A biochemical oscillator explains several aspects of Myxococcus xanthus behavior during development

The Limits of Our Explanation: A Case Study in Myxococcus xanthus Cooperation

In this article, I demonstrate two ways in which our major theories of the evolution of cooperation may fail to capture particular social phenomena. The first shortcoming of our current major theories stems from the possibility of mischaracterizing the cooperative problem in game theory. The second shortcoming of our current major theories is the insensitivity of these explanatory models to ecological and genomic context. As a case study to illustrate these points, I will use the cooperative interaction of a species of myxobacteria called Myxococcus xanthus. M. xanthus cooperate in many areas of their life cycle-in quorum sensing, social motility, fruiting body formation, and predation. I focus in particular on predation as we have not yet discovered an adequate explanation of how they sustain cooperative predation in the face of developmental cheats. In explaining why we have not, I draw generalizable conclusions that shed light on our use of simplified models to explain real-world behaviors in a variety of organisms.

Analytical refractory period distribution for a class of time-variant biochemical systems with second-order reactions

Refractory period (RP), the waiting time between signals, can induce complex signaling dynamics, such as acceleration, adaptation, and oscillation, within many cellular biochemical networks. However, its underlying molecular mechanisms are still unclear. Rigorously estimating the RP distribution may be essential to identify its causal regulatory mechanisms. Traditional methods of estimating the RP distribution depend on solving the underlying Chemical Master Equations (CMEs), the dominant modeling formalism of biochemical systems. However, exact solutions of the CME are only known for simple reaction systems with zero- and first-order reactions or specific systems with second-order reactions. General solutions still need to be derived for systems with bimolecular reactions. It is even more challenging if large state-space and nonconstant reaction rates are involved. Here, we developed a direct method to gain the analytical RP distribution for a class of second-order reaction systems with nonconstant reaction rates and large state space. Instead of using the CME, we used an equivalent path-wise representation, which is the solution to a transformed martingale problem of the CME. This allowed us to bypass solving a CME. We then applied the method to derive the analytical RP distribution of a real complex biochemical network with second-order reactions, the Drosophila phototransduction cascade. Our approach provides an alternative to the CMEs in deriving the analytical RP distributions of a class of second-order reaction systems. Since the bimolecular reactions are common in biological systems, our approach could enhance understanding real-world biochemical processes.

A general model-based causal inference method overcomes the curse of synchrony and indirect effect

To identify causation, model-free inference methods, such as Granger Causality, have been widely used due to their flexibility. However, they have difficulty distinguishing synchrony and indirect effects from direct causation, leading to false predictions. To overcome this, model-based inference methods that test the reproducibility of data with a specific mechanistic model to infer causality were developed. However, they can only be applied to systems described by a specific model, greatly limiting their applicability. Here, we address this limitation by deriving an easily testable condition for a general monotonic ODE model to reproduce time-series data. We built a user-friendly computational package, General ODE-Based Inference (GOBI), which is applicable to nearly any monotonic system with positive and negative regulations described by ODE. GOBI successfully inferred positive and negative regulations in various networks at both the molecular and population levels, unlike existing model-free methods. Thus, this accurate and broadly applicable inference method is a powerful tool for understanding complex dynamical systems.

Unorthodox regulation of the MglA Ras-like GTPase controlling polarity in Myxococcus xanthus

Motile cells have developed a large array of molecular machineries to actively change their direction of movement in response to spatial cues from their environment. In this process, small GTPases act as molecular switches and work in tandem with regulators and sensors of their guanine nucleotide status (GAP, GEF, GDI and effectors) to dynamically polarize the cell and regulate its motility. In this review, we focus on Myxococcus xanthus as a model organism to elucidate the function of an atypical small Ras GTPase system in the control of directed cell motility. M. xanthus cells direct their motility by reversing their direction of movement through a mechanism involving the redirection of the motility apparatus to the opposite cell pole. The reversal frequency of moving M. xanthus cells is controlled by modular and interconnected protein networks linking the chemosensory-like frizzy (Frz) pathway - that transmits environmental signals - to the downstream Ras-like Mgl polarity control system - that comprises the Ras-like MglA GTPase protein and its regulators. Here, we discuss how variations in the GTPase interactome landscape underlie single-cell decisions and consequently, multicellular patterns.

Inferring causality in biological oscillators

MOTIVATION

Fundamental to biological study is identifying regulatory interactions. The recent surge in time-series data collection in biology provides a unique opportunity to infer regulations computationally. However, when components oscillate, model-free inference methods, while easily implemented, struggle to distinguish periodic synchrony and causality. Alternatively, model-based methods test the reproducibility of time series given a specific model but require inefficient simulations and have limited applicability.

RESULTS

We develop an inference method based on a general model of molecular, neuronal and ecological oscillatory systems that merges the advantages of both model-based and model-free methods, namely accuracy, broad applicability and usability. Our method successfully infers the positive and negative regulations within various oscillatory networks, e.g. the repressilator and a network of cofactors at the pS2 promoter, outperforming popular inference methods.

AVAILABILITY AND IMPLEMENTATION

We provide a computational package, ION (Inferring Oscillatory Networks), that users can easily apply to noisy, oscillatory time series to uncover the mechanisms by which diverse systems generate oscillations. Accompanying MATLAB code under a BSD-style license and examples are available at https://github.com/Mathbiomed/ION. Additionally, the code is available under a CC-BY 4.0 License at https://doi.org/10.6084/m9.figshare.16431408.v1.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Linking single-cell decisions to collective behaviours in social bacteria

Social bacteria display complex behaviours whereby thousands of cells collectively and dramatically change their form and function in response to nutrient availability and changing environmental conditions. In this review, we focus on Myxococcus xanthus motility, which supports spectacular transitions based on prey availability across its life cycle. A large body of work suggests that these behaviours require sensory capacity implemented at the single-cell level. Focusing on recent genetic work on a core cellular pathway required for single-cell directional decisions, we argue that signal integration, multi-modal sensing and memory are at the root of decision making leading to multicellular behaviours. Hence, Myxococcus may be a powerful biological system to elucidate how cellular building blocks cooperate to form sensory multicellular assemblages, a possible origin of cognitive mechanisms in biological systems. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.

Interplay of mesoscale physics and agent-like behaviors in the parallel evolution of aggregative multicellularity

Myxobacteria and dictyostelids are prokaryotic and eukaryotic multicellular lineages, respectively, that after nutrient depletion aggregate and develop into structures called fruiting bodies. The developmental processes and resulting morphological outcomes resemble one another to a remarkable extent despite their independent origins, the evolutionary distance between them and the lack of traceable homology in molecular mechanisms. We hypothesize that the morphological parallelism between the two lineages arises as the consequence of the interplay within multicellular aggregates between generic processes, physical and physicochemical processes operating similarly in living and non-living matter at the mesoscale (~10^-3-10^-1 m) and agent-like behaviors, unique to living systems and characteristic of the constituent cells, considered as autonomous entities acting according to internal rules in a shared environment. Here, we analyze the contributions of generic and agent-like determinants in myxobacteria and dictyostelid development and their roles in the generation of their common traits. Consequent to aggregation, collective cell-cell contacts mediate the emergence of liquid-like properties, making nascent multicellular masses subject to novel patterning and morphogenetic processes. In both lineages, this leads to behaviors such as streaming, rippling, and rounding-up, as seen in non-living fluids. Later the aggregates solidify, leading them to exhibit additional generic properties and motifs. Computational models suggest that the morphological phenotypes of the multicellular masses deviate from the predictions of generic physics due to the contribution of agent-like behaviors of cells such as directed migration, quiescence, and oscillatory signal transduction mediated by responses to external cues. These employ signaling mechanisms that reflect the evolutionary histories of the respective organisms. We propose that the similar developmental trajectories of myxobacteria and dictyostelids are more due to shared generic physical processes in coordination with analogous agent-type behaviors than to convergent evolution under parallel selection regimes. Insights from the biology of these aggregative forms may enable a unified understanding of developmental evolution, including that of animals and plants.

Dynamical patterning modules and network motifs as joint determinants of development: Lessons from an aggregative bacterium

Development and evolution are dynamical processes under the continuous control of organismic and environmental factors. Generic physical processes, associated with biological materials and certain genes or molecules, provide a morphological template for the evolution and development of organism forms. Generic dynamical behaviors, associated with recurring network motifs, provide a temporal template for the regulation and coordination of biological processes. The role of generic physical processes and their associated molecules in development is the topic of the dynamical patterning module (DPM) framework. The role of generic dynamical behaviors in biological regulation is studied via the identification of the associated network motifs (NMs). We propose a joint DPM-NM perspective on the emergence and regulation of multicellularity focusing on a multicellular aggregative bacterium, Myxococcus xanthus. Understanding M. xanthus development as a dynamical process embedded in a physical substrate provides novel insights into the interaction between developmental regulatory networks and generic physical processes in the evolutionary transition to multicellularity.

The effect of habitats and fitness on species coexistence in systems with cyclic dominance

Cyclic dominance between species may yield spiral waves that are known to provide a mechanism enabling persistent species coexistence. This observation holds true even in presence of spatial heterogeneity in the form of quenched disorder. In this work we study the effects on spatio-temporal patterns and species coexistence of structured spatial heterogeneity in the form of habitats that locally provide one of the species with an advantage. Performing extensive numerical simulations of systems with three and six species we show that these structured habitats destabilize spiral waves. Analyzing extinction events, we find that species extinction probabilities display a succession of maxima as function of time, that indicate a periodically enhanced probability for species extinction. Analysis of the mean extinction time reveals that as a function of the parameter governing the advantage of one of the species a transition between stable coexistence and unstable coexistence takes place. We also investigate how efficiency as a predator or a prey affects species coexistence.

Dynamic polarity control by a tunable protein oscillator in bacteria

In bacteria, cell polarization involves the controlled targeting of specific proteins to the poles, defining polar identity and function. How a specific protein is targeted to one pole and what are the processes that facilitate its dynamic relocalization to the opposite pole is still unclear. The Myxococcus xanthus polarization example illustrates how the dynamic and asymmetric localization of polar proteins enable a controlled and fast switch of polarity. In M. xanthus, the opposing polar distribution of the small GTPase MglA and its cognate activating protein MglB defines the direction of movement of the cell. During a reversal event, the switch of direction is triggered by the Frz chemosensory system, which controls polarity reversals through a so-called gated relaxation oscillator. In this review, we discuss how this genetic architecture can provoke sharp behavioral transitions depending on Frz activation levels, which is central to multicellular behaviors in this bacterium.

Allosteric regulation of a prokaryotic small Ras-like GTPase contributes to cell polarity oscillations in bacterial motility

Mutual gliding motility A (MglA), a small Ras-like GTPase; Mutual gliding motility B (MglB), its GTPase activating protein (GAP); and Required for Motility Response Regulator (RomR), a protein that contains a response regulator receiver domain, are major components of a GTPase-dependent biochemical oscillator that drives cell polarity reversals in the bacterium Myxococcus xanthus. We report the crystal structure of a complex of M. xanthus MglA and MglB, which reveals that the C-terminal helix (Ct-helix) from one protomer of the dimeric MglB binds to a pocket distal to the active site of MglA. MglB increases the GTPase activity of MglA by reorientation of key catalytic residues of MglA (a GAP function) combined with allosteric regulation of nucleotide exchange by the Ct-helix (a guanine nucleotide exchange factor [GEF] function). The dual GAP-GEF activities of MglB accelerate the rate of GTP hydrolysis over multiple enzymatic cycles. Consistent with its GAP and GEF activities, MglB interacts with MglA bound to either GTP or GDP. The regulation is essential for cell polarity, because deletion of the Ct-helix causes bipolar localization of MglA, MglB, and RomR, thereby causing reversal defects in M. xanthus. A bioinformatics analysis reveals the presence of Ct-helix in homologues of MglB in other bacterial phyla, suggestive of the prevalence of the allosteric mechanism among other prokaryotic small Ras-like GTPases.

A study on the mechanism of cell polarity oscillations in Myxococcus xanthus reveals a novel allosteric regulatory mechanism for a small Ras-like GTPase. The motility protein MglB is the first example of both GTPase activating protein (GAP) and guanosine nucleotide exchange factor (GEF) activities being integrated into a single regulator of the small Ras-like GTPase MglA.

Agent-Based Modeling Reveals Possible Mechanisms for Observed Aggregation Cell Behaviors

Myxococcus xanthus is a soil bacterium that serves as a model system for biological self-organization. Cells form distinct, dynamic patterns depending on environmental conditions. An agent-based model was used to understand how M. xanthus cells aggregate into multicellular mounds in response to starvation. In this model, each cell is modeled as an agent represented by a point particle and characterized by its position and moving direction. At low agent density, the model recapitulates the dynamic patterns observed by experiments and a previous biophysical model. To study aggregation at high cell density, we extended the model based on the recent experimental observation that cells exhibit biased movement toward aggregates. We tested two possible mechanisms for this biased movement and demonstrate that a chemotaxis model with adaptation can reproduce the observed experimental results leading to the formation of stable aggregates. Furthermore, our model reproduces the experimentally observed patterns of cell alignment around aggregates.

Period-amplitude co-variation in biomolecular oscillators

The period and amplitude of biomolecular oscillators are functionally important properties in multiple contexts. For a biomolecular oscillator, the overall constraints in how tuning of amplitude affects period, and vice versa, are generally unclear. Here, the authors investigate this co-variation of the period and amplitude in mathematical models of biomolecular oscillators using both simulations and analytical approximations. The authors computed the amplitude-period co-variation of 11 benchmark biomolecular oscillators as their parameters were individually varied around a nominal value, classifying the various co-variation patterns such as a simultaneous increase/decrease in period and amplitude. Next, the authors repeated the classification using a power norm-based amplitude metric, to account for the amplitudes of the many biomolecular species that may be part of the oscillations, finding largely similar trends. Finally, the authors calculate 'scaling laws' of period-amplitude co-variation for a subset of these benchmark oscillators finding that as the approximated period increases, the upper bound of the amplitude increases, or reaches a constant value. Based on these results, the authors discuss the effect of different parameters on the type of period-amplitude co-variation as well as the difficulty in achieving an oscillation with large amplitude and small period.

Dissipative structures in biological systems: bistability, oscillations, spatial patterns and waves

The goal of this review article is to assess how relevant is the concept of dissipative structure for understanding the dynamical bases of non-equilibrium self-organization in biological systems, and to see where it has been applied in the five decades since it was initially proposed by Ilya Prigogine. Dissipative structures can be classified into four types, which will be considered, in turn, and illustrated by biological examples: (i) multistability, in the form of bistability and tristability, which involve the coexistence of two or three stable steady states, or in the form of birhythmicity, which involves the coexistence between two stable rhythms; (ii) temporal dissipative structures in the form of sustained oscillations, illustrated by biological rhythms; (iii) spatial dissipative structures, known as Turing patterns; and (iv) spatio-temporal structures in the form of propagating waves. Rhythms occur with widely different periods at all levels of biological organization, from neural, cardiac and metabolic oscillations to circadian clocks and the cell cycle; they play key roles in physiology and in many disorders. New rhythms are being uncovered while artificial ones are produced by synthetic biology. Rhythms provide the richest source of examples of dissipative structures in biological systems. Bistability has been observed experimentally, but has primarily been investigated in theoretical models in an increasingly wide range of biological contexts, from the genetic to the cell and animal population levels, both in physiological conditions and in disease. Bistable transitions have been implicated in the progression between the different phases of the cell cycle and, more generally, in the process of cell fate specification in the developing embryo. Turing patterns are exemplified by the formation of some periodic structures in the course of development and by skin stripe patterns in animals. Spatio-temporal patterns in the form of propagating waves are observed within cells as well as in intercellular communication. This review illustrates how dissipative structures of all sorts abound in biological systems.This article is part of the theme issue 'Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)'.

A gated relaxation oscillator mediated by FrzX controls morphogenetic movements in Myxococcus xanthus

Dynamic control of cell polarity is of critical importance for many aspects of cellular development and motility. In Myxococcus xanthus, MglA, a G protein, and MglB, its cognate GTPase-activating protein, establish a polarity axis that defines the direction of movement of the cell and that can be rapidly inverted by the Frz chemosensory system. Although vital for collective cell behaviours, how Frz triggers this switch has remained unknown. Here, we use genetics, imaging and mathematical modelling to show that Frz controls polarity reversals via a gated relaxation oscillator. FrzX, which we identify as a target of the Frz kinase, provides the gating and thus acts as the trigger for reversals. Slow relocalization of the polarity protein RomR then creates a refractory period during which another switch cannot be triggered. A secondary Frz output, FrzZ, decreases this delay, allowing rapid reversals when required. Thus, this architecture results in a highly tuneable switch that allows a wide range of reversal frequencies.

Parameter-robustness analysis for a biochemical oscillator model describing the social-behaviour transition phase of myxobacteria

We develop a tool based on bifurcation analysis for parameter-robustness analysis for a class of oscillators and, in particular, examine a biochemical oscillator that describes the transition phase between social behaviours of myxobacteria. Myxobacteria are a particular group of soil bacteria that have two dogmatically different types of social behaviour: when food is abundant they live fairly isolated forming swarms, but when food is scarce, they aggregate into a multicellular organism. In the transition between the two types of behaviours, spatial wave patterns are produced, which is generally believed to be regulated by a certain biochemical clock that controls the direction of myxobacteria's motion. We provide a detailed analysis of such a clock and show that, for the proposed model, there exists some interval in parameter space where the behaviour is robust, i.e. the system behaves similarly for all parameter values. In more mathematical terms, we show the existence and convergence of trajectories to a limit cycle, and provide estimates of the parameter under which such a behaviour occurs. In addition, we show that the reported convergence result is robust, in the sense that any small change in the parameters leads to the same qualitative behaviour of the solution.

Dissipative structures and biological rhythms

Sustained oscillations abound in biological systems. They occur at all levels of biological organization over a wide range of periods, from a fraction of a second to years, and with a variety of underlying mechanisms. They control major physiological functions, and their dysfunction is associated with a variety of physiological disorders. The goal of this review is (i) to give an overview of the main rhythms observed at the cellular and supracellular levels, (ii) to briefly describe how the study of biological rhythms unfolded in the course of time, in parallel with studies on chemical oscillations, (iii) to present the major roles of biological rhythms in the control of physiological functions, and (iv) the pathologies associated with the alteration, disappearance, or spurious occurrence of biological rhythms. Two tables present the main examples of cellular and supracellular rhythms ordered according to their period, and their role in physiology and pathophysiology. Among the rhythms discussed are neural and cardiac rhythms, metabolic oscillations such as those occurring in glycolysis in yeast, intracellular Ca⁺⁺ oscillations, cyclic AMP oscillations in Dictyostelium amoebae, the segmentation clock that controls somitogenesis, pulsatile hormone secretion, circadian rhythms which occur in all eukaryotes and some bacteria with a period close to 24 h, the oscillatory dynamics of the enzymatic network driving the cell cycle, and oscillations in transcription factors such as NF-ΚB and tumor suppressors such as p53. Ilya Prigogine's concept of dissipative structures applies to temporal oscillations and allows us to unify within a common framework the various rhythms observed at different levels of biological organization, regardless of their period and underlying mechanism.

Mesoscale pattern formation of self-propelled rods with velocity reversal

We study self-propelled particles with velocity reversal interacting by uniaxial (nematic) alignment within a coarse-grained hydrodynamic theory. Combining analytical and numerical continuation techniques, we show that the physics of this active system is essentially controlled by the reversal frequency. In particular, we find that elongated, high-density, ordered patterns, called bands, emerge via subcritical bifurcations from spatially homogeneous states. Our analysis reveals further that the interaction of bands is weakly attractive and, consequently, bands fuse upon collision in analogy with nonequilibrium nucleation processes. Moreover, we demonstrate that a renormalized positive line tension can be assigned to stable bands below a critical reversal rate, beyond which they are transversally unstable. In addition, we discuss the kinetic roughening of bands as well as their nonlinear dynamics close to the threshold of transversal instability. Altogether, the reduction of the multiparticle system onto the dynamics of bands provides a unified framework to understand the emergence and stability of nonequilibrium patterns in this self-propelled particle system. In this regard, our results constitute a proof of principle in favor of the hypothesis in microbiology that velocity reversal of gliding rod-shaped bacteria regulates the transitions between various self-organized patterns observed during the bacterial life cycle.

Regulations governing the multicellular lifestyle of Myxococcus xanthus

In living organisms, cooperative cell movements underlie the formation of differentiated tissues. In bacteria, Myxococcus xanthus uses cooperative group movements, to predate on prey and to form multicellular fruiting bodies, where the cells differentiate into dormant spores. Motility is controlled by a central signaling Che-like pathway, Frz. Single cell studies indicate Frz regulates the frequency at which cells reverse their direction of movement by transmitting signals to a molecular system that controls the spatial activity of the motility engines. This regulation is central to all Myxococcus multicellular behaviors but how Frz signaling generates ordered patterns is poorly understood. In this review, we first discuss the genetic structure of the Frz pathway and possible regulations that could explain its action during Myxococcus development.

Colony Expansion of Socially Motile Myxococcus xanthus Cells Is Driven by Growth, Motility, and Exopolysaccharide Production

Myxococcus xanthus, a model organism for studies of multicellular behavior in bacteria, moves exclusively on solid surfaces using two distinct but coordinated motility mechanisms. One of these, social (S) motility is powered by the extension and retraction of type IV pili and requires the presence of exopolysaccharides (EPS) produced by neighboring cells. As a result, S motility requires close cell-to-cell proximity and isolated cells do not translocate. Previous studies measuring S motility by observing the colony expansion of cells deposited on agar have shown that the expansion rate increases with initial cell density, but the biophysical mechanisms involved remain largely unknown. To understand the dynamics of S motility-driven colony expansion, we developed a reaction-diffusion model describing the effects of cell density, EPS deposition and nutrient exposure on the expansion rate. Our results show that at steady state the population expands as a traveling wave with a speed determined by the interplay of cell motility and growth, a well-known characteristic of Fisher’s equation. The model explains the density-dependence of the colony expansion by demonstrating the presence of a lag phase–a transient period of very slow expansion with a duration dependent on the initial cell density. We propose that at a low initial density, more time is required for the cells to accumulate enough EPS to activate S-motility resulting in a longer lag period. Furthermore, our model makes the novel prediction that following the lag phase the population expands at a constant rate independent of the cell density. These predictions were confirmed by S motility experiments capturing long-term expansion dynamics.

Collective motility is a key mechanism bacteria use to self-organize into multicellular structures and to adapt to various environments. An important example of such behavior is social (S) motility in the gram-negative bacterium Myxococcus xanthus. S-motile cells are restricted to movement in groups and do not move as individual cells. S-motility is powered by type IV pili (TFP)–multi-subunit filaments, which extrude from the cell poles, adhere to the substrate and retract, pulling the cell forward. TFP retraction or adhesion is suggested to be triggered by extracellular exopolysaccharides (EPS) deposited by cells on the substrate. As individual cells synthesize both pili and EPS, it is unclear why S-motile cells only exhibit group movement. Moreover, the experimentally observed initial cell-density dependence of S-motility remains unexplained. To understand these phenomena, we developed a mathematical model for the colony expansion of S-motile cells. Our model hypothesizes that the EPS level regulates the TFP activity that initiates collective cell movements. With this assumption, the model quantitatively matches the density-dependent expansion rate. Moreover, the model predicts two phases during colony expansion: an initial density-dependent lag phase with a slow expansion rate, followed by a faster expansion phase with a density-independent rate. These model predictions were confirmed by long-term colony expansion experiments.

Coordination of cell decisions and promotion of phenotypic diversity in B. subtilis via pulsed behavior of the phosphorelay

The phosphorelay of Bacillus subtilis, a kinase cascade that activates master regulator Spo0A ~ P in response to starvation signals, is the core of a large network controlling the cell's decision to differentiate into sporulation and other phenotypes. This article reviews recent advances in understanding the origins and purposes of the complex dynamical behavior of the phosphorelay, which pulses with peaks of activity coordinated with the cell cycle. The transient imbalance in the expression of two critical genes caused by their strategic placement at opposing ends of the chromosome proved to be the key for this pulsed behavior. Feedback control loops in the phosphorelay use these pulses to implement a timer mechanism, which creates several windows of opportunity for phenotypic transitions over multiple generations. This strategy allows the cell to coordinate multiple differentiation programs in a decision process that fosters phenotypic diversity and adapts to current conditions.

A survey of HK, HPt, and RR domains and their organization in two-component systems and phosphorelay proteins of organisms with fully sequenced genomes

Two Component Systems and Phosphorelays (TCS/PR) are environmental signal transduction cascades in prokaryotes and, less frequently, in eukaryotes. The internal domain organization of proteins and the topology of TCS/PR cascades play an important role in shaping the responses of the circuits. It is thus important to maintain updated censuses of TCS/PR proteins in order to identify the various topologies used by nature and enable a systematic study of the dynamics associated with those topologies. To create such a census, we analyzed the proteomes of 7,609 organisms from all domains of life with fully sequenced and annotated genomes. To begin, we survey each proteome searching for proteins containing domains that are associated with internal signal transmission within TCS/PR: Histidine Kinase (HK), Response Regulator (RR) and Histidine Phosphotranfer (HPt) domains, and analyze how these domains are arranged in the individual proteins. Then, we find all types of operon organization and calculate how much more likely are proteins that contain TCS/PR domains to be coded by neighboring genes than one would expect from the genome background of each organism. Finally, we analyze if the fusion of domains into single TCS/PR proteins is more frequently observed than one might expect from the background of each proteome. We find 50 alternative ways in which the HK, HPt, and RR domains are observed to organize into single proteins. In prokaryotes, TCS/PR coding genes tend to be clustered in operons. 90% of all proteins identified in this study contain just one of the three domains, while 8% of the remaining proteins combine one copy of an HK, a RR, and/or an HPt domain. In eukaryotes, 25% of all TCS/PR proteins have more than one domain. These results might have implications for how signals are internally transmitted within TCS/PR cascades. These implications could explain the selection of the various designs in alternative circumstances.

Dual biochemical oscillators may control cellular reversals in Myxococcus xanthus

Myxococcus xanthus is a Gram-negative, soil-dwelling bacterium that glides on surfaces, reversing direction approximately once every 6 min. Motility in M. xanthus is governed by the Che-like Frz pathway and the Ras-like Mgl pathway, which together cause the cell to oscillate back and forth. Previously, Igoshin et al. (2004) suggested that the cellular oscillations are caused by cyclic changes in concentration of active Frz proteins that govern motility. In this study, we present a computational model that integrates both the Frz and Mgl pathways, and whose downstream components can be read as motor activity governing cellular reversals. This model faithfully reproduces wildtype and mutant behaviors by simulating individual protein knockouts. In addition, the model can be used to examine the impact of contact stimuli on cellular reversals. The basic model construction relies on the presence of two nested feedback circuits, which prompted us to reexamine the behavior of M. xanthus cells. We performed experiments to test the model, and this cell analysis challenges previous assumptions of 30 to 60 min reversal periods in frzCD, frzF, frzE, and frzZ mutants. We demonstrate that this average reversal period is an artifact of the method employed to record reversal data, and that in the absence of signal from the Frz pathway, Mgl components can occasionally reverse the cell near wildtype periodicity, but frz- cells are otherwise in a long nonoscillating state.

Describing Myxococcus xanthus aggregation using Ostwald ripening equations for thin liquid films

When starved, a swarm of millions of Myxococcus xanthus cells coordinate their movement from outward swarming to inward coalescence. The cells then execute a synchronous program of multicellular development, arranging themselves into dome shaped aggregates. Over the course of development, about half of the initial aggregates disappear, while others persist and mature into fruiting bodies. This work seeks to develop a quantitative model for aggregation that accurately simulates which will disappear and which will persist. We analyzed time-lapse movies of M. xanthus development, modeled aggregation using the equations that describe Ostwald ripening of droplets in thin liquid films, and predicted the disappearance and persistence of aggregates with an average accuracy of 85%. We then experimentally validated a prediction that is fundamental to this model by tracking individual fluorescent cells as they moved between aggregates and demonstrating that cell movement towards and away from aggregates correlates with aggregate disappearance. Describing development through this model may limit the number and type of molecular genetic signals needed to complete M. xanthus development, and it provides numerous additional testable predictions.

Changes in oscillatory dynamics in the cell cycle of early Xenopus laevis embryos

During the early development of Xenopus laevis embryos, the first mitotic cell cycle is long (∼85 min) and the subsequent 11 cycles are short (∼30 min) and clock-like. Here we address the question of how the Cdk1 cell cycle oscillator changes between these two modes of operation. We found that the change can be attributed to an alteration in the balance between Wee1/Myt1 and Cdc25. The change in balance converts a circuit that acts like a positive-plus-negative feedback oscillator, with spikes of Cdk1 activation, to one that acts like a negative-feedback-only oscillator, with a shorter period and smoothly varying Cdk1 activity. Shortening the first cycle, by treating embryos with the Wee1A/Myt1 inhibitor PD0166285, resulted in a dramatic reduction in embryo viability, and restoring the length of the first cycle in inhibitor-treated embryos with low doses of cycloheximide partially rescued viability. Computations with an experimentally parameterized mathematical model show that modest changes in the Wee1/Cdc25 ratio can account for the observed qualitative changes in the cell cycle. The high ratio in the first cycle allows the period to be long and tunable, and decreasing the ratio in the subsequent cycles allows the oscillator to run at a maximal speed. Thus, the embryo rewires its feedback regulation to meet two different developmental requirements during early development.

A semi-mechanistic integrated toxicokinetic-toxicodynamic (TK/TD) model for arsenic(III) in hepatocytes

BACKGROUND

A systems engineering approach is presented for describing the kinetics and dynamics that are elicited upon arsenic exposure of human hepatocytes. The mathematical model proposed here tracks the cellular reaction network of inorganic and organic arsenic compounds present in the hepatocyte and analyzes the production of toxicologically potent by-products and the signaling they induce in hepatocytes.

METHODS AND RESULTS

The present modeling effort integrates for the first time a cellular-level semi-mechanistic toxicokinetic (TK) model of arsenic in human hepatocytes with a cellular-level toxicodynamic (TD) model describing the arsenic-induced reactive oxygen species (ROS) burst, the antioxidant response, and the oxidative DNA damage repair process. The antioxidant response mechanism is described based on the Keap1-independent Nuclear Factor-erythroid 2-related factor 2 (Nrf2) signaling cascade and accounts for the upregulation of detoxifying enzymes. The ROS-induced DNA damage is simulated by coupling the TK/TD formulation with a model describing the multistep pathway of oxidative DNA repair. The predictions of the model are assessed against experimental data of arsenite-induced genotoxic damage to human hepatocytes; thereby capturing in silico the mode of the experimental dose-response curve.

CONCLUSIONS

The integrated cellular-level TK/TD model presented here provides significant insight into the underlying regulatory mechanism of Nrf2-regulated antioxidant response due to arsenic exposure. While computational simulations are in a fair good agreement with relevant experimental data, further analysis of the system unravels the role of a dynamic interplay among the feedback loops of the system in controlling the ROS upregulation and DNA damage response. This TK/TD framework that uses arsenic as an example can be further extended to other toxic or pharmaceutical agents.

Myxobacterial tools for social interactions

Myxobacteria exhibit complex social traits during which large populations of cells coordinate their behaviors. An iconic example is their response to starvation: thousands of cells move by gliding motility to build a fruiting body in which vegetative cells differentiate into spores. Here we review mechanisms that the model species Myxococcus xanthus uses for cell-cell interactions, with a focus on developmental signaling and social gliding motility. We also discuss a newly discovered cell-cell interaction whereby myxobacteria exchange their outer membrane (OM) proteins and lipids. The mechanism of OM transfer requires physical contact between aligned cells on a hard surface and is apparently mediated by OM fusion. The TraA and TraB proteins are required in both donor and recipient cells for transfer, suggesting bidirectional exchange, and TraA is thought to serve as a cell surface adhesin. OM exchange results in phenotypic changes that can alter gliding motility and development and is proposed to represent a novel microbial interacting platform to coordinate multicellular activities.

The mechanistic basis of Myxococcus xanthus rippling behavior and its physiological role during predation

Myxococcus xanthus cells self-organize into periodic bands of traveling waves, termed ripples, during multicellular fruiting body development and predation on other bacteria. To investigate the mechanistic basis of rippling behavior and its physiological role during predation by this Gram-negative soil bacterium, we have used an approach that combines mathematical modeling with experimental observations. Specifically, we developed an agent-based model (ABM) to simulate rippling behavior that employs a new signaling mechanism to trigger cellular reversals. The ABM has demonstrated that three ingredients are sufficient to generate rippling behavior: (i) side-to-side signaling between two cells that causes one of the cells to reverse, (ii) a minimal refractory time period after each reversal during which cells cannot reverse again, and (iii) physical interactions that cause the cells to locally align. To explain why rippling behavior appears as a consequence of the presence of prey, we postulate that prey-associated macromolecules indirectly induce ripples by stimulating side-to-side contact-mediated signaling. In parallel to the simulations, M. xanthus predatory rippling behavior was experimentally observed and analyzed using time-lapse microscopy. A formalized relationship between the wavelength, reversal time, and cell velocity has been predicted by the simulations and confirmed by the experimental data. Furthermore, the results suggest that the physiological role of rippling behavior during M. xanthus predation is to increase the rate of spreading over prey cells due to increased side-to-side contact-mediated signaling and to allow predatory cells to remain on the prey longer as a result of more periodic cell motility.

Myxococcus xanthus cells collectively move on solid surfaces and reorganize their colonies in response to environmental cues. Under some conditions, cells exhibit an intriguing form of collective motility by self-organizing into bands of travelling alternating-density waves termed ripples. These waves are distinct from the waves originating from Turing instability in diffusion-reaction systems, as these counter-traveling waves do not annihilate but appear to pass through each other. Here we developed a new mathematical model of rippling behavior based on a recently observed contact signaling mechanism – cells that make side-to-side contacts can signal one another to reverse. We hypothesize that this signaling is enhanced by the presence of prey-associated macromolecules and compare modeling predictions with experimentally observed waves generated on E. coli prey cells. The model predicts a modified relationship between the wavelength and individual predatory cell motility parameters and provides a physiological role for rippling during predation. We show that ripples allow predatory cells to increase the rate of their spreading to quickly envelope the prey, and subsequently to decrease their random drift to remain in the prey region for longer. These and other predictions are confirmed by the experimental observations.

Systems biology of cellular rhythms

Rhythms abound in biological systems, particularly at the cellular level where they originate from the feedback loops present in regulatory networks. Cellular rhythms can be investigated both by experimental and modeling approaches, and thus represent a prototypic field of research for systems biology. They have also become a major topic in synthetic biology. We review advances in the study of cellular rhythms of biochemical rather than electrical origin by considering a variety of oscillatory processes such as Ca++ oscillations, circadian rhythms, the segmentation clock, oscillations in p53 and NF-κB, synthetic oscillators, and the oscillatory dynamics of cyclin-dependent kinases driving the cell cycle. Finally we discuss the coupling between cellular rhythms and their robustness with respect to molecular noise.

Collective dynamics of self-propelled sphere-dimer motors

The collective dynamics of ensembles of chemically powered sphere dimer motors is investigated. Sphere dimers are self-propelled nanomotors built from linked catalytic and noncatalytic spheres. They consume fuel in the environment and utilize the resulting self-generated concentration gradients to produce directed motion along their internuclear axes. In collections of such motors, the individual motors interact through forces that arise from concentration gradients, hydrodynamic coupling, and direct intermolecular forces. Under nonequilibrium conditions it is found that the sphere dimer motors self-assemble into transient aggregates with distinctive structural correlations and exhibit swarming where the aggregates propagate through the system. The mean square displacement of a dimer motor in the ensemble displays short-time ballistic and long-time diffusive regimes and, for ensembles containing many motors, an increasingly prominent intermediate regime. The self-diffusion coefficient of a motor in a many-motor system behaves differently from that of an isolated motor, and the decay of orientational correlations is a nonmonotonic function of the number of motors. The results presented here illustrate the phenomena to be expected in applications, such as cargo transport, where many motors may act in consort.

From individual cell motility to collective behaviors: insights from a prokaryote, Myxococcus xanthus

In bird flocks, fish schools, and many other living organisms, regrouping among individuals of the same kin is frequently an advantageous strategy to survive, forage, and face predators. However, these behaviors are costly because the community must develop regulatory mechanisms to coordinate and adapt its response to rapid environmental changes. In principle, these regulatory mechanisms, involving communication between individuals, may also apply to cellular systems which must respond collectively during multicellular development. Dissecting the mechanisms at work requires amenable experimental systems, for example, developing bacteria. Myxococcus xanthus, a Gram-negative delatproteobacterium, is able to coordinate its motility in space and time to swarm, predate, and grow millimeter-size spore-filled fruiting bodies. A thorough understanding of the regulatory mechanisms first requires studying how individual cells move across solid surfaces and control their direction of movement, which was recently boosted by new cell biology techniques. In this review, we describe current molecular knowledge of the motility mechanism and its regulation as a lead-in to discuss how multicellular cooperation may have emerged from several layers of regulation: chemotaxis, cell-cell signaling, and the extracellular matrix. We suggest that Myxococcus is a powerful system to investigate collective principles that may also be relevant to other cellular systems.

An introduction to dynamical systems

This Teaching Resource provides lecture notes, slides, and a problem set that can assist in teaching concepts related to dynamical systems tools for the analysis of ordinary differential equation (ODE)-based models. The concepts are applied to familiar biological problems, and the material is appropriate for graduate students or advanced undergraduates. The lecture explains how equations describing biochemical signaling networks can be derived from diagrams that illustrate the reactions in graphical form. Because such reactions are most frequently described using systems of ODEs, the lecture discusses and illustrates the principles underlying the numerical solution of ODEs. Methods for determining the stability of steady-state solutions of one or two-dimensional ODE systems are covered and illustrated using standard graphical methods. The concept of a bifurcation, a condition at which a system's behavior changes qualitatively, is also introduced. A problem set is included that (i) requires students to implement an ODE model of biochemical reactions using MATLAB and (ii) allows them to explore dynamical systems concepts.

Myxococcus xanthus swarms are driven by growth and regulated by a pacemaker

The principal social activity of Myxococcus xanthus is to organize a dynamic multicellular structure, known as a swarm. Although its cell density is high, the swarm can grow and expand rapidly. Within the swarm, the individual rod-shaped cells are constantly moving, transiently interacting with one another, and independently reversing their gliding direction. Periodic reversal is, in fact, essential for creating a swarm, and the reversal frequency controls the rate of swarm expansion. Chemotaxis toward nutrient has been thought to drive swarming, but here the nature of swarm growth and the impact of genetic deletions of members of the Frz family of proteins suggest otherwise. We find that three cytoplasmic Frz proteins, FrzCD, FrzF, and FrzE, constitute a cyclic pathway that sets the reversal frequency. Within each cell these three proteins appear to be connected in a negative-feedback loop that produces oscillations whose frequencies are finely tuned by methylation and by phosphorylation. This oscillator, in turn, drives MglAB, a small G-protein switch, to oscillate between its GTP- and GDP-bound states that ultimately determine when the cell moves forward or backward. The periodic reversal of interacting rod-shaped cells promotes their alignment. Swarm organization ensures that each cell can move without blocking the movement of others.

Quantifying aggregation dynamics during Myxococcus xanthus development

Under starvation conditions, a swarm of Myxococcus xanthus cells will undergo development, a multicellular process culminating in the formation of many aggregates called fruiting bodies, each of which contains up to 100,000 spores. The mechanics of symmetry breaking and the self-organization of cells into fruiting bodies is an active area of research. Here we use microcinematography and automated image processing to quantify several transient features of developmental dynamics. An analysis of experimental data indicates that aggregation reaches its steady state in a highly nonmonotonic fashion. The number of aggregates rapidly peaks at a value 2- to 3-fold higher than the final value and then decreases before reaching a steady state. The time dependence of aggregate size is also nonmonotonic, but to a lesser extent: average aggregate size increases from the onset of aggregation to between 10 and 15 h and then gradually decreases thereafter. During this process, the distribution of aggregates transitions from a nearly random state early in development to a more ordered state later in development. A comparison of experimental results to a mathematical model based on the traffic jam hypothesis indicates that the model fails to reproduce these dynamic features of aggregation, even though it accurately describes its final outcome. The dynamic features of M. xanthus aggregation uncovered in this study impose severe constraints on its underlying mechanisms.

Experimentally guided computational model discovers important elements for social behavior in myxobacteria

Identifying essential factors in cellular interactions and organized movement of cells is important in predicting behavioral phenotypes exhibited by many bacterial cells. We chose to study Myxococcus xanthus, a soil bacterium whose individual cell behavior changes while in groups, leading to spontaneous formation of aggregation center during the early stage of fruiting body development. In this paper, we develop a cell-based computational model that solely relies on experimentally determined parameters to investigate minimal elements required to produce the observed social behaviors in M. xanthus. The model verifies previously known essential parameters and identifies one novel parameter, the active turning, which we define as the ability and tendency of a cell to turn to a certain angle without the presence of any obvious external factors. The simulation is able to produce both gliding pattern and spontaneous aggregation center formation as observed in experiments. The model is tested against several known M. xanthus mutants and our modification of parameter values relevant for the individual mutants produces good phenotypic agreements. This outcome indicates the strong predictive potential of our model for the social behaviors of uncharacterized mutants and their expected phenotypes during development.

Open cascades as simple solutions to providing ultrasensitivity and adaptation in cellular signaling

Cell signaling is achieved predominantly by reversible phosphorylation-dephosphorylation reaction cascades. Up until now, circuits conferring adaptation have all required the presence of a cascade with some type of closed topology: negative-feedback loop with a buffering node, or incoherent feed-forward loop with a proportioner node. In this paper--using Goldbeter and Koshland-type expressions--we propose a differential equation model to describe a generic, open signaling cascade that elicits an adaptation response. This is accomplished by coupling N phosphorylation-dephosphorylation cycles unidirectionally, without any explicit feedback loops. Using this model, we show that as the length of the cascade grows, the steady states of the downstream cycles reach a limiting value. In other words, our model indicates that there are a minimum number of cycles required to achieve a maximum in sensitivity and amplitude in the response of a signaling cascade. We also describe for the first time that the phenomenon of ultrasensitivity can be further subdivided into three sub-regimes, separated by sharp stimulus threshold values: OFF, OFF-ON-OFF, and ON. In the OFF-ON-OFF regime, an interesting property emerges. In the presence of a basal amount of activity, the temporal evolution of early cycles yields damped peak responses. On the other hand, the downstream cycles switch rapidly to a higher activity state for an extended period of time, prior to settling to an OFF state (OFF-ON-OFF). This response arises from the changing dynamics between a feed-forward activation module and dephosphorylation reactions. In conclusion, our model gives the new perspective that open signaling cascades embedded in complex biochemical circuits may possess the ability to show a switch-like adaptation response, without the need for any explicit feedback circuitry.

Self-propelled nanodimer bound state pairs

A pair of chemically powered self-propelled nanodimers can exist in a variety of bound and unbound states after undergoing a collision. In addition to independently moving unbound dimers, bound Brownian dimer pairs, whose center-of-mass exhibits diffusive motion, self-propelled moving dimer pairs with directed motion, and bound rotating dimer pairs, were observed. The bound pairs arise from a solvent depletion interaction, which depends on the nonequilibrium concentration field in the vicinity of dimers. The phase diagram reported in the paper shows regions in monomer interaction energy-diameter plane where these bound and unbound states are found. Particle-based simulations and analytical calculations are used to provide insight into the nature of interaction between dimers that gives rise to the observed bound states.

Statistical image analysis reveals features affecting fates of Myxococcus xanthus developmental aggregates

Starving Myxococcus xanthus bacteria use their motility systems to self-organize into multicellular fruiting bodies, large mounds in which cells differentiate into metabolically inert spores. Despite the identification of the genetic pathways required for aggregation and the use of microcinematography to observe aggregation dynamics in WT and mutant strains, a mechanistic understanding of aggregation is still incomplete. For example, it is not clear why some of the initial aggregates mature into fruiting bodies, whereas others disperse, merge, or split into two. Here, we develop high-throughput image quantification and statistical analysis methods to gain insight into M. xanthus developmental aggregation dynamics. A quantitative metric of features characterizing each aggregate is used to deduce the properties of the aggregates that are correlated with each fate. The analysis shows that small aggregate size but not neighbor-related parameters correlate with aggregate dispersal. Furthermore, close proximity is necessary but not sufficient for aggregate merging. Finally, splitting occurs for those aggregates that are unusually large and elongated. These observations place severe constraints on the underlying aggregation mechanisms and present strong evidence against the role of long-range morphogenic gradients or biased cell exchange in the dispersal, merging, or splitting of transient aggregates. This approach can be expanded and adapted to study self-organization in other cellular systems.

Bacterial polarity

Many recent studies have revealed exquisite subcellular localization of proteins, DNA, and other molecules within bacterial cells, giving credence to the concept of prokaryotic anatomy. Common sites for localized components are the poles of rod-shaped cells, which are dynamically modified in composition and function in order to control cellular physiology. An impressively diverse array of mechanisms underlies bacterial polarity, including oscillatory systems, phospho-signaling pathways, the sensing of membrane curvature, and the integration of cell cycle regulators with polar maturation.

Myxobacteria, polarity, and multicellular morphogenesis

Myxobacteria are renowned for the ability to sporulate within fruiting bodies whose shapes are species-specific. The capacity to build those multicellular structures arises from the ability of M. xanthus to organize high cell-density swarms, in which the cells tend to be aligned with each other while constantly in motion. The intrinsic polarity of rod-shaped cells lays the foundation, and each cell uses two polar engines for gliding on surfaces. It sprouts retractile type IV pili from the leading cell pole and secretes capsular polysaccharide through nozzles from the trailing pole. Regularly periodic reversal of the gliding direction was found to be required for swarming. Those reversals are generated by a G-protein switch which is driven by a sharply tuned oscillator. Starvation induces fruiting body development, and systematic reductions in the reversal frequency are necessary for the cells to aggregate rather than continue to swarm. Developmental gene expression is regulated by a network that is connected to the suppression of reversals.

A bacterial Ras-like small GTP-binding protein and its cognate GAP establish a dynamic spatial polarity axis to control directed motility

Directional control of bacterial motility is regulated by dynamic polarity inversions driven by pole-to-pole oscillation of a Ras family small G-protein and its associated GTPase-activating protein.

Regulated cell polarity is central to many cellular processes. We investigated the mechanisms that govern the rapid switching of cell polarity (reversals) during motility of the bacterium Myxococcus xanthus. Cellular reversals are mediated by pole-to-pole oscillations of motility proteins and the frequency of the oscillations is under the control of the Frz chemosensory system. However, the molecular mechanism that creates dynamic polarity remained to be characterized. In this work, we establish that polarization is regulated by the GTP cycle of a Ras-like GTPase, MglA. We initially sought an MglA regulator and purified a protein, MglB, which was found to activate GTP hydrolysis by MglA. Using live fluorescence microscopy, we show that MglA and MglB localize at opposite poles and oscillate oppositely when cells reverse. In absence of MglB, MglA-YFP accumulates at the lagging cell end, leading to a strikingly aberrant reversal cycle. Spatial control of MglA is achieved through the GAP activity of MglB because an MglA mutant that cannot hydrolyze GTP accumulates at the lagging cell end, despite the presence of MglB. Genetic and cell biological studies show that the MglA-GTP cycle controls dynamic polarity and the reversal switch. The study supports a model wherein a chemosensory signal transduction system (Frz) activates reversals by relieving a spatial inhibition at the back pole of the cells: reversals are allowed by Frz-activated switching of MglB to the opposite pole, allowing MglA-GTP to accumulate at the back of the cells and create the polarity switch. In summary, our results provide insight into how bacteria regulate their polarity dynamically, revealing unsuspected conserved regulations with eukaryots.

Motile cells have evolved complex regulatory networks to respond to environmental cues and change their direction of movement appropriately. In this process, an arsenal of receptor-coupled small G-proteins acts as a cellular compass to dynamically polarize the leading edge and regulate the motility response. However, the precise mechanism of action of these G-proteins in controlling bacteria movement on solid surfaces has remained an enigma. We investigate this process in Gram negative Myxococcus xanthus cells. Surprisingly, we find that the Ras-like small G-protein MglA polarizes the cell by accumulating at the leading cell pole in its active GTP-bound form. This localization is dependent on MglB, a GTPase-activating protein that converts MglA to its inactive form specifically at the opposite, lagging cell pole. Furthermore, we show that a receptor-coupled signal transduction cascade can activate re-localization of MglA and MglB at opposite poles in a synchronous manner, resulting in inversion of the polarity axis and cell movement in the opposite direction. Thus, a simple, eukaryote-like signaling module also governs dynamic polarity mechanisms in bacteria, demonstrating broader conservation of these signaling systems than initially suspected.

Some possible dynamical constraints for life's origin

Oscillating biochemical reactions are common in cell dynamics and could be closely related to the emergence of the life phenomenon itself. In this work, we study the dynamical features of some classical chemical or biochemical oscillators where the effect of cell volume changes is explicitly considered. Such analysis enables us to find some general conditions about the cell membrane to preserve such oscillatory patterns, of possible relevance to hypothetical primitive cells in which these structures first appeared.

Deciphering the hunting strategy of a bacterial wolfpack

Myxococcus xanthus is a common soil bacterium with an intricate multicellular lifestyle that continues to challenge the way in which we conceptualize the capabilities of prokaryotic organisms. Myxococcus xanthus is the preferred laboratory representative from the Myxobacteria, a family of organisms distinguished by their ability to form highly structured biofilms that include tentacle-like packs of surface-gliding cell groups, synchronized rippling waves of oscillating cells and massive spore-filled aggregates that protrude upwards from the substratum to form fruiting bodies. But most of the Myxobacteria are also predators that thrive on the degradation of macromolecules released through the lysis of other microbial cells. The aim of this review is to examine our understanding of the predatory life cycle of M. xanthus. We will examine the multicellular structures formed during contact with prey, and the molecular mechanisms utilized by M. xanthus to detect and destroy prey cells. We will also examine our understanding of microbial predator-prey relationships and the prospects for how bacterial predation mechanisms can be exploited to generate new antimicrobial technologies.

Localization of a bacterial cytoplasmic receptor is dynamic and changes with cell-cell contacts

Directional motility in the gliding bacterium Myxococcus xanthus requires controlled cell reversals mediated by the Frz chemosensory system. FrzCD, a cytoplasmic chemoreceptor, does not form membrane-bound polar clusters typical for most bacteria, but rather cytoplasmic clusters that appear helically arranged and span the cell length. The distribution of FrzCD in living cells was found to be dynamic: FrzCD was localized in clusters that continuously changed their size, number, and position. The number of FrzCD clusters was correlated with cellular reversal frequency: fewer clusters were observed in hypo-reversing mutants and additional clusters were observed in hyper-reversing mutants. When moving cells made side-to-side contacts, FrzCD clusters in adjacent cells showed transient alignments. These events were frequently followed by one of the interacting cells reversing. These observations suggest that FrzCD detects signals from a cell contact-sensitive signaling system and then re-localizes as it directs reversals to distributed motility engines.

Periodic reversal of direction allows Myxobacteria to swarm

Many bacteria can rapidly traverse surfaces from which they are extracting nutrient for growth. They generate flat, spreading colonies, called swarms because they resemble swarms of insects. We seek to understand how members of any dense swarm spread efficiently while being able to perceive and interfere minimally with the motion of others. To this end, we investigate swarms of the myxobacterium, Myxococcus xanthus. Individual M. xanthus cells are elongated; they always move in the direction of their long axis; and they are in constant motion, repeatedly touching each other. Remarkably, they regularly reverse their gliding directions. We have constructed a detailed cell- and behavior-based computational model of M. xanthus swarming that allows the organization of cells to be computed. By using the model, we are able to show that reversals of gliding direction are essential for swarming and that reversals increase the outflow of cells across the edge of the swarm. Cells at the swarm edge gain maximum exposure to nutrient and oxygen. We also find that the reversal period predicted to maximize the outflow of cells is the same (within the errors of measurement) as the period observed in experiments with normal M. xanthus cells. This coincidence suggests that the circuit regulating reversals evolved to its current sensitivity under selection for growth achieved by swarming. Finally, we observe that, with time, reversals increase the cell alignment, and generate clusters of parallel cells.