proteins help localize the Z ring to the center of the Escherichia coli cell. MinC, which inhibits Z-ring assembly, is a passenger on MinD. Previous studies have shown that MinC-MinD from E. coli and Aquifex aeolicus assemble in vitro into extended filaments with a 1:1 stoichiometry. However, a recent study has raised questions about the function of the MinC-MinD copolymer in vivo, because its assembly appears to require a high concentration of these two proteins and has a long lag time, and its blockade does not affect in vivo activities. Here, we found that MinC and MinD from Pseudomonas aeruginosa coassemble into filaments with a 1:1 stoichiometry. We also found that the minimal concentration of ∼4 μm required for assembly applies only to MinD because above 4 μm MinD, even very low MinC concentrations sustained coassembly. As previously reported, the MinC-MinD coassembly exhibited a long lag of ∼100 s when initiated by ATP. Premixing MinD with ATP eliminated this lag, suggesting that it may be due to slow MinD dimerization following ATP activation. We also discovered that MinC-MinD copolymers quickly bound FtsZ filaments and formed huge bundles. Our results resolve previous questions about the low concentration of MinC and the lag time, insights that may inform future investigations into the exact role of the MinC-MinD copolymer in vivo.

How cells sense their own shape - mechanisms to probe cell geometry and their implications in cellular organization and function

Cells come in a variety of shapes that most often underlie their functions. Regulation of cell morphogenesis implies that there are mechanisms for shape sensing that still remain poorly appreciated. Global and local cell geometry features, such as aspect ratio, size or membrane curvature, may be probed by intracellular modules, such as the cytoskeleton, reaction-diffusion systems or molecular complexes. In multicellular tissues, cell shape emerges as an important means to transduce tissue-inherent chemical and mechanical cues into intracellular organization. One emergent paradigm is that cell-shape sensing is most often based upon mechanisms of self-organization, rather than determinism. Here, we review relevant work that has elucidated some of the core principles of how cellular geometry may be conveyed into spatial information to guide processes, such as polarity, signaling, morphogenesis and division-plane positioning.

Mechanistic insights of the Min oscillator via cell-free reconstitution and imaging

The MinD and MinE proteins of Escherichia coli self-organize into a standing-wave oscillator on the membrane to help align division at mid-cell. When unleashed from cellular confines, MinD and MinE form a spectrum of patterns on artificial bilayers-static amoebas, traveling waves, traveling mushrooms, and bursts with standing-wave dynamics. We recently focused our cell-free studies on bursts because their dynamics recapitulate many features of Min oscillation observed in vivo. The data unveiled a patterning mechanism largely governed by MinE regulation of MinD interaction with membrane. We proposed that the MinD to MinE ratio on the membrane acts as a toggle switch between MinE-stimulated recruitment and release of MinD from the membrane. In this review, we summarize cell-free data on the Min system and expand upon a molecular mechanism that provides a biochemical explanation as to how these two 'simple' proteins can form the remarkable spectrum of patterns.

Dynamic blue light-switchable protein patterns on giant unilamellar vesicles

The photoswitchable iLID/Nano interaction allows for specific, non-invasive, reversible and dynamic protein photopatterning on GUVs with high spatiotemporal control.

Shedding light on biology of bacterial cells

To understand basic principles of living organisms one has to know many different properties of all cellular components, their mutual interactions but also their amounts and spatial organization. Live-cell imaging is one possible approach to obtain such data. To get multiple snapshots of a cellular process, the imaging approach has to be gentle enough to not disrupt basic functions of the cell but also have high temporal and spatial resolution to detect and describe the changes. Light microscopy has become a method of choice and since its early development over 300 years ago revolutionized our understanding of living organisms. As most cellular components are indistinguishable from the rest of the cellular contents, the second revolution came from a discovery of specific labelling techniques, such as fusions to fluorescent proteins that allowed specific tracking of a component of interest. Currently, several different tags can be tracked independently and this allows us to simultaneously monitor the dynamics of several cellular components and from the correlation of their dynamics to infer their respective functions. It is, therefore, not surprising that live-cell fluorescence microscopy significantly advanced our understanding of basic cellular processes. Current cameras are fast enough to detect changes with millisecond time resolution and are sensitive enough to detect even a few photons per pixel. Together with constant improvement of properties of fluorescent tags, it is now possible to track single molecules in living cells over an extended period of time with a great temporal resolution. The parallel development of new illumination and detection techniques allowed breaking the diffraction barrier and thus further pushed the resolution limit of light microscopy. In this review, we would like to cover recent advances in live-cell imaging technology relevant to bacterial cells and provide a few examples of research that has been possible due to imaging.

This article is part of the themed issue ‘The new bacteriology’.

Engineering Compartmentalized Biomimetic Micro- and Nanocontainers

Compartmentalization of biological content and function is a key architectural feature in biology, where membrane bound micro- and nanocompartments are used for performing a host of highly specialized and tightly regulated biological functions. The benefit of compartmentalization as a design principle is behind its ubiquity in cells and has led to it being a central engineering theme in construction of artificial cell-like systems. In this review, we discuss the attractions of designing compartmentalized membrane-bound constructs and review a range of biomimetic membrane architectures that span length scales, focusing on lipid-based structures but also addressing polymer-based and hybrid approaches. These include nested vesicles, multicompartment vesicles, large-scale vesicle networks, as well as droplet interface bilayers, and double-emulsion multiphase systems (multisomes). We outline key examples of how such structures have been functionalized with biological and synthetic machinery, for example, to manufacture and deliver drugs and metabolic compounds, to replicate intracellular signaling cascades, and to demonstrate collective behaviors as minimal tissue constructs. Particular emphasis is placed on the applications of these architectures and the state-of-the-art microfluidic engineering required to fabricate, functionalize, and precisely assemble them. Finally, we outline the future directions of these technologies and highlight how they could be applied to engineer the next generation of cell models, therapeutic agents, and microreactors, together with the diverse applications in the emerging field of bottom-up synthetic biology.

Large-scale modulation of reconstituted Min protein patterns and gradients by defined mutations in MinE's membrane targeting sequence

The E. coli MinDE oscillator is a paradigm for protein self-organization and gradient formation. Previously, we reconstituted Min protein wave patterns on flat membranes as well as gradient-forming pole-to-pole oscillations in cell-shaped PDMS microcompartments. These oscillations appeared to require direct membrane interaction of the ATPase activating protein MinE. However, it remained unclear how exactly Min protein dynamics are regulated by MinE membrane binding. Here, we dissect the role of MinE’s membrane targeting sequence (MTS) by reconstituting various MinE mutants in 2D and 3D geometries. We demonstrate that the MTS defines the lower limit of the concentration-dependent wavelength of Min protein patterns while restraining MinE’s ability to stimulate MinD’s ATPase activity. Strikingly, a markedly reduced length scale—obtainable even by single mutations—is associated with a rich variety of multistable dynamic modes in cell-shaped compartments. This dramatic remodeling in response to biochemical changes reveals a remarkable trade-off between robustness and versatility of the Min oscillator.

Artificial cell mimics as simplified models for the study of cell biology

Living cells are hugely complex chemical systems composed of a milieu of distinct chemical species (including DNA, proteins, lipids, and metabolites) interconnected with one another through a vast web of interactions: this complexity renders the study of cell biology in a quantitative and systematic manner a difficult task. There has been an increasing drive towards the utilization of artificial cells as cell mimics to alleviate this, a development that has been aided by recent advances in artificial cell construction. Cell mimics are simplified cell-like structures, composed from the bottom-up with precisely defined and tunable compositions. They allow specific facets of cell biology to be studied in isolation, in a simplified environment where control of variables can be achieved without interference from a living and responsive cell. This mini-review outlines the core principles of this approach and surveys recent key investigations that use cell mimics to address a wide range of biological questions. It will also place the field in the context of emerging trends, discuss the associated limitations, and outline future directions of the field. Impact statement Recent years have seen an increasing drive to construct cell mimics and use them as simplified experimental models to replicate and understand biological phenomena in a well-defined and controlled system. By summarizing the advances in this burgeoning field, and using case studies as a basis for discussion on the limitations and future directions of this approach, it is hoped that this minireview will spur others in the experimental biology community to use artificial cells as simplified models with which to probe biological systems.

DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos

Spatial ordering of macromolecular components inside cells is important for cellular physiology and replication. In bacteria, ParA/B systems are known to generate various intracellular patterns that underlie the transport and partitioning of low-copy-number cargos such as plasmids. ParA/B systems consist of ParA, an ATPase that dimerizes and binds DNA upon ATP binding, and ParB, a protein that binds the cargo and stimulates ParA ATPase activity. Inside cells, ParA is asymmetrically distributed, forming a propagating wave that is followed by the ParB-rich cargo. These correlated dynamics lead to cargo oscillation or equidistant spacing over the nucleoid depending on whether the cargo is in single or multiple copies. Currently, there is no model that explains how these different spatial patterns arise and relate to each other. Here, we test a simple DNA-relay model that has no imposed asymmetry and that only considers the ParA/ParB biochemistry and the known fluctuating and elastic dynamics of chromosomal loci. Stochastic simulations with experimentally derived parameters demonstrate that this model is sufficient to reproduce the signature patterns of ParA/B systems: the propagating ParA gradient correlated with the cargo dynamics, the single-cargo oscillatory motion, and the multicargo equidistant patterning. Stochasticity of ATP hydrolysis breaks the initial symmetry in ParA distribution, resulting in imbalance of elastic force acting on the cargo. Our results may apply beyond ParA/B systems as they reveal how a minimal system of two players, one binding to DNA and the other modulating this binding, can transform directionally random DNA fluctuations into directed motion and intracellular patterning.